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21 fall: Biochem > lecture 7 > Flashcards

lecture 7 Flashcards

1
Q

your patient seems prematurely old, and suffers from osteoporosis, kyphosis (curve of spine), cachexia(muscle wasting) and infertility
What is the problem

A

defect in NER (nucleotide excision repair) leading to Trichothiodystrrophy (TTD)

NER fix UV light defects (thymine dimers)

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2
Q

your patient has balance disorder, depressed immune system, cerebellar degeneration, extreme sensitivity to Xrays and has developed cancer.
What is the problem

A

Ataxia Telangiectasia caused by mutation of the ATM gene

ATM protein can see DCB and causes the cell to fix them

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3
Q

P has colon cancer

What gene is mutated?

A

genes in mismatch DNA repair pathway

heriditary non-polyposis colon cancer HNPPC

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4
Q

how is DNA bonded

A

sugar-phosphate backbone of DNA

5’ to 3’

helix

GC (stronger 3 hydrogen bones) and AT (weaker 2 hydrogen bonds)

purines attaches to pyrimidines

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5
Q

DNA replication

A
  • topological constraints
  • unmasking of chromosomal proteins
  • large genome size (needs to be fast) (1000 nucleotides per second), can occur at a bunch of spots on DNA at same time
  • accuracy

Semiconservative and bidirectional

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6
Q

explain semiconservative DNA replication

A

new copy has one strand old one strand new

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7
Q

explain bidirectional DNA replication

A

starts and then goes in both directions

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8
Q

DNA polymerase can only go ___ to ___. DNA polymerase can only elongate an ____ of DNA or RNA

A

5’ to 3’

existing primer, only double stranded, with free 3’hydroxyl group available to bind

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9
Q

lagging strand fragments

A

okazaki

can only go 5’ to 3 ‘

DNA polymerase needs a primer to start

RNA polymerase can start. will attach and will put down RNA which DNA can see and copy. RNA primer will eventually get eaten and replaced by DNA polymerase

at the end of the strand will have RNA primer at end of chromosome
- cant be eaten
-RNA easily degraded
leaving single strand which also gets degraded- BAD cell death

Enzyme telomerase adds repeated sequence at ends to protect DNA from being broken down

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10
Q

ways to damage DNA

A

radiation
DNA polymerase
heat
ect.

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11
Q

how does DNA know something went wrong

A

protein sensors
-usually phosphorylation cascade
= stop cell cycle, cell death, turn on genes that fix the problem, and then fix the problem

ATM is one of these proteins
ATM sees double stranded breaks and is a transducer that initiates signaling pathways to inform the cell the DNA is damaged

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12
Q

Defects in ATM leads to

A

Ataxia telangiectasia

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13
Q

explain BER

A

base excision repair

PARP is needed to recruit proteins to DNA damage

  1. recognize problem
    glycosylases recognize 1 base error and cut the base out
  2. cut out the damage
    endonuclease (ape1) cuts the sugar out of the DNA backbone
  3. fill in proper sequence
    DNA polmerase beta fills in the correct nucleotide
  4. close the DNA backbone with ligase
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14
Q

explain NER

A

nucleotide excision repair

  1. recognize problem
    UV light damage (thymine dimers)
    XPA, XPE find problem
    TFIIH(XPB and XPD) unwind the helix
  2. cut out the damage
    XPF/ERRC1 and XPG cut out section
  3. fill in proper sequence
    DNA polymerase put in right section
  4. close the DNA backbone with ligase
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15
Q

explain MMR

A

mismatch repair
usually seen in colon cancer

in BACTERIA

  1. recognize problem
    will recognize problem and nick DNA
    MutS, MutL, MutH, ATP
  2. cut out the damage
    Will eat bases and error
    Exonuclease, Helicase II ATP
  3. fill in proper sequence
    DNA polymerase
  4. close the DNA backbone with ligase
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16
Q

explain HR

A

homologous recombination

Double stranded breaks (DSB)

bring broken ends together and join them with ligase.

