transcription,translation and genetic code(cell biology)by welfredo yu

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TRANSCRIPT

Cells are governed by a cellular chain of

command

DNA RNA protein

Transcription

Is the synthesis of RNA under the direction of

DNA

Produces messenger RNA (mRNA)

Translation

Is the actual synthesis of a polypeptide which

occurs under the direction of mRNA

Occurs on ribosomes

The Genetic Code

a non-overlapping sequence with each amino

acid plus polypeptide initiation and termination

specified by RNA codons composed of three

nucleotides

Genes can be expressed at different efficiencies

bull Gene A is transcribed much more efficiently than gene B

bull This allows the amount of protein A in the cell to be

greater than protein B

bull The lower expression of gene B is a reason behind

incomplete dominance

BIOL211

RNA is the bridge between

genes and the proteins for

which they code

what is RNA

Monomers of proteins are amino acids

what are proteins made of

Codons

bull A codon is three nucleotides in a row on an RNA

molecule that codes for a single amino acid

bull A specific three-nucleotide sequence encodes for each

amino acid

Template Strand

bull During transcription one of the two DNA

strands called the template strand provides

a template for ordering the sequence of

complementary nucleotides in an RNA

transcript

ndash The template strand is always the same strand for

a given gene

ndash However different genes may be on opposite

strands

bull The genetic code is nearly

universal shared by the simplest

bacteria to the most complex

animals

ndash Some species prefer certain

codons (codon bias)

bull Genes can be transcribed and

translated after being

transplanted from one species

to another

EVOLUTION OF THE CODE

History linking genes and proteins

1900rsquos Archibald Garrod Inborn errors of metabolism inherited human

metabolic diseases (more information) Genes are the inherited factors

Enzymes are the biological molecules that drive metabolic reactions

Enzymes are proteins

Question

How do the inherited factors the genes control the structure and activity of enzymes (proteins)

History linking genes and proteins

Beadle and Tatum (1941) PNAS USA 27 499ndash506

Hypothesis If genes control structure and activity of metabolic enzymes

then mutations in genes should disrupt production of required nutrients and that disruption should be heritable

Method Isolated ~2000 strains from single irradiate spores

(Neurospora) that grew on rich but not minimal medium Examples defects in B1 B6 synthesis

Conclusion Genes govern the ability to synthesize amino acids purines

and vitamins

History linking genes and proteins

1950s sickle-cell anemia Glu to Val change in hemoglobin

Sequence of nucleotides in gene determines sequence of amino acids in protein

Single amino acid change can alter the function of the protein

Tryptophan synthase gene in E coli Mutations resulted in single amino acid change

Order of mutations in gene same as order of affected amino acids

Ribosomal structure

EP A

Large subunit

Peptidyl-tRNA binding site

Aminoacyl-tRNA binding site

mRNA

5rsquo

Exit

site

Small subunit

3rsquo

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Genes can be expressed at different efficiencies

bull Gene A is transcribed much more efficiently than gene B

bull This allows the amount of protein A in the cell to be

greater than protein B

bull The lower expression of gene B is a reason behind

incomplete dominance

BIOL211

RNA is the bridge between

genes and the proteins for

which they code

what is RNA

Monomers of proteins are amino acids

what are proteins made of

Codons

bull A codon is three nucleotides in a row on an RNA

molecule that codes for a single amino acid

bull A specific three-nucleotide sequence encodes for each

amino acid

Template Strand

bull During transcription one of the two DNA

strands called the template strand provides

a template for ordering the sequence of

complementary nucleotides in an RNA

transcript

ndash The template strand is always the same strand for

a given gene

ndash However different genes may be on opposite

strands

bull The genetic code is nearly

universal shared by the simplest

bacteria to the most complex

animals

ndash Some species prefer certain

codons (codon bias)

bull Genes can be transcribed and

translated after being

transplanted from one species

to another

EVOLUTION OF THE CODE

History linking genes and proteins

1900rsquos Archibald Garrod Inborn errors of metabolism inherited human

metabolic diseases (more information) Genes are the inherited factors

Enzymes are the biological molecules that drive metabolic reactions

Enzymes are proteins

Question

How do the inherited factors the genes control the structure and activity of enzymes (proteins)

