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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
hydrophobic effects
hydrophobic bases inside charged backbone inside
26
Van der waals stacking forces
4 kJ/mol
27
major groove
22 A wide info rich txn factors read sequence w/o unwinding seq specific DNA binding
28
minor groove
12A wide info poor binding alters DNA
29
A-DNA
RH 2.3 A/ b 25.3 A pitch 19 degree tilt 2.6 nm diameter
30
B-DNA
RH 3.4A/b 35.4A pitch 1 degree bp tilt 2.4 nm diameter
31
Z-DNA
LH 3.8 A / base 45.6 A pitch 9 degree bp tilt 1.8nm diameter
32
watson and crick base-pairing consequences
bulges tertiary interactions matched/ mismatched bp
33
semi-conservative replication proof
meselson and stahl 1958
34
Meselson and stahl semi conservative proof
15N medium placed in 1st generation 14 N medium and replicated each generation microfuged
35
dNTP precursors
(DNA)n + dNTP > (DNA)n+1 + PPi
36
semi-conservative replication process
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
oriC
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
DnaB helicase action
recruited by DnaA loaded around ssDNA ATPase-dependent translocation strand exclusion model
39
single stranded binding protein SSB
loaded onto SSDNA wrapped around SSB tetramers prevents secondary structure formation
40
pre-priming complex stages
initiation loading activation
41
initiation
DnaA assembly stimulates AT-rich array unwinding recruits DnaB/helicase
42
loading
DnaC/ loading factor complexes w C-terminus of DnaB after helicase closure, DnaC hydrolyzes ATP and dissociates
43
activation
DnaG synthesizes RNA oligonucleotides in DNA replication
44
DnaG primase
synthesizes RNA primer recruited by DnaG
45
topoisomerase II
catalyzes untangling of DNA duplexes 1. cleavage of both strands 2. passage separate duplex molecule through break 3. break resealed
46
topoisomerase I
catalyzes relaxation of supercoiled DNA 1. cleavage of one strand 2. passage of cut end under other strand 3. reseals break
47
DNA polymerase III core components
alpha polymerase unit exonuclease domain sliding clamp klenow fragment
48
sliding clamp
35A diameter hole accomodates dsDNA keeps polyym III in contact w DNA ^ processivity 1-5Kb added before enzyme falls off
49
okazaki fragments length
1-2 Kb long
50
DNA polymerase III holoenzyme
2 DNA polymerase follow single DnaB helicase to coordinate synthesis of leading/ lagging strands
51
trombone model
looping of lagging strand, releases after 1000nt's new loop then formed (lengthened and shortened)
52
DNA damaging agents
DNA replicative stress 0 radicals/ ionizing radiation polyaromatic hydrocarbons/ UV light chemotherapeutics
53
DNA replicative stress
base mismatches mismatch repair
54
ionizing radiation effect on DNA
ssDNA breaks abasic sites 8 onoguanine
55
chemotherapeutics damage
breaks intra-strand cross-links dsDNA break repair homologous recombination
56
polyaromatic hydrocarbons damage
DNA adducts/ intrastrand crosslinks nucleotide excision repair
57
dideoxy sequencing
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
pros of dideoxy sequencing w fluorescent ddNTPs
enabled genome sequencing
59
cons of dideoxy sequencing w fluorescent ddNTPs
limited to small genomes slow expensive
60
capillary sequencing
Sanger method capillary tube filled w viscous gel automation
61
NGS pros
next generation sequencing quick/ cheap/ large genomes
62
impacts of individual genome sequencing
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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