Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry I > Cell cycle + DNA repair > Flashcards

Cell cycle + DNA repair Flashcards

1
Q

What are the 4 phases of the cell cycle?

A

cell enters cell cycle to duplicate its DNA content for production of 2 daughter cells

  1. G1: cell prepares for replication of DNA
  2. S: replication of DNA
  3. G2: cell prepares for cell division
  4. M: mitosis

induced in response to growth signal

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How do you call the phase when cells are not dividing?

Why does it happen?

A

quiescent, G0 phase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Explain the terms ploidy, haploid, diploid, tri- and tetraploid.

A

​ploidy ​= number of sets of chromosomes in a cell

  • haploid (n): 1 set of chromosomes present (in zygotes)
  • diploid (2n): 1 pair of homolog chromomosomes present (in somatic cells)
  • triploid (3n): third chromosome present (i.e. in Down syndrome)
  • tetraploid (4n): DNA content of somatic cell after S-phase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

So what are euploidy and anploidy?

A
  • euploidy: “good ploidy”, so only exact multiple of the haploid number (n) should be present
  • anploidy: chromosomal number of a cell is not a multiple of the haploid number (n) (often in tumors) → causes chromosomal instability
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Give an example for a synthetic nucleotide analog.

Medical application?

A

​​5-fluorodeoxyuridine

  • inhibit enzymes for DNA replication
  • incorporation into nucleic acids causing disruption of base pairing

⇒ chemotherapy, sometimes also used for organ transplantation to suppress immunologic rejection

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What do colchine or taxol do?

How are they used in medical practice?

A

both disrupt mitotic spindle

  • colchicine used for karyotype analysis
  • taxol used as cytostaticum
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What does FACS do?

A

fluorescence-activated cell sorter, special type of flow cytometry

sorts a mixture of biological cells into 2+ containers, one cell at a time, based upon the specific light scattering/fluorescent characteristics

→ dependent on chromatin layout present in cell, shows DNA content of diff. cell phases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How was the concept of permissive and restrictive temperatures discovered?

A

yeast strains were incubated at different temperatures

  • permissive (low) temperature → only those strains could enter cell cycle and proliferate
  • restrictive (high) temperature T → caused denaturation of enzymes, no proliferation

→ then used mutated yeast strains, observed that they could adapt to restrictive temperatures and still proliferated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Which proteins are directly involved the regulation of the cell cycle?

A
  • cyclins
  • cyclin-dependent kinases (Cdks)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are cyclins?

Features.

A

group of proteins controlling progression through cell cycle past restriction points by binding and activating Cdks

  • don’t have enzyme activity
  • can interact w/ different Cdks

NOTE: have changing conc. during cell cycle due to regulated synthesis/degradation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are Cdks?

What would be another name?

During which phases can they be found?

A

cyclin-dependent kinases,
also called cdcs (_cell division cycle strain_s)

are protein kinases w/ 2 domains:

  • kinase domain for phosphorylation of targets
  • regulatory domain for cyclin binding

NOTE: unlike cyclins their concentration does NOT fluctuate during cell cycle

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

The concentration of cyclins fluctuates during the cell cycle.

What is the function of the different cyclins?

Which Cdks do they bind?

A
  1. cyclin D causes progression from G1 to S phase
    → Cdk4, 6
  2. cyclin E initiates DNA replication in early S phase
    → Cdk2
  3. cyclin A governs transition from S to G2 phase, also remains until early M phase
    → Cdk2, 1
  4. cyclin B appears during G2 phase, causes transition to M phase
    → Cdk1

REMEMBER: DEAB 6,4 / 2 / 2,1 / 1​

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are SPF and MPF?

A

cyclin/Cdk complexes

  • SPF (S-phase promoting factor): cyclin E + Cdk2 → initiates DNA replication
  • MPF (maturation promoting factor): cyclin B + Cdk1 → initiates mitosis
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

List the mechanisms that regulate the presence cyclin/Cdk complexes in the nucleus.

A
  • de-/phosphorylation of Cdks
  • ubquitination + proteasomal degradation of cyclins and Cdks
  • Cdk inhibitor proteins (CKIs)
  • translocation of Cdks into nucleus
  • regulation on level of transcription by p53, pRB
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How are the cyclin/Cdk complexes generally activated?

A

have low activity when phosphorylated

→ need to be dephosphorylated and rephosphorylated at a different AA to be active

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is the function of MPF?

How is it activated?

A

mitosis-promoting factor, induces mitosis

  1. when inactive, active center of Cdk1 phosphorylated by Wee and Myt kinase
  2. for activation, Cdk1 phosphorlyated by Cak
  3. now cdc25 phosphatase dephosphorylates active center

→ active MPF now causing all its effects, incl. further activation of cdc25 phosphatase (feedforward)

(cyclin B/Cdk1 complex)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

When and how is MPF inactivated?