History linking genes and proteins

Beadle and Tatum (1941) PNAS USA 27 499ndash506

Hypothesis If genes control structure and activity of metabolic enzymes

then mutations in genes should disrupt production of required nutrients and that disruption should be heritable

Method Isolated ~2000 strains from single irradiate spores

(Neurospora) that grew on rich but not minimal medium Examples defects in B1 B6 synthesis

Conclusion Genes govern the ability to synthesize amino acids purines

and vitamins

History linking genes and proteins

1950s sickle-cell anemia Glu to Val change in hemoglobin

Sequence of nucleotides in gene determines sequence of amino acids in protein

Single amino acid change can alter the function of the protein

Tryptophan synthase gene in E coli Mutations resulted in single amino acid change

Order of mutations in gene same as order of affected amino acids

Ribosomal structure

EP A

Large subunit

Peptidyl-tRNA binding site

Aminoacyl-tRNA binding site

mRNA

5rsquo

Exit

site

Small subunit

3rsquo

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

RNA is the bridge between

genes and the proteins for

which they code

what is RNA

Monomers of proteins are amino acids

what are proteins made of

Codons

bull A codon is three nucleotides in a row on an RNA

molecule that codes for a single amino acid

bull A specific three-nucleotide sequence encodes for each

amino acid

Template Strand

bull During transcription one of the two DNA

strands called the template strand provides

a template for ordering the sequence of

complementary nucleotides in an RNA

transcript

ndash The template strand is always the same strand for

a given gene

ndash However different genes may be on opposite

strands

bull The genetic code is nearly

universal shared by the simplest

bacteria to the most complex

animals

ndash Some species prefer certain

codons (codon bias)

bull Genes can be transcribed and

translated after being

transplanted from one species

to another

EVOLUTION OF THE CODE

History linking genes and proteins

1900rsquos Archibald Garrod Inborn errors of metabolism inherited human

metabolic diseases (more information) Genes are the inherited factors

Enzymes are the biological molecules that drive metabolic reactions

Enzymes are proteins

Question

How do the inherited factors the genes control the structure and activity of enzymes (proteins)

History linking genes and proteins

Beadle and Tatum (1941) PNAS USA 27 499ndash506

Hypothesis If genes control structure and activity of metabolic enzymes

then mutations in genes should disrupt production of required nutrients and that disruption should be heritable

Method Isolated ~2000 strains from single irradiate spores

(Neurospora) that grew on rich but not minimal medium Examples defects in B1 B6 synthesis

Conclusion Genes govern the ability to synthesize amino acids purines

and vitamins

History linking genes and proteins

1950s sickle-cell anemia Glu to Val change in hemoglobin

Sequence of nucleotides in gene determines sequence of amino acids in protein

Single amino acid change can alter the function of the protein

Tryptophan synthase gene in E coli Mutations resulted in single amino acid change

Order of mutations in gene same as order of affected amino acids

Ribosomal structure

EP A

Large subunit

Peptidyl-tRNA binding site

Aminoacyl-tRNA binding site

mRNA

5rsquo

Exit

site

Small subunit

3rsquo

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Monomers of proteins are amino acids

what are proteins made of

Codons

bull A codon is three nucleotides in a row on an RNA

molecule that codes for a single amino acid

bull A specific three-nucleotide sequence encodes for each

amino acid

Template Strand

bull During transcription one of the two DNA

strands called the template strand provides

a template for ordering the sequence of

complementary nucleotides in an RNA

transcript

ndash The template strand is always the same strand for

a given gene

ndash However different genes may be on opposite

strands

bull The genetic code is nearly

universal shared by the simplest

bacteria to the most complex

animals

ndash Some species prefer certain

codons (codon bias)

bull Genes can be transcribed and

translated after being

transplanted from one species

to another

EVOLUTION OF THE CODE

History linking genes and proteins

1900rsquos Archibald Garrod Inborn errors of metabolism inherited human

metabolic diseases (more information) Genes are the inherited factors

Enzymes are the biological molecules that drive metabolic reactions

Enzymes are proteins

Question

How do the inherited factors the genes control the structure and activity of enzymes (proteins)

