•Nucleic acids are polymers that are specialized for storage and transmission of information

•Two types of nucleic acid are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

•DNA encodes hereditary information and transfers information to RNA molecules (Transcription)

•The information in RNA is decoded to specify the sequence of amino acids in proteins (Translation)

Nucleic Acids: Informational Macromolecules

That Can Be Catalytic

Nucleic Acids: Informational Macromolecules

That Can Be Catalytic•Nucleic acids are polymers of nucleotides,the

monomeric unit of Nucleic acids

•A nucleotide consists of a pentose sugar, a phosphate group, and a nitrogen-containing base

•The pentose sugar and the nitrogen-containing base alone is called a nucleoside

HAS THREE COMPONENTS

1.Nitrogen base: purine (A, G) or pyrimidine (C, T, or U for RNA)

2.Pentose Sugar: deoxyribose or ribose for RNA

3.Phosphate group

1’

5’

1

3’ o

Monomeric Unit of Nucleic Acids: Nucleotide

Nitrogen Bases

• The ribonucleotide ATP acts as an energy transducer

• The ribonucleotide GTP powers protein synthesis

• cAMP (cyclic AMP) functions as a second messenger

• Coenzymes in catalytic reactions

Nucleotides Have Other Important Nucleotides Have Other Important RolesRoles

• αα phosphate of the incoming phosphate of the incoming nucleotide attacks the hydroxy group nucleotide attacks the hydroxy group on the 3’ carbon at the end of the on the 3’ carbon at the end of the polynucleotide chainpolynucleotide chain

• This results in the formation of a This results in the formation of a phospho-diester bond between 3’ phospho-diester bond between 3’ carbon and 5’ carbon of the adjacent carbon and 5’ carbon of the adjacent nucleotidesnucleotides

• ββ γγ phosphates and 3’ hydroxyl are phosphates and 3’ hydroxyl are lostlost

• Polynucleotides have chemically Polynucleotides have chemically distinct endsdistinct ends

• Polymer grow from 5’ to 3’Polymer grow from 5’ to 3’

PolymerizatiPolymerizati

onon

•Catalyzed by two Catalyzed by two classes of enzyemesclasses of enzyemes

•DNA – DNA DNA – DNA polymerasepolymerase

•RNA – RNA polymeraseRNA – RNA polymerase

Discovering the structure of the Discovering the structure of the DNADNA

• Chargaff’s base ratiosChargaff’s base ratios

• X-ray diffraction experiments by Wilkins and X-ray diffraction experiments by Wilkins and FranklinFranklin

• Elucidation of the structure by Watson and Crick Elucidation of the structure by Watson and Crick (1953)(1953)

Erwin ChargaffErwin Chargaff• Break molecule into Break molecule into

mononucleotide mononucleotide components using components using acid or alkaliacid or alkali

• Paper Paper chromotography with chromotography with n-butanol as the n-butanol as the mobile phasemobile phase

• Resulting spots were Resulting spots were cut out and dissolved cut out and dissolved in aqueous solutionin aqueous solution

• Concentrations were Concentrations were measuredmeasured

Chargaff’s RuleChargaff’s Rule

• Conc. A approximated Conc. Conc. A approximated Conc. T T

• Conc. G approximated Conc. Conc. G approximated Conc. CC

• GC content varied GC content varied considerably depending on considerably depending on the organismthe organism

X-Ray Diffraction studiesX-Ray Diffraction studies

• Rosalind Franklin and Rosalind Franklin and Maurice WilkinsMaurice Wilkins

• Took photos of X-ray Took photos of X-ray diffraction patterns of DNAdiffraction patterns of DNA

• DNA Crystal is bombarded DNA Crystal is bombarded with x-rayswith x-rays

• Angles the x-rays pass Angles the x-rays pass through are determined by through are determined by the structure of the the structure of the molecule in the crystal.molecule in the crystal.

