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Nucleic Acids, DNA, RNA and Protein Synthesis Nucleic Acids, DNA, RNA and Protein Synthesis

Nucleic Acids, DNA, RNA and Protein Synthesis - PowerPoint Presentation

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Nucleic Acids, DNA, RNA and Protein Synthesis - PPT Presentation

CHM 341 Suroviec Fall 2016 I Nucleotides Nucleic Acids and Bases Bases Planar aromatic heterocyclic Purine 2 rings Pyrimidine 1 ring Adenine A Guanine G Thyamine T ID: 741358

rna dna polymerase strand dna rna strand polymerase mrna base trna replication amino synthesis protein iii acids binds bases

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Slide1

Nucleic Acids, DNA, RNA and Protein Synthesis

CHM

341

Suroviec

Fall

2016Slide2

I. Nucleotides, Nucleic Acids and Bases

Bases

Planar, aromatic, heterocyclic

Purine (2 rings)Pyrimidine (1 ring)

Adenine (A)

Guanine (G)

Thyamine (T)

Cytosine ( C)

Uracil (U)Slide3

B. Nucleosides

Ribonucleotides

sugar = ribose

DeoxyriboneculeotideSugar = 2´-deoxyriboseSlide4

C. Nucleotides (total molecule)

Have a phosphate on carbon #5

Can have up to 3 phosphates

Monophosphate (NMP)Diphosphate (NDP)

Triphosphate (NTP)Where N is any one of the nucleic acidsSlide5

II. Nucleic Acid Structure

Can be found singly

Most often found in a polymer

DNA (or RNA) polymerizes 5´ phosphate to 3´ OH

Makes phosphodiester bondPolymer of non-identical residues has a property that individual monomers do not.Slide6

A. Base composition of DNA

1940’s Erwin Chargaff discovered that when measuring the amount of each base A = T and G = C. Lead to Chargaff’s rules

.

Maurie

Wilkins and Rosalind Franklin made and X-ray that indicated that DNA was helical in nature

Watson and Crick took this data and other material that hinted that DNA stacked to propose that DNA was double stranded.Put the bases together in such a way so that the complimentary H-bonds were formed and the width of the base pairs would be similar.Slide7

Characteristics of DNA model

DNA strands run in opposite directions (antiparallel)

Sugar phosphate backbone is found on outside, bases inside and pair up

Each base is H-bonded with a base on the opposite strand with the same number of H-bonds

A complete turn takes 34 Å

and has 10 bases per turn2 helical polynucleotide chains coiled around a central axis (diameter = 20 Å)DNA strand is quite stiff and will not bend much around the axisSlide8

- DNA

Helix is right handedSlide9

III. Overview of Nucleic Acid Function

Carries genetic info

Directs protein synthesis

Double stranded nature allows for easy replication

DNA replicationW-C model allows each DNA strand to act as template for replication

2 hypothesis for replication came forth:Conservative: where the parental DNA strand retains both old stands and creates new ds DNASemi conservative: where the created DNA has one old strand and one new strand. Shown to be how DNA replicatedSlide10

DNA, RNA & Protein Synthesis

DNA directs its own replication and is also transcribed into RNA.

RNA then translates into proteins.

CENTRAL DOGMA of MOLECULAR BIOLOGY

Transcription: transferring into from DNA --> RNATranslation: transferring info from RNA --> proteinsSlide11

IV. Replication

Involves 20+ proteins

Helicases: opens the double strand, splits the strands apart starting at replication fork rich in A-T

SSB: bind to the single strand DNA

stablizing itPrimase: adds short stretches of RNA and allows the the DNA polymerase to start.

DNA polymerase I: catalyzes the addition of deoxynucleotides to the chain

DNA Polymerase I & III:

add DNA

with high fidelity to

the

newly growing DNA strand.

Ligase: closes up gaps

in

the DNASlide12

DNA polymerase I

DNA polymerase I catalyzes addition of a addition of dNTP to chain

Requires

dATP, dGTP,

TTp, dCTP and Mg2+Elongation occurs 5´ to 3´ where 3´ hydroxyl bind to the new

deoxyribonucleotideDNA polymerase is a “template directed enzyme”Slide13

DNA polymerase III

Adds nucleotides to the 3´ end of the chain

New strand reads 5´ to 3´

Needs a primer with free 3´ hydroxyl group to start addition of new DNA

The strand is going to be started with a RNA primer that is later removed and replaced

The incoming dNTP first forms an appropriate base pair and then the DNA polymerase III links the incoming bases togetherBinds complementary DNA nucleotides starting at the 3´ end of the RNA primer at a rate of 1000/secondMakes a mistake 1/108Slide14

