Nucleic Acids: Informational Macromolecules That Can Be Catalytic

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 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

Monomeric Unit of Nucleic Acids: Nucleotide

1 5

1
3
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

Nitrogen Bases

Nucleotides Have Other Important Roles

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

 phosphate of the incoming nucleotide attacks the hydroxy group on the 3 carbon at the end of the polynucleotide chain This results in the formation of a phospho-diester bond between 3 carbon and 5 carbon of the adjacent nucleotides phosphates and 3 hydroxyl are lost Polynucleotides have chemically distinct ends Polymer grow from 5 to 3

Polymerization
Catalyzed by two classes of enzyemes DNA DNA polymerase

RNA RNA polymerase

Discovering the structure of the DNA

Chargaffs base ratios X-ray diffraction experiments by Wilkins and Franklin Elucidation of the structure by Watson and Crick (1953)

Erwin Chargaff
Break molecule into mononucleotide components using acid or alkali Paper chromotography with n-butanol as the mobile phase Resulting spots were cut out and dissolved in aqueous solution

Concentrations were measured

Chargaffs Rule
Conc. A approximated Conc. T
Conc. G approximated Conc. C GC content varied considerably depending on the organism

X-Ray Diffraction studies

Rosalind Franklin and Maurice Wilkins

Took photos of X-ray diffraction patterns of DNA

DNA Crystal is bombarded with x-rays Angles the x-rays pass through are determined by the structure of the molecule in the crystal. X-ray beam exposes film after passing through the crystal

Watson and Crick Model

After earlier models proved impossible, finally settled on double helix

Based on Chargaffs ratios and X-ray diffraction studies

Watson and Crick Model

2 polynucleotide chains Anti-parallel double helix

Right handed helix

Nitrogenous bases on the inside Sugar-Phosphate backbone (vely charged)

Base pairs perpendicular to the helix

10 base pairs per helical turn Each turn occurs at 34 A

Base Pairing

The bases pairs are held together by Hydrogen bonds

What does DNA look like?

Sugar Phosphate Backbone (Sides of the Ladder)

Nitrogenous Base (Rungs of the Ladder)

DNA is polymeric

Poly nucleotides can be of any length and can have any sequence No chemical restrictions on how they join A polynucleotide of 10 nucleotides can have 410 or 1,048,576 possible sequences Variability enables genetic material to exist in an infinite number of forms

Nucleic Acids: RNA

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

Structure of the RNA

Similarities between DNA and RNA : Sugar-phosphate backbone and nitrogenous bases Main differences between DNA and RNA: Ribose instead of deoxyribose sugar Uracil instead of Thymine RNA occurs as a single polynucleotide while DNA occur as two polynucleotides wrapped around each other in a double helix

Nucleic Acids: RNA can be catalytic

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

Comparison of DNA and RNA Deoxyribose

Deamination

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 10mm 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

Packing of the chromosome

Double helix Nucleosomes histoneDNA complex which forms the nucleosome string 30 nm solenoid coil of string of nucleosomes

Formation of folded loops

Formation of radial loops The chromosome

Chromosomes

Chromosomes (Colored body) may differ in their staining patterns, size and shape Contains a constriction called the centromere

The two ends of the DNA strand contains repeated G rich sequence (TTAGGG)n

These are called telomeres that prevent that protect the ends

The Central Dogma

Replicatio n DNA duplicates

Transcripti Reverse on RNA Transcripti synthesis on

Translatio n protein synthesis

DNA Replication
Before a cell divides it must produce a new copy of its chromosomes This occurs during a specific part of the cell cycle, the DNA synthesis phase or S Phase By the end of the S phase each chromosome has produced two complete copies which remained joined to each other by the centromere until the M phase About a dozen enzymes and proteins are involved in replication

Overall View of the DNA Replication

DNA replication is accomplished by a multi enzyme complex These include: Helicase Primase SSBs

DNA Polymerases
Clamp Proteins DNA ligase Gyrase Telomerase

DNA Helicase

DNA Primase

Single-strand Binding Proteins (SSBs)

DNA Polymerase
Can add new nucleotides to a free 3 end (5 3 polymerase activity) Has 3 5 Proof reading ability

DNA Ligase

DNA Topoisomerase

1. Helicase - Unwinds the DNA and melts it

A Summary of Proteins Involved in Replication

2. Primase - Provides an RNA primer to start polymerization 3. Single Strand Binding Proteins - Keep the DNA single stranded after it has been melted by helicase

4. DNA Polymerase - Matches the correct nucleotides then joins adjacent nucleotides to each other
5. Ligase - Joins adjacent DNA strands together (fixes nicks) 6. Gyrase - A topisomerase that Relieves torsional strain in the DNA molecule 7. Telomerase - Finishes off the ends of DNA strands

Polynucleotides Store Information (Gene)

Regulatory region
coding region

DNA contains information for making RNA and polypeptides Gene may also include cis acting elements (found in the same DNA molecule as the gene) such as promoters, operators and enhancers Gene may also be regulated by trans acting elements (produced by another gene on a different DNA molecule) such as repressors and transcription factors

Genetic Info is Written in Code

4 RNA bases have to code for 20 amino acids

If 1 base = 1 aa, only 4 aas

If 2 bases = 1 aa, only 16 aas If 3 bases = 1 aa, 64 possible aas

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

The Genetic Code

Coding ratio is three (3) Highly degenerate (several codons code for same aa) Degeneracy is logical (first two letters are the same when multiple code words)

Not ambiguous (no codon codes for multiple aas)

3 chain termination (nonsense) codons One initiation codon

Universal

Transcription of Genes
Stages: Initiation: binding of RNA polymerase and start of synthesis Elongation: RNA synthesis continues, RNA strands begins to peel away from DNA template Termination: RNA polymerase gets to stop codon, and transcription ends Makes mRNA, tRNA, rRNA

mRNA is used in translation

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

RNA Polymerase

DNA Polymerase

Polymerization of Ribonucleotides Needs a template

Does not need a primer Does not have exonuclease activity Relatively high error rate 1 mismatch/104 nucleotides

Polymerization of Deoxyribonucleotides
Needs a template Needs a primer Express exonuclease activity Relatively low error rate 1 mismatch/109 nucleotides

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

Translation Has 3 Phases

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

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

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

AA transferred from tRNA to polypeptide chain

tRNA in P-site leaves ribosome; tRNA in A-site moves to Psite; new tRNA enters A-site Continues until stop codon

Termination

The presence of a stop codon in the A site of the ribosome causes translation to terminate The completed protein is released

Post-translational modification

After synthesis a protein can undergo one or more modifications Tertiary structure: regulated by chaperons Glycosidation: addition of sugars

Proteolitic cleavage
Phosphorylation: addition of phosphate groups to Tyr, Thr and Ser. Other....