• X-ray beam exposes film X-ray beam exposes film after passing through the after passing through the crystalcrystal

Watson and Crick ModelWatson and Crick Model

•After earlier models proved impossible, After earlier models proved impossible, finally settled on double helixfinally settled on double helix

•Based on Chargaff’s ratios and X-ray Based on Chargaff’s ratios and X-ray diffraction studiesdiffraction studies

Watson and Crick ModelWatson and Crick Model

• 2 polynucleotide chains2 polynucleotide chains

• Anti-parallel double helixAnti-parallel double helix

• Right handed helixRight handed helix

• Nitrogenous bases on the Nitrogenous bases on the insideinside

• Sugar-Phosphate backbone Sugar-Phosphate backbone (-vely charged) (-vely charged)

• Base pairs perpendicular to Base pairs perpendicular to the helixthe helix

• 10 base pairs per helical 10 base pairs per helical turnturn

• Each turn occurs at 34 AEach turn occurs at 34 A

Base PairingBase Pairing

The bases pairs are held The bases pairs are held together by Hydrogen bondstogether by Hydrogen bonds

What does DNA look like?What does DNA look like?

Sugar PhosphateSugar PhosphateBackboneBackbone

(Sides of the Ladder)(Sides of the Ladder)

Nitrogenous Nitrogenous BaseBase

(Rungs of the (Rungs of the Ladder)Ladder)

DNA is polymericDNA is polymeric

•Poly nucleotides can be of any length Poly nucleotides can be of any length and can have any sequenceand can have any sequence

•No chemical restrictions on how they joinNo chemical restrictions on how they join•A polynucleotide of 10 nucleotides can A polynucleotide of 10 nucleotides can

have 4have 410 10 or 1,048,576 possible or 1,048,576 possible sequencessequences

•Variability enables genetic material to Variability enables genetic material to exist in an infinite number of formsexist in an infinite number of forms

•RNA is also a polynucleotide

•Instead of the base thymine, RNA uses the base uracil

•Most RNA molecules consist of only a single polynucleotide chain

•Intra chain Hydrogen bonding between ribonucleotides in RNA can result in complex three-dimensional shapes

Nucleic Acids: RNA

Structure of the RNAStructure of the RNA

Similarities between DNA and RNA : Similarities between DNA and RNA : •Sugar-phosphate backbone and Sugar-phosphate backbone and

nitrogenous basesnitrogenous bases

Main differences between DNA and RNA:Main differences between DNA and RNA:•Ribose instead of deoxyribose sugarRibose instead of deoxyribose sugar•Uracil instead of ThymineUracil instead of Thymine•RNA occurs as a single polynucleotide RNA occurs as a single polynucleotide

while DNA occur as two while DNA occur as two polynucleotides wrapped around each polynucleotides wrapped around each other in a double helixother in a double helix

•Certain RNA molecules called ribozymes can act as catalysts

•The discovery of ribozymes provided a solution to the question of whether proteins or nucleic acids came first when life originated

•Since RNA can be informational and catalytic, it could have acted as a catalyst for its own replication as well as for the synthesis of proteins

Nucleic Acids: RNA can be catalytic

Deoxyribose

Comparison of DNA and RNA

9

DeaminationDeamination

From DNA to Chromosome In a typical human cell there are approximately

6,000,000,000 bp or 2m of DNA that has to be packaged into a nucleus of 10m

Therefore the problem faced by the cell is how to package this DNA to fit in the nucleus at the same time making it sure that the DNA can be replicated and transcribed when necessary

All organisms have solved this problem by using proteins called histones to package their DNA or RNA

• Double helix

• Nucleosomes – histone-DNA complex which forms the nucleosome string

• 30 nm solenoid – coil of string of nucleosomes

• Formation of folded loops

• Formation of radial loops

• The chromosome

Packing of the Packing of the chromosomechromosome

• Chromosomes (Colored body) Chromosomes (Colored body) may differ in their staining may differ in their staining patterns, patterns, size and shape size and shape

• Contains a constriction called Contains a constriction called the centromerethe centromere

• The two ends of the DNA The two ends of the DNA

strand contains repeated G strand contains repeated G

rich sequencerich sequence (TTAGGG)n(TTAGGG)n

• These are called telomeres These are called telomeres

that prevent that protect the that prevent that protect the

endsends

Chromosomes

The Central Dogma

Reverse Transcrip

tion

Replication DNA duplicat

es

Transcription RNA synthesis

Translation

protein synthesi

s

DNA ReplicationDNA Replication• Before a cell divides it must Before a cell divides it must

produce a new copy of it’s produce a new copy of it’s chromosomeschromosomes

• This occurs during a specific This occurs during a specific part of the cell cycle, the DNA part of the cell cycle, the DNA synthesis phase or S Phasesynthesis phase or S Phase

