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Biochemistry > Final exam review > Flashcards

Final exam review Flashcards

1
Q

delta G

A

free energy

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2
Q

delta H

A

enthalpy
heat (K)

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3
Q

delta S

A

entropy
disorder

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4
Q

relationship between delta G and Keq

A

delta G = -RT(ln)Keq

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5
Q

enthalpy is caused by

A

bonds breaking and forming

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6
Q

entropy represents

A

order vs disorder

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7
Q

DG0

A

free energy located at the BOTTOM of the curve

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8
Q

if delta G is POSITIVE, do we have more products or reactants

A

reactants

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9
Q

if delta G is NEGATIVE, do we have more products or reactants

A

products

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10
Q

negative delta G

A

spont

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11
Q

positive delta G

A

non-spont

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12
Q

ln of a number less than one is

A

negative

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13
Q

moving delta G to the left of the curve

A

more negative

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14
Q

moving delta G to the right of the curve

A

more positive

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15
Q

ln of 1

A

0

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16
Q

energy =

A

heat + disorder

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17
Q

delta G =

A

delta H - (T) delta S

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18
Q

for delta G to be negative

A

S must be NEGATIVE

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19
Q

negative delta H

A

exothermic

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20
Q

negative delta S

A

increased order

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21
Q

positive delta H
negative delta S

A

positive delta G

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22
Q

reactions tend to occur in a way that dissipates energy and leads to an

A

increased order

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23
Q

gibbs free energy equation

A

delta G = DG0 + RT(ln) ([C][D]/[A][B])

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24
Q

henderson hasselbalch equation

A

pH = pKa + log ([conj base]/[weak acid])

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25
Q

how to determine the pH of a STRONG acid from a given concentration

A

take the -log of the concentration

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26
Q

how to determine the pH of a STRONG base from a given concentration

A

find pOH: -log of concentration

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27
Q

how do you calculate [H+] from a given pH

A

[H+] = 10^-pH

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28
Q

[OH-] =

A

[OH-] = 10^(14-pH)

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29
Q

1 pH unit is a _____ fold difference

A

10

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30
Q

nucleotides vs nucleosides

A

nucleotides contain nitrogenous base, sugar, and phosphate group
nucleosides contain nitrogenous base and sugar

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31
Q

hydrogen bonding between nucleotides

A

AT has 2 H bonds between them
CG has 3 H bonds between them

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32
Q

complementary base-pairings and their relative strength

A

AT (DNA) AU (RNA)
CG - strongest bc of 3 H bonds

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33
Q

approximate amount of DNA in a cell

A

6 billion base pairs

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34
Q

number of chromosomes per cell

A

23 pairs
46 total chromosomes

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35
Q

chromatin structure

A

base unit: nucleosome
nucleosomes are 147 base pairs wrapped around histones

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36
Q

bacterial transcription

A

transcription and translation occur simultaneously in the cytoplasm

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37
Q

eukaryotic transcription occurs in the _____________ and translation occurs in the ____________

A

nucleus, cytoplasm

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38
Q

3 major modifications to most eukaryotic mRNA transcripts prior to translation

A

5’-capping, splicing of introns, polyA tails

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39
Q

purpose of the 5’ cap

A

methylated cap protects the transcript from being degraded

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40
Q

cis regulatory elements

A

promoters, enhancers, silencers
regulate nearby genes on one chromosomal allele

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41
Q

trans regulatory elements

A

transcription factors, long noncoding RNAs
regulate expression of distant genes on both alleles

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42
Q

prokaryotic operons vs eukaryotic operons

A

polycistronic - genomic (introns and exons)
Exons = Expressed

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43
Q

transcription regulators in prokaryotes

A

activators

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44
Q

transcription regulators in eukaryotes

A

repressors

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45
Q

splice junctions

A

strongly conserved parts of eukaryotic genes
border exon/intron junction and aid in the process of removing introns by RNA splicing

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46
Q

alternative splicing

A

exons from the same gene are joined in different combinations, leading to different mRNA transcripts

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47
Q

poly-A tail

A

long chain of adenine nucleotides
increases stability and prevents degredation

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48
Q

purines vs pyrimidines

A

purines have two rings (AG)
pyrimidines have one ring (TCU)

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49
Q

ribo vs deobyribo sugars

A

ribose sugars have an OH at C2
deoxyribo sugars have a H at C2

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50
Q

silent mutation

A

nucleotide change that does not affect the protein

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51
Q

missense mutation

A

single base pair substitution alters

52
Q

nonsense mutation

A

sense codon is replaced with a stop codon

53
Q

insertion and deletion mutations

A

insertion: adding one or more nucleotides to the gene
deletion: removing one or more nucleotides from the gene

54
Q

frame-shift mutations

A

caused by insertion of deletion that results in the remainder of the codon to be read differently

55
Q

impact of wobble base pairing

A

alpha helix/beta sheet is disrupted

56
Q

codon anticodon relationship

A

codons and anticodons bind together during translation (protein synthesis)
codons are on mRNA, anticodons are tRNA

57
Q

codons are ________ unit that ______________

A

3 nucleotide unit, codes for an amino acid

58
Q

operator

A

regulatory sequence lying adjacent to the promoter

59
Q

promoter

A

nucleotide sequence that binds to RNA polymerase

60
Q

attenuator

A

results in the premature termination of transcription

61
Q

attenuator

A

results in the premature termination of transcription

62
Q

enhancer sites

A

increase transcription

63
Q

ribonucleotides

A

phosphate group, ribose sugar, nucleobase (AGCU)

64
Q

transcriptional repression vs depression

A

repression: impedes binding of RNA polymerase
depression: causes conformational change

65
Q

most transcriptional activators bind to

A

enhancers

66
Q

transcription regulators in prokaryotes

A

activators

67
Q

transcription regulators in eukaryotes

A

repressors

68
Q

RNA polymerase 1

A

synthesis of rRNA genes
(nucleolus)

69
Q

RNA polymerase 2

A

synthesis of mRNA genes

70
Q

RNA polymerase 3

A

synthesis of tRNA genes

71
Q

DNA replication is ______, __________, and ________

A

semi-conservative, bidirectional, discontinuous

72
Q

RNA replication is ________ and __________

A

unidirectional and continuous

73
Q

start codon

A

AUG

74
Q

termination codons

A

UGA, UAA, UAG

75
Q

mRNA role in protein synthesis

A

carry coding sequences for protein synthesis

76
Q

rRNA role in protein synthesis

A

hold the construction of protein amino acid sequences

77
Q

tRNA role in protein synthesis

A

supply and configure the protein sequence coded on the mRNA

78
Q

primary protein structure

A

amino acid chains
peptide bonds

79
Q

secondary protein structure

A

alpha helix and beta sheets
hydrogen bonds

80
Q

tertiary protein structure

A

3D folding structure
disulfide bonds, hydrogen bonds, ionic bond
aka side chain interactions

81
Q

quaternary protein structure

A

proteins consisting of more than one amino acid chain
hydrogen bonds and van der waal forces

82
Q

amino acids in the body are what configuration

A

L

83
Q

all amino acids except __________ are _________

A

glycine, chiral

84
Q

Km

A

michaelis constant
concentration at which 1/2 the active sites of enzymes are occupied by the substrate (1/2 of Vmax)

85
Q

Kd

A

disassociation constant
lower the Kd, higher substrate affinity

86
Q

Kcat

A

first order rate constant
turnover number

87
Q

Vmax

A

maximum velocity
rate of reaction when enzyme has the highest turnover

88
Q

relationship between substrate concentration [S] and reaction velocity (v)

A

low [S], v is linearly proportional to S
at high [S], v is independent of S

89
Q

Ki

A

inhibitor constant
binding affinity between the inhibitor and the enzyme

90
Q

polar amino acids

A

serine
threonine
cysteine
asparagine
glutamine
tyrosine

91
Q

nonpolar amino acids

A

glycine
alanine
valine
leucine
isoleucine
methionine
phenylalanine
tryptophan
proline

92
Q

aromatic amino acids

A

phenylalanine
tryptophan
tyrosine
histidine*

93
Q

“structural” amino acids

A

glycine
proline

94
Q

what is unique about glycine

A

not chiral
no unique R-group, just “H”

95
Q

what is unique about proline

A

side chain “loops back” and forms circle when it bonds with the NH2

96
Q

peptide bonds between AA’s are also known as

A

amide bonds

96
Q

peptide bonds between AA’s are also known as

A

amide bonds

97
Q

amino acids that can form disulfide bonds contain a ______ group

A

thiol (SH)
cysteine

98
Q

D sugars

A

-OH on right side

99
Q

L sugars

A

-OH on left side

100
Q

alpha sugars

A

-OH is down

101
Q

beta sugars

A

-OH is up

102
Q

enzyme proteins are almost always __________ proteins

A

globular

103
Q

substrates bind to specific

A

active sites

104
Q

enzyme active sites often contain ________, _________, ________

A

weak acids (D, E), weak bases (R, K), nucleophiles

105
Q

things that assist enzymes

A

enzyme cofactors

106
Q

in metabolism, ____ is a waste product and ____ is the saved product

A

C, H

107
Q

oxidation

A

gaining electrons

108
Q

reduction

A

loss of electrons

109
Q

spend ATP and utilize NADH to

A

make fatty acids

110
Q

gradient is a way of ________, creates a ______ gradient without the use of ______

A

storing energy, proton, ATP

111
Q

what type of transport requires ATP

A

active transport

112
Q

what type of transport requires ATP

A

active transport

113
Q

saturated fats

A

no double bonds

114
Q

unsaturated fats

A

cis double bond (bent)

115
Q

trans fats

A

trans double bond (straight)

116
Q

phospholipids

A

lipid containing phosphate group
glycerol backbone
2 fatty acid groups
in cell membrane

117
Q

sphingolipids

A

fatty acid derivatives
cell membranes of NERVOUS tissue
do NOT contain first fatty acid group

118
Q

fatty acid tails

A

one is saturated, one is unsaturated with a cis double bond

119
Q

impact of cholesterol

A

stiffens a specific region of fatty acid tail/reduces fluidity
effects the ability of things to pass through

120
Q

N form that can be incorporated into other biological molecules

A

NH4 and bioamines

121
Q

in order for ammonia to use krebs cycle, it is added to

A

glutamic acid

122
Q

how nitrogen gets incorporates into something that can leave the body

A

urea cycle

123
Q

Ns from arginine end up in

A

urea

124
Q

nitrogen needs to be converted into

A

ammonia

Biochemistry (10 decks)

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