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Y2 Mol Bio > Genetics > Flashcards

Genetics Flashcards

1
Q

Which phase can individual chromosomes be distinguished?

A

Metaphase

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2
Q

What is a karotype?

A

Organised representation of all the chromosomes in a eukaryotic cell at metaphase as they condense

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3
Q

Describe the different types of DNA coiling

A

(heterochromatin)- 30nm
(euchromatin)- 10nm

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4
Q

What histones are contained in a typical nucleosome?

A

2 H2A
2 H2B
2 H3
2 H4

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5
Q

What do the N-terminals of histone subunits do?

A

Interact with other proteins
Facilitate regulation and function of chromatin

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6
Q

What do linker histones (e.g H1) do?

A

Attach DNA onto histone octamers, limiting DNA movement
Stabilises formation of 30nm fibre which is transcriptionally silent
Rich in Lys and Arg, making it basic and can bind DNA
The chromatin scaffold can be remodelled to accommodate protein complexes for gene transcription and DNA replication

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7
Q

What does interphase chromatin contain which condense and decondense?

A

Set of fractal globules (globules within globules) which condense and decondese without knotting

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8
Q

What is contained in the nuclear periphery of interphase cells?

A

Transcriptionally inactive DNA
RNA transcripts are excluded

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9
Q

What do specialised DNA sequences ensure for complete interphase?

A

Facilitates complete DNA replication
Segregation of duplicated chromosomes in cell division

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10
Q

What does telomerase synthesise?

A

TTAGGG repeats on the 3’ overhang of chromosomes

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11
Q

How are centromeres defined?

A

171bp alpha satellite repeats that form condensed chromatin with histone octamers

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12
Q

What do kinetochore inner plate proteins bind to?

A

alpha satellite DNA

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13
Q

What do kinetochore outer plate proteins bind to?

A

protein components of the mitotic spindle

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14
Q

Describe a yeast centromere bound to a microtubule

A

Single nucleosome of centromeric chromatin is linked to a single microtubule with a basket structure

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15
Q

What increases with biological complexity?

A

Protein coding DNA
Non-protein coding DNA

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16
Q

What does non-protein coding DNA encode?

A

regulating transcription and organising access to protein-coding genes
Cis-regulatory information which determines when and where adjacent protein coding genes are transcribed

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17
Q

Describe transposons

A

Mobile genetic elements that jump around the genome
Can be non-replicative and replicative

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18
Q

Give three examples of transposons

A

P-element in flies, Activator/dissociator in maize where coloured kernals jump around the genome, Tn3/Tn10 in E.coli

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19
Q

Describe retroviral-like transposons

A

Replicate via RNA intermediates
Produce new DNA copies which integrate at new genomic locations
Self-encoded reverse transcriptase
Do not encode fully active infective viruses

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20
Q

Describe non-retroviral transposons

A

Abundant in vertebrate genomes
Replicates via an RNA intermediate with its own reverse transcriptase
Replicative

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21
Q

Give some examples of non-retroviral transposons

A

LINEs
SINEs
Human L1 elements
Human Alu elements
Mouse B1 elements

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22
Q

Describe an L1 insertion in humans

A
  1. L1 RNA synthase generates an ssRNA strand
  2. An endonuclease cleaves the first strand of target DNA
  3. DNA-primed reverse transcription takes place and a complimentary strand is synthesised
  4. The strand reintegrates with the inserted gene
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23
Q

What is an example of a disease caused by an L1 insertion?

A

Haemophilia

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24
Q

What initiates DNA synthesis at molecular level?

A

DNA helicase forming a replication fork

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25
Q

What machinery is involved in DNA replication?

A

DNA helicase- spliting DNA strands
DNA primase- synthesise short RNA primers
Sliding clamp
Clamp loader
DNA polymerase- adds nucleotides

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26
Q

What does DNA polymerase require to add nucleotides?

A

A pre-existing primer chain
Polymerase extends the RNA primer once it is in place

27
Q

What removes the RNA primer from DNA?

A

Ribonuclease H

28
Q

When the RNA pirmer is removed from DNA, what seals the nick?

A

DNA ligase

29
Q

What can mutations in DNA helicase lead to?

A

Werner syndrome (premature aging)
Autosomal recessive in RecQ helicase gene WRN

30
Q

What can a loss of function mutation in RecQ-family DNA helicase lead to?

A

Bloom syndrome- extreme sensitivity to sun exposure
Autosomal recessive

31
Q

What increases the processivity of DNA polymerases?

A

Sliding clamp helps move DNA pol forward
When DNA pol interacts with the primer, template junction is maintained and nucleotides are rapidly added

32
Q

What keeps the sliding clamp close to the primer:template junction?

A

Clamp loader

33
Q

How is ssDNA kept available as a template during semi-conservative replication?

A

ssDNA binding proteins (SSBs) which keep the replication fork open and allow DNA pol to function

34
Q

Describe DNA topoisomerases

A

Prevent DNA becoming tangled during replication, increasing processivity of DNA pol
This is because helicase unwinding parental DNA at the replication fork introduces tension in DNA
Topoisomerases nick and reseal DNA

35
Q

What is the difference between type I and type II DNA topoisomerases?

