TEST 1 Flashcards
(157 cards)
1
Q
A
carboxylic acid
2
Q
A
ketone
3
Q
A
amine
4
Q
A
ester
5
Q
A
aldehyde
6
Q
A
peptide bond
7
Q
A
aromatic ring
8
Q
A
alcohol
9
Q
A
organic phosphate
10
Q
A
thiol
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
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
13
Q
AT H bonds
A
2 h bonds
14
Q
GC H bonds
A
3 h bonds
15
Q
defining chemical features of water
A
overall polar
high electron density at oxygen
low electron density on both hydrogens
16
Q
1x10^-7 H = ?pH
A
7
17
Q
1x10^-1 H = ?pH
A
1
18
Q
pH equation
A
19
Q
H x OH = what
A
20
Q
4 classes of biomolecules
A
proteins
nucleic acids
carbohydrates
lipids
21
Q
carbs functions
A
fuel
structural roles
extracellular receptors
22
Q
lipid functions
A
hydrophobic
held together through hydrophobic interactions
fuel
intracellular signaling molecules
separates internal and external environment
23
Q
eukaryotes
A
large
internal organelles
nucleus
usually multicellular
24
Q
prokaryotes
A
small
no nucleus
cell wall
25
van der waal bond
-shortest bond length
-1
-weakest bond
-bond formed through different charges of its parent molecule
26
ionic bond
longest bond length
3
second strongest bond
27
covalent bond
medium bond length
1.5
strongest bond
28
hydrogen bond
1.5-2.6
second weakest bond
29
breaking a bond
always requires energy to break a bond
energy is always released when a bond is broken
30
polar
hydrophilic
ex glucose
31
nonpolar
hydrophobic
lipids o2 n2 co2
32
amphipathic
both polar and nonpolar
33
-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
34
gibbs free energy
35
hydrophobic effect when two nonpolar molecules are suspended in water
they join by the increase of entropy of the water molecules surrounding
(creation of plasma membrane increases entropy)
36
autoionization of water equation
h20 == h + oh
h20+h20==h30 + oh
37
equilibirum constant expression
kw= [H+][OH-]=1.0x10^-14
38
pH equation
pH= -log[H+]
39
acid disassociation equation
Ka = [H+][A-]/[HA]
Ka= acid dissociation constant
H+=hydrogen concentation
A-=anion
HA=weak acid
as ka gets bigger, the acid gets stronger
40
COOH
carboxylic acid, H on an acid of the carboxylic acid is most likely to dissociate
41
pka equation
pKa= -logKa
as pka gets lower = stronger acid
as pka gets higher = weaker acid
42
when pka = pH
pka < pH
pka > pH
[HA] = [A-] acid and conjugate base are in equal amounts
[HA] < [A-] deprotonated conjugate base
[HA] > [A-] protonated acid
43
Buffering equation
44
amino acid constituents
carboxylic acid
amino group
variable side group
central carbon
ONLY L form of amino acids
45
GO OVER L/D isomer
46
proteins
-all made from 20 amino acids
-contain 20 different side groups
47
amino acid pka
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
48
Glycine
non polar
49
Alanine
non polar
50
Valine
non polar
51
Leucine
non polar
52
Isoleucine
non polar
53
Methionine
non polar
54
proline
non polar
55
phenylalanine
non polar
56
Tryptophan
non polar
57
serine
polar
58
Threonine
polar
59
Tyrosine
polar
pka of oh hydrogen = 11
60
glutamine
polar
61
asparagine
polar
62
cysteine
polar
pka of sulfur hydrogen = 8
63
Lysine
positively charged
polar
pka of amino group = 11
64
Arginine
positively charged
pka of amino group = 12.5
65
histidine
positively charged
pka of amino group in pentyl group = 6
66
aspartate
negatively charged
67
Glutamate
negatively charged
68
most proteins amino acid count
50-2000
69
psi bond
Alpha carbon of amino acid bonded to carbon of carboxylic acid
70
phi bond
Alpha carbon of amino acid bonded to nitrogen of amino group
71
when a peptide bond forms what is lost?
H20
72
secondary structure of a protein
-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
primary structure of a protein
-sequence of amino acids linked by peptide bonds
74
alpha helix
-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
beta pleated sheets
-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
turns/loops
-secondary structure
-hydrophilic r groups
-on surface of protein
77
tertiary structure of a protein
-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
Quaternary Structure of a protein
-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
Denaturation
loss of secondary, tertiary or quaternary
structure of a protein
80
active site
-site of enzyme catalysis and substate binding
-small 3D pocket
-binds via multiple weak
interactions (not usually covalent)
81
induced fit model
-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
transition states
-unstable molecule
-higher in free energy than substrate or product
83
catalysts
-lowers energy required to achieve transition state
-only affects the rate at which equilibrium is achieved
-doesnt change final equilibruim position
84
enzyme catalysts
-highly specific, usually only catalyzes one reaction or very closely related reactions
85
lock and key model
-substrate and active site fit identically into each other
-not correct
86
coenzymes
small organic cofactors derived from vitamins
87
tightly bound coenzymes
prosthetic groups
88
loosly bound coenzymes
cosubstrates
89
enzymes + cofactor
holoenzymes
90
enzyme without cofactor
apoenzyme
91
cofactors
2 main groups making up larger whole
92
-activation energy
-rate of reaction/how fast reaction will proceed
-lowering this value will speed up the reaction
93
-∆G
spontaneous reaction
keq < 1
favors products
94
+∆G
non spontaneous reaction
favors reactants
keq > 1
95
kcat
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
specific activity
product formed/time/mg enzyme
97
Vmax
highest velocity of product created
dependent on enzyme concentration
98
Km
independant of enzyme concentration
substrate concentration ( required for half Vmax)
99
low km
enzyme only requires small amount of substrate to become saturated
100
high km
enzyme requires large amount of substrate to become saturated
101
catalytic efficiency
kcat/km
used to compare enzyme preference for substrates
102
Covalent Catalysis
active site contains a reactive group that becomes temporarily covalently modified
103
General Acid-Base Catalysis
molecule other than water plays the role of proton donor or acceptor
104
Metal Ion Catalysis
metal ion may serve as electrophilic catalyst, may generate a nucleophile, may bind
to substrate
105
Approximation and Orientation
full complement of interactions only when substrate is in transition state (transition
state stabilization)
106
chymotrypsin
protease specific for peptide bonds on carboxyl-
terminal side of large aromatic, hydrophobic amino acids
-functions at pH 8
107
2 phases of chymotrypsin peptide bond formation
acylation
deacylation
108
acylation
-peptide bond cleavage, ester
linkage formed between peptide carbonyl
carbon and enzyme
109
Competitive Inhibition
-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
Noncompetitive
Inhibition
-inhibitor binds to a site other than the active site
-cannot be overcome by increasing substrate concentration
-lower v max
-km unchanged
111
deacylation
-ester linkage hydrolyzed and
nonacylated enzyme regenerated
112
hydrophobic pocket
-functions in enzyme specificity
-preference for cleaving peptide bonds just past resides with large hydrophobic side chains
113
oxyanion hole
-negative charge on carbonyl oxygen during formation of intermediate stabilized by hydrogen bonds
114
catalytic triad
serine histidine asparagine
115
allosteric control
-the binding of a ligand to one site affects the binding properties of another site on the same protein
116
bonding techniques used by the catalytic triad of chymotrypsin
general acid/base catalysis
covalent catalysis
approximation and orientation
NOT metal ion catalysis
117
buffer ranges
+/- 1pH around pKa value
118
hemoglobin
-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
myoglobin
-found in muscle
-diffuses o2 to sites requiring 02, provides reserve supply of 02
-difficult to dissociate 02
120
T state
deoxy, low affinity for oxygen- oxygen desaturated
121
R state
oxy, high affinity for oxygen- oxygen saturated
122
intermediate states between r and t state
-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
other allosteric regulators for hemoglobin
2,3 biphosphoglycerate
C02- as c02 increases 02 affinity decreases
H+ - as
124
Bar Headed Goose
-Changes in hemoglobin amino acid sequence that stabilizes R form
-allows for survival in low 02 concentration environment
125
sickle cell anemia mutation
Glutamate to Valine amino acid 6
126
Isozymes
Different variants of the same enzyme
127
fetal Hb
⍺ 2 ɣ 2
gamma subunits are similar to Beta subunits however they have a lower affinity for BPG and increased affinity for 02
128
hexokinase and glucokinase
isozymes
129
hexokinase
isozyme of glucokinase
hexokinase:
located in all tissues
low km
inhibited by glucose 6 phosphate
130
glucokinase
isozyme of hexokinase
located in liver pancrease and brain
high km
not inhibited by glucose 6 phosphate
131
Reversible Covalent Modification
Addition or removal of a group to a protein via an
enzyme
132
phosphorylation
occurs only in groups w OH group
Tyr Ser Thr His
133
proteolysis
cleavage of a peptide into its
active form
ex, Proinsulin to insulin
134
DNA
store genetic info and pass info to next generation
deoxyribose - has H in 2' spot
135
RNA
transmits and expresses info in DNA into proteins w cellular functions
ribose- has OH in 2' spot
135
nucleotide composition
nitrogenous base
sugar
phosphate
can have up to 3 phosphate
135
purine
2 rings
GA
135
pyrimidine
1 ring
TCU
136
oligonucleotide
few nucleotides linked together
137
polynucleotide
many nucleotides linked together
138
nucleoside
base + sugar
139
glycosidic linkage
1' carbon of nitrogenous base to sugar
140
pauling and corey model
3 strands of DNA
bases on outside
phosphates on inside
141
watson and crick
2 strands of dna
phosphates on outside
paired bases on inside
142
DNA secondary structure
-double helical structure
-anitparallel complementary backbones
-right handed helix
-minor and major grooves
143
chargraffs rules
ratio of purine to pyrimidine bases is equal
144
hydrophobic stabilizing interaction
hydrogen bonds linking complementary bases
and
van der waal interactions between bps
145
hydrophilic stabilizing interactions
stabilized by hydrogen bonds with the aqueous environment
146
A form of DNA
right handed
favored by DNA/DNA RNA/RNA complexes
most compact form of DNA
147
B form of DNA
right handed
standard accepted human form
found by watson and crick
148
Z form of DNA left handed
left handed
least compact form of DNA
149
stem loops
secondary structure of RNA
150
tertiary structure of prokaryotic DNA
circular plasmid DNA
151
tertiary structures of eukaryotic DNA
chromatids
152
quaternary structures of DNA
histones wound around DNA
153
what amino acids bind to DNA
positively charged ones
mostly arginine or lysine
154
