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Biochemistry semester 1 > Molecular building blocks of life II > Flashcards

Molecular building blocks of life II Flashcards

1
Q

DNA functions

A

genetic code
storage in cell
meiosis
genome integrity
replication
transcription accessibility

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2
Q

scientists demonstrating DNA as a transforming molecule

A

Griffiths 1928
Avery, macleod mccarthy 1944
hershey and chase 1952

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3
Q

Hershey and chase experiment 1952

A
  1. mix marked phages w bacteria
  2. agitate in blender, separating phages outside of bacteria
  3. centrifuge
  4. measure radioactivity in pellet/ liquidq
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4
Q

nucleic acid composition

A

heterocyclic base
sugar
phosphate

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5
Q

purines

A

adenine
guanine
N9>C1

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6
Q

pyrimidines

A

cytosine
thymine
uracil
N1> C1

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7
Q

nucleoside

A

base + sugar

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8
Q

cytodine/ deoxycytidine

A

pyrmidine N1 attaches to sugar C1

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9
Q

adenosine/ deoxyadenosine

A

purine N9 attaches to sugar C1

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10
Q

phosphodiester bond formation

A

phosphate oxygen lost
hexose hydroxyl lost
water produced

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11
Q

polymeric structure of DNA/ RNA

A

linear polymer formed by 3’-5’ phosphodiester bonds
acidic/ - charge sugar phosphate backbone
written 5’ (phosphate) > 3’ (hydroxyl) direction

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12
Q

DNA vs RNA

A

DNA: 100* more stable, resistant to hydrolysis, long-term info storage
RNA: base-catalyzed hydrolysis of RNA backbone, temporary info

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13
Q

Chargaff’s rules

A
  1. [A] = [T] / [G]=[C]
  2. [A] + [T]/ [C]+[G] varies depending on species
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14
Q

DNA structure

A

RH double helix
2 anti-parallel strands w complementary base-pairing
H bonds between bases

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15
Q

meridian angle

A

60 degrees

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16
Q

rise per base

A

0.34 nm

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17
Q

DNA spacing

A

3.4 nm

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18
Q

alpha helical radius

A

1nm

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19
Q

alpha helical diameter

A

2nm

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20
Q

number H bonds per G-C

A

3

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21
Q

number H bonds per A-T

A

2

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22
Q

H bond energy

A

5 kj/ mol

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23
Q

C-H covalent energy

A

418 kj/mol

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24
Q

DNA structural stability

A

hydrophobic effects
Bp H bonding
cooperativity
-charge

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25
Q

hydrophobic effects

A

hydrophobic bases inside
charged backbone inside

26
Q

Van der waals stacking forces

A

4 kJ/mol

27
Q

major groove

A

22 A wide
info rich
txn factors
read sequence w/o unwinding
seq specific DNA binding

28
Q

minor groove

A

12A wide
info poor
binding alters DNA

29
Q

A-DNA

A

RH
2.3 A/ b
25.3 A pitch
19 degree tilt
2.6 nm diameter

30
Q

B-DNA

A

RH
3.4A/b
35.4A pitch
1 degree bp tilt
2.4 nm diameter

31
Q

Z-DNA

A

LH
3.8 A / base
45.6 A pitch
9 degree bp tilt
1.8nm diameter

32
Q

watson and crick base-pairing consequences

A

bulges
tertiary interactions
matched/ mismatched bp

33
Q

semi-conservative replication proof

A

meselson and stahl 1958

34
Q

Meselson and stahl semi conservative proof

A

15N medium placed in 1st generation 14 N medium and replicated
each generation microfuged

35
Q

dNTP precursors

A

(DNA)n + dNTP > (DNA)n+1 + PPi

36
Q

semi-conservative replication process

A
  1. new DNA chain assembled on existing DNA template
    - catalysis of phosphodiester bond formation
  2. primer enables synthesis initiation
    - 5’-3’ direction
  3. mistake correction as mismatched nucleotides removed via 3’-5’ exonuclease activity
37
Q

oriC

A

origin of replication
circular 4.6*10^6 genome
5 copies of DNAa binding sequence
AT-rich tandem array of 13mers
DNAa assembly stimulates unwinding of AT-rich array

38
Q

DnaB helicase action

A

recruited by DnaA
loaded around ssDNA
ATPase-dependent translocation
strand exclusion model

39
Q

single stranded binding protein
SSB

A

loaded onto SSDNA
wrapped around SSB tetramers
prevents secondary structure formation

40
Q

pre-priming complex stages

A

initiation
loading
activation

41
Q

initiation

A

DnaA assembly stimulates AT-rich array unwinding
recruits DnaB/helicase

42
Q

loading

A

DnaC/ loading factor complexes w C-terminus of DnaB
after helicase closure, DnaC hydrolyzes ATP and dissociates

43
Q

activation

A

DnaG synthesizes RNA oligonucleotides in DNA replication

44
Q

DnaG primase

A

synthesizes RNA primer
recruited by DnaG

45
Q

topoisomerase II

A

catalyzes untangling of DNA duplexes
1. cleavage of both strands
2. passage separate duplex molecule through break
3. break resealed

46
Q

topoisomerase I

A

catalyzes relaxation of supercoiled DNA
1. cleavage of one strand
2. passage of cut end under other strand
3. reseals break

47
Q

DNA polymerase III core components

A

alpha polymerase unit
exonuclease domain
sliding clamp
klenow fragment

48
Q

sliding clamp

A

35A diameter hole accomodates dsDNA
keeps polyym III in contact w DNA ^ processivity
1-5Kb added before enzyme falls off

49
Q

okazaki fragments length

A

1-2 Kb long

50
Q

DNA polymerase III holoenzyme

A

2 DNA polymerase follow single DnaB helicase to coordinate synthesis of leading/ lagging strands

51
Q

trombone model

A

looping of lagging strand, releases after 1000nt’s
new loop then formed (lengthened and shortened)

52
Q

DNA damaging agents

A

DNA replicative stress
0 radicals/ ionizing radiation
polyaromatic hydrocarbons/ UV light
chemotherapeutics

53
Q

DNA replicative stress

A

base mismatches
mismatch repair

54
Q

ionizing radiation effect on DNA

A

ssDNA breaks
abasic sites
8 onoguanine

55
Q

chemotherapeutics damage

A

breaks intra-strand cross-links
dsDNA break repair
homologous recombination

56
Q

polyaromatic hydrocarbons damage

A

DNA adducts/ intrastrand crosslinks
nucleotide excision repair

57
Q

dideoxy sequencing

A

2’,3’ dideoxy analogues spike DNA polym reactions > truncated products
new DNA strands separated and electrophoresed
4 reactions dd(A/T/G/C)TP
sequence read from gel electrophoresis

58
Q

pros of dideoxy sequencing w fluorescent ddNTPs

A

enabled genome sequencing

59
Q

cons of dideoxy sequencing w fluorescent ddNTPs

A

limited to small genomes
slow
expensive

60
Q

capillary sequencing

A

Sanger method
capillary tube filled w viscous gel
automation

61
Q

NGS pros

A

next generation sequencing
quick/ cheap/ large genomes

62
Q

impacts of individual genome sequencing

A

bacteria/ virus (drug resistance)
crops (high yield)
humans (genome seq at birth, cancer genome project, disease susceptibility, pharmacogenomics)

Biochemistry semester 1 (7 decks)

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