nucleic acids dna, rna & protein synthesis sdk september 24, 2013
DESCRIPTION
NUCLEIC ACIDS DNA, RNA & Protein Synthesis SDK September 24, 2013. Road Map. What is nucleic Acid Types of nucleic acid Structural and functional characeristics of nucleic acid Nomenclature of Nucleic Acid Components DNA Definition Structure of DNA Types of DNA DNA & Chromosomes - PowerPoint PPT PresentationTRANSCRIPT
NUCLEIC ACIDSDNA, RNA &
Protein SynthesisSDK
September 24, 2013
Road Map
1. What is nucleic Acid1. Types of nucleic acid2. Structural and functional characeristics of nucleic acid3. Nomenclature of Nucleic Acid Components
2. DNA1. Definition2. Structure of DNA3. Types of DNA4. DNA & Chromosomes
3. RNA1. Definition2. Structure& function of RNA
4. Difference between DNA & RNA5. Protein and Gene Expression
1. Protein Synthesis2. Transcription3. DNA Intones and Exons4. Translation5. Polypeptide chain6. Termination codon7. Summary
6. Brain Work
Nucleic Acids• Are the organic molecules derived from the
nucleus.
Friedrich Miescher in 1869• Isolated what he called nuclein from the nuclei of pus
cells• Nuclein was shown to have acidic properties, hence it
became called nucleic acid
Types of Nucleic Acid
• Deoxyribonucleic acid (DNA)• Ribonucleic acid (RNA)
The Distribution of Nucleic Acids in The Human Cell
• DNA is found in the nucleus with small amounts in mitochondria
• RNA is found throughout the cell
Nucleic Acid Structure
• Nucleic acids are polynucleotides
• Their building blocks are nucleotides
Nucleic Acid Structure
1. Primary- Basic component of NA
2. Secondary- Nucleoside and nucleotides
3. Tertiary- Formation of poly nucleotide chain
4. Quaternary- Pairing of two poly nucleotide
chains
Basic structure of Purine & Pyrimidine
Pyrimidines
Purines
Nucleic Acid Structure
O
N
N
NH2
O
CH2OPO
O-O-
OH
O
N
N
NH2
CH2OPO
O-
OH
O
N
N
AMP
CMP
3
5
Nomenclature of Nucleic Acid Components
Base Nucleoside Nucleotide Nucleicacid
PurinesAdenine Adenosine Adenylate RNA
Deoxyadenosine Deoxyadenylate DNA-------------------------------------------------------------------------------------Guanine Guanosine Guanylate RNA
Deoxy guanosine Deoxyguanylate DNA------------------------------------------------------------------------------------- PyrimidinesCytosine Cytidine Cytidylate RNA
Deoxycytidine Deoxycytidylate DNA-------------------------------------------------------------------------------------Thymine Thymidine Thymidylate DNA-------------------------------------------------------------------------------------Uracil Uridine Uridylate RNA
5-Fluorouracil 6-Mercaptopurine
Anticancer agents
Azidothymidine Dideoxyinosine
Antiretroviral agents
Nucleoside and base analogs can be used as anti-cancer and anti-virus drugs
DNA
Double Helix of DNA• DNA, or deoxyribonucleic acid, is the hereditary material in
humans and almost all other organisms.
• Nearly every cell in a person’s body has the same DNA. • Most DNA is located in the cell nucleus (where it is called
nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).
• Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people.
Why the people are different from each other
The order, or sequence, of these bases determines the information available for building and maintaining an organism, similar to the way in which letters of the alphabet appear in a certain order to form words and sentences.
• DNA contains two strands of nucleotides• H bonds hold the two strands in a double-helix
structure• A helix structure is like a spiral stair case• Bases are always paired as A–T and G-C• Thus the bases along one strand complement the
bases along the other
Traditionally, a DNA sequence is drawn from 5’ to 3’ end.
A shorthand notation for this sequence is ACGTA
The primary structure of DNA is the sequence
The 2ndry structure of DNA is a Double Helix of DNA
DNA TypesProperty A-DNA B-DNA Z-DNAHelix Handedness Right Right Left
Base Pairs per turn 11 10.4 12
Rise per base pair along axis
0.23nm 0.34nm 0.38nm
Pitch 2.46nm 3.40nm 4.56nm
Diameter 2.55nm 2.37nm 1.84nm
Width Widest Intermediate Narrowest
Conformation of Glycosidic bond
anti anti Alternating anti and syn
Major Groove Present Present Absent
Minor Groove Present Present Deep cleft
Helix : right handedBase pairs: almost perpendicular to the helix axis; 3.4 Å apartOne turn of the helix: 36 Å; ~10.4 base pairs Minor groove: 12 Å acrossMajor groove: 22 Å across
Normally DNA is B-form DNA
In eukaryotic cells,
DNA is folded into chromatin
DNA Tertiary Structure
DNA double helical structure coils round histones.