IV. Replication

Opening of the DNA

Double stranded DNA is opened by helicase

Kept open by SSB

Exposed DNA bind DNA polymerase III and RNA synthesizing protein primaseThis makes the replication forkSlide15

IV. Replication

Leading strand synthesis begins with synthesis of primase of short RNA primer

dNTPs are added by DNA polymerase III

Continously

added to this strand toward the forkSlide16

Replication

Lagging strand synthesis is done in short bursts

Needs multiple RNA primers

Synthesized in opposite direction of the fork

DNA primase moves 5’ to 3’ and makes RNA primer to which DNA is then added by DNA polymerase IIISlide17

Replication

Keeping the DNA sequence correct is important: 1

mispair

per 109 base pairs

Polymerase reaction occurs in 2 stagesIncoming dNTP base pairs with the template while enzyme is open catalytically inactivePolymerization only occurs after polymerase has closed around base pair which positions residuesSlide18

Transcription

DNA is in the nucleus

Protein synthesis takes place in the ribosome

RNA is the intermediate

Cells contain 3 types of RNARibosomal RNA (rRNA)Transfer RNA (tRNA)

Messenger RNA (mRNA)Slide19

RNA polymerase

RNAP couples together the ribonucleotide triphosphates on DNA templates

Builds RNA in the 5’

3’ direction (reads the DNA in the 3’ --> 5’ direction)Slide20

RNA polymerase

3’ hydroxyl group attacks the triphosphate

Creates phosphodiester bond

Releases PPi

Does not need a primerSlide21

RNA polymerase

Initiation of RNA synthesis occurs only at promoters

Usually starts at GTP or ATP

New RNA strand base pairs temporarily with DNA template to form DNA/RNA template

DNA must unwind then rewind Template strandNontemplate

strand or coding strandSlide22

RNA polymerase

RNA polymerase lacks ability to proof read

No 3’--> 5’ exonuclease activity

One error in 104 ribonucleotides addedSlide23

Post transcription of RNA

In Eukaryotes RNA is further modified

mRNA undergoes gene splicing where introns are removed and exons are rejoined

5’ obtains a cap3’ gets polyA

tailSlide24

Characteristics of RNA

Contains AUGC

Uracil is less “energy expensive”

Normally single stranded

Has –OH on 2’ carbon of riboseSeven roles of RNA

mRNA – carries DNA code to make proteinsrRNA – forms complex of 2/3 RNA, 1/3 protein to form protein in ribosometRNA – carries the amino acids to the mRNAsnRNA – helps splice exonsRibozymes – RNA capable of catalytic activityAntisense RNA – act to bind RNA to stop translationViral RNA – carry hereditary informationSlide25

Translation

mRNA to proteins

Need mRNA, ribosome and

tRNAmRNA is produced from DNAmRNA read from ribosomes and

tRNASlide26

Ribosome

Large protein/RNA complex

2 units (large/small)

Synthesis begins at start codon near 5’ end

Smaller unit (usually has tRNA bound) binds to AUG codon on mRNA binds to large subunit

Large unit then bindsLarge unit has 3 tRNA binding sites (APE)A: aminoacyl-tRNAP:peptidyl-tRNAE: free-tRNASlide27

Initiation

AUG signals the beginning of polypeptide chains

Read the code off of the mRNA and translate into amino acids

One start codon3 stop codonSlide28

tRNA

Read the code on the mRNA and translate into the correct amino acid

Acceptor stem

5’ terminal nucleotide and 3’ terminal nucleotide (-OH group where amino acid binds)

3’end always has CCA sequenceSpecific linkage is catalyzed by amino acyl-tRNA

synthetase (tranferase). Anticodon recognizes the complementary codon on the mRNASlide29

Aminoacylation

Process of adding an aminoacyl group to a compound

Produces

tRNA molecules with their CCA 3’ ends covalently linked to an amino acidAminoacyl

tRNA synthetase (one specific for each amino acid)Needs ATP to drive the reactionSlide30

Initiation and Elongation

mRNA bearing the code for the polypeptide binds to the small ribosome unit

Aminoacyl-

tRNA then binds followed by larger ribosomal unitAminoacyl-

tRNA base-pairs with mRNA codon AUG to start the polypeptide

Chain is elongated by addition of amino acidsAdded by individual tRNAPolypeptides are grown from amino-terminal end to carboxyl-endSlide31

Elongation

mRNA passes through ribosome

AUG is held in P site

2nd amino acid binds in the A site

Make peptide bondRibosome then moves toward 3’ end using GTP and leaving A site open