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Molecular and cell biology > Chromosomes and DNA > Flashcards

Chromosomes and DNA Flashcards

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AP® Biology flashcards Biology 101 flashcards
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
Q

How do DNA transponons move?

A

by a cut and paste mechanism without self-duplication, requiring enzyme transposase

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26
Q

Non-retroviral polyA retrotransponsons

A

abundant in vertebrate genomes
replicates via an RNA intermediate using its own encoded reverse transcriptase

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27
Q

What do products of L1 reverse transcription do?

A

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

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28
Q

Evolution of transposing elements

A

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

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29
Q

How is DNA synthesis initiated?

A

creating a replication fork where the DNA strands are seperated by DNA helicase

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30
Q

What direction does DNA replication happen?

A

5’ → 3’

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31
Q

Why is there a leading and lagging strand?

A

antiparallel orientation of parental strands
unidirectional orientation of new DNA synthesis
both new strands can’t be synthesised continuously

32
Q

What strand has continuous synthesis?

A

leading strand

33
Q

Why are primers needed?

A

DNA polymerases can’t start making a DNA chain from scratch
requires a pre-existing chain or short stretch of nucleotides

34
Q

How is the short RNA primer synthesised?

A

using template and NTPs by DNA primase
once the primer is in place DNA polymerase extends it

35
Q

What enzymes does lagging strand synthesis require?

A

DNA primase
DNA polymerase
ribonuclease H
DNA ligase

36
Q

Lagging strand synthesis

A

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
Q

Werner syndrome

A

caused by mutations in genes encoding DNA helicases + accessory 3’ exonuclease
causes premature ageing, genome instability + cancer in several sites

38
Q

Sliding clamp

A

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
Q

Single stranded DNA binding proteins

A

expose single stranded DNA in the replication fork
makes it available for templating synthesis of the new DNA strand and eases fork progression

40
Q

DNA topoisomerases

A

prevent DNA from becoming tangled during DNA replication and enhance processivity of DNA polymerase

41
Q

What is the function of topoisomerases?

A

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
Q

Origin of replication

A

single point where DNA replication starts
specific DNA sequences recruit replication initiator proteins

43
Q

What are the 2 phases of DNA replication in eukaryotes?

A
  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
Q

Eukaryotic replicator selection

A

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
Q

Ribonuclease H

A

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
Q

What are the 2 types of things cells are under constant attack from?

A

endogenous sources
exogenous sources

47
Q

What are endogenous sources?

A

reactions with other molecules within the cell like hydrolysis, oxygen species and by-products of metabolism

48
Q

What are exogenous sources?

A

reactions with molecules from outside the cell like UV, x rays, carcinogens and chemotherapeutics

49
Q

Types of endogenous DNA damage

A

depurination
deamination
methylation

50
Q

Types of exogenous DNA damage

A

pyrimidine dimers
double strand breaks
interstrand crosslinks

51
Q

What DNA damage effects both strands of the alpha helix?

A

double strand breaks
interstrand crosslinks

52
Q

Deamination

A

removal of the amino group by hydrolysis
results in changes to the DNA bases

53
Q

Transition mutations

A

more likely than transversions
less likely to result in amino acid substitutions

54
Q

Depurination

A

the N-glycosidic bond is a common substrate for hydrolysis as it is an abasic site
more frequent at purine bases

55
Q

What effect does UV light have on DNA?

A

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
Q

Double backbone break inducers

A

x rays
ionising radiation
topoisomerase II inhibitors

57
Q

Single backbone break inducers

A

reactive oxygen species
hydroxyurea
camptothecin

58
Q

NER

A

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
Q

Translesion synthesis

A

translesional DNA polymerases can replicate highly damaged DNA
lack precision in template recognition and substrate base choice

60
Q

What does translesion synthesis cause?

A

base substitution and single nucleotide deletion mutations

61
Q

What are the 2 mechanisms to repair double strand breaks?

A

non-homologous end joining NHEJ
homologous recombination

62
Q

Non-homologous end joining NHEJ

A

error prone
restricted to G1 phase
usually results in the loss of nucleotides surrounding the break site and important genetic information

63
Q

Homologous recombination

A

error free and accurate repair
occurs only in S phase by using intact sister chromatids as a template

64
Q

What 3 places in the cell cycle can DNA damage be detected?

A

G1
entry to S phase
entry to mitosis

65
Q

How is damage detected?

A

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
Q

Xeroderma pigmentosum

A

autosomal recessive disease associated with a defect in NER
skin cancer, UV sensitivity, neurological abnormalities

67
Q

BRCA2 deficient cells

A

exhibit genomic stability+ sensitive to DNA damaging elements
defective in HR
breast, ovarian and prostate cancer

68
Q

What are the two types of topoisomerase?

A

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
Q

What enzymes are involved in base excision repair?

A

DNA glycosylase
AP endonuclease + phosphodiesterase
DNA polymerase
DNA ligase

70
Q

DNA glycosylase

A

removes base that has been deaminated from DNA sequence

71
Q

AP endonuclease + phosphodiesterase

A

remove sugar phosphate that incorrect base was attached to from backbone

72
Q

DNA polymerase + ligase role in BER and NER

A

DNA polymerase adds in correct base(s) into gap created
DNA ligase seals the nick

73
Q

What enzymes are involved in nucleotide excision repair?

A

excision nuclease
DNA helicase
DNA polymerase + ligase

74
Q

Translesion synthesis process

A

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
Q

BRCA1 mutations

A

defective homologous recombination
breast ovarian cancer

76
Q

Bloom syndrome

A

defective DNA helicase needed for recombination
cancer at several sites, stunted growth + genome instability`

Molecular and cell biology (8 decks)

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