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Molecular and cell biology > Chromosomes and DNA > Flashcards

Chromosomes and DNA Flashcards

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1
Q

When individual chromosomes be easily distinguished?

A

during metaphase of mitosis

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2
Q

Diploid eukaryotic cells

A

contain two copies of each chromosome
each chromosome pair differs in size and DNA sequence

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3
Q

What is the karyotype of the parent organism?

A

organisaed representation of all the chromosomes in a eukaryotic cell at metaphase
individual chromosomes occupy distinct subnuclear territories even in interphase

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4
Q

Chromosome

A

highly coiled fibre of chromatin
under electron microscope interphase chromatin resembles beads on a string
beads are nucleosomes

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5
Q

Nucleosomes

A

a protein core with DNA wound around it
protein subunits are core histones

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6
Q

Core histones structure

A

N-terminal tails of core histone subunits project out from the nucleosome core and are free to interact with otehr proteins
faciliate regulation of chromatin structure and function

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7
Q

Linker histones

A

strap DNA onto histone octamers and limit movement of DNA relative to the histone octamer
facilitates establishment of transcriptionally silent heterochromatin

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8
Q

How is DNA packed?

A

by histone octamers into a compact, flexible 30nm chromatin scaffold that can be remodelled to accomodate protein complexes involved in gene transcription and DNA replication

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9
Q

Chromatin is engineered to permit…

A

flexible responses to altered transcription factor activity caused by changes in cell differentiation status + signalling pathway activities

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10
Q

Interphase chromatin

A

comprises of a set of dynamic fractal globules that can reversible condense and decondense without becoming knotted

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11
Q

Nuclear periphery in interphase cells

A

composed of transcriptionally inactive DNA
RNA transcripts are excluded from the periphery

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12
Q

Chromosomes contain specialised DNA sequences that facilitate:

A

reliable and complete DAN replication
segregation of duplicated chromosomes during cell division

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13
Q

Telomeres

A

specialised repetitive DNA sequences at the ends of chromosomes
define chromosome ends and maintain their integrity

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14
Q

Telomerase

A

specialised DNA polymerse that replicated telomeres
synthesises single stranded 3’ overhanging TTAAGGG repeat arrays
ribonucleoprotein with an intrinsic RNA component that acts as a template

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15
Q

Centromeres

A

contain specialised proteins and DNA sequences that facilitate chromosome segregation during cell division

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16
Q

Alpha-satellite DNA repeats

A

in centromeres
readily form condensed chromatin with histone octamers containing unusual subunits

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17
Q

Kinetochore outer plate proteins

A

bind to protein components of the mitotic spindle

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18
Q

What is the function of kinetochore proteins?

A

part of the mechanism of ensuring faithful segregation of sister chromatids at cell division

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19
Q

Yeast kinetochore

A

basket that links a single nucleosome of centromeric chromatin to a single microtubule

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20
Q

Parasitic DNA

A

repeated DNA sequence elements that make up half of the human genome
copies of retrotransponons

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21
Q

Increasing biological complexity is accompanied by

A

increasing numbers of protein coding genes
increasing amounts of non-protein-coding DNA for regulating transcription and organising access to protein coding genes

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22
Q

Cis-regulatory information

A

encoded by non-protein-coding DNA sequences
determines where and when in the body adjacent protein-coding genes are transcribed

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23
Q

What are the 3 different types of transponons?