DNA bound to histones forms nucleosomes (10nm fibres)
Nucleosomes contain 146 nucleotidesNucleosomes
Repeating globular subunits of chromatin that consist of a complex of DNA and histone.
Compaction of DNA in a eukaryotic Chromosome
Supercoil = coil over coil
Functions of DNA and summary of structure
DNA consists of four bases—A, G, C, and T—that are held in linear array by phosphodiester bonds through the 3' and 5' positions of adjacent deoxyribose .
DNA is organized into two strands by the pairing of bases A to T and G to C on complementary strands. These strands form a double helix around a central axis.
The 3 x 109 base pairs of DNA in humans are organized into the haploid complement of 23 chromosomes.
Ribonucleic acid (RNA)
Ribonucleic acid (RNA)• Definition: RNA is polymer of ribonucleotides held
together by 3′,5′-phosphodiester bonds.
• The RNA is made from four types of ribonucleotides, ATP,GTP,CTP and UTP.
• These ribonucleotides are made from: Nitrogenous bases ; Adenine, Guanine, Uracil and Cytosine.Sugar –ribosePhosphate group
• Single stranded but usually forms intra-molecular base
pairs
• major and minor grooves are less pronounced
• Uracil instead of thymine
• Structural, adaptor and transfer roles of RNA are all
involved in decoding the information carried by DNA
RNA Structure
Type of RNA
Short name Functions
Messenger RNA mRNA Transfers genetic information from genes to ribosomes for synthesis of proteins
Transfer RNA tRNA Acts as an adaptors between mRNA and amino acids in protein synthesis
Ribosomal RNA rRNA •Provides structural framework for ribosomes. •Also helps in peptide bond formation (as an enzyme)
Types and functions of RNA Three major types:
Messenger RNA: 5-10%
Transfer RNA : 10-20%
Ribosomal RNA: 50-80%
Minor Types of RNA
Heterogeneous nuclear RNA
hnRNA Serves as precursor for mRNA and rRNA
Small nuclear RNA snRNA Involved in mRNA processing
Small nucleolar RNA
snoRNA Plays a key role in the processing of rRNA molecules.
Small cytoplasmic RNA
scRNA Involved in the selection of proteins for export
Micro RNA miRNA Involved in translation and mRNA degradation
Non-coding RNA ncRNA Involved in telomere synthesis, protein transport , tRNA processing etc
Messenger RNA (m-RNA)
Comprises only 5% of the RNA in the cellMost heterogeneous in size and base sequenceAll members of the class function as messengers carrying the information in a gene to the protein synthesizing machinery
Structural Characteristics of m-RNA
The 5’ terminal end is capped by 7- methyl guanosine triphosphate cap.
The cap is involved in the recognition of mRNA by the translating machinery
It stabilizes m RNA by protecting it from 5’ exonuclease
The 3’end of most m-RNAs have a polymer of Adenylate residues( 20-250) The tail prevents the attack by 3’ exonucleasesHistones and interferons do not contain poly A tails On both 5’ and 3’ end there are non coding sequences which are not translated (NCS)The intervening region between non coding sequences present between 5’ and 3’ end is called coding region. This region encodes for the synthesis of a protein.
Structural Characteristics of m-RNA
Structural Characteristics of m-RNA
5’ cap and 3’ tail impart stability to m RNA by protecting from specific exo nucleases.
The m- RNA molecules are formed with the help of DNA template during the process of transcription.The sequence of nucleotides in m RNA is complementary to the sequence of nucleotides on template DNA.The sequence carried on m -RNA is read in the form of codons.A codon is made up of 3 nucleotidesThe m-RNA is formed after processing of heterogeneous nuclear RNA
Structural Characteristics of m-RNA
Heterogeneous nuclear RNA(hnRNA)
In mammalian nuclei , hnRNA is the immediate product of gene transcription The nuclear product is heterogeneous in size (Variable) and is very large.75 % of hnRNA is degraded in the nucleus, only 25% is processed to mature m RNA
Mature m –RNA is formed from primary transcript by capping, tailing, splicing and base modification.
Heterogeneous nuclear RNA(hnRNA)
Transfer RNA (t- RNA)
Transfer RNA (t- RNA)
Transfer RNA are the smallest of three major species of RNA moleculesThey have 74-95 nucleotide residuesThey transfer the amino acids from cytoplasm to the protein synthesizing machinery, hence the name t RNA.They are also called Adapter molecules, since they act as adapters for the translation of the sequence of nucleotides of the m RNA in to specific amino acidsThere are at least 20 species of t RNA one corresponding to each of the 20 amino acids required for protein synthesis.
