NUCLEIC ACIDS DNA, RNA & Protein Synthesis SDK September 24, 2013

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NUCLEIC ACIDS DNA, RNA & Protein Synthesis SDK September 24, 2013

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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 Presentation

Transcript of NUCLEIC ACIDS DNA, RNA & Protein Synthesis SDK September 24, 2013

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NUCLEIC ACIDSDNA, RNA &Protein SynthesisSDKSeptember 24, 2013

Road MapWhat is nucleic AcidTypes of nucleic acidStructural and functional characeristics of nucleic acidNomenclature of Nucleic Acid ComponentsDNADefinitionStructure of DNATypes of DNADNA & ChromosomesRNADefinitionStructure& function of RNADifference between DNA & RNAProtein and Gene ExpressionProtein SynthesisTranscriptionDNA Intones and ExonsTranslationPolypeptide chainTermination codonSummaryBrain Work

Nucleic AcidsAre the organic molecules derived from the nucleus. Friedrich Miescher in 1869Isolated what he called nuclein from the nuclei of pus cellsNuclein was shown to have acidic properties, hence it became called nucleic acid

Types of Nucleic Acid Deoxyribonucleic acid (DNA)Ribonucleic acid (RNA)4The Distribution of Nucleic Acids in The Human Cell DNA is found in the nucleus with small amounts in mitochondria

RNA is found throughout the cell5Nucleic Acid StructureNucleic acids are polynucleotidesTheir building blocks are nucleotides6Nucleic Acid StructurePrimary- Basic component of NASecondary- Nucleoside and nucleotidesTertiary- Formation of poly nucleotide chainQuaternary- Pairing of two poly nucleotide chains

Basic structure of Purine & Pyrimidine

Pyrimidines

Purines

Nucleic Acid Structure

35Nomenclature of Nucleic Acid Components

BaseNucleoside Nucleotide NucleicacidPurinesAdenineAdenosine Adenylate RNADeoxyadenosine Deoxyadenylate DNA-------------------------------------------------------------------------------------GuanineGuanosine Guanylate RNADeoxy guanosine Deoxyguanylate DNA------------------------------------------------------------------------------------- PyrimidinesCytosineCytidine Cytidylate RNADeoxycytidine Deoxycytidylate DNA-------------------------------------------------------------------------------------ThymineThymidine Thymidylate DNA-------------------------------------------------------------------------------------UracilUridineUridylate RNA

5-Fluorouracil6-MercaptopurineAnticancer agents

AzidothymidineDideoxyinosineAntiretroviral agentsNucleoside and base analogs can be used as anti-cancer and anti-virus drugs

DNADouble Helix of DNADNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms.

Nearly every cell in a persons 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 nucleotidesH bonds hold the two strands in a double-helix structureA helix structure is like a spiral stair caseBases are always paired as AT and G-CThus 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 sequenceThe 2ndry structure of DNA is a Double Helix of DNA

DNA TypesPropertyA-DNAB-DNAZ-DNAHelix HandednessRightRightLeftBase Pairs per turn1110.412Rise per base pair along axis0.23nm0.34nm0.38nmPitch2.46nm3.40nm4.56nmDiameter2.55nm2.37nm1.84nmWidthWidestIntermediateNarrowestConformation of Glycosidic bondantiantiAlternating anti and synMajor GroovePresentPresentAbsentMinor GroovePresentPresentDeep cleftHelix : right handedBase pairs: almost perpendicular to the helix axis; 3.4 apartOne turn of the helix: 36 ; ~10.4 base pairs Minor groove: 12 acrossMajor groove: 22 acrossNormally DNA is B-form DNA

In eukaryotic cells, DNA is folded into chromatin

DNA Tertiary StructureDNA double helical structure coils round histones.

DNA bound to histones forms nucleosomes (10nm fibres)

Nucleosomes contain 146 nucleotidesNucleosomesRepeating globular subunits of chromatin that consist of a complex of DNA and histone.