A

inactivated to leave mitosis

  1. Kap phosphatase dephosphorylates earlier phosphorylation site of Cak
  2. cyclin B is ubiquinated + degraded by proteasome

→ cdk1 can reassociate w/ new cyclins, becomes phosphorylated in active site again

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Which AA of Cdk1 are exactly phosphorylated/dephosphorylated to activate/inactivate MPF?

A
  • Wee, Myt kinase phosphorylate Thr14, Tyr15
    → inactivating b/c in active center
  • Cak phosphorylates Thr160
    → required for full activation of MPF
  • Kap dephosphorylates Thr160
    → inactivates MPF again
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the functions of the activated MPF complex?

A

causes multiple events to initiate mitosis

  • breaks down nuclear envelope
  • condensates chromatin
  • leads to cytoskeletal rearrangements, formation of centrosome
  • activates APC
  • activates SCF
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Which signals induce a transition from G1 to S phase?

A

GFs bind to mitogen-Rs on cell surface, activate gene regulatory proteins like transcription factor c-myc that induces the synthesis of cyclin D

→ forms synthesis-promoting factor (SPF) w/ Cdk4 or Cdk6

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What does SPF do?

A

phosphorylates tumor suppressor protein pRB (retinoblastoma protein)

unphopshorylated pRB binds transcription factor E2F, but releases it when phosphorylated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What does E2F do?

Give examples for induced proteins. Outcome?

A

stimulates synthesis of S-phase proteins following a cascade induced by GF binding

  • cyclin E: forms complex w/ Cdk2, further phosphorylates pRB → feedforward
  • DNA polymerase: starts DNA replication
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Which CKIs do you know?

What is their effect?

A

2 families of CKIs

  • INK Cdk inhibitors:
    p15, p16, p18, p19 → basically inhibit all exc. SPF
    ⇒ causing senescence
  • KIP/CIP Cdk inhibitors:
    p21, p27, p57 → inhibit SPF (cyclin A/Cdk2)
    ⇒ causing cell cycle arrest
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is cellular senescence?

A

cells that stopped dividing, “grow old”

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is contact inhibition?

A

regulatory mechanism that keeps cells from growing if in too close contact

→ no progression from G1 to S-phase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Explain the process of ubiquination.

A

cytosolic proteins receive ubiquitin as a mark for degradation by proteasomes

  1. E1 = ubiquitin-activating enzyme
    ubiquitin binds to E1 via thioester, ATP hydrolyzed to AMP
  2. E2 = ubiquitin-conjugating enzyme
    ubiquitin transferred from E1 to E2
  3. E3 = ubiquitin ligase
    ubiquitin transferred from E2 to substrate protein, forming an iso__peptide bond
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

The concentration of p53 is normally held low.

How?

A

forms tetramer, each p53 binds the ubiquitin ligase Mdm2 → marked for ubiquitination + proteasomal degradation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is the function of SCF?

A

Skp1/cullin/F-box protein, E3 ubiquitin ligase

activated by MPF

→ ubiquinates p27 (inhibitor of cyclin D+E) → disinhibition of of G1-S phase + S-phase cdks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What is the function of APC?

A

anaphase-promoting complex, E3 ubiquitin ligase

activated by MPF

  • ubiquinates anaphase inhibitors → transition from meta- to anaphase
  • ubiquinates cyclin B → cell returns to G1 phase after finishing mitosis
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What are restriction points?

A

chromosomal integrity monitored throughout cell cycle

  • G1/S transition: checks for DNA-damage and if enough nucleotides present
  • G2/M transition: checks for DNA-damage and if DNA successfully replicated
  • meta-/anaphase transition: checks if all chromosomes attached to mitotic spindle
31
Q

Which restriction point mediators are responsible for.. ?

  • G1/S transition
  • G2/M transition
  • meta-/anaphase transition
A
  • G1/S transition: p21, CHK1/2
  • G2/M transition: p21
  • meta-/anaphase transition: APC
32
Q

What are CHK1 and CHK2?

A

part of G1/S phase checkpoint control

phosphorylated/activated by ATM/ATR in response to DNA damage

→ phosphorylate/inactivate cdc25, hence no activation of SPF

33
Q

What are seliciclib and alvocidib?

A

experimental CKIs

34
Q

What is replication licensing?

A

marking of chromatin after S phase to prevent further DNA replication until the cell passes again through mitosis

  • phosphorylation/degradation of cyclin-cdk complexes
  • ubiquitination of origin binding proteins
35
Q

What are oncogenes and oncoviruses?

Mechanisms.

