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MSAP > Week 1 - Biochemistry > Flashcards

Week 1 - Biochemistry Flashcards

1
Q

two purines

A

adenine and guanine

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2
Q

three pyrimidines

A

thymine, cytosine and uracil

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3
Q

U replaces what?

A

T

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4
Q

5’ end has what?

A

phosphate group

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5
Q

3’ end has what

A

hydroxyl group

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6
Q

name 3 levels of packing in DNA in order

A

nucleosomes, loops of fibers (beads on a string), and 30 nm fibers

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7
Q

how do prokaryotes pack their dna?

A

negative supercoiling and HU proteins

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8
Q

how many oriC in prokaryotes?

A

one

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9
Q

how many origins of replication in eukarytoes?

A

many many many

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10
Q

2 sequences of the OriC

A

3x 13-mer sequence and 4x 9-nucleotide sequence

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11
Q

importance of 13 mer tandem sequences?

A

AT rich so will break easily

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12
Q

DnaA binds to what?

A

9-nucleotide region

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13
Q

what happens after DnaA binds?

A

13 mer sequence opens

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14
Q

what delivers DnaB?

A

DnaC - helicase inhibitor

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15
Q

what is DnaB?

A

helicase

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16
Q

what does helicase do?

A

wraps around both strands of DNA to unwind DNA in both directions away from the OriC

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17
Q

what is DnaA

A

initiatior protein

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18
Q

what is DnaB

A

helicase

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19
Q

what are the importance of single stranded binding proteins?

A

they hold everything open (ssbp)

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20
Q

main enzyme of DNA replication?

A

DNA pol III

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21
Q

direction of DNA pol III

A

5’-3’, lays down leading and lagging strands

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22
Q

what is released after complementary nucleotide is seale

A

pyrophosphate

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23
Q

what special thing can DNA pol III do?

A

3’-5’ exonuclease activity

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24
Q

what is DNA primase?

A

lays down RNA template so that DNA pol III can begin

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25
Q

what is DNA pol I?

A

removes and replaced RNA primer

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26
Q

what is DNA ligase?

A

ligates okazaki fragments together

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27
Q

describe leading and lagging strand

A

DNA pol III will lay down both, 2 separate going in both directions, leading continuous, lagging has to lay down short bits known as Okazaki fragments

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28
Q

what is the central dogma of biology?

A

DNA –> RNA –> protein

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29
Q

direction of RNA pol?

A

5’-3’

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30
Q

template strand?

A

read by RNA pol to generate mRNA

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31
Q

another name for template strand?

A

antisense strand

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32
Q

another name for the non-template strand?

A

sense strand

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33
Q

non-template strand?

A

not read by RNA pol to generate mRNA but is the sense strand, meaning the mRNA generated is an exact copy except for the U instead of T

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34
Q

is a primer needed for RNA pol?

A

no

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35
Q

name the 4 types of RNA

A

mRNA, tRNA, rRNA, and snRNA

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36
Q

how many RNA pol in bacteria?

A

one

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37
Q

how many RNA in euk?

A

3

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38
Q

RNA pol I?

A

makes rRNA

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39
Q

RNA pol II?

A

mRNA and some snRNA

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40
Q

RNA pol III?

A

tRNA and some snRNA

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41
Q

3 regions of prokaryote gene?

A

promotor, RNA coding sequence, and terminator

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42
Q

the holoenzyme form of prok RNA pol has what?

A

sigma factor

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43
Q

when does sigma factor fall off?

A

after 8-9 nucleotides in

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44
Q

pribnow box?

A

prokaryote promotor region -10, there is also some at -35

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45
Q

in euk what is the major sequence in the promotor?

A

tata box

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46
Q

what is TFIID?

A

distorts DNA helix, has TATA box binding protein

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47
Q

what is TFIIB?

A

part of RNA pol interaction

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48
Q

what is TFIIH?

A

DNA helicase, activates RNA polymerase through phosphorylation

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49
Q

what is TFIIE?

A

positions RNA polymerase

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50
Q

what increases levels of transcription in euk?

A

activators and adaptor molecules

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51
Q

what does transcription do to the coils ahead and behind?

A

positive supercoils in front, and negative supercoils behind

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52
Q

what does the cell do during transcription to solve supercoiling

A

gyrase in front, topoisomerase in back

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53
Q

two types of transcription termination?

A

intrinsic-palindromic region forms hairpin, G-C rich region followed by Us
extrensic-rho factor

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54
Q

during post transcriptional processing what happens?

A

introns spliced out, 5’ cap added which is methylated, poly A tail added

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55
Q

describe the general structure of an amino acid

A

central carbon bonded to hydrogen, R group, amino group, and carboxyl group

56
Q

2 amino acids are bound together by a?

A

peptide bond

57
Q

name the 4 types of amino acids?

A

acidic, basic, neutral/nonpolar, neutral polar

58
Q

who deciphered the genetic code?

A

Nirenburg

59
Q

what are the characteristics of the genetic code?

A

triplet, comma free, nonoverlapping, almost universal, degenerate (more than one codon occurs for each amino acid), start and stop

60
Q

describe base-pairing wobble

A

if cells do not carry tRNAs for all codons the 5’ end of tRNA can wobble as it attaches to the 3’ end of mRNA

61
Q

deletion?

A

causes frameshift mutation

62
Q

addition?

A

reversion of deletion mutation

63
Q

amino acid attached to what end of tRNA?

A

3’

64
Q

describe charging of tRNA?

A

tRNA synthetase (one for each amino acid), adds amino acid onto ATP, AMP left, then add that new structure to 3’ end of tRNA

65
Q

prok ribosome structure?

A

30s. 50s, 70s

66
Q

euk ribosome structure?

A

40s, 60s, 80s

67
Q

describe initiation of prok transcription

A

30s + initiation factors + GTP bind to fMet initiator tRNA, all that ish binds to shin-delgrano sequence, 50s comes along to form 70s, GTP hydrolyzed as initiation factors pop off

68
Q

describe initiation of euk transcription

A

40s binds to methylated 5’ cap then migrates to first AUG

69
Q

how are appropriate tRNA brought to A site?

A

elongation factors and GTP

70
Q

role of peptidyl transferase

A

forms peptide bond between P site and A site leaving elongated chain on A site

71
Q

what is a polysome?

A

a number of ribosomes each translating the same mRNA sequentially

72
Q

how is translation terminated?

A

releasing factors associated with UAG, UAA, and UGA, euk have 1 releasing factor, prok 3 releasing factors

73
Q

what does an oxidoreductase do?

A

oxidation-reduction

74
Q

what does a transferase do?

A

transfer of C N and P

75
Q

what does a hydrolase do?

A

adds water

76
Q

what does a lyase do?

A

cleaves carbon sulfer or nitrogen bond

77
Q

what does an isomerase do?

A

rearranges

78
Q

what does a ligase do

A

formation of bonds coupled to ATP hydrolasis

79
Q

what does a kinase do?

A

adds an phosphate to something

80
Q

what does a phosphatase do?

A

cuts a phosphate off something

81
Q

what is a cofactor?

A

inorganic component

82
Q

what is a coenzyme?

A

non-protein component like a vitamin

83
Q

what is a holoenzyme?

A

enzyme plus cofactor

84
Q

apoenzyme

A

enzyme without cofactor

85
Q

porsthetic group

A

a coenzyme that is tightly (usually covalently) attached

86
Q

what is proteolytic cleavage?

A

zymogen to active form through truncation

87
Q

what is covalent modification?

A

increase or decrease activity through phosphorylation

88
Q

what is sequestration?

A

enzyme=inactive polymers

89
Q

what is allosteric regulation?

A

other site regulation; homotropic positive and heterotropic negative

90
Q

what is induction?

A

upregulation through gene expression

91
Q

what is repression?

A

downregulation through gene expression

92
Q

what are isozymes?

A

catalyze the same reaction but are different molecular sizes

93
Q

shape of curve with allosteric enzymes?

A

sigmoid

94
Q

shape of curve with Michaelis-Menten kinetics

A

hyperbolic

95
Q

Describe michaelis-menten kinetics

A

km=concentration of substrate at 1/2Vmax, high concentration velocity zero order meaning high velocity and not dependant on concentration, low concentration velocity first order meaning proportional to substrate concentration

96
Q

what is reversible inhibition?

A

weak, non-covalent bonds readily dissociate, enzyme inactive when inhibitor is present

97
Q

what is irreversible inhibition?

A

covalent bonds, or strong non-covalent

98
Q

examples of reversible inhibition

A

competitive inhibitors which resemble sustrate, non-competitive inhibitors that bind other site, uncompetative - binds to other site but only during ES complex

99
Q

examples of irreversible inhibition

A

permanently inactive enzymes, heavy metals and such

100
Q

what does a competitive inhibitor do to the graph?

A

vmax same, km increased

101
Q

what does a non-competitive inhibitor do to the graph?

A

vmax decreased, km same

102
Q

what does a uncompetitive inhibitor do to the graph?

A

vmax decreased, km decreased

103
Q

how many amino acids?

A

20

104
Q

how many organization levels of proteins?

A

4: primary, secondary, tertiary, and quaternary

105
Q

key to primary structure

A

sequence of amino acids, peptide bond which is very strong

106
Q

characteristics of the peptide bond

A

doesn’t rotate, trans configuration, uncharged but polar so can experience hydrogen bonding, rigid and planar

107
Q

how is a peptide bond formed

A

condensation reaction

108
Q

how to determine protein composition

A

acid hydrolysis, chromatography, quantitative with ninhydrin (spectrophotometry)

109
Q

how to sequence a protein

A

Edman’s reagent breaks off piece by piece

110
Q

key to secondary structure

A

hydrogen bonding

111
Q

3 structures of secondary structure

A

alpha helices, beta sheets and random chain

112
Q

what disrupts alpha helices

A

proline and glycine, high number of charged aas, or aas with bulky R groups

113
Q

characteristics of parallel beta sheets

A

up and down, same direction

114
Q

characteristics of anti parallel beta sheets

A

up and down, opposite directions

115
Q

characteristics of the beta bend

A

proline, glycine, charged, hydrogen bonding

116
Q

what is three demensional structure

A

3D structure of the protein

117
Q

characteristics of globular proteins

A

spherical, good water solubility, dynamic metabolic function

118
Q

quarternary structure

A

two or more subunits

119
Q

what stabilizes tertiary structure?

A

hydrogen bonds, disulfide bonds between Cysteines, hydrophobic interactions, ionic and polar interactions

120
Q

what helps protein folding?

A

chaperones

121
Q

what can denature a protein?

A

heat, organic solvents, mechanical shearing, heavy metals, detergents, chaotropic agents; may be reversible or irreversible, loss of biologic activity

122
Q

name a protein that can renature

A

ribonuclease

123
Q

what stabilizes Quaternary structure?

A

hydrogen bonds, hydrophobic interactions, electrostatic interactions

124
Q

features of catabolism

A

degradation, convergence, oxidation

125
Q

products of catabolism

A

ATP, FADH2, NADH, NADPH

126
Q

features of anabolism

A

synthesis, reduction, divergence, uses ATP

127
Q

products of anabolism

A

NAD+, FAD, ADP, NADP+

128
Q

stages of catabolism

A

I - hydrolysis of complex molecules, II - conversion to acetyl CoA, III - oxidation of acetyl CoA

129
Q

what does regulation depend on?

A

intercellular signals, and intracellular signals

130
Q

types of intercellular signals

A

synaptic (nerves), endocrine (hormones), direct (gap junctions)

131
Q

4 types of signal transduction

A

steroid, gated ion, receptor enzyme (or catylitic receptor), G-protein coupled receptor

132
Q

example of steroid receptor

A

goes inside the cell for upregulation or downregulation of genes

133
Q

example of gated ion receptor

A

receptor linked to ligand, voltage-gated ion; ex nicotinic ACh

134
Q

example of receptor or catalytic receoptor

A

insulin and tyrosine kinase

135
Q

example of G-protein coupled receptor

A

produce second messenger (beta andrenergic receptor), cAMP, IP3, DAG, Calcium

136
Q

describe complete process of adynelate cyclase system

A

1) Epinephrine or Norepinephrine binding
2) GDP replaced by GTP on Gs
3) Gs (alpha subunit) moves to adenylyl cyclase and activates it
4) adenylyl cyclase catalyzes formation of cAMP from ATP
5) protein kinase A activated by cAMP
6) protein kinase A phosphorylates other proteins
7) cAMP is degraded by cyclic nucleotide phosphodiesterase

137
Q

describe complete process of phosphoinositide system

A

1) ligand binds
2) GDP replaced by GTP on Gq
3) Gq (alpha subunit) moves to phospholipase C and activates it
4) phopholipase C cleaves PIP2 to IP3 and DAG
5) IP3 causes calcium to be released from the ER lumen
6) protein kinase C activated by DAG in cell membrane and calcium released from ER lumen
7) protein kinase C then phosphorylates proteins

MSAP (6 decks)

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