Structural characteristics of t- RNA
1) Primary structure- The nucleotide sequence of all the t RNA molecules allows extensive intrastand complimentarity that generates a secondary structure.2) Secondary structure- Each single t- RNA shows extensive internal base pairing and acquires a clover leaf like structure. The structure is stabilized by hydrogen bonding between the bases and is a consistent feature.
Secondary structure (Clover leaf structure)
All t-RNA contain 5 main arms or loops which are as follows-a) Acceptor armb) Anticodon armc) D armd) TΨ C arme) Extra arm
Secondary structure of t- RNA Acceptor arm The acceptor arm is at 3’ end It has 7 base pairs The end sequence is unpaired Cytosine, Cytosine-
Adenine at the 3’ end The 3’ OH group terminal of Adenine binds with
carboxyl group of amino acids The t RNA bound with amino acid is called Amino
acyl t RNA CCA attachment is done post transcriptionally
b) Anticodon arm Lies at the opposite end of acceptor arm5 base pairs longRecognizes the triplet codon present in the m RNABase sequence of anticodon arm is complementary to the base sequence of m RNA codon. Due to complimentarity it can bind specifically with m RNA by hydrogen bonds.
Secondary structure of t- RNA
c) DHU arm It has 3-4 base pairsServes as the recognition site for the enzyme (amino acyl t RNA synthetase) that adds the amino acid to the acceptor arm.d) TΨC armThis arm is opposite to DHU armSince it contains pseudo uridine that is why it is so named It is involved in the binding of t RNA to the ribosomes
Secondary structure of t- RNA
e) Extra arm or Variable arm About 75 % of t RNA molecules possess a short extra armIf about 3-5 base pairs are present the t-RNA is said to be belonging to class 1. Majority t -RNA belong to class 1. The t –RNA belonging to class 2 have long extra arm, 13-21 base pairs in length.
Secondary structure of t- RNA
Tertiary structure of t- RNA The L shaped tertiary structure is formed by further folding of the clover leaf due to hydrogen bonds between T and D arms. The base paired double helical stems get arranged in to two double helical columns, continuous and perpendicular to one another.
Ribosomal RNA and Ribosomes
Ribosomal RNA and Ribosomes
• Ribosomal RNA (rRNA) is a component of the ribosomes, the protein synthesis factories in the cell.
• Eukaryotic ribosome (80S) made up of two dissimilar subunits.
Large subunit (60S) made up of about 50 proteins and 3 types of rRNA (5S, 5.8 S and 28 S rRNA)
Small subunit (40S) made up of about 35 proteins and 1 type of rRNA(18 S rRNA)
AE P
Large Subunit
Small Subunit
A - Amino acyl siteP - Peptidyl siteE - Exit site
Ribosomal RNA (rRNA)
Ribosomal RNA (rRNA)The functions of the ribosomal RNA molecules in the ribosomal particle are not fully understood, but they are necessary for ribosomal assembly and seem to play key roles in the binding of mRNA to ribosomes and its translationRecent studies suggest that an rRNA component performs the peptidyl transferase activity and thus is an enzyme (a ribozyme).
Comparisons of DNA and RNAFeature DNA RNABases
Purines Adenine, Guanine Adenine, Guanine
Pyrimidines Cytosine, Thymine Cytosine, Uracil
Sugar Deoxy-D-ribose D-Ribose
Size 103 to 109 bp • tRNA: 80 to 120 nt• mRNA: 500 to 10,000 nt• rRNA: 120 to 3,000 nt
Shape base-paired double-stranded helix Single-stranded random coils (tRNA is about 75% base paired)
Associated substances histones, protamines, enzymes, spermine etc.
Ribosomal proteins with rRNA
Cellular distribution Mostly in nucleus; some in mitochondria
Highest in cytoplasm but much in nucleus and nucleolus
Differences between RNA and DNAS.No. RNA DNA
1) Single stranded mainly except when self complementary sequences are there it
forms a double stranded structure (Hair pin structure)
Double stranded (Except for certain viral DNA s which are single stranded)
2) Ribose is the main sugar The sugar moiety is deoxy ribose
3) Pyrimidine components differ. Thymine is never found(Except
tRNA)
Thymine is always there but uracil is never found
4) Being single stranded structure- It does not follow Chargaff’s rule
It does follow Chargaff's rule. The total purine content in a double stranded DNA is always equal to
pyrimidine content.
Differences between RNA and DNAS.No. RNA DNA
5) RNA can be easily destroyed by alkalies to cyclic diesters of mono nucleotides.
DNA resists alkali action due to the absence of OH group at 2’ position
6) RNA is a relatively a labile molecule, undergoes easy and spontaneous
degradation
DNA is a stable molecule. The spontaneous degradation is very 2
slow. The genetic information can be stored for years together without
any change.
7) Mainly cytoplasmic, but also present in nucleus (primary transcript and small
nuclear RNA)
Mainly found in nucleus, extra nuclear DNA is found in
mitochondria, and plasmids etc
8) The base content varies from 100- 5000. The size is variable.