A

disrupt G1/S phase restriction point, causing uncontrolled cell growth

  • bind to Rb → E2F const. free
  • bind + inactivate p53 → no activation of p21
  • ubiquination of p53
36
Q

What are protooncogenes?

A

normal gene that could become an oncogene due to mutations or incr. expression

37
Q

Differentiate btw the 2 types of substitution mutations.

A

​single-base changes on DNA/mRNA

  • transition: pyrimidine replaced by diff. pyrimidine, same for purines
  • transversion: purine replaced by pyrimidine + vice versa
38
Q

List the 3 different “standard” effects of mutations.

A

can be either

  • silent mutations
  • missense mutation
  • ​nonsense mutation
39
Q

What are silent mutations?

A

mutation doesn’t have any effect

most likely due to wobble and degeneracy of 3rd base pair in codon

40
Q

What are missense mutations?

NOTE: only 2 “s” instead of “misssense”

A

single-base changes on mRNA causes translation of different AA, can have different effects

  • protein still has still same function
  • protein has partial, yet abnormal function (gain or loss)
  • protein either defect or totally abnormal function
41
Q

Why are missense mutations often “buffered” by the genetic code?

A

most single-base mutations only cause replacement of an AA by an AA with a similar functional group

42
Q

What is the effect of nonsense mutations?

A

cause premature termination of translation, only parts of protein synthesized

→ often leading to defect protein

43
Q

What are dominant negative mutations?

A

in heterozygotes

mutated gene product affects function of normal gene product

44
Q

What is a back mutation?

Another name.

A

also, reversion

reversal process whereby mutated gene returns to its original, non-mutated state

45
Q

Besides substition mutations there are also frameshift mutations.

Explain.

A

can result either from deletion or insertion of a nucleotide

depending on how many nucleotides are inserted/deleted, can result in

  • nonsense codons, leading to premature termination of translation
  • changed protein if 1 or 2 bases are inserted/deleted
  • only 1 additional AA if 3 bases inserted/deleted
46
Q

What does proflavin do?

A

is a mutagen, causes frameshift mutations

(adds or deletes base pairs)

47
Q

Give an example of a single-base mutation.

A

factor V Leiden mutation
Arg506 replaced by Gln

48
Q

Give an example for a frameshit mutation where 3 nucleotides are deleted.

A

gene coding for CFTR
F508 deleted, causing a missing Phe

→ if 2 copies of this mutation: cystic fibrosis

49
Q

What does ataluren do?

A

makes ribosomes less sensitive to premature stop codons → induces synthesis of functioning protein

e.g. for treatment of cystic fibrosis

50
Q

What are triplet expansions?

What would be an example for a disease caused by triplet expansion?

A

mutation where trinucleotide repeated multiple times, causing a gene defect

ex: CAG repeat in Huntington’s chorea

51
Q

Differentiate btw horizontal and vertical transfer of mutations.

A
  • horizontal transfer: mutation of somatic cells
  • vertical transfer: mutation of gametes, inherited to progeny
52
Q

What can be tested by conducting the Ames assay?

A

used to identify chemical carcinogens

uses Salmonella typhimurium that require His for growth, but cannot produce it

  1. bacteria spread on an agar plate with small amount of His, allows the bacteria to grow for an initial time and have the opportunity to mutate
  2. when all His depleted, only mutated bacteria that are able to produce its own His will survive
53
Q

List the 5 types of DNA repair systems in eukaryotes.

A
  • mismatch repair (MMR)
  • base-excision repair (BER)
  • nucleotide-excision repair (NER)
  • nonhomologous end-joining (NHEJ)
  • homologous recombination (HR)
54
Q

What are the 3 reasons for high-fidelity DNA synthesis?

A
  • 5’ → 3’ polymerization w/ 1 error/105bps
  • 3’ → 5’ exonucleolytic proofreading w/ 1 error/102bps
  • strand-directed mismatch repair w/ 1 error/102bps

⇒ consequence: 1 error/109 bps

55
Q

Which types of DNA damages are repaired by mismatch repair?

A
  • insertions/deletions
  • base mismatches
56
Q

Explain the mechanism of methyl-directed mismatch-repair in e. coli.

A

after replication methyl transferases methylate first parental, then daughter strand

→ mismatch-repair system checks for mutations after methylation of parental strand

  1. tetramer of 2 MutS, 2 MutL proteins bind to parental strand
  2. when mismatch detected, recruits MutH endocnuclease → cleaves sequence w/ mutation in daughter strand
  3. helicase unwinds defect sequence + exonuclease removes it
  4. DNA polymerase synthesizes excized DNA piece + DNA ligase seals nick
57
Q

What is HNPCC?