History linking genes and proteins

Beadle and Tatum (1941) PNAS USA 27 499ndash506

Hypothesis If genes control structure and activity of metabolic enzymes

then mutations in genes should disrupt production of required nutrients and that disruption should be heritable

Method Isolated ~2000 strains from single irradiate spores

(Neurospora) that grew on rich but not minimal medium Examples defects in B1 B6 synthesis

Conclusion Genes govern the ability to synthesize amino acids purines

and vitamins

History linking genes and proteins

1950s sickle-cell anemia Glu to Val change in hemoglobin

Sequence of nucleotides in gene determines sequence of amino acids in protein

Single amino acid change can alter the function of the protein

Tryptophan synthase gene in E coli Mutations resulted in single amino acid change

Order of mutations in gene same as order of affected amino acids

Ribosomal structure

EP A

Large subunit

Peptidyl-tRNA binding site

Aminoacyl-tRNA binding site

mRNA

5rsquo

Exit

site

Small subunit

3rsquo

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Codons

bull A codon is three nucleotides in a row on an RNA

molecule that codes for a single amino acid

bull A specific three-nucleotide sequence encodes for each

amino acid

Template Strand

bull During transcription one of the two DNA

strands called the template strand provides

a template for ordering the sequence of

complementary nucleotides in an RNA

transcript

ndash The template strand is always the same strand for

a given gene

ndash However different genes may be on opposite

strands

bull The genetic code is nearly

universal shared by the simplest

bacteria to the most complex

animals

ndash Some species prefer certain

codons (codon bias)

bull Genes can be transcribed and

translated after being

transplanted from one species

to another

EVOLUTION OF THE CODE

History linking genes and proteins

1900rsquos Archibald Garrod Inborn errors of metabolism inherited human

metabolic diseases (more information) Genes are the inherited factors

Enzymes are the biological molecules that drive metabolic reactions

Enzymes are proteins

Question

How do the inherited factors the genes control the structure and activity of enzymes (proteins)

History linking genes and proteins

Beadle and Tatum (1941) PNAS USA 27 499ndash506

Hypothesis If genes control structure and activity of metabolic enzymes

then mutations in genes should disrupt production of required nutrients and that disruption should be heritable

Method Isolated ~2000 strains from single irradiate spores

(Neurospora) that grew on rich but not minimal medium Examples defects in B1 B6 synthesis

Conclusion Genes govern the ability to synthesize amino acids purines

and vitamins

History linking genes and proteins

1950s sickle-cell anemia Glu to Val change in hemoglobin

Sequence of nucleotides in gene determines sequence of amino acids in protein

Single amino acid change can alter the function of the protein

Tryptophan synthase gene in E coli Mutations resulted in single amino acid change

Order of mutations in gene same as order of affected amino acids

Ribosomal structure

EP A

Large subunit

Peptidyl-tRNA binding site

Aminoacyl-tRNA binding site

mRNA

5rsquo

Exit

site

Small subunit

3rsquo

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Template Strand

bull During transcription one of the two DNA

strands called the template strand provides

a template for ordering the sequence of

complementary nucleotides in an RNA

transcript

ndash The template strand is always the same strand for

a given gene

ndash However different genes may be on opposite

strands

bull The genetic code is nearly

universal shared by the simplest

bacteria to the most complex

animals

ndash Some species prefer certain

codons (codon bias)

bull Genes can be transcribed and

translated after being

transplanted from one species

to another

EVOLUTION OF THE CODE

History linking genes and proteins

1900rsquos Archibald Garrod Inborn errors of metabolism inherited human

metabolic diseases (more information) Genes are the inherited factors

Enzymes are the biological molecules that drive metabolic reactions

Enzymes are proteins

Question

How do the inherited factors the genes control the structure and activity of enzymes (proteins)

History linking genes and proteins

Beadle and Tatum (1941) PNAS USA 27 499ndash506

Hypothesis If genes control structure and activity of metabolic enzymes

then mutations in genes should disrupt production of required nutrients and that disruption should be heritable

