Biol 1107 Topic 9: DNA Replication

Who discovered DNA’s helical structure using X-ray diffraction?

Maurice Wilkins and Rosalind Franklin

Who constructed the double-helix model for DNA?

Watson and Crick

What is Chargaff’s Rule?

Nitrogenous bases occur in definite ratios; Amt of A’s=Amt of T’s; Amt of G’s=Amt of C’s

Nucleotides

Basic building block of DNA and RNA

What 3 parts make up a Nucleotide?

Phosphate group, Pentose sugar, Nitrogenous base

What pentose sugar is in DNA?

Deoxyribose

What pentose sugar is in RNA?

Ribose

Purine

Nitrogenous base; 2 rings; adenine and guanine

Pyrimidine

Nitrogenous base; 1 ring; Cytosine, uracil, thymine

Phosphodiester bond

Covalent bonds that link NTs into a chain

How do nucleotides form?

Phosphate group on the 5’ carbon of one NT; Bonds to 3’ hydroxyl of the next NT; through a dehydration reaction, sugar phosphate backbone with 5’→3’ directionality

How can polymerases add NTs?

Only to the 3’ -OH

How many hydrogen bonds are needed for A-T base pairing?

2 Hydrogen bonds

How many hydrogen bonds are needed for G-C base pairing?

3 Hydrogen bonds

What replaces A-T in RNA?

A-U

Structure of DNA

Double helix; created by the complimentary NBs paired together in parallel strands with Hydrogen bonds'

What does the helical twist of DNA allow for?

Allows for optimal alignment of those NBs, more efficient for strong genetic material

DNA directionality

Replication bubble split in 2, two more strands synthesized on top of those; strands will always run in opposite directions; strands are synthesized in the 5’ to 3’ direction

What directions will DNA strands run in?

Opposite directions

Which way are DNA strands synthesized in?

In the 5’ to 3’ direction

What direction are the template strands read in?

In the 3’ to 5’ direction

Semiconservative replicaition

Used by ALL forms of life; Each new DNA molecule contains one original (parental) strand and one newly synthesized strand; Half of the original DNA is “conserved” in each daughter molecule

Conservative replication

The entire original DNA molecule stays intact, and a completely new copy is made; One daughter molecule = 100% old DNA and the other daughter molecule = 100% new DNA

Dispersive replication

Each daughter DNA molecule is a mix of old and new DNA within each strand - patchwork segments; Both strands are hybrids of old + new DNA interspersed throughout

Replication bubble

Bubble formed to replicate DNA, DNA being separated; Has 4 areas; 2 lagging strands diagonal from each other; 2 leading strands; multiple replication bubbles throughout DNA

Leading strand

strand that’s built continuously

Lagging strand

strand that’s built discontinuously

Origin of Replication

Where the DNA is opened by the helicase

Replication Fork

A Y-shaped structure where the double helix is being unwound from

Okazaki fragments

the pieces added to the lagging strand

How does the replication Bubble work?

Helicase unwinds DNA by breaking Hydrogen bonds

Topoisomerase

On either end of the bubble; stops the DNA from getting too twisted

DNA polymerase III

The main replicating enzyme; builds both the leading and lagging strands; fast and highly processive

RNA primase

Matched the base pairs between the different sections

Single strand binding protein (SSBs)

Proteins that bind to separated DNA strands during replication to keep them from re-annealing or forming secondary structures; right behind the helicase on the replication fork

DNA polymerase I

The cleanup and repair enzyme; removes RNA primers using 5’→3’ exonuclease activity and replaces them with DNA; works on Okazaki fragments during lagging-strand synthesis

DNA polymerase II

DNA repair enzyme; not use during normal replication; functions mainly in DNA repair pathways; has 3’→5’ exonuclease proofreading; helps restart replication when DNA is damaged

Ligase

Fuses Okazaki fragments together

Telomeres

A sequence of NTs that don’t code for anything and act as a buffer so that we don’t lose important genetic material; synthesized extensions of DNA via reverse transcriptase

Transverse transcriptase

An enzyme that builds/ synthesizes DNA from an RNA template

Types of Repair for Replication Errors

Proofreading, Mismatched repair, Base Excision repair, Nucleotide Excision repair

Proofreading

Occurs during replication; DNA polymerase III moves from 3’ to 5’; If wrong NT is added, it can reverse and go 3’ to 5’ and remove and replace mismatched NT; DNA polymerase III 5’ to 3’; it can only go back ONE NT

Mismatched repair

Occurs during replication (AFTER proofreading); Have enzymes that recognize the mismatch, cut out/ taking out bad section (of a couple NTs); DNA polymerase I replaces NT and ligase will seal the gap

Base Excision repair

Corrects DNA damage; Multiple things affected by this kind of repair; Double helix is damaged/ disrupted; Path of NTs is removed and replaced; Things can still go wrong and get past these layers (mutations)

Types of Mutations

Base Pair Mutations and Chromosomal Mutations

Types of Base Pair Mutations

Missense, Nonsense, Silent, Frameshift

Types of Chromosomal Mutations

Duplication, Deletion, Insertion, Translocation, Inversion

Codon

3 pairs of DNA that codes Amino Acid that the whole segment codes for a protein

Missense Mutation

Codon that now signals a different amino acid; creates an entirely new protein

Nonsense mutation

Stop codons: UAA, UAG, UGA; Codon that has changed to a stop codon (signals the ribosome to stop translation, ending protein synthesis)

Silent mutation

Codon is changed to a different codon; still codes for some AA → unchanged function

Frameshift mutation

Single base pair is inserted or deleted; alters reading frame; rest of AA are read completely differently

Duplication

A segment of chromosome is replicated

Deletion

A segment of the chromosome is deleted

Insertion

Insertion of one or a few NTs in the sequence; also altering the reading frame

Translocation

Where a chromosomal segment is going to be moved to a different position along the chromosome

Inversion

When a segment of the chromosome is broken off and when it is, it is going to be reinserted to a different loci; reinserted in the reverse direction

Loci

The location of a gene on the chromosome