A

Type I- nick and reseal 1 DNA strand (no ATP)
Type II- nick and reseal both DNA strands (requires ATP)

36
Q

What is the difference between human and yeast origins of replication?

A

Yeast- autonomously replicating sequences (ARS)
Human- sequences near LMNB2, MYC

37
Q

Why is initiation of eukaryotic DNA replication biphasic?

A

Two stages:
1. Replicator selection in G1 phase where pre-replicative complex forms
2. Origin activation occurs at the start of S-phase where DNA unwinds and DNA polymerase is recruited

38
Q

What does temporal selection when initiating DNA replication ensure?

A

Each origin is used and each chromosome replicates once per cell cycle

39
Q

What does an origin recognition complex bind to?

A

Replicator sequence in the origin, e.g ARS in yeast

40
Q

Outline formation of the pre-recognition complex in G1 phase?

A
  1. The ORC binds to the replicator sequence
  2. Cdc6 and Cdt1 bind to the ORC
  3. Helicase Mem2-7 binds and the pre-recognition complex forms
41
Q

What activates the pre-recognition complex?

A

Cyclin-dependent kinase (Cdk) in S-phase. This inhibits new pre-recognition complexes forming

42
Q

What ensures chromosomes are replicated exactly once per cell cycle?

A

There is close relationship between pre-RC function, Cdk levels and cell cycle

43
Q

How is DNA replication finished with the unsealed gap?

A

At chromosome ends, pol or ligase haven’t sealed a gap. This is next to an RNA primer which is removed by ribonuclease H, shortening newly synthesised DNA strands at the 5’ ends
This can risk losing valuable coding information- premature aging and mutations

44
Q

Outline how telomerase functions

A
  1. Adds TTAGGG repeats on 3’ end to compensate for loss of telomere sequences from RNA primer removal
  2. DNA primase binds and initiates RNA primer synthesis
  3. DNA polymerase extends this as an extra okazaki fragment
45
Q

What is the telomerase shuffle?

A

Telomerase RNA component acts as a template where the telomere repeat sequences are synthesised in a step-wise process

46
Q

When there are errors in DNA, what can happen to it?

A

DNA repair
cell death
Stay mutated and replicate

47
Q

What are some endogenous causes of DNA damage?

A

Reactions with other molecules in the cell
Hydrolysis
Reactive oxygen species

48
Q

What are some exogenous causes of DNA damage?

A

UV
X-rays
Carcinogens
Chemotherapies

49
Q

What are some consequences of endogenous DNA damage?

A

Depurination
Deamination
Methylation
Replication errors

50
Q

What are some consequences of exogenous DNA damage?

A

Pyrimidine dimers
Double strand links
Interstrand crosslinks

51
Q

Are transversions or transition mutations more likely>

A

Transitions (pyrimadines to pyrimidine, vice versa)

52
Q

Explain the outcome of a depurination of adenine

A

A purine is cleaved off by the N-glycosidic bond, causing a wobble base
A frameshift can occur, generating missense proteins

53
Q

What mutations can UV light cause?

A

Pyrimidine dimers due to DNA to distorting
Interstrand DNA crosslinks- DNA cannot unwind for replication
DNA-protein crosslinks

54
Q

What can induce single strand breaks in DNA?

A

X-rays
Ionising radiation
Topoisomerase II inhibitors

55
Q

What can induce double strand breaks in DNA?

A

ROS
Hydroxyurea
Camptocthecin

56
Q

Outline base excision repair (BER)

A
  1. DNA glycosylase removed damaged base
  2. AP endonuclease and phosphodiesterase remove the sugar phosphate
  3. Pol and ligase add a new nucleotide and seal the nick
    Repairs abasic sites and deamination
57
Q

Outline nucleotide excision repair (NER)

A

Endonuclease cuts phosphate bonds
DNA helicase removes short stretches of ssDNA.
Pol and ligase seal the nick

58
Q

Outline how translesion DNA polymerase replicates damaged DNA

A
  1. When polymerase encounters DNA damage, the sliding clamp is covalently modified
  2. DNA pol is released and translesion polymerase is loaded onto DNA
  3. DNA is synthesised and covalent modifications are removed.
  4. Translesion DNA pol is replaced by replicative DNA pol again
59
Q

What is the double strand break repair that happens in G1?

A

Non-homologous end joining:
Error prone
Results in loss of nucleotides around break site
Ku70/80 and DNA PKes facilitate end joining
Ligase IV seals gaps

60
Q

What is the double strand break repair that happens in S phase?

A

Homologous recombination:
Error free repair that uses sister chromatids as a template

61
Q

How is DNA damage initially detected?

A
  1. ATM/ATR kinase associate with the site of DNA damage
  2. Chk1/Chk2 kinase activates and phosphorylates p53
  3. p53 dissociates from mdm2 and binds to a regulatory region of the p21 gene
  4. This inactivates G1/S-CDK and S-CDK complexes, preventing the cell cycle progressing
62
Q

What is xeroderma pigmentosum?

A

Autosomal recessive condition that increases skin cancer risk 2000 fold
Associated with a defective NER pathway (UV damage)

63
Q

How are cells with DNA damage studied?

A

Comet assay- electrophoresis to look at overall damage and find marks of DNA damage

Y2 Mol Bio (10 decks)

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