Method Isolated ~2000 strains from single irradiate spores

(Neurospora) that grew on rich but not minimal medium Examples defects in B1 B6 synthesis

Conclusion Genes govern the ability to synthesize amino acids purines

and vitamins

History linking genes and proteins

1950s sickle-cell anemia Glu to Val change in hemoglobin

Sequence of nucleotides in gene determines sequence of amino acids in protein

Single amino acid change can alter the function of the protein

Tryptophan synthase gene in E coli Mutations resulted in single amino acid change

Order of mutations in gene same as order of affected amino acids

Ribosomal structure

EP A

Large subunit

Peptidyl-tRNA binding site

Aminoacyl-tRNA binding site

mRNA

5rsquo

Exit

site

Small subunit

3rsquo

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

bull The genetic code is nearly

universal shared by the simplest

bacteria to the most complex

animals

ndash Some species prefer certain

codons (codon bias)

bull Genes can be transcribed and

translated after being

transplanted from one species

to another

EVOLUTION OF THE CODE

History linking genes and proteins

1900rsquos Archibald Garrod Inborn errors of metabolism inherited human

metabolic diseases (more information) Genes are the inherited factors

Enzymes are the biological molecules that drive metabolic reactions

Enzymes are proteins

Question

How do the inherited factors the genes control the structure and activity of enzymes (proteins)

History linking genes and proteins

Beadle and Tatum (1941) PNAS USA 27 499ndash506

Hypothesis If genes control structure and activity of metabolic enzymes

then mutations in genes should disrupt production of required nutrients and that disruption should be heritable

Method Isolated ~2000 strains from single irradiate spores

(Neurospora) that grew on rich but not minimal medium Examples defects in B1 B6 synthesis

Conclusion Genes govern the ability to synthesize amino acids purines

and vitamins

History linking genes and proteins

1950s sickle-cell anemia Glu to Val change in hemoglobin

Sequence of nucleotides in gene determines sequence of amino acids in protein

Single amino acid change can alter the function of the protein

Tryptophan synthase gene in E coli Mutations resulted in single amino acid change

Order of mutations in gene same as order of affected amino acids

Ribosomal structure

EP A

Large subunit

Peptidyl-tRNA binding site

Aminoacyl-tRNA binding site

mRNA

5rsquo

Exit

site

Small subunit

3rsquo

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

History linking genes and proteins

1900rsquos Archibald Garrod Inborn errors of metabolism inherited human

metabolic diseases (more information) Genes are the inherited factors

Enzymes are the biological molecules that drive metabolic reactions

Enzymes are proteins

Question

How do the inherited factors the genes control the structure and activity of enzymes (proteins)

History linking genes and proteins

Beadle and Tatum (1941) PNAS USA 27 499ndash506

Hypothesis If genes control structure and activity of metabolic enzymes

then mutations in genes should disrupt production of required nutrients and that disruption should be heritable

Method Isolated ~2000 strains from single irradiate spores

(Neurospora) that grew on rich but not minimal medium Examples defects in B1 B6 synthesis

Conclusion Genes govern the ability to synthesize amino acids purines

and vitamins

History linking genes and proteins

1950s sickle-cell anemia Glu to Val change in hemoglobin

Sequence of nucleotides in gene determines sequence of amino acids in protein

Single amino acid change can alter the function of the protein

Tryptophan synthase gene in E coli Mutations resulted in single amino acid change

Order of mutations in gene same as order of affected amino acids

Ribosomal structure

EP A

Large subunit

Peptidyl-tRNA binding site

Aminoacyl-tRNA binding site

mRNA

5rsquo

Exit

site

Small subunit

3rsquo

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

History linking genes and proteins

Beadle and Tatum (1941) PNAS USA 27 499ndash506

Hypothesis If genes control structure and activity of metabolic enzymes

then mutations in genes should disrupt production of required nutrients and that disruption should be heritable

Method Isolated ~2000 strains from single irradiate spores

(Neurospora) that grew on rich but not minimal medium Examples defects in B1 B6 synthesis