Compaction of DNA in a eukaryotic Chromosome

Supercoil = coil over coilFunctions of DNA and summary of structureDNA consists of four basesA, G, C, and Tthat 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

3737 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 Structure38700-800 rRNA and 497 tRNA genes Type of RNA Short nameFunctionsMessenger RNAmRNATransfers genetic information from genes to ribosomes for synthesis of proteinsTransfer RNA tRNAActs as an adaptors between mRNA and amino acids in protein synthesisRibosomal RNArRNAProvides 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 RNAhnRNAServes as precursor for mRNA and rRNASmall nuclear RNAsnRNAInvolved in mRNA processingSmall nucleolar RNAsnoRNAPlays a key role in the processing of rRNA molecules.Small cytoplasmic RNAscRNAInvolved in the selection of proteins for exportMicro RNAmiRNA Involved in translation and mRNA degradationNon-coding RNAncRNAInvolved in telomere synthesis, protein transport , tRNA processing etcMessenger 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-RNAThe 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 3end 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-RNAStructural Characteristics of m-RNA5 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 RNAStructural 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- RNA1) 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-Acceptor armAnticodon armD armT C armExtra arm

Secondary structure of t- RNAAcceptor armThe acceptor arm is at 3 endIt has 7 base pairsThe end sequence is unpaired Cytosine, Cytosine-Adenine at the 3 endThe 3 OH group terminal of Adenine binds with carboxyl group of amino acidsThe t RNA bound with amino acid is called Amino acyl t RNACCA 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) TC 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- RNAe) 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- RNATertiary 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 Ribosomes5757Ribosomal RNA and RibosomesRibosomal 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)

AEP Large SubunitSmall SubunitA - Amino acyl siteP - Peptidyl siteE - Exit siteRibosomal 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 RNAFeatureDNARNABasesPurinesAdenine, GuanineAdenine, Guanine PyrimidinesCytosine, ThymineCytosine, UracilSugarDeoxy-D-riboseD-RiboseSize103 to 109 bp

tRNA: 80 to 120 nt mRNA: 500 to 10,000 nt rRNA: 120 to 3,000 ntShapebase-paired double-stranded helixSingle-stranded random coils (tRNA is about 75% base paired)Associated substanceshistones, protamines, enzymes, spermine etc.Ribosomal proteins with rRNACellular distributionMostly in nucleus; some in mitochondriaHighest in cytoplasm but much in nucleus and nucleolus

Differences between RNA and DNAS.No.RNADNA1)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 sugarThe sugar moiety is deoxy ribose3)Pyrimidine components differ. Thymine is never found(Except tRNA)Thymine is always there but uracil is never found4) Being single stranded structure- It does not follow Chargaffs ruleIt 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.RNADNA5)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 position6) RNA is a relatively a labile molecule, undergoes easy and spontaneous degradationDNA 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 etc8) The base content varies from 100- 5000. The size is variable.Millions of base pairs are there depending upon the organismDifferences between RNA and DNAS.No.RNADNA9)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 cellSingle copy of DNA is present per cell.Proteins/ Gene Expression Proteins/ Gene Expression

Proteins make up all living materials66Proteins are composed of amino acids there are 20 different amino acidsDifferent proteins are made by combining these 20 amino acids in different combinations

67Proteins 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 WordsATC GCA GGA AUU AUG

These words make sentences

Protein Synthesis

DNA and Protein Synthesis DNA contains the genetic information to make amino acidsAmino 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!

70Transcription 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 & TranslationDNA 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 ProteinTranscriptionFirst Step: Copying of genetic information from DNA to RNA called TranscriptionPart of DNA temporarily unzips and is used as a template to assemble complementary nucleotides into messenger RNA (mRNA).

73Transcription 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 RNAMessenager (mRNA)Transfer (tRNA)Ribsomal (rRNA)Site of Transcription&TranslationA U G G G C U U A A A G C A G U G C A C G U UThis is a molecule of messenger RNA.It was made in the nucleus by transcription from a DNA molecule.

mRNA moleculeCodon Messenger RNAA U G G G C U U A A A G C A G U G C A C G U UA 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 UIt brings an amino acid to the first three bases (codon) on the mRNA. Amino acidtRNA moleculeanticodon U A CA 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 UAnother tRNA molecule comes into place, bringing a second amino acid. U A C C C GIts 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 UA 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 UThe 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 GThe 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 UAnother tRNA molecule brings the next amino acid into place. C C G A A UA U G G G C U U A A A G C A G U G C A C G U UA peptide bond joins the second and third amino acids to form a polypeptide chain. C C G C C G Polypeptide ChainA U G G G C U U A A A G C A G U G C A C G U UThe 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) codonDNA and Protein Synthesis - Summary

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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___________/___________/___________/____________HistidineProlineTryptophanStop

AUG/AAC/GAC/UAA

___________/___________/___________/____________MethionineAsparagineAspartic AcidStopThank You