DNA

DNA review

DNA codes for all information necessary for life

The information is stored in the sequence of nucleotide bases

It is a quaternary code… The sequence is important

– Human Genome Project: Sequence of roughly

3.2 billion bases in human DNA!

A Perfect Copy

When a cell divides, each new cell receives a complete set of chromosomes. This means that each new cell has a complete set of the DNA code. Before a cell can divide, the DNA must be copied so that there are two sets ready to be distributed to the new cells.

DNA structure

Recall that once Watson and Crick made the correct model, they instantly realized a copying mechanism.

Due to the structure of DNA (specifically the base-pairing arrangement), if the order of nucleotides on one chain is known, the order on the other chain is obvious.

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DNA is copied through a process called DNA replication.

The process, though seemingly simple, is actually quite complex.

Energy is required.– Comes from which molecule?

Many enzymes and proteins are required for DNA replication.

Where does replication happen?

Eukaryotes?

Prokaryotes?

In a nutshell…

To start, an enzyme breaks the hydrogen bonds that hold base-pairs together.

This process “unzips” the DNA molecule. Other enzymes find and correctly match free-

floating nucleotides to the two sides of the now open DNA molecule.

This process continues until the entire molecule has been replicated.

Replication fork… what happens

Many different enzymes are needed to open up the DNA helix for replication

Two strands must be separated first Helicases do this … Pry apart the hydrogen bonds of the two

DNA strands…

Template Strands and New Strands

DNA polymerases build new strands.

Growth

Growth

Replication fork

DNA polymerase

New strandOriginal strand

DNA polymerase

Nitrogenous bases

Replication fork

Original strand

New strand

DNA Replication fork is asymmetrical

Leading and lagging strands are different The leading strand is continuous The lagging strand has fragments and is

synthesized discontinuously.– Okazaki fragments

High fidelity requires proof reading

DNA polymerase synthesizes in a 5’ to 3’ direction

Proof reading is in a 3’-5’ direction Can take out mismatched bases with reverse

action

Fig 5-9

Helicases…

Many different helicases have been identified Single stranded binding proteins are

important in maintaining the single stranded nature at the replication fork & so no hair pins can form

Replication starts at replication origins.

• Each eukaryotic chromosome contains one DNA double helix

• Average ~106 base pairs long

• With a replication rate of 2 kb/minute, replicating one human chromosome would require ~35 days.

• Solution ---> DNA replication initiates at many different sites simultaneously.

Rates are cell specific!

Three main features of the DNA synthesis reaction:

1. DNA polymerase catalyzes formation of phosphodiester bondbetween deoxyribose and the phosphate on the new strand.

• Energy for this reaction is derived from the release of two of the three phosphates on the free nucleotide.

2. DNA polymerase “finds” the correct complementary nucleotideat each step in the lengthening process.

• rate 50-1000 bases/second• low error rate (~1/107)

3. Direction of synthesis is 5’ to 3’ Image credit:Protein Data Bank

DNA Replication Overview

Replication Animation