Lecture G2 (DNA Replication)

Basic structure of a DNA molecule

Made up of two strands forming a double helix

Three components of a DNA nucleotide

• nitrogenous base

• Pentose sugar (deoxyribose)

• Phosphate group

Purines

• Aromatic organic compound with two rings

• Bases: Adenine and Guanine

Pyrimidines

• Aromatic organic compound with one ring

• Bases: Thymine and Cytosine

What forms the backbone of the DNA molecule?

sugar-phosphate chain; the phosphate group of one nucleotide is attached to the sugar of the next

What does it mean that DNA strands are antiparallel?

the subunits run in opposite directions

Chargaff’s rules

• the base composition of DNA varies between species

• In any species, the number of A and T bases is equal, and the number of G and C bases is equal

Which bases pair with each other in DNA? How are they held together?

• Adenine (A) paired with Thymine (T)

• Guanine (G) paired with Cytosine (C)

• Held together by hydrogen bonds

How do base pairing rules explain DNA structure?

Uniform width results from pairing a purine with a pyrimidine; this explains Chargaff’s rules (A=T and G=C)

Why is DNA replication necessary before cell division?

Prior to meiosis

• Ensures genetic information is inherited from generation to generation and explains the resemblance of offspring to parents

Prior to mitosis

• Ensures genetic information is transmitted from a parent cell to daughter cells

What happens during base pairing to a template strand?

• The parental molecule has two complementary strands

• Each strand serves as a template for building a new strand

What is the result of replication?

Complementary nucleotides are connected to form the sugar-phosphate backbones of the new “daughter” strands, yielding two exact replicas of the “parental” molecule

What is the model of DNA replication?

Semiconservative model

• each daughter molecule has one old strand (conserved from the parental molecule) and one newly made strand

What are origins of replication?

• multiple replication bubbles form

  • Replication proceeds in both direction from each origin

  • Bubbles eventually fuse, speeding up the copying

Replication fork

• Y-shaped region where DNA strands are being unwound

• Found at the end of each replication bubble

Function of topoisomerase

Facilitates DNA replication by reducing molecular tension caused by unwinding ahead of the replication fork

Function of single-strand binding proteins

Bind to the unpaired DNA strands, keeping them from re-pairing; stabilize single-strand DNA

Role of DNA polymerases

• Catalyze the synthesis of new DNA

• Add nucleotides to the 3’ end of a preexisting chain

• Require a short RNA primer synthesized by primase

What does antiparallel elongation mean?

The two DNA strands are oriented in opposite directions, which affects replication

What is the leading strand?

DNA polymerase III adds nucleotides to the free 3’ end continuously, moving toward the replication fork

What is the lagging strand?

DNA polymerase III works away from the replication fork, synthesizing short segments called Okazaki fragments

What happens after Okazaki fragments are made?

DNA polymerase I replaces the RNA nucleotides of the primer with DNA nucleotides, and DNA ligase joins all the fragments into a continuous strand

How is synthesis coordinated?

Synthesis occurs concurrently and at the same rate; the lagging strand template DNA loops through the complex

How does the cell proofread and repair DNA?

• DNA polymerase replace incorrect nucleotides in the newly made DNA

• Nucleotide excision repair: nuclease cuts out incorrect or damaged nucleotides, DNA polymerase replaces them

• DNA can be damaged by chemical or physical agents (cigarette smoke, x-rays, etc.)

What are eukaryotic chromosomes made of?

Linear DNA molecules combined with proteins called chromatin; histones are responsible for the main level of DNA packing

What is a nucleosome?

• “bead”

• DNA wound twice around a core of eight histones

Difference between euchromatin and heterochromatin

Euchromatin

• loosely packed chromatin

• DNA is accessible for transcription

Heterochromatin

• highly condensed chromatin

• DNA is inaccessible for transcription

How are chromosomes arranged in the interphase nucleus?

Occupy specific restricted regions in the nucleus; fibers of different chromosomes do not entangle; most chromatin is loosely packed (euchromatin)