17
Q

explain NHEJ

what might it help with

A

nonhomologous end joining

Double stranded breaks (DSB)

bring broken ends together and join them with ligase. Somatic recombination of immunoglobulin genes

18
Q

explain TS

A

translesion DNA synthesis

error prone DNA polymerase copy over mutated DNA (ehh it will probably be okay)

Somatic Hypermutation of immunoglobulin genes

19
Q

how does PARP inhibitors help kill cancer cells

A

PARP is used to fix 1 strand errors (BER base excision repair)

stop PARP and 1 strand error becomes two stranded error

BRCA tries to come and fix the problem

in cancer BRCA fucks up and causes more breaks

if we stop PARP we stop BRCA and more breaks causes cell to die

20
Q

NER defects leads to

A

NER (nucleotide excision repair)

xeroderma pigmentosa
cockayne’s syndrome
trichothiodystrophy

21
Q

explain xeroderma pigmentosa

A

NER defect (nucleotide excision repair)

  • 7-8 genes cause defect on XPA (finds problem) and XPG (cuts problem)
  • unable to repair UV damage (thymine dimers)
  • 1000-2000 fold increase in sun-induced skin cancer
  • neurological defects in most severe cases
22
Q

explain cockayne’s syndrome

A

NER defect (nucleotide excision repair)

caused by mutation of a subset of XP genes (TFIIH XPB, XPD)

no increase risk of cancer

impaired neurological development

dwarfism

premature aging

23
Q

explain trichothiodystrophy

A

defect in NER (nucleotide excision repair)

share many of the same conditions as C.S(cockayne’s syndrome)

brittle hair and nails, scaly skin

reduced stature, curved spine (kyphosis)

reproductive problems

24
Q

how does mismatch repair know which strand is right

A

old strand has Ch3 (methyl group)

old strand must be right, will attack and fix new strand

25
Q

HNPCC

A

heriditary non-polyposis colon cancer

mutations in Mismatch repair

bacteria to human
MutS is similar to MSH1-6
MutL is similar to MLH1, MLH2, PMS1 and PMS2

MLH1 30%
MSH2 60%
PMS1 and PMS2 are sometimes mutated as well

26
Q

*** a defect in the enzyme, ApeI will affect which DNA repair pathway

A

base excision repair

Step 2
ApeI is used to cut out the sugar out of the DNA backbone

27
Q

*** choose one of the DNA repair pathways we discussed in class. Describe it

A

NER
nucleotide excision repair

  • repairs larger lesions in DNA (UV damage thymine dimers)
  • XPA and XPE detect the damge
  • TFIIH (XPB and XPD) act as helicase and unwind DNA
  • XPF and XPG cut out the error
  • DNA polymerase then relace the correct base
  • ligase then seals the DNA
28
Q

3 ways DNA sequence are stored

A
  • single copy DNA
  • moderately repetive DNA
  • Highly repetitive DNA
29
Q

explain single copy DNA

A

occur only once, or a few times

70% of genome

encode proteins and spacer DNA

30
Q

explain moderately repetitive DNA

A

100- 1000 copies

20%

ribosomal and tRNA, retrotransposons which replicated themselves and reinsert into the genome

31
Q

highly repetitive DNA

A

100,000 copies

families of repetitive sequences that can be species specific

10%

SINES- short interspersed DNA sequences 150-300 bp
LINES- long interspersed DNA sequences 5000-6000 bp

32
Q

type of protein that finds single stranded breaks in DNA

A

ATR (ATM and Rad3-related protein)

33
Q

___ is needed in somatic hypermutation of immunoglobulin genes

A

translesion DNA synthesis.

Error prone polymerases

34
Q

what happens at the end of the lagging strand

A

at the end of the strand will have RNA primer at end of chromosome
- cant be eaten
-RNA easily degraded
leaving single strand which also gets degraded- BAD cell death

Enzyme telomerase adds repeated sequence at ends to protect DNA from being broken down

35
Q

___ is a protein sensor that can see double stranded breaks in DNA

A

ATM

36
Q

symptoms of Ataxia telangiectasia

A

ataxia
extreme sensitivity to Xrays
depressed immune system

37
Q

6 type of DNA repair

A 
base excision repair (BER)
nucleotide excision repair (NER)
mismatch repair (MMR)
homologous recombination (HR)
nonhomologous end joining (NHEJ)
translesion DNA synthesis (TS)
38
Q

PARP is in what type of DNA repair

A

BER

39
Q

examples of glycosylases that are used in BER

A

TDG, MBD4,UNG

21 fall: Biochem (44 decks)

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