dr. maha daghestani dna structure and function dr. maha daghestani november 2007
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Dr. Maha Daghestani
DNA structure and function
Dr. Maha Daghestani
November 2007
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Dr. Maha Daghestani
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Dr. Maha Daghestani
DNA Structure: Double Helix
• 1953 - Watson and Crick 3-D structure of DNA
• DNA is a double helix (ll-stranded)
• Polymer of nucleotides (phosphate, sugar, base)
• DNA has 4 base types (adenine, thymine, guanine, cytosine)
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Dr. Maha Daghestani
DNA
1. Double Stranded Helix
2. Hydrogen Bonds between Nitrogenous Base Pairs
3. Adenine-Thymine and Guanine-Cytosine
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Dr. Maha Daghestani
DNA in a cell1. Which organelles contain DNA ?
• Eukaryotic cells contain several organelles. • The nucleus contains most of the DNA in a cell and
this DNA is called the chromosomal DNA. It is separated from the rest of the cell (cytoplasm) by a double layer of membrane.
• The mitochondria, which have a role in the oxidative degradation of nutrient molecules, also contain DNA, called the mitochondrial DNA.
• Eucariotic cells that are capable of photosynthesis contain chloroplasts with chloroplast DNA.
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Dr. Maha Daghestani
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Dr. Maha Daghestani
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Dr. Maha Daghestani
DNA StructureDNA Structure
DNA compositionDNA compositionPhosphatePhosphate
SugarSugarNucleic acids (bases)Nucleic acids (bases)
DNA StructureDNA Structure
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Dr. Maha Daghestani
1-Basic chemical units
1-Basic chemical units
A 5 carbon sugar - deoxyribose phosphate - link between sugars
bases: purines = adenine and guaninepyrimidines = thymine and cytosine
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Dr. Maha Daghestani
.Nucleotides
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Dr. Maha Daghestani
This is
the five-carbon sugarfound in RNA.
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Dr. Maha Daghestani
This is
the five-carbon sugarfound in DNA.
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Dr. Maha Daghestani
How are they different?
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Dr. Maha Daghestani
phosphate
sugar
ADENINE (A) THYMINE (T)
CYTOSINE (C)GUANINE (G)
base
4 DNA Nucleotides
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Dr. Maha Daghestani
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Dr. Maha Daghestani
Nitrogen bases
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Dr. Maha Daghestani
Nitrogen bases
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Dr. Maha Daghestani
ADENINE (A)
ADENINE (A)
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Dr. Maha Daghestani
GUANINE (G)
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Dr. Maha Daghestani
THYMINE (T)
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Dr. Maha Daghestani
CYTOSINE (C)
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Dr. Maha Daghestani
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Dr. Maha Daghestani
• Gene:- segment of DNA that contains all the information needed for regulated synthesis of an RNA or protein product.
• Genome:- the entire DNA sequence content of an organism (nuclear DNA)
Some Important Definitions
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Dr. Maha Daghestani
Genotype and PhenotypeGenotype and Phenotype
• Genotype1. Genetic Composition of an
Organism2. Represents the Potential Properties
• Phenotype1. The Expression of the Genes2. What You See
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Dr. Maha Daghestani
Gene Expression
• DNA codes for genes
• Genes are expressed as proteins
• Gene expression is regulated
• The genome of every cell in your body is identical
• Cell type is determined by the genes the cells express
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Dr. Maha Daghestani
What are genes
• Genes are working subunits of DNA. • Genes, which are made up of DNA, act as
instructions to make molecules called proteins
• In humans, genes vary in size from a few hundred DNA bases to more than 2 million bases.
• The Human Genome Project has estimated that humans have between 20,000 and 25,000 genes. Every person has two copies of each gene, one inherited from each parent.
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Dr. Maha Daghestani
Genes
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Dr. Maha Daghestani
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Dr. Maha Daghestani
ReplicationReplication
• The duplication of DNA which occurs during the S phase of Interphase.
• 1 Strand 2 Complementary Strands
• DNA Polymerase
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Dr. Maha Daghestani
DNA Replication
• Must be completed prior to cell division
• Helicase enzymes open the DNA
• Polymerase enzymes generate a new DNA strand on each old template
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Dr. Maha Daghestani
by adding one nucleotide after
anotherto a growing daughter
strand.
the enzyme
can build long strandsof DNA
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can only add nucleotides
if they contain the sugar
deoxyribose
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Dr. Maha Daghestani
Noticethe
deoxyribosesugar
in eachof these
molecules.