A

in HNPCC (hereditary nonpolyposis colorectal cancer)
or Lynch syndrome

autosomal dominantly inherited, mutation of gene involved in mismatch-repair system

esp. important for intestinal epithelium b/c of its high regenerative activity (DNA replication)

58
Q

In which cases is base-excision repair used?

A
  • deaminiation
  • depurination
59
Q

How does deamination of DNA induce DNA damage?

How can it be caused?

A

removal of an amino group from a nucleotide base, resulting in

  • C → U
  • A → hypoxanthine

NOTE: both bases are usually NOT present in DNA, would cause changed replicated sequence

can be spontaneous or induced by nitrous acid (or precursors), ionizing radiation

60
Q

How does depurination induce DNA damage?

How can it be caused?

A

hydrolysis of N-glycosidic bond → purine base lost, only phosphate and deoxyribose left

AP (apurinic) site formed

mutated parental strand lacks one bp → replication would lead to frameshift due to deletion of bp

happens spontaneously

61
Q

Explain the mechanism of base-excision repair.

A
  1. DNA gylcosylase detects deaminated nucleotide
  2. AP endonuclease + phosphodiesterase remove sugar phosphate
  3. DNA polymerase adds new nucleotide, DNA ligase seals nick

NOTE: DNA glycosylase obv not required in case of depurination

62
Q

For which types of DNA damage is nucleotide-excision repair used?

A
  • in case of bulky adducts
  • when pyrimidine dimers (TC, CT, CC) formed
  • in case of base alkylation (induced by carcinogen)
  • intrastrand crosslinks
63
Q

Give an example of a well known cytostatic drug.

How does it induce DNA damage?

A

cisplatin forms intrastrand crosslinks btw adjacent purines (esp. GpG, also some ApG)

→ causes replicational arrest, elicits DNA repair, activates apoptosis when repair impossible

64
Q

What are reasons for the formation of pyrimidine dimers?

A

induced by UV-light, radiation, X-ray

→ causes formation of thymine dimers

65
Q

How does base alkylation induce DNA damage?

How can it be caused?

A

methylation/alkylation of DNA affects base pairing

can happen spontaneously, or induced by PAHs (i.e. benzpyrene in smoke)

66
Q

What is the product of Aspergillus flavus?

How can it cause DNA damage?

A

= mold

produces aflatoxin B1, most potent carcinogen known

forms bulky DNA adduct
aflatoxin-N7-guanine, biomarker for mold exposure in urine

67
Q

Explain the mechanism of nucleotide-excision repair in e.coli.

A
  1. UvrA, B, C complex (excision nuclease) recognizes topographical irregularities on DNA strand, cleaves phosphodiester bonds 8 upstream, 4 downstream of DNA damage
  2. DNA helicase removes 12 nucleotide ssDNA segment
  3. DNA polyermase fills gap + DNA ligase seals nick
68
Q

What causes xeroderma pigmentosum?

How is it inherited?

A

autosomal recessively inherited, caused by defect in nucleotide-excision repair

→ thymine dimers formed in response to UV light cannot be repaired

⇒ pts are extremely sensitive to sunlight, high predisposition for skin cancer

69
Q

How is DNA double-strand break repair initiated?

A
  1. MRN complex recognizes double-strand break, also initiates DNA doube strand-break repair
  2. activates ATM and ATR (“master kinases”), phosphorylate and activate p53
  3. p53 = transcription factor, induces protein transcription mediating cellular outcome

just remember this stupid cascade

70
Q

What is ataxia telangiectasia?

How is it caused?

A

Louis-Bar syndrome
caused by mutation of ATM

progressive neurodegenerative disease, leading to immunodeficiency and incr. tumor formation

71
Q

Which proteins are induced by p53?

A
  • p16, p19 (= CKIs): causing senescence by inhibiting cyclin D/Cdk4, 6
  • p21 (= CKI): causing cell cycle arrest by inhibition of SPF
  • when in very high conc., BAX: activates apoptocic pathways
72
Q

What are the ways to repair DNA double-strand break?

A
  • non-homologous end joining
  • homologous recombination
73
Q

Explain the mechanism of non-homologous end-joining.

A

double-strand break →

  1. end recognition by KU80/KU70 heterodimer
  2. recruits add. proteins to process DNA ends, for repair synthesis and ligation

BUT: partial deletion and no control-mechanism
→ low fidelity repair

74
Q

Explain the mechanism of homologous recombination.

A

double-strand break →

  1. MRN complex cleaves off short sequences from both ends
  2. ends are processed + strand invasion happens: exchange of DNA single strands btw 2 homolog chromosomes, involves BRCA1
  3. DNA polymerase synthesizes missing DNA sequence using the homolog chromosome as template, nick sealed by DNA ligase

​⇒ high-fidelity repair, but not possible for haploid gametes, male X/Y chromosomes

Biochemistry I (13 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions