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CH531—Biochemistry > Chp 4—Nucleic Acids & Molecular Cloning > Flashcards

Chp 4—Nucleic Acids & Molecular Cloning Flashcards

1
Q

purines

A

A
G

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2
Q

pyrimidines

A

C
T
U

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3
Q

double-ringed bases

A

purines

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4
Q

how to tell A from G?

A

A has NH2 next to N furthest from bridge

G has carbonyl next to N furthest from bridge, and NH2 between Ns

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5
Q

how to tell C from T?

A

C has NH2 directly above R

T has carbonyl directly above R, and methyl on the left side

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6
Q

how to tell T from U?

A

T has methyl on carbon next to carbonyl

U does not

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7
Q
A

adenine

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8
Q
A

guanine

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9
Q
A

cytosine

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10
Q
A

thymine

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11
Q
A

uracil

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12
Q

nucleoside

A

base + sugar

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13
Q

ribose vs deoxyribose

A

ribose has 2’ OH

deoxyribose does not

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14
Q

nucleotide

A

base + sugar + phosphate(s)

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15
Q

phosphate is bonded to…

A

5’ flag of sugar

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16
Q

names of 3 phosphates on NTP

A

alpha
beta
gamma

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17
Q

sugar in ATP

A

ribose

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18
Q

bonds joining nucleotides

A

phosphodiester bonds

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19
Q

reaction steps for formation of phosphodiester bonds

A
  1. free base deprotonates 3’ OH
  2. (-) oxygen attacks alpha phosphorus on an NTP
  3. 2 other Ps leave
  4. strand now has a 5’ end (old) and a 3’ end (new)
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20
Q

2 hydroxyls involved in the phosphodiester bonds

A

3’ OH
5’ OH

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21
Q

explain phosphodiester bond hydrolysis

A

in an alkaline environment, free base deprotonates the 2’ OH on ribose

O- attacks nearby phosphorus, breaking the bond with the next nucleotide

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22
Q

H-bonds between A & T
H-bonds between C & G

A

2
3

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23
Q

chargaff’s rules (4)

A
  1. base comp of DNA varies from species to species
  2. DNA from different tissues have same comp
  3. base comp does not change with age, nutrition, environment
  4. A + G = C + T
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24
Q

A + T hydrogen bonds

A
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25
Q

C + G hydrogen bonds

A
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26
Q

number of non-canonical base pairings

A

28

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27
Q

base stacking is via …. interactions

28
Q

base stacking bond strength

A

pur/pur&raquo_space; pur/pyr&raquo_space; pyr/pyr

29
Q

4 contributors to DNA structure

A
  1. base pairing; H bonds
  2. base stacking; pi pi
  3. syn & anti conformers
  4. ribose conformers
30
Q

(anti/syn) conformer is preferred

31
Q

sugar pucker function

A

minimizes non-bonded interactions between substituents

32
Q

common sugar puckers

A

C2’ - endo
C3’ - endo

33
Q

Z-DNA conformers

A

alternating syn and anti conformers along backbone

34
Q

continuity of DNA replication

A

semi-discontinuous

35
Q

helicase

A

unzips DNA

36
Q

primase

A

adds RNA primer

37
Q

DNA polymerase

A

binds RNA primer and adds bases

38
Q

exonuclease

A

removes RNA primers

39
Q

ligase

A

seals replicated DNA together

40
Q

30-50 divisions

A

Hayflick limit

41
Q

3 stages of transcription and translation

A
  1. initiation
  2. elongation
  3. termination
42
Q

transcribes DNA to mRNA

A

RNA polymerase

43
Q

RNA read…

A

5’ to 3’

44
Q

AAs synthesized…

A

N’ to C’

45
Q

start codon

46
Q

stop codons

47
Q

translational repression requires…

A

partial complementarity between miRNA and mRNA

48
Q

translational degradation requires…

A

perfect complementarity between miRNA and mRNA

49
Q

stem and loop shaped RNA

50
Q

ribosome sites

51
Q

5 main base modifications

A

methylation
deamination
sulfur substitution
base isomerization
double bond saturation

52
Q

why is there thymine instead of uracil in DNA?

A
  1. uracil subject to more modifications
  2. thymine more expensive to make
  3. methyl on thymine protects it/makes it more stable
  4. cytosines deaminate many times a day to give uracil, which could not be corrected if uracil was in DNA already
53
Q

length of chromosomes

54
Q

avg length of chromosome

55
Q

histone/DNA arrangement models

A

solenoid
zigzag

56
Q

protein synthesis steps

A
  1. make complementary DNA strand from template
  2. change Ts to Us to give complementary RNA strand
  3. flip RNA strand to give a 5-3’ RNA (direction of reading)
  4. use codon chart to get polypeptide
57
Q

12 steps of molecular cloning

A
  1. amplification of gene via PCR
  2. digestion of gene with restriction enzymes
  3. digestion of host vector with restriction enzymes
  4. isolation & purification of BOTH gene and vector with gel
  5. sequencing of BOTH with fluorophores
  6. ligation of gene + vector to give recom.plasmid
  7. identification of product via gel
  8. transformation of recom.plasmid into host cells
  9. selection of host cells carrying plasmid
  10. isolation & purification of recom.plasmid
  11. diagnostic digestion & gel
  12. sequencing of recom.plasmid
58
Q

steps of PCR

A

denaturing
annealing
elongation

59
Q

what not to do do a plasmid with restriction enzymes

A

cut through the origin or your selection genes

60
Q

nucleotide + fluorophore

61
Q

ligation uses…

A

DNA ligase

62
Q

PCR uses enzyme…

A

Taq polymerase

63
Q

2 methods of transformation

A

heat shock/chemical
electric shock/electroporation

64
Q

transduction

A

virus brings plasmid into cells

65
Q

transfection

A

plasmid brought into eukaryotic cells
difficult

66
Q

2018 Nobel Prize
2020 Nobel Prize

A

Directed Evolution
CRISPR

CH531—Biochemistry (11 decks)

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