Conclusion Genes govern the ability to synthesize amino acids purines

and vitamins

History linking genes and proteins

1950s sickle-cell anemia Glu to Val change in hemoglobin

Sequence of nucleotides in gene determines sequence of amino acids in protein

Single amino acid change can alter the function of the protein

Tryptophan synthase gene in E coli Mutations resulted in single amino acid change

Order of mutations in gene same as order of affected amino acids

Ribosomal structure

EP A

Large subunit

Peptidyl-tRNA binding site

Aminoacyl-tRNA binding site

mRNA

5rsquo

Exit

site

Small subunit

3rsquo

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

History linking genes and proteins

1950s sickle-cell anemia Glu to Val change in hemoglobin

Sequence of nucleotides in gene determines sequence of amino acids in protein

Single amino acid change can alter the function of the protein

Tryptophan synthase gene in E coli Mutations resulted in single amino acid change

Order of mutations in gene same as order of affected amino acids

Ribosomal structure

EP A

Large subunit

Peptidyl-tRNA binding site

Aminoacyl-tRNA binding site

mRNA

5rsquo

Exit

site

Small subunit

3rsquo

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Ribosomal structure

EP A

Large subunit

Peptidyl-tRNA binding site

Aminoacyl-tRNA binding site

mRNA

5rsquo

Exit

site

Small subunit

3rsquo

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

From gene to protein transcription

Gene sequence (DNA) recopied or transcribed to RNA sequence

Product of transcription is a messenger molecule that delivers the genetic instructions to the protein synthesis machinery messenger RNA (mRNA)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription evidence for mRNA

Brenner S Jacob F and Meselson M (1961) Nature190 576ndash81

Question How do genes work

Does each one encode a different type of ribosome which in turn synthesizes a different protein OR

Are all ribosomes alike receiving the genetic information to create each different protein via some kind of messenger molecule

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription evidence for mRNA

E coli cells switch from making bacterial proteins to phage proteins when infected with bacteriophage T4

Grow bacteria on medium containing ldquoheavyrdquo nitrogen (15N) and carbon (13C)

Infect with phage T4

Immediately transfer to ldquolightrdquo medium containing radioactive uracil

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription evidence for mRNA

If genes encode different ribosomes the newly synthesized phage ribosomes will be ldquolightrdquo

If genes direct new RNA synthesis the RNA will contain radiolabeled uracil

Results Ribosomes from phage-infected cells were ldquoheavyrdquo

banding at the same density on a CsCl gradient as the original ribosomes

Newly synthesized RNA was associated with the heavy ribosomes

New RNA hybridized with viral ssDNA not bacterial ssDNA

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription evidence for mRNA

Conclusion

Expression of phage DNA results in new phage-specific RNA molecules (mRNA)

These mRNA molecules are temporarily associated with ribosomes

Ribosomes do not themselves contain the genetic directions for assembling individual proteins

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription overview

Transcription requires

ribonucleoside 5acute triphosphates

ATP GTP CTP and UTP

bases are adenine guanine cytosine and uracil

sugar is ribose (not deoxyribose)

DNA-dependent RNA polymerase

Template (sense) DNA strand

Animation of transcription

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription overview

Features of transcription

RNA polymerase catalyzes sugar-phosphate bond between 3acute-OH of ribose and the 5acute-PO4

Order of bases in DNA template strand determines order of bases in transcript

Nucleotides are added to the 3acute-OH of the growing chain

RNA synthesis does not require a primer

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription overview

In prokaryotes transcription and translation are coupled Proteins are synthesized directly from the primary transcript as it is made

In eukaryotes transcription and translation are separated Transcription occurs in the nucleus and translation occurs in the cytoplasm on ribosomes

Figure comparing eukaryotic and prokaryotic transcription and translation

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription RNA Polymerase

DNA-dependent

DNA template ribonucleoside 5acute triphosphates and Mg2+

Synthesizes RNA in 5acute to 3acute direction

E coli RNA polymerase consists of 5 subunits

Eukaryotes have three RNA polymerases

RNA polymerase II is responsible for transcription of protein-coding genes and some snRNA molecules

RNA polymerase II has 12 subunits

Requires accessory proteins (transcription factors)

Does not require a primer

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Stages of Transcription

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription promoter recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase

DNA is bound first in a closed complex Then RNA polymerase denatures a 12ndash15 bp segment of the DNA (open complex)

The site where the first base is incorporated into the transcription is numbered ldquo+1rdquo and is called the transcription start site

Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Promoter recognition promoter sequences

Promoter sequences vary considerably

RNA polymerase binds to different promoters with different strengths binding strength relates to the level of gene expression

There are some common consensus sequences for promoters Example E coli ndash35 sequence (found 35 bases 5acute to the

start of transcription)

Example E coli TATA box (found 10 bases 5acute to the start of transcription)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Promoter recognition enhancers

Eukaryotic genes may also have enhancers

Enhancers can be located at great distances from the gene they regulate either 5acute or 3acute of the transcription start in introns or even on the noncoding strand

One of the most common ways to identify promoters and enhancers is to use a reporter gene

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Promoter recognition other players

Many proteins can regulate gene expression by modulating the strength of interaction between the promoter and RNA polymerase

Some proteins can activate transcription (upregulate gene expression)

Some proteins can inhibit transcription by blocking polymerase activity

Some proteins can act both as repressors and activators of transcription

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription chain initiation

Chain initiation

RNA polymerase locally denatures the DNA

The first base of the new RNA strand is placed complementary to the +1 site

RNA polymerase does not require a primer

The first 8 or 9 bases of the transcript are linked Transcription factors are released and the polymerase leaves the promoter region

Figure of bacterial transcription initiation

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription chain elongation

Chain elongation

RNA polymerase moves along the transcribed or template DNA strand

The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription chain termination

Most known about bacterial chain termination

Termination is signaled by a sequence that can form a hairpin loop

The polymerase and the new RNA molecule are released upon formation of the loop

Review the transcription animation

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription mRNA synthesisprocessing

Prokaryotes mRNA transcribed directly from DNA template and used immediately in protein synthesis

Eukaryotes primary transcript must be processed to produce the mRNA

Noncoding sequences (introns) are removed

Coding sequences (exons) spliced together

5acute-methylguanosine cap added

3acute-polyadenosine tail added

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription mRNA synthesisprocessing

Removal of introns and splicing of exons can occur several ways For introns within a nuclear transcript a spliceosome is

required

Splicesomes protein and small nuclear RNA (snRNA)

Specificity of splicing comes from the snRNA some of which contain sequences complementary to the splice junctions between introns and exons

Alternative splicing can produce different forms of a protein from the same gene

Mutations at the splice sites can cause disease

Thalassemia bull Breast cancer (BRCA 1)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Transcription mRNA synthesisprocessing

RNA splicing inside the nucleus on particles called spliceosomes

Splicesomes are composed of proteins and small RNA molecules (100ndash200 bp snRNA)

Both proteins and RNA are required but some suggesting that RNA can catalyze the splicing reaction

Self-splicing in Tetrahymena the RNA catalyzes its own splicing

Catalytic RNA ribozymes

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

From gene to protein genetic code

Central Dogma

Information travels from DNA to RNA to Protein

Is there a one-to-one correspondence between DNA RNA and Protein

DNA and RNA each have four nucleotides that can form them so yes there is a one-to-one correspondence between DNA and RNA

Proteins can be composed of a potential 20 amino acids only four RNA nucleotides no one-to-one correspondence

How then does RNA direct the order and number of amino acids in a protein

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

From gene to protein genetic code

How many bases are required for each amino acid (4 bases)2basesaa = 16 amino acidsmdashnot enough

(4 bases)3basesaa = 64 amino acid possibilities

Minimum of 3 basesaa required

What is the nature of the code Does it have punctuation Is it overlapping

Crick FH et al (1961) Nature 192 1227ndash32 (httpprofilesnlmnihgovSCBCBJ )

3-base nonoverlapping code that is read from a fixed point

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

From gene to protein genetic code

Nirenberg and Matthaei in vitro protein translation

Found that adding rRNA prolonged cell-free protein synthesis

Adding artificial RNA synthesized by polynucleotide phosphorylase (no template UUUUUUUUU) stimulated protein synthesis more

The protein that came out of this reaction was polyphenylalanine (UUU = Phe)

Other artificial RNAs AAA = Lys CCC =Pro

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

From gene to protein genetic code

Nirenberg

Triplet binding assay add triplet RNA ribosomes binding factors GTP and radiolabeled charged tRNA (figure)

UUU trinucleotide binds to Phe-tRNA

UGU trinucleotide binds to CYS-tRNA

By fits and starts the triplet genetic code was worked out

Each three-letter ldquowordrdquo (codon) specifies an amino acid or directions to stop translation

The code is redundant or degenerate more than one way to encode an amino acid

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

From gene to protein Translation

Components required for translation

mRNA

Ribosomes

tRNA

Aminoacyl tRNA synthetases

Initiation elongation and termination factors

Animation of translation

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Translation initiation

Ribosome small subunit binds to mRNA

Charged tRNA anticodon forms base pairs with the mRNA codon

Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine

mRNA-small subunit-tRNA complex recruits the large subunit

Eukaryotic and prokaryotic initiation differ slightly

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Translation initiation

The large subunit of the ribosome contains three binding sites

Amino acyl (A site)

Peptidyl (P site)

Exit (E site)

At initiation

The tRNAfMet occupies the P site

A second charged tRNA complementary to the next codon binds the A site

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Translation elongation

Elongation

Ribosome translocates by three bases after peptide bond formed

New charged tRNA aligns in the A site

Peptide bond between amino acids in A and P sites is formed

Ribosome translocates by three more bases

The uncharged tRNA in the A site is moved to the E site

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Translation elongation

EF-Tu recruits charged tRNA to A site Requires hydrolysis of GTP

Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids)

Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

Translation termination

Termination

Elongation proceeds until STOP codon reached UAA UAG UGA

No tRNA normally exists that can form base pairing with a STOP codon recognized by a release factor

tRNA charged with last amino acid will remain at P site

Release factors cleave the amino acid from the tRNA

Ribosome subunits dissociate from each other

Review the animation of translation

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

48

Genetic code

Def Genetic code is the nucleotide base sequence on DNA ( and

subsequently on mRNA by transcription) which will be translated into a

sequence of amino acids of the protein to be synthesized

The code is composed of codons

Codon is composed of 3 bases ( eg ACG or UAG) Each codon is

translated into one amino acid

The 4 nucleotide bases (AGC and U) in mRNA are used to produce the

three base codons There are therefore 64 codons code for the 20 amino

acids and since each codon code for only one amino acids this means

that there are more than one cone for the same amino acid

How to translate a codon (see table)

This table or dictionary can be used to translate any codon sequence

Each triplet is read from 5prime rarr 3prime direction so the first base is 5prime base

followed by the middle base then the last base which is 3prime base

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

49

Examples 5prime- A UG- 3prime codes for methionine

5prime- UCU- 3prime codes for serine

5prime - CCA- 3prime codes for proline

Termination (stop or nonsense) codons

Three of the 64 codons UAA UAG UGA do not code for any amino

acid They are termination codes which when one of them appear in

mRNA sequence it indicates finishing of protein synthesis

Characters of the genetic code

1- Specificity the genetic code is specific that is a specific codon

always code for the same amino acid

2- Universality the genetic code is universal that is the same codon is

used in all living organisms procaryotics and eucaryotics

3- Degeneracy the genetic code is degenerate ie although each codon

corresponds to a single amino acidone amino acid may have more than

one codons eg arginine has 6 different codons (give more examples

from the table)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

50

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

51

Gene mutation (altering the nucleotide sequence)