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Dr. Maha Daghestani
andthis hydrogen
Cells removethis OH
as a moleculeof H2O
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- H2O
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Dr. Maha Daghestani
Two empty bonds
remain afterthe molecule
of waterhas been removed.
- H2O
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Dr. Maha Daghestani
a new
forms at this location, joining the two nucleotides.
bond
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Dr. Maha Daghestani
a new
forms at this location, joining the two nucleotides.
bond
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Dr. Maha Daghestani
Growing daughter strands
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Dr. Maha Daghestani
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Dr. Maha Daghestani
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One More Time!
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Dr. Maha Daghestani
thymine
adenine
cytosine
guanine
phosphate
deoxyribose sugar
DNA nucleotide
Deoxyribose sugar
phosphate
Nitrogenous base (guanine)
RNA nucleotide
ribose sugar
phosphate
Nitrogenous base (uracil)
Sugar / phosphate “strand”Nitrogenous base “rung”
Hydrogen bond(H-bonds)
DNA Replication
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Dr. Maha Daghestani
Step 1: Hydrogen bonds between complimentary bases break
DNA “unzips”
DNA Replication
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Dr. Maha Daghestani
Step 2: DNA strandspull apart from each other
DNA Replication
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Dr. Maha Daghestani
Step 3: DNA nucleotides in the cellmatch up with each side of the “unzipped” DNA
each “unzipped’ strands forms a template for a new strand
DNA Replication
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Dr. Maha Daghestani
Step 4: Each “old’ strandforms a template for a “new” strand
two identical DNA molecules form
“old” (original) strand
“new” strand, identicalsequence to the original
DNA Replication
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Central Dogma
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Central Dogma of Genetics
DNA
RNA
Protein
Replication
Transcription
Translation
Reverse Transcription
aa aa aa aa aa aa
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Replication Replication Transcription Transcription TranslationTranslation
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Dr. Maha Daghestani
protein• For a cell to make protein, the information from
a gene is copied, base by base, from DNA into new strands of messenger RNA (mRNA).
• Then mRNA travels out of the nucleus into the cytoplasm, to cell organelles called ribosomes. There, mRNA directs the assembly of amino acids that fold into completed protein molecule.
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Dr. Maha Daghestani
DNA DNA RNA RNA ProteinProtein
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Dr. Maha Daghestani
Protein SynthesisProtein Synthesis
• The production (synthesis) of proteinsproteins.
• 3 phases3 phases:
1.1. TranscriptionTranscription
2.2. RNA processingRNA processing
3.3. TranslationTranslation
• RememberRemember:: DNA DNA RNA RNA ProteinProtein
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Dr. Maha Daghestani
Question:Question:
• How does RNARNA (ribonucleic (ribonucleic acid) acid) differ from DNA DNA
(deoxyribonucleic acid)(deoxyribonucleic acid)?
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Dr. Maha Daghestani
RNARNA differs from DNADNA
1. RNARNA has a sugar ribosesugar ribose
DNADNA has a sugar deoxyribosesugar deoxyribose
2. RNARNA contains uracil (U)uracil (U)
DNADNA has thymine (T)thymine (T)
3. RNARNA molecule is single-single-strandedstranded
DNADNA is double-strandeddouble-stranded
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Dr. Maha Daghestani
1. Transcription1. Transcription
• The transfer of information in the nucleusnucleus from a DNADNA molecule to an RNARNA molecule.
• Only 1 1 DNADNA strand serves as the templatetemplate
• Starts at promoter DNADNA (TATA box)
• Ends at terminator DNADNA (stop)
• When complete, pre-RNApre-RNA molecule is released.
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Dr. Maha Daghestani
Question:Question:
• What is the What is the enzymeenzyme responsible for responsible for the production of the RNA the production of the RNA molecule?molecule?
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Dr. Maha Daghestani
Answer:Answer: RNA PolymeraseRNA Polymerase
• Separates the DNADNA molecule by breaking the H-bonds between the bases.
• Then moves along one of the DNA DNA strandsstrands and links RNARNA nucleotides together.
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Dr. Maha Daghestani
1. Transcription1. Transcription
DNADNA
pre-mRNApre-mRNA
RNA PolymeraseRNA Polymerase
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Question:Question:
• What would be the complementary RNARNA strand for the following DNADNA sequence?
