Microbial and eukaryotic genomes

Question 1

3 ways in which incorrect bases can be repaired?

Answer 1

by DNA polymerase: ‘–>3’ polymerisation
3’–>5’ exonuclease proofreading
strand driected mismatch repair

Question 2

describe how 5’–>3’ polymerisation protects against incorrect bases
what is the error rate

Answer 2

1 in 10^5
correct nucleotide has higher affinity to active stie
DNAp needs to undergo a conf change before covalent binding - easier with correct one

Question 3

describe 3’–>5’ exonuclease proofreading

what is the error rate

Answer 3

1 in 10^2
tautomeric form can be integrated; then switch to regular form, causing a kink in the train.
exonuclease finds this nucleotide, gets rid of the whole strand beginning frmo the error, and continues polymerisation

Question 4

describe strand directed mismatch repair

error rate?

Answer 4

1 in 10^3 errors
the template strand is distinguished from the newly synthesised strand
errors are found and removed

Question 5

how is the new strand found in prokaryotes?

Answer 5

soon after replication, A’s in GATC will be methylated

Question 6

how is new strand found in eukaryotes? how to proteins function to remove errors?

Answer 6

new strand has nicks
MutS binds to incorrect nucleotide
MutL finds nick
this segment is destroyed and replaced.

Question 7

where is eukaryotic DNA found?

Answer 7

extranuclear or in chromosomes

Question 8

what are chromosomes?

Answer 8

chromatin: DNA + histones

Question 9

describe nucleosomes

Answer 9

contain an 8 histone octomer 2x(H2A, H2B, H3, H4)

146 bp linker sequence with H1 histone in the middle.

Question 10

what is the purpose of nucleosomes?

Answer 10

DNA wraps tightly around it; enabling the DNA to be consdensed

Question 11

describe interphase

Answer 11

g1: organelles replicated
s: DNA replicated
g2: cell checks for chromosomal errors

Question 12

describe mitosis

Answer 12

prophase: nuclear membrane dissolves
metaphase: chromosomes line up on equator of cell
anaphase: spindles contract, and take chromatids to poles of cell
telophase: nuclear membranes reform and cell divides

Question 13

describe centromere structure

Answer 13

one per chromosome

contains short highly repettive sequenceof DNA (satellite DNA)

Question 14

describe centromere function

Answer 14

site at which sister chromatids are paired; interacts with microtubles and proteins to split the chromatids

Question 15

what is the problem at the end of chromosomes

Answer 15

Leading strand is synthesised as normal.
For the lagging strand (3’ end of template); okazaki fragments are filled as normal (with ligase) EXCEPT the terminal one. This leads to 3’ overhang of the template

Question 16

what could the 3’ overhang problem lead to

Answer 16

DNA will get smaller and smaller, until the chromosomes are defective.

• usually, cell will stop dividing, protecting against uncontrolled cell div but leading to ageing
• sometimes, cell can keep dividing, leading to uncontrolled cell growth and cancer

Question 17

how is the DNA prevented from getting shorter

Answer 17

Telomerase has repetitive RNA sequence attached; does RNA templated DNA synthesis on the 3’ template strand
this allows DNA p to polymerise the lagging strand till the end of the original template
shelterin protects the new 3’ overhang from digestion