• By the end of the S phase By the end of the S phase each chromosome has each chromosome has produced two complete produced two complete copies which remained joined copies which remained joined to each other by the to each other by the centromere until the M phasecentromere until the M phase

• About a dozen enzymes and About a dozen enzymes and proteins are involved in proteins are involved in replicationreplication

Overall View of the DNA Overall View of the DNA ReplicationReplication• DNA replication DNA replication

is accomplished is accomplished by a multi by a multi enzyme enzyme complex complex

• These include:These include:

HelicaseHelicase

PrimasePrimase

SSB’sSSB’s

DNA DNA PolymerasesPolymerases

Clamp ProteinsClamp Proteins

DNA ligaseDNA ligase

GyraseGyrase

TelomeraseTelomerase6

DNA HelicaseDNA Helicase DNA PrimaseDNA Primase

Single-strand Single-strand Binding Binding Proteins Proteins (SSB’s)(SSB’s)

DNA DNA PolymerasePolymerase•Can add new Can add new

nucleotides to a free “3’ nucleotides to a free “3’ end” (5’end” (5’ 3’ 3’ polymerase activity)polymerase activity)

•Has 3’ Has 3’ 5’ Proof 5’ Proof reading abilityreading ability

DNA LigaseDNA Ligase DNA DNA TopoisomeraseTopoisomerase

A Summary of Proteins Involved in Replication

1.1. Helicase - Unwinds the DNA and melts itHelicase - Unwinds the DNA and melts it

2.2. Primase - Provides an RNA primer to start Primase - Provides an RNA primer to start polymerizationpolymerization

3.3. Single Strand Binding Proteins - Keep the DNA single Single Strand Binding Proteins - Keep the DNA single stranded after it has been melted by helicase stranded after it has been melted by helicase

4.4. DNA Polymerase - Matches the correct nucleotides DNA Polymerase - Matches the correct nucleotides then joins adjacent nucleotides to each otherthen joins adjacent nucleotides to each other

5.5. Ligase - Joins adjacent DNA strands together (fixes Ligase - Joins adjacent DNA strands together (fixes “nicks”)“nicks”)

6.6. Gyrase - A topisomerase that Relieves torsional strain Gyrase - A topisomerase that Relieves torsional strain in the DNA moleculein the DNA molecule

7.7. Telomerase - Finishes off the ends of DNA strandsTelomerase - Finishes off the ends of DNA strands

• DNA contains information for making RNA and DNA contains information for making RNA and polypeptidespolypeptides

• Gene may also include cis acting elements (found in the Gene may also include cis acting elements (found in the same DNA molecule as the gene) such as promoters, same DNA molecule as the gene) such as promoters, operators and enhancersoperators and enhancers

• Gene may also be regulated by trans acting elements Gene may also be regulated by trans acting elements (produced by another gene on a different DNA (produced by another gene on a different DNA molecule) such as repressors and transcription factorsmolecule) such as repressors and transcription factors

Regulatory region coding region

Polynucleotides Store Information (Gene)

•4 RNA bases have to code for 20 amino 4 RNA bases have to code for 20 amino acidsacids

•If 1 base = 1 aa, only 4 aa’sIf 1 base = 1 aa, only 4 aa’s

•If 2 bases = 1 aa, only 16 aa’sIf 2 bases = 1 aa, only 16 aa’s

•If 3 bases = 1 aa, 64 possible aa’sIf 3 bases = 1 aa, 64 possible aa’s

•Two scientists Gobind Khorana and Two scientists Gobind Khorana and Marshall Nirenberg were mainly Marshall Nirenberg were mainly responsible for figuring out the genetic responsible for figuring out the genetic codecode

Genetic Info is Written in CodeGenetic Info is Written in Code

The Genetic Code

• Coding ratio is three Coding ratio is three (3)(3)

• Highly degenerate Highly degenerate (several codons code (several codons code for same aa)for same aa)

