Week 1 Flashcards
(156 cards)
1
Q
primary structure
A
linear sequence of amino acids in a polypeptide chain
2
Q
primary structure is written
A
from the amino terminus (N) to the carboxyl terminus (C)
3
Q
main secondary structures
A
alpha helix
beta sheets
4
Q
alpha helix is formed when
A
the carbonyl group of the peptide bond forms a hydrogen bond with the amide hydrogen located 4 residues down the chain
5
Q
alpha helix peptide backbone is formed
A
by hydrogen bonds between each carbonyl oxygen atom and the amide hydrogen located 4 residues down the chain
6
Q
this comprises a third of all secondary structures
A
alpha helix
7
Q
proline and alpha helices
A
not normally found in them
creates a kink in the helix
8
Q
beta sheets are formed
A
when beta strands are connected laterally by at least two or three backbone hydrogen bonds formed between C-O groups of either strand and NH groups of either strand
9
Q
beta sheet r groups
A
- protrude to the top or bottom
- may make the protein hydrophobic or hydrophilic depending on which R group is part of the protein
10
Q
bends, turns, loops
A
secondary structure
short stretches of the polypeptide chain form these structures that are stabilized by hydrogen bonds
11
Q
supersecondary structure aka
A
tertiary structure
12
Q
tertiary structure
A
total 3D conformation of an entire polypeptide chain including interactions between alpha helices, betas sheet, and any other loops, turns, or bends
13
Q
rossman fold
A
type of tertiary structure
14
Q
structural domain
A
a section of protein sufficient to perform a particular chemical or physical task
defined regions with specific function conserved in function and sequence across other proteins
15
Q
motifs
A
common arrangements of secondary structures to generate a tertiary structure
16
Q
quaternary structure
A
a combination of two or more tertiary subunits that work together as one functioning unit
17
Q
tertiary and quaternary structures are stabilized by
A
hydrophobic interaction
hydrogen bonds
salt bonds
18
Q
apoprotein
A
a protein missing its ligand or ligands
ex. hemoglobin without -porphyrin ring
19
Q
holoprotein
A
a protein with its ligand so it is able to function
ex. hemoglobin bound to heme
20
Q
myoglobin
A
- monomer
- 8 alpha helices linked by alpha turns
- hydrophobic pocket with heme with a ferrous iron atom bound to histidine R-group at center for oxygen binding
21
Q
what stabilizes the reduced state of myoglobin
A
the fact that ferrous iron is bound to a histidine R-group of the alpha helix
22
Q
myoglobin binding is
A
hyperbolic
23
Q
heme is a
A
prosthetic group
24
Q
hemoglobin
A
- heterotetramer
- 2 alpha and 2 beta subunits each with its own heme
25
hemoglobin can bind
4 oxygen molecules
26
cooperativity (hemoglobin)
when O2 binds to the ferrous iron at one of the Hb binding sites, it pulls on the histidine which pulls on the alph helix changing the conformation making the other hemes more likely to bind a second molecule of oxygen
27
which binds oxygen more strongly - hemo or myoglobin?
myoglobin
28
When hemoglobin releases an oxygen,
this facilitates the loss of additional oxygen molecules
29
hemoglobin conformations
T-state
| R-state
30
T-state
tense state of Hb
| low affinity for oxygen
31
R-state
relaxed state of Hb
| high affinity for oxygen
32
Bohr effect
impact of pH on oxygen binding hemoglobin
decreased pH decreases hemoglobin saturation
effectors
- 2,3 BPG
- pH
- CO2
33
enzyme reaction takes place
away from from water solution
34
enzymes change conformation due to
the interactions between the amino acid side chain groups of the enzyme and the functional groups of the substrate so the outside solution can't take part in rxn
35
how do enzymes increase the rate of rxn?
