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BIOCHEM > TEST 1 > Flashcards

TEST 1 Flashcards

1
Q
A

carboxylic acid

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2
Q
A

ketone

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3
Q
A

amine

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4
Q
A

ester

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5
Q
A

aldehyde

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6
Q
A

peptide bond

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7
Q
A

aromatic ring

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8
Q
A

alcohol

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9
Q
A

organic phosphate

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10
Q
A

thiol

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11
Q

rank the following from strongest to least
hydrogen bond
covalent bond
van der waal bond
ionic bond

A

covalent
ionic
hydrogen
van der waal

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12
Q

what are the variables in this equation and what is it finding?

A

Energy= (Charge on particle 1*charge on particle 2) / Distance

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13
Q

AT H bonds

A

2 h bonds

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14
Q

GC H bonds

A

3 h bonds

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15
Q

defining chemical features of water

A

overall polar
high electron density at oxygen
low electron density on both hydrogens

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16
Q

1x10^-7 H = ?pH

A

7

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17
Q

1x10^-1 H = ?pH

A

1

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18
Q

pH equation

A
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19
Q

H x OH = what

A
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20
Q

4 classes of biomolecules

A

proteins
nucleic acids
carbohydrates
lipids

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21
Q

carbs functions

A

fuel
structural roles
extracellular receptors

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22
Q

lipid functions

A

hydrophobic
held together through hydrophobic interactions
fuel
intracellular signaling molecules
separates internal and external environment

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23
Q

eukaryotes

A

large
internal organelles
nucleus
usually multicellular

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24
Q

prokaryotes

A

small
no nucleus
cell wall

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25
Q

van der waal bond

A

-shortest bond length
-1
-weakest bond
-bond formed through different charges of its parent molecule

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26
Q

ionic bond

A

longest bond length
3
second strongest bond

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27
Q

covalent bond

A

medium bond length
1.5
strongest bond

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28
Q

hydrogen bond

A

1.5-2.6
second weakest bond

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29
Q

breaking a bond

A

always requires energy to break a bond
energy is always released when a bond is broken

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30
Q

polar

A

hydrophilic
ex glucose

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31
Q

nonpolar

A

hydrophobic
lipids o2 n2 co2

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32
Q

amphipathic

A

both polar and nonpolar

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33
Q
A

-second law of entropy
-for anything to be spontaneous it must increase entropy
-entropy of universe can still increase if the surroundings entropy of the surroundings increases while the systems entropy decreases

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34
Q
A

gibbs free energy

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35
Q

hydrophobic effect when two nonpolar molecules are suspended in water

A

they join by the increase of entropy of the water molecules surrounding
(creation of plasma membrane increases entropy)

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36
Q

autoionization of water equation

A

h20 == h + oh
h20+h20==h30 + oh

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37
Q

equilibirum constant expression

A

kw= [H+][OH-]=1.0x10^-14

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38
Q

pH equation

A

pH= -log[H+]

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39
Q

acid disassociation equation

A

Ka = [H+][A-]/[HA]

Ka= acid dissociation constant
H+=hydrogen concentation
A-=anion
HA=weak acid
as ka gets bigger, the acid gets stronger

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40
Q

COOH

A

carboxylic acid, H on an acid of the carboxylic acid is most likely to dissociate

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41
Q

pka equation

A

pKa= -logKa
as pka gets lower = stronger acid
as pka gets higher = weaker acid

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42
Q

when pka = pH
pka < pH
pka > pH

A

[HA] = [A-] acid and conjugate base are in equal amounts
[HA] < [A-] deprotonated conjugate base
[HA] > [A-] protonated acid

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43
Q

Buffering equation

A
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44
Q

amino acid constituents

A

carboxylic acid
amino group
variable side group
central carbon
ONLY L form of amino acids

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45
Q

GO OVER L/D isomer

A
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46
Q

proteins

A

-all made from 20 amino acids
-contain 20 different side groups

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47
Q

amino acid pka

A

Carboxylic acid group pka = ~3
protonated- COOH charge close to 0
deprotonated- COO- charge close to -1

amino group pka = ~9
protonated- NH3+
deprotonated- NH2

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48
Q
A

Glycine
non polar

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49
Q
A

Alanine
non polar

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50
Q
A

Valine
non polar

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51
Q
A

Leucine
non polar

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52
Q
A

Isoleucine
non polar

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53
Q
A

Methionine
non polar

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54
Q
A

proline
non polar

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55
Q
A

phenylalanine
non polar

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56
Q
A

Tryptophan
non polar

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57
Q
A

serine
polar

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58
Q
A

Threonine
polar

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59
Q
A

Tyrosine
polar
pka of oh hydrogen = 11

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60
Q
A

glutamine
polar

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61
Q
A

asparagine
polar

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62
Q
A

cysteine
polar
pka of sulfur hydrogen = 8

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63
Q
A

Lysine
positively charged
polar
pka of amino group = 11

64
Q
A

Arginine
positively charged
pka of amino group = 12.5

65
Q
A

histidine
positively charged
pka of amino group in pentyl group = 6

66
Q
A

aspartate
negatively charged

67
Q
A

Glutamate
negatively charged

68
Q

most proteins amino acid count

A

50-2000

69
Q

psi bond

A

Alpha carbon of amino acid bonded to carbon of carboxylic acid

70
Q

phi bond

A

Alpha carbon of amino acid bonded to nitrogen of amino group

71
Q

when a peptide bond forms what is lost?

A

H20

72
Q

secondary structure of a protein

A

-local folded protein structure that is due to interactions between atoms in the protein backbone
-held together mostly by hydrogen bonds
-alpha helixs
-beta folded sheets

73
Q

primary structure of a protein

A

-sequence of amino acids linked by peptide bonds

74
Q

alpha helix

A

-3.6 amino acid residues per turn
-only right handed helixes
-hydorgen bond occurs between amino and carboxyl group 4 amino acids ahead for each amino acid

75
Q

beta pleated sheets

A

-links strands of amino acids running parallel/antiparallel
-links dont need to be close in sequence to bond
-bonds amino and carboxyl groups
-many adopt a twisted shape
-can beta pleated sheet bond with 2 other sheets

76
Q

turns/loops

A

-secondary structure
-hydrophilic r groups
-on surface of protein

77
Q

tertiary structure of a protein

A

-overall three-dimensional structure resulting
from folding and covalent cross-linking of a polypeptide
-result of the interaction between R-groups
-interior usually non-polar
-exterior usually polar
-contains secondary structure inside it
-overall globular connected by short strands of peptides

78
Q

Quaternary Structure of a protein

A

-multiple polypeptide chains (subunits) that
assemble into a functional protein
-held together by hydrogen bonds, van der Waals
interactions, electrostatic interactions
-subunits can be variable or uniform
ex. ⍺, β, ɣ
⍺2 β1 ɣ3 = 1 protein

79
Q

Denaturation

A

loss of secondary, tertiary or quaternary
structure of a protein

80
Q

active site

A

-site of enzyme catalysis and substate binding
-small 3D pocket
-binds via multiple weak
interactions (not usually covalent)

81
Q

induced fit model

A

-binding of substrate and active site that creates a
conformational change in shape of protein
-makes binding site more
complementary to substrate
-correct model

82
Q

transition states

A

-unstable molecule
-higher in free energy than substrate or product

83
Q

catalysts

A

-lowers energy required to achieve transition state
-only affects the rate at which equilibrium is achieved
-doesnt change final equilibruim position

84
Q

enzyme catalysts

A

-highly specific, usually only catalyzes one reaction or very closely related reactions

85
Q

lock and key model

A

-substrate and active site fit identically into each other
-not correct

86
Q

coenzymes

A

small organic cofactors derived from vitamins

87
Q

tightly bound coenzymes

A

prosthetic groups

88
Q

loosly bound coenzymes

A

cosubstrates

89
Q

enzymes + cofactor

A

holoenzymes

90
Q

enzyme without cofactor

A

apoenzyme

91
Q

cofactors

A

2 main groups making up larger whole

92
Q
A

-activation energy
-rate of reaction/how fast reaction will proceed
-lowering this value will speed up the reaction

93
Q

-∆G

A

spontaneous reaction
keq < 1
favors products

94
Q

+∆G

A

non spontaneous reaction
favors reactants
keq > 1

95
Q

kcat

A

turnover number
number of substrate molecules that an enzyme can convert to a product in a given unit of time
independant of enzyme concentration

96
Q

specific activity

A

product formed/time/mg enzyme

97
Q

Vmax

A

highest velocity of product created
dependent on enzyme concentration

98
Q

Km

A

independant of enzyme concentration
substrate concentration ( required for half Vmax)

99
Q

low km

A

enzyme only requires small amount of substrate to become saturated

100
Q

high km

A

enzyme requires large amount of substrate to become saturated

101
Q

catalytic efficiency

A

kcat/km
used to compare enzyme preference for substrates

102
Q

Covalent Catalysis

A

active site contains a reactive group that becomes temporarily covalently modified

103
Q

General Acid-Base Catalysis

A

molecule other than water plays the role of proton donor or acceptor

104
Q

Metal Ion Catalysis

A

metal ion may serve as electrophilic catalyst, may generate a nucleophile, may bind
to substrate

105
Q

Approximation and Orientation

A

full complement of interactions only when substrate is in transition state (transition
state stabilization)

106
Q

chymotrypsin

A

protease specific for peptide bonds on carboxyl-
terminal side of large aromatic, hydrophobic amino acids
-functions at pH 8

107
Q

2 phases of chymotrypsin peptide bond formation

A

acylation
deacylation

108
Q

acylation

A

-peptide bond cleavage, ester
linkage formed between peptide carbonyl
carbon and enzyme

109
Q

Competitive Inhibition

A

-inhibitor resembles substrate and binds to the active site
results : apparent km is higher to reach vmax ; vmax unchanged ; km turns into kapp (apparent needed to then reach vmax with an increased concentration)

110
Q

Noncompetitive
Inhibition

A

-inhibitor binds to a site other than the active site
-cannot be overcome by increasing substrate concentration
-lower v max
-km unchanged

111
Q

deacylation

A

-ester linkage hydrolyzed and
nonacylated enzyme regenerated

112
Q

hydrophobic pocket

A

-functions in enzyme specificity
-preference for cleaving peptide bonds just past resides with large hydrophobic side chains

113
Q

oxyanion hole

A

-negative charge on carbonyl oxygen during formation of intermediate stabilized by hydrogen bonds

114
Q

catalytic triad

A

serine histidine asparagine

115
Q

allosteric control

A

-the binding of a ligand to one site affects the binding properties of another site on the same protein

116
Q

bonding techniques used by the catalytic triad of chymotrypsin

A

general acid/base catalysis
covalent catalysis
approximation and orientation

NOT metal ion catalysis

117
Q

buffer ranges

A

+/- 1pH around pKa value

118
Q

hemoglobin

A

-a2B2
-more dynamic to changes in oxygen pressure in body
-when iron binds to 02 it pulls the iron into the plane of the hemoglobin, rather than hang outside of it

119
Q

myoglobin

A

-found in muscle
-diffuses o2 to sites requiring 02, provides reserve supply of 02
-difficult to dissociate 02

120
Q

T state

A

deoxy, low affinity for oxygen- oxygen desaturated

121
Q

R state

A

oxy, high affinity for oxygen- oxygen saturated

122
Q

intermediate states between r and t state

A

-out of 4 overall subunits, 1 fills with oxygen, it then influences other subunits to bind to more 02
-Hb with 1 02 bound binds 02 3x as strongly as fully deoxygenated Hb
-Hb with 3 02 bound 4 site has 20x greater affinity for 02 than fully deoxygenated Hb

123
Q

other allosteric regulators for hemoglobin

A

2,3 biphosphoglycerate
C02- as c02 increases 02 affinity decreases
H+ - as

124
Q

Bar Headed Goose

A

-Changes in hemoglobin amino acid sequence that stabilizes R form
-allows for survival in low 02 concentration environment

125
Q

sickle cell anemia mutation

A

Glutamate to Valine amino acid 6

126
Q

Isozymes

A

Different variants of the same enzyme

127
Q

fetal Hb

A

⍺ 2 ɣ 2
gamma subunits are similar to Beta subunits however they have a lower affinity for BPG and increased affinity for 02

128
Q

hexokinase and glucokinase

A

isozymes

129
Q

hexokinase

A

isozyme of glucokinase
hexokinase:
located in all tissues
low km
inhibited by glucose 6 phosphate

130
Q

glucokinase

A

isozyme of hexokinase
located in liver pancrease and brain
high km
not inhibited by glucose 6 phosphate

131
Q

Reversible Covalent Modification

A

Addition or removal of a group to a protein via an
enzyme

132
Q

phosphorylation

A

occurs only in groups w OH group
Tyr Ser Thr His

133
Q

proteolysis

A

cleavage of a peptide into its
active form
ex, Proinsulin to insulin

134
Q

DNA

A

store genetic info and pass info to next generation
deoxyribose - has H in 2’ spot

135
Q

RNA

A

transmits and expresses info in DNA into proteins w cellular functions
ribose- has OH in 2’ spot

135
Q

nucleotide composition

A

nitrogenous base
sugar
phosphate
can have up to 3 phosphate

135
Q

purine

A

2 rings
GA

135
Q

pyrimidine

A

1 ring
TCU

136
Q

oligonucleotide

A

few nucleotides linked together

137
Q

polynucleotide

A

many nucleotides linked together

138
Q

nucleoside

A

base + sugar

139
Q

glycosidic linkage

A

1’ carbon of nitrogenous base to sugar

140
Q

pauling and corey model

A

3 strands of DNA
bases on outside
phosphates on inside

141
Q

watson and crick

A

2 strands of dna
phosphates on outside
paired bases on inside

142
Q

DNA secondary structure

A

-double helical structure
-anitparallel complementary backbones
-right handed helix
-minor and major grooves

143
Q

chargraffs rules

A

ratio of purine to pyrimidine bases is equal

144
Q

hydrophobic stabilizing interaction

A

hydrogen bonds linking complementary bases
and
van der waal interactions between bps

145
Q

hydrophilic stabilizing interactions

A

stabilized by hydrogen bonds with the aqueous environment

146
Q

A form of DNA

A

right handed
favored by DNA/DNA RNA/RNA complexes
most compact form of DNA

147
Q

B form of DNA

A

right handed
standard accepted human form
found by watson and crick

148
Q

Z form of DNA left handed

A

left handed
least compact form of DNA

149
Q

stem loops

A

secondary structure of RNA

150
Q

tertiary structure of prokaryotic DNA

A

circular plasmid DNA

151
Q

tertiary structures of eukaryotic DNA

A

chromatids

152
Q

quaternary structures of DNA

A

histones wound around DNA

153
Q

what amino acids bind to DNA

A

positively charged ones
mostly arginine or lysine

154
Q
A

BIOCHEM (8 decks)

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