A

DNA transponons
retroviral trasnponons
non-retroviral polyA retrotransponons

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24
Q

Transponons

A

repeated DNA sequences
mobile genetic elements that jump around the genome

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25
How do DNA transponons move?
by a cut and paste mechanism without self-duplication, requiring enzyme transposase
26
Non-retroviral polyA retrotransponsons
abundant in vertebrate genomes replicates via an RNA intermediate using its own encoded reverse transcriptase
27
What do products of L1 reverse transcription do?
integrated directly into the genome at a new location without the need to be packaged into virus like particles some are known to disrupt genes and cause diseases such as haemophilia
28
Evolution of transposing elements
non retroviral retrotransponsons have expanded hugely in numbers in evolution of higher mammals most of the copies of transposing elements in the genome are defective and ancient relics of formerly functional elements
29
How is DNA synthesis initiated?
creating a replication fork where the DNA strands are seperated by DNA helicase
30
What direction does DNA replication happen?
5’ → 3’
31
Why is there a leading and lagging strand?
antiparallel orientation of parental strands unidirectional orientation of new DNA synthesis both new strands can't be synthesised continuously
32
What strand has continuous synthesis?
leading strand
33
Why are primers needed?
DNA polymerases can't start making a DNA chain from scratch requires a pre-existing chain or short stretch of nucleotides
34
How is the short RNA primer synthesised?
using template and NTPs by DNA primase once the primer is in place DNA polymerase extends it
35
What enzymes does lagging strand synthesis require?
DNA primase DNA polymerase ribonuclease H DNA ligase
36
Lagging strand synthesis
DNA primase makes RNA primer → DNA polymerase- extends RNA primer which requires primer-template junction → ribonuclease H removes RNA primer → DNA polymerase extends across gap → DNA ligase seals the nick
37
Werner syndrome
caused by mutations in genes encoding DNA helicases + accessory 3' exonuclease causes premature ageing, genome instability + cancer in several sites
38
Sliding clamp
increases the processivity of DNA polymerase once frist step of DNA synthesis has been accomplished interaction of enzyme with primer-template junction is maintained makes addition of further nucleotides very rapid ATP dependent
39
Single stranded DNA binding proteins
expose single stranded DNA in the replication fork makes it available for templating synthesis of the new DNA strand and eases fork progression
40
DNA topoisomerases
prevent DNA from becoming tangled during DNA replication and enhance processivity of DNA polymerase
41
What is the function of topoisomerases?
helicase unwinding introduces superhelical tension into the DNA helix → tension is relaxed by DNA topoisomerases which nick and reseal the backbone of the helix
42
Origin of replication
single point where DNA replication starts specific DNA sequences recruit replication initiator proteins
43
What are the 2 phases of DNA replication in eukaryotes?
1. replicator selection in G1 phase- formation of pre-replicative complex 2. origin activation in S phase- unwinding of DNA and recruitment of DNA polymerase
44
Eukaryotic replicator selection
origin recognition complex binds to replicator sequence (ARS in yeast) → helicase loading proteins Cdc6 and Cdt1 bind to ORC → the helicase Mnm2-7 binds to complete formation of pre-RC → inactive
45
Ribonuclease H
removes RNA primers which further shortens the newly synthesised DNA strands at 5' ends of chromosomes chromosome shortening risks loss of valuble coding info
46
What are the 2 types of things cells are under constant attack from?
endogenous sources exogenous sources
47
What are endogenous sources?
reactions with other molecules within the cell like hydrolysis, oxygen species and by-products of metabolism
48
What are exogenous sources?
reactions with molecules from outside the cell like UV, x rays, carcinogens and chemotherapeutics
49
Types of endogenous DNA damage
depurination deamination methylation
50
Types of exogenous DNA damage
pyrimidine dimers double strand breaks interstrand crosslinks
51
What DNA damage effects both strands of the alpha helix?
double strand breaks interstrand crosslinks
52
Deamination
removal of the amino group by hydrolysis results in changes to the DNA bases
53
Transition mutations
more likely than transversions less likely to result in amino acid substitutions
54
Depurination
the N-glycosidic bond is a common substrate for hydrolysis as it is an abasic site more frequent at purine bases
55
What effect does UV light have on DNA?
induces the formation of pyrimidine dimers distorts DNA and can also cause interstrand DNA crosslinks and DNA protein crosslinks these block relpication and transcription so are highly toxic
56
Double backbone break inducers
x rays ionising radiation topoisomerase II inhibitors
57
Single backbone break inducers
reactive oxygen species hydroxyurea camptothecin
58
NER
nucleotide excision repair repairs DNA damage when more than one base is involved such as pyrimidine dimers involves excision of short patches of single stranded DNA to remove affected bases
59
Translesion synthesis
translesional DNA polymerases can replicate highly damaged DNA lack precision in template recognition and substrate base choice
60
What does translesion synthesis cause?
base substitution and single nucleotide deletion mutations
61
What are the 2 mechanisms to repair double strand breaks?
non-homologous end joining NHEJ homologous recombination
62
Non-homologous end joining NHEJ
error prone restricted to G1 phase usually results in the loss of nucleotides surrounding the break site and important genetic information
63
Homologous recombination
error free and accurate repair occurs only in S phase by using intact sister chromatids as a template
64
What 3 places in the cell cycle can DNA damage be detected?
G1 entry to S phase entry to mitosis
65
How is damage detected?
ATM/ATR get activated and associate with the site of DNA damage and this activates other kinases to block the cell cycle → p53 is stabilised and activates p21 → p21 renders the G1/S-CDK and its complexes inactive → preventing cycle progression → DNA is repaired and if this isn’t possible, apoptosis
66
Xeroderma pigmentosum
autosomal recessive disease associated with a defect in NER skin cancer, UV sensitivity, neurological abnormalities
67
BRCA2 deficient cells
exhibit genomic stability+ sensitive to DNA damaging elements defective in HR breast, ovarian and prostate cancer
68
What are the two types of topoisomerase?
type I topoisomerases nick and reseal one of the 2 DNA strands so no ATP is required → type II topoisomerases nick and reseal both DNA strands which requires ATP
69
What enzymes are involved in base excision repair?
DNA glycosylase AP endonuclease + phosphodiesterase DNA polymerase DNA ligase
70
DNA glycosylase
removes base that has been deaminated from DNA sequence
71
AP endonuclease + phosphodiesterase
remove sugar phosphate that incorrect base was attached to from backbone
72
DNA polymerase + ligase role in BER and NER
DNA polymerase adds in correct base(s) into gap created DNA ligase seals the nick
73
What enzymes are involved in nucleotide excision repair?
excision nuclease DNA helicase DNA polymerase + ligase
74
Translesion synthesis process
covalent modifications to sliding clamp when it encounters damaged DNA replicative DNA polymerase released translesion DNA polymerase loaded by assembly factors DNA synthesis continues
75
BRCA1 mutations
defective homologous recombination breast ovarian cancer
76
Bloom syndrome
defective DNA helicase needed for recombination cancer at several sites, stunted growth + genome instability`

Molecular and cell biology (8 decks)

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