IB Biology - 7.1

DNA Structure & Replication

Rosalind Franklin

Woman who used X-ray diffraction to research DNA structure. She improved the resolution to obtain precise pattern measurements, finding the double helix structure of DNA

Watson and Crick

Men who used calculations and a model of DNA structure using Rosalind Franklin's information

Nucleosomes

A core of eight histones with DNA coiled around them. It has 2 copies of 4 types of histones. An H1 protein binds the DNA to the octamer

Linker DNA strand

A short strand of DNA connecting nucleosomes

Supercoiling

The twisting of DNA to make it pack into a tiny nucleus

Complementary base pairing

Structure of DNA where each base is bonded to another complementary base to form a complementary strand

Semiconservative model of replication

Model of DNA replication where each strand of DNA is a template strand for a new DNA helix, and new strands are synthesized based on that strand

Origins of replication

Where DNA replication begins (there are many of these in eukaryotes, but only one in prokaryotes)

Direction in which replication occurs

It occurs in both directions away from the origin, appearing as a replication bubble. Nucleotides are added to the 3' carbon at the end of the chain, so replication occurs in a 5' to 3' direction

Deoxyribose phosphate

The ribose sugar-phosphate backbone of DNA

Nucleoside

A base connected to a sugar

Nucleotide

A base and sugar connected to a phosphate group

Structure of the DNA helix

Double helix arranged in an anti-parallel way. This means synthesis must occur differently on each strand

Replication fork

Region where the DNA is split into two separate strands by helicase

Leading strand

Strand of DNA during replication which is made continuously following the fork as it opens

Lagging strand

Strand of DNA during replication which is made in fragments, moving *away* from the replication fork

Okazaki fragments

Fragments of DNA replicated on the lagging strand (which do not have phosphodiester bonds)

Phosphodiester bonds

Bonds between sugars in the sugar-phosphate backbone, using a phosphate group and O's on either side

Covalent bonds in DNA structure

Occur between C5 and the phosphate group

Helicase

Unwinds DNA at the replication fork

DNA gyrase

(AKA topoisomerase II) Releases the strain developing ahead of the helicase (isolating breaking so it is happening solely at the helicase)

SSB's

Single-stranded binding proteins keep strands apart until after being separated long enough to allow the template to be replicated

DNA primase

Adds one RNA primer on the leading strand at initiation and many primers on the lagging strand

DNA polymerase III

Covalently links deoxyribonucleotide monophosphates (nucleotides) to the 3' end of the growing strand. It begins off the RNA primer

DNA polymerase I

Removes RNA primers on replicated strands, replacing them with DNA

DNA ligase

Connects gaps between Okazaki fragments by creating phosphodiester bonds

Coding sequences

DNA that codes for polypeptides

Non-coding sequences

Sequences of DNA which do not make polypeptides. They can:
(1) Allow tRNA production
(2) Regulate gene expression with *silencers and enhancers*
(3) Be introns

Satellite DNA

Highly repetitive sequences of non-coding DNA

Telomeres

Ends of chromosomes with repetitive non-coding DNA which protect it during interphase because in DNA replication, *replication does not occur to the end of the chromosome*. This prevents genes from being lost, instead losing the telomeres

How X-ray diffraction works

(1) X-rays are directed at a material, and some is scattered through diffraction
(2) X-rays' wavelengths are sensitive to diffraction by DNA
(3) DNA is arranged in an orderly way (as if it were crystallized, but as DNA cannot be crystallized, this was done) for diffraction patterns to be obtained
(4) X-ray detector placed close to the sample to collect scattered rays
(5) Sample is rotated to see pattern of scattering
(6) Diffraction recorded with X-ray film

What Franklin deduced about DNA

(1) Cross in centre showed the molecule was helical
(2) Angle of cross shape showed steepness of helix
(3) Distance between horizontal bars showed turns in the helix were 3.4nm apart
(4) Distance between middle of the pattern and the top showed there were repeating structures with 0.34nm between repeats

How base sequence is typically determined

(1) Many copies of unknown DNA are placed into test tubes with deoxyribonucleotides and enzymes for replication
(2) Small amounts of "dide"oxyribonucleotides are added, labelled with fluorescent markers
(3) They are incorporated into some of the new DNA, stopping replication where they are added
(4) Fragments synthesized are separated by electrophoresis
(5) Base sequence is analyzed by comparing colour of fluorescence with fragment length

Variable number tandem repeat

Short sequence which is repeated a different number of times in different people, inherited as an allele. This allows DNA profiling.

Typical DNA profiling techniques

Finding father: analyzing short tandem repeats from the Y-chromosome
Finding mother: analyzing mitochondrial DNA variations in single nucleotides in hyper-variable regions

Hershey and CHase

Scientists who worked with T2 phages, some with sulfur-35 and others with phosphorus-32. The ones with radioactive 32P did not have radioactive material, but 35S did. This indicated that nucleic acids were responsible for genetic material