• DNA 5’-GCGTATG-3’DNA 5’-GCGTATG-3’
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Dr. Maha Daghestani
Answer:Answer:
• DNA 5’-GCGTATG-3’DNA 5’-GCGTATG-3’
• RNA 3’-CGCAUAC-5’RNA 3’-CGCAUAC-5’
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Dr. Maha Daghestani
2. RNA Processing2. RNA Processing
• Maturation of pre-RNApre-RNA molecules.
• Also occurs in the nucleus.nucleus.
• IntronsIntrons spliced out by splicesome-enzymesplicesome-enzyme and exonsexons come together.
• End product is a mature RNA moleculemature RNA molecule that leaves the nucleusnucleus to the cytoplasm.cytoplasm.
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Dr. Maha Daghestani
2. RNA Processing2. RNA Processing
pre-RNA molecule
intron
intronexon exon exon
exon exon exon
Mature RNA moleculeMature RNA molecule
exon exon exon
intron intron
splicesome splicesome
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Dr. Maha Daghestani
During transcription, one DNA strand, the template strand, provides a template for ordering the sequence of nucleotides
in an RNA transcript
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Types of RNATypes of RNA
• Three types ofThree types of RNARNA:
A.A. messenger RNA (mRNA)messenger RNA (mRNA)
B.B. transfer RNA (tRNA)transfer RNA (tRNA)
C.C. ribosome RNA (rRNA)ribosome RNA (rRNA)
• Remember: all produced in theRemember: all produced in the nucleusnucleus!!
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Dr. Maha Daghestani
A. Messenger RNA (mRNA)A. Messenger RNA (mRNA)
• Carries the information for a specific proteinprotein.
• Made up of 500 to 1000 nucleotides nucleotides long.
• Made up of codons codons (sequence of three bases: AUG - methionine).
• Each codoncodon, is specific for an amino acidamino acid.
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Dr. Maha Daghestani
A. Messenger RNA (mRNA)A. Messenger RNA (mRNA)
methionine glycine serine isoleucine glycine alanine stopcodon
proteinprotein
A U G G G C U C C A U C G G C G C A U A AmRNAmRNA
startcodon
Primary structure of a proteinPrimary structure of a protein
aa1 aa2 aa3 aa4 aa5 aa6
peptide bonds
codon 2 codon 3 codon 4 codon 5 codon 6 codon 7codon 1
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Dr. Maha Daghestani
B. Transfer RNA (tRNA)B. Transfer RNA (tRNA)
• Made up of 75 to 80 nucleotides long.
• Picks up the appropriate amino acidamino acid floating in the cytoplasm (amino amino acid activating enzymeacid activating enzyme)
• Transports amino acids amino acids to the mRNAmRNA.
• Have anticodonsanticodons that are complementary to mRNAmRNA codonscodons.
• Recognizes the appropriate codonscodons on the mRNAmRNA and bonds to them with H-bonds.
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• A tRNA molecule consists of a strand of about 80 nucleotides that folds back on itself to form a three-dimensional structure.– It includes a loop containing the anticodon and an
attachment site at the 3’ end for an amino acid.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 17.13
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C. Ribosomal RNA (rRNA)C. Ribosomal RNA (rRNA)
• Made up of rRNrRNAA is 100 to 3000 nucleotides long.
• Important structural component of a ribosomeribosome..
• Associates with proteins proteins to form ribosomes.ribosomes.
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RibosomesRibosomes• Large and small subunits.Large and small subunits.• Composed of rRNA (40%) rRNA (40%) and proteins (60%).proteins (60%).
• Both units come together and help bind the mRNAmRNA and tRNA.tRNA.
• Two sites forTwo sites for tRNAtRNA
a. P siteP site (first and last tRNA will attachtRNA will attach)
b. A siteA site
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• Each ribosome has a binding site for mRNA and three binding sites for tRNA molecules.
– The P site holds the tRNA carrying the growing polypeptide chain.
– The A site carries the tRNA with the next amino acid.
– Discharged tRNAs leave the ribosome at the E site.
Fig. 17.15b &c
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• Translation can be divided into three stages: initiation elongation termination
• All three phase require protein “factors” that aid in the translation process.
• Both initiation and chain elongation require
energy provided by the hydrolysis of GTP.
Translation
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• Initiation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits.
– First, a small ribosomal subunit binds with mRNA and a special initiator tRNA, which carries methionine and attaches to the start codon.
– Initiation factors bring in the large subunit such that the initiator tRNA occupies the P site.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 17.17
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• Elongation consists of a series of three stepcycles as each amino acid is added to the proceeding one.
• During codon recognition, an elongation factor assists hydrogen bonding between the mRNA codon under the A site with the corresonding anticodon of tRNA carrying the appropriateamino acid.
– This step requires the hydrolysis of two GTP.
Elongation
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• The three steps of elongation continue codon by codon to add amino acids until the polypeptide chain is completed.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin CummingsFig. 17.18
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• Termination occurs when one of the three stop codons reaches the A site.
• A release factor binds to the stop codon and hydrolyzes the bond between the polypeptide and its tRNA in the P site.
• This frees the polypeptide and the translation complex
disassembles.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 17.19
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3. Translation3. Translation
Nuclearmembrane
TranscriptionTranscription
RNA ProcessingRNA Processing
TranslationTranslation
DNA
Pre-mRNA
mRNA
Ribosome
Protein
Eukaryotic Eukaryotic CellCell
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3. Translation3. Translation
• Synthesis of proteinsproteins in the cytoplasmcytoplasm
• Involves the following:Involves the following:
1. mRNA (codons)mRNA (codons)
2. tRNA (anticodons)tRNA (anticodons)
3. rRNArRNA
4. ribosomesribosomes
5. amino acidsamino acids
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3. Translation3. Translation• Three parts:
1. initiationinitiation: start codon (AUG)
2. elongationelongation:
3. terminationtermination: stop codon (UAG)
• Let’s make a PROTEIN!!!!PROTEIN!!!!.
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3. Translation3. Translation
PSite
ASite
Largesubunit
Small subunit
mRNAmRNA
A U G C U A C U U C G
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InitiationInitiation
mRNAmRNA
A U G C U A C U U C G
2-tRNA
G
aa2
A U
A
1-tRNA
U A C
aa1
anticodon
hydrogenbonds codon
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mRNAmRNA
A U G C U A C U U C G
1-tRNA 2-tRNA
U A C G
aa1 aa2
A UA
anticodon
hydrogenbonds codon
peptide bond
3-tRNA
G A A
aa3
ElongationElongation
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mRNAmRNA
A U G C U A C U U C G
1-tRNA
2-tRNA
U A C
G
aa1
aa2
A UA
peptide bond
3-tRNA
G A A
aa3
Ribosomes move over one codon
(leaves)
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mRNAmRNA
A U G C U A C U U C G
2-tRNA
G
aa1
aa2
A UA
peptide bonds
3-tRNA
G A A
aa3
4-tRNA
G C U
aa4
A C U
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mRNAmRNA
A U G C U A C U U C G
2-tRNA
G
aa1aa2
A U
A
peptide bonds
3-tRNA
G A A
aa3
4-tRNA
G C U
aa4
A C U
(leaves)
Ribosomes move over one codon
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mRNAmRNA
G C U A C U U C G
aa1aa2
A
peptide bonds
3-tRNA
G A A
aa3
4-tRNA
G C U
aa4
A C U
U G A
5-tRNA
aa5
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mRNAmRNA
G C U A C U U C G
aa1aa2
A
peptide bonds
3-tRNA
G A A
aa3
4-tRNA
G C U
aa4
A C U
U G A
5-tRNA
aa5
Ribosomes move over one codon
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mRNAmRNA
A C A U G U
aa1
aa2
U
primaryprimarystructurestructureof a proteinof a protein
aa3
200-tRNA
aa4
U A G
aa5
C U
aa200
aa199
terminatorterminator or stopor stop codoncodon
TerminationTermination
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End ProductEnd Product
• The end products of protein synthesis is a primary structure of a proteinprimary structure of a protein.
• A sequence of amino acid amino acid bonded together by peptide bondspeptide bonds.
aa1
aa2 aa3 aa4aa5
aa200
aa199
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PolyribosomePolyribosome
• Groups of ribosomes reading same mRNA mRNA simultaneously producing many proteins proteins (polypeptides).(polypeptides).
incominglargesubunit
incomingsmall subunit polypeptidepolypeptide
mRNAmRNA1 2 3 4 5 6 7
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Question:Question:
• The anticodon The anticodon UACUAC belongs to a tRNA belongs to a tRNA that recognizes and binds to a that recognizes and binds to a particular particular amino acid.amino acid.
• What would be theWhat would be the DNA base code DNA base code for for thisthis amino acid?amino acid?
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Answer:Answer:
• tRNA tRNA - UAC (anticodon)- UAC (anticodon)
• mRNAmRNA - AUG (codon)- AUG (codon)
• DNA DNA - TAC- TAC
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Thank youThank you