Millions of base pairs are there depending upon the organism
Differences between RNA and DNAS.No. RNA DNA
9) There are various types of RNA – mRNA, r RNA, t RNA, Sn RNA, Si RNA,
mi RNA and hn RNA. These RNAs perform different and specific
functions.
DNA is always of one type and performs the function of storage and
transfer of genetic information.
10) RNA is synthesized from DNA, it can not form DNA(except by the action of reverse transcriptase). It can not
duplicate (except in certain viruses where it is a genomic material )
DNA can form DNA by replication, it can also form RNA by transcription.
11) Many copies of RNA are present per cell
Single copy of DNA is present per cell.
Proteins/ Gene Expression
Proteins/ Gene Expression • Proteins make up all living materials
• Proteins are composed of amino acids – there are 20 different amino acids
• Different proteins are made by combining these 20 amino acids in different combinations
• Proteins are manufactured in the ribosomes under the strict control and order of DNA.
• The DNA language is made up of letters which are ATGCATATGGAATCAG
• These letters forms Words• ATC GCA GGA AUU AUG
• These words make sentences
•
Protein Synthesis
DNA and Protein Synthesis• DNA contains the genetic information to make amino acids•Amino acids combine to make proteins
• These proteins determine the physical traits of an organism and control cellular functions.
• Proteins do everything, and DNA gets all the credit!
Transcription is the Reading of the DNA and Changing the code to mRNA.
Translation is changing the mRNA into a trait by using tRNA to interpret the mRNA.
Transcription & Translation
• DNA has regions of coding and non-coding. The regions of DNA that code for proteins or traits are called EXONS, while the regions that do not code for proteins are called INTRONS.
Introns & Exons
Making a Protein—Transcription•First Step: Copying of genetic information from DNA to RNA called Transcription
•Part of DNA temporarily unzips and is used as a template to assemble complementary nucleotides into messenger RNA (mRNA).
• Transcription occurs inside the nucleus in a two step sequence of events.– Pre-mRNA includes both introns and exons for the
gene.– mRNA is only the coding portion (exons).
• Translation occurs in the cytoplasm at the ribosomes.– Reminder: There are three (3) types of RNA• Messenager (mRNA)• Transfer (tRNA)• Ribsomal (rRNA)
Site of Transcription&Translation
A U G G G C U U A A A G C A G U G C A C G U U
This is a molecule of messenger RNA.It was made in the nucleus by transcription from a
DNA molecule.
mRNA molecule
Codon
Messenger RNA
A U G G G C U U A A A G C A G U G C A C G U U
A ribosome on the rough endoplasmic reticulum attaches to the mRNA
molecule.
Ribosome
Ribosome
A U G G G C U U A A A G C A G U G C A C G U U
It brings an amino acid to the first three bases (codon) on the mRNA.
Amino acid
tRNA molecule
anticodon
U A C
A transfer RNA molecule arrives.
The three unpaired bases (anticodon) on the tRNA link up with the codon.
Transfer RNA
A U G G G C U U A A A G C A G U G C A C G U U
Another tRNA molecule comes into place, bringing a second amino acid.
U A C C C G
Its anticodon links up with the second codon on the mRNA.
Transfer RNA
A U G G G C U U A A A G C A G U G C A C G U U
A peptide bond forms between the two amino acids.
Peptide bond
C C G U A C
Transfer RNA
A U G G G C U U A A A G C A G U G C A C G U U
The first tRNA molecule releases its amino acid and moves off into the cytoplasm.
C C G U A C
Transfer RNA
A U G G G C U U A A A G C A G U G C A C G U U C C G
The ribosome moves along the mRNA to the next codon.
Transfer RNA
A U G G G C U U A A A G C A G U G C A C G U U
Another tRNA molecule brings the next amino acid into place.
C C G
A A U
A U G G G C U U A A A G C A G U G C A C G U U
A peptide bond joins the second and third amino acids to form a polypeptide chain.
C C G C C G
Polypeptide Chain
A U G G G C U U A A A G C A G U G C A C G U U
The polypeptide chain gets longer.
G U C
A C G
The process continues.
This continues until a termination (stop) codon is reached.
The polypeptide is then complete.
Termination (stop) codon
DNA and Protein Synthesis - Summary
Use the codon charts on the next page to find the amino acid sequence coded for by the following mRNA strands.
CAC/CCA/UGG/UGA
___________/___________/___________/____________
AUG/AAC/GAC/UAA
___________/___________/___________/____________
CAC/CCA/UGG/UGA
___________/___________/___________/____________Histidine Proline Tryptophan Stop
AUG/AAC/GAC/UAA
___________/___________/___________/____________Methionine Asparagine Aspartic Acid Stop
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