1- Point mutation changing in a single nucleotide base on the mRNA

can lead to any of the following 3 results

i- Silent mutation ie the codon containg the changed base may code

for the same amino acid For example in serine codon UCA if A is

changed to U giving the codon UCU it still code for serine See table

ii- Missense mutation the codon containing the changed base may code

for a different amino acid For example if the serine codon UCA is

changed to be CCA ( U is replaced by C) it will code for proline not

serine leading to insertion of incorrect amino acid into polypeptide chain

iii- Non sense mutation the codon containing the changed base may

become a termination codon For example serine codon UCA becomes

UAA if C is changed to A UAA is a stop codon leading to termination

of translation at that point

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

52

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

53

Types of point mutation

U A A (termination codon) Nonsense mutation

uarr

U C A rarr U C U Silent mutation

(codon for serine) (codon for serine)

darr

C C A ( codon for proline) Missense mutation

Give other examples on missense mutation which leads to some Hb

disease

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

54

2- Frame- shift mutation

deletion or addition of one or two base to

message sequence leading to change in

reading frame (reading sequence) and the

resulting amino acid seuence may become

completely different from this point

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

55

TranslationComponents required for protein synthesis1- Amino acids all amino acids involved in thefinished protein must be present at the time ofprotein synthesis2- Ribosomes the site of protein synthesis They arelarge complexes of protein and rRNA In humanthey consist of two subunits one large (60S) and onesmall (40S)

3- tRNA at least one specific type of tRNA is required to transfer

one amino acid There about 50 tRNA in human for the 20 amino

acids this means some amino acids have more than one specific

tRNA The role of tRNA in protein synthesis is discussed before

(amino acid attachment and anticodon loop)

4- aminoacyl-tRNA synthetase This is the enzyme that catalyzes the

attachment of amino acid with its corresponding tRNA forming

aminoacyl tRNA

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

56

5- mRNA that carry code for the protein to be synthesized

6- protein factors Initiation elongation and termination (or release)

factors are required for peptide synthesis

7- ATP and GTP are required as source of energy

Steps (movie)

1- Initiation

Initiation (start) codon is usually AUG which is the codon of

methionine so the initiator tRNA is methionnyl tRNA (Met tRNA)

a- The initiation factors (IF-1 IF-2 and IF-3) binds the Met tRNA with

small ribosomal subunit then to mRNA containing the code of the

protein to be synthesized IFs recognizes mRNA from its 5 cap

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

57

b-This complex binds to large ribosomal subunit forming initiation complex in which Met tRNA is present in P- site of 60 ribosomal subunitNB- tRNA bind with mRNA by base pairing between codon on mRNA and anticodon

on tRNA - mRNA is read from 5prime rarr 3prime direction

P-site is the peptidyl site of the ribosome to which methionyl tRNA is placed (enter)

2- Elongation elongation factors (EFs) stimulate the stepwise elongation of polypeptide chain as follow

a- The next aminoacyl tRNA (tRNA which carry the next amino acid specified by recognition of the next codon on mRNA) will enter A site of ribosome

A site or acceptor site or aminoacyl tRNA siteIs the site of ribosome to which each new incoming aminoacyl tRNA will enter

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

b) ribosomal peptidyl transferase enzyme will transfer methionine

from methionyl tRNA into A site to form a peptide bond between

methionine and the new incoming amino acid to form dipeptidyl

tRNA

c) Elongation factor-2 (EF-2) (called also translocase) moves

mRNA and dipeptidyl tRNA from A site to P site leaving A site free to

allow entrance of another new aminoacyl tRNA

The figure shows the repetitive cycle of elongation of chain Each

cycle is consisting of

1) codon recognition and the entrance of the new aminoacyl tRNA

acid ( amino acid carried on tRNA) into A site

2) The growing chain in P site will moved to A site with peptide

bond formation with the new amino acid

3) Translocation of growing chain to P site allowing A site free for

enterance of new amino acid an so onhelliphelliphelliphelliphelliphelliphellip Resulting in

elongation of poly peptide chain

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

59repetitive cycle of elongation

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)

60

3- Termination occurs when one of the three stop codons (UAA UAG orUGA) enters A site of the ribosome These codons are recognized by releasefactors (RFs) which are RF-1 RF-2 RF-3 RFs cause the newly synthesizedprotein to be released from the ribosomal complex and dissociation ofribosomes from mRNA (ie cause dissolution of the complex)