• Degeneracy is logical Degeneracy is logical (first two letters are (first two letters are the same when the same when multiple code words)multiple code words)

• Not ambiguous (no Not ambiguous (no codon codes for codon codes for multiple aa’s)multiple aa’s)

• 3 chain termination 3 chain termination (nonsense) codons(nonsense) codons

• One initiation codonOne initiation codon

• UniversalUniversal

Transcription of Genes

• Stages:Stages:• Initiation: binding of RNA polymerase and start of Initiation: binding of RNA polymerase and start of

synthesissynthesis• Elongation: RNA synthesis continues, RNA strands Elongation: RNA synthesis continues, RNA strands

begins to peel away from DNA templatebegins to peel away from DNA template• Termination: RNA polymerase gets to stop codon, Termination: RNA polymerase gets to stop codon,

and transcription endsand transcription ends

• Makes mRNA, tRNA, rRNAMakes mRNA, tRNA, rRNA

• mRNA is used in translationmRNA is used in translation

• Before leaving nucleus, mRNA is processed Before leaving nucleus, mRNA is processed (eukaryotic)(eukaryotic)• 5’ cap and poly A tail5’ cap and poly A tail• Splicing/ Removal of introns (non-coding regions of Splicing/ Removal of introns (non-coding regions of

DNA)DNA)

RNA PolymeraseRNA Polymerase

•Polymerization of Polymerization of Ribonucleotides Ribonucleotides

•Needs a templateNeeds a template

•Does not need a Does not need a primerprimer

•Does not have Does not have exonuclease activityexonuclease activity

•Relatively high error Relatively high error rate 1 mismatch/10rate 1 mismatch/1044 nucleotidesnucleotides

DNA PolymeraseDNA Polymerase

•Polymerization of Polymerization of Deoxy-Deoxy-ribonucleotides ribonucleotides

•Needs a templateNeeds a template

•Needs a primerNeeds a primer

•Express Express exonuclease exonuclease activityactivity

•Relatively low error Relatively low error rate 1 rate 1 mismatch/10mismatch/1099 nucleotidesnucleotides

Prokaryote genes are uninterrupted while the Prokaryote genes are uninterrupted while the eukaryotic genes are interrupted by noncoding eukaryotic genes are interrupted by noncoding

regionsregions

Translation Has 3 PhasesTranslation Has 3 Phases

InitiationInitiation

• mRNA molecules binds to a small ribosomal mRNA molecules binds to a small ribosomal subunit, 1subunit, 1stst tRNA pairs with the mRNA (start tRNA pairs with the mRNA (start codon codes for methionine)codon codes for methionine)

• Large ribosomal subunit binds to small unit, Large ribosomal subunit binds to small unit, making ribosome functional, tRNA fits into making ribosome functional, tRNA fits into binding site on ribosome (P-site)binding site on ribosome (P-site)

ElongationElongation

•Anticodon of incoming tRNA molecule (carrying an aa) Anticodon of incoming tRNA molecule (carrying an aa) pairs with mRNA codon at the A-sitepairs with mRNA codon at the A-site

•AA transferred from tRNA to polypeptide chainAA transferred from tRNA to polypeptide chain

• tRNA in P-site leaves ribosome; tRNA in A-site moves tRNA in P-site leaves ribosome; tRNA in A-site moves to P-site; new tRNA enters A-siteto P-site; new tRNA enters A-site

•Continues until stop codonContinues until stop codon

TerminationTermination

•The presence of a stop codon in the A site of The presence of a stop codon in the A site of the ribosome causes translation to terminatethe ribosome causes translation to terminate

•The completed protein is releasedThe completed protein is released

Post-translational modificationPost-translational modification•After synthesis a protein can undergo After synthesis a protein can undergo one or more modificationsone or more modifications

•Tertiary structure: regulated by Tertiary structure: regulated by chaperonschaperons

•Glycosidation: addition of sugarsGlycosidation: addition of sugars

•Proteolitic cleavageProteolitic cleavage

•Phosphorylation: addition of Phosphorylation: addition of phosphate groups to Tyr, Thr and phosphate groups to Tyr, Thr and Ser.Ser.

•Other....Other....