DNA repair, maintenance and packaging

Question 1

What enzyme proofreads DNA?

Answer 1

DNA Polymerase, replace any incorrect nucleotides using exonuclease action

Question 2

Exonuclease action

Answer 2

DNA polymerase has a higher affinity of correctly paired nucleotides, making incorrectly paired nucleotides more likely to disassociate, allowing the correct pairing to be added. hese polymerases “read” each base after it is added to the new strand. If the newly-added base is incorrect, the polymerase reverses direction (moving from 3’ to 5’) and uses an exonucleolytic domain to cut off the incorrect base. Subsequently, it is replaced with the correct base.

Question 3

Mismatch repair of DNA

Answer 3

repairs single base pair errors that have been missed by proofreading

Question 4

Proofreading and repair of DNA

Answer 4

DNA can be damaged by chemicals,radioactive emissions, X-rays, UV light and certain chemicals…..
e.g. thymine dimers formed by covalent bonds between adjacent T-T bases in response to UV radiation

Question 5

How thymine dimers are removed

Answer 5

A thymine dimer distorts the DNA molecule
A nuclease enxyme cuts the DNA strand at two points and the damaged section is removed
Repair synthesis by a DNA polymerase fills in the missing nucleotides
A DNA ligase seals the free end of the new DNA to the old DNA making the strand complete

Question 6

DNA packing - Bacterial ‘chromosomes’

Answer 6

The bacterial genome typically comprises a double-stranded, circular DNA molecule – sometimes referred to as a bacterial chromosome

Question 7

What causes the DNA to coil and supercoil

Answer 7

Proteins cause the DNA to coil and supercoil  denser packing. Located in a region (not bound) called the nucleoid.
* Multiple proteins act together to fold and condense prokaryotic DNA (1980’s-1990’s) e.g HU, IHF etc.
* Work with topoisomerase I to bind DNA and introduce sharp bends in the chromosome, generating the tension necessary for supercoiling.
* Folded DNA is then organized into a variety of conformations, maintained by DNA topoisomerase I, DNA gyrase, and other maintenance proteins

Question 8

What also carries genes

Answer 8

Additional plasmids (circular DNAs) also carry genes which may, e.g., confer resistance to antibiotics

Question 9

DNA Packing - Eukaryotic chromosomes

Answer 9

• The eukaryotic genome is made up of true chromosomes, each comprising a double-stranded, linear DNA, which is associated with proteins (histones), and coiled and supercoiled to form chromatin
• Average human chromosome = 1.5 x 108 nucleotide pairs; about 4 cm long when completely unwound and stretched out
• Located in the nucleus of the cell

Question 10

Chromosome dynamics

Answer 10

• Chromosomes are dynamic structures  change form during the cell cycle
• Most chromatin is loosely packed in the nucleus during interphase (euchromatin); condenses prior to mitosis
• During interphase some chromatin remains highly condensed (heterochromatin); dense packing of heterochromatin makes gene expression in
  these regions difficult

Question 11

Telomeres

Answer 11

Protect chromosome ends from DNA degradation,
recombination, and DNA end fusions, and they are
important for nuclear architecture.

Question 12

What happens when we age

Answer 12

• Chromosomes shorten with age.