decreasing the activation energy
| ex. stabilizing the transition state
36
general classes of enzymes
- oxidoreductase
- transferase
- hydrolase
- lyase
- isomerase
- ligase
37
oxidoreductase
catalyze oxidation reduction rxns
38
transferase
catalyze group transfer rxns
39
hydrolase
in hydrolysis rxns C-O, C-N, and C-S bonds are cleaved by the addition of h2O in the form of Oh- and H+ to the atoms forming the bond
40
lyase
cleave C-C, C-O, C-N, and C-S bonds by means other than hydrolysis or oxidation
41
isomerase
rearrange the exisiting atoms of a molecule to create isomers of the starting material
42
ligase
synthesize C-C, C-S, C-O, and C-N bonds in rxns coupled ot the cleavage of high energy phosphate bonds in ATP or some other nucleotide
43
amylase
CHO digestion
dx acute pancreatitis
44
ALT
use to transfer amino groups from an amino acid to a ketoacid
dx viral hepatitis
45
lactate dehydrogenase
anaerobic glycolysis to convert glucose ot lactate
dx. liver disease
46
lipase
located on endothelial cells and hydrolyzes triacylglycerol into free FAs to be stored in adipose
dx acute pancreatitis
47
beta-glucocerebrosidase
complex lipid metabolism
dx. gaucher disease
48
transketolase
participates in the nonoxidative portion of PPP and requires thiamin as a cofactor
dx. reduced activity indicates a thiamine deficiency
49
categories of cofactors
coenzymes
metal ions
prosthetic groups
50
coenzyme
any organic cofactor that binds to the enzyme and is necessary for the rxn
51
metal ions
inorganic and may be part of prosthetic group
| cofactor
52
prosthetic groups
tightly bound within an enzyme through non covalent mechanisms
cofactor
53
NAD/FAD
used in redox rxns
54
pantothenic acid (CoA)
acyl group carriers
55
thiamin pyrophosphate
decarboxylation rxns
56
pyridoxal phosphate
transmination
57
biotin
carboxylation rxns
58
cobalamin
carbon transfers
59
heme
required for oxygen carrying
60
induced fit model
the enzyme changes its conformation when it binds to a substrate and this "induced" conformation is due to the interactions between the AA side chains of the active site and the functional groups of the substrate
substrate also changes conformation in response to the enzyme
61
transition state
when an intermediate that resembles both substrate and product, and contains the most free energy, exists
the enzyme stabilizes this by lowering its activation energy
62
activation energy
energy necessary to achieve the transition state
| determines how fast a rxn will go
63
rxn types of enyzmes
- acid-base catalysis
- covalent catalysis
- catalysis by proximity
- catalysis by strain
64
acid-base cataysis
activates the substrate by interaction with an acidic or basic AA R group to initiate a rxn
can be specific or general
65
covalent catalysis
relies on the enzyme becoming modified and therefore becomes a reactant in the rxn reducing the activation energy and speeding up rxn
ex. transamination using pyridoxal phosphate
66
catalysis by proximity
the higher the concentration of reactants the more likely they will interact
67
catalysis by strain
cleavage through the physical distortion by mimicking the transition state intermediate
68
secondary structures are stabilized through
hydrogen bonding
69
are beta-sheets or alpha-helices more stable? why?
beta sheets due to increased hydrogen bonding
70
loops are stabilized through
a variety of bonds such as hydrogen, salt bridges, hydrophobic interactions
71
all kinases transfer
the gamma phosphoryl group of ATP to protein or peptides
72
describe adult hemoglobin
2 alpha-globulin and two beta-globulin chains
| each independent subunit has own biding site for the porphyrin ring heme
73
do muscle cells contain myoglobin or hemoglobin
myoglobin
74
when a fully saturated hemoglobin loses 1 oxygen, what happens?
conformational change in one of the subunits which facilitates the offloading of the other oxygen until the hemoglobin is fully deoxygenated and will return to the lungs to become oxygenated
75
fully oxygenated state of hemoglobin is the
relaxed state
76
fully deoxygenated state of hemoglobin is the
tense state
77
term for myoglobin and hemoglobin when heme is present
holoproteins
78
heme group is required for
oxygen transport
79
term for myoglobin and hemoglobin when heme ring is not present
apoprotein
80
heme is considered a
prosthetic group
81
how is heme stabilized in its interaction with myo/hemoglobin
interaction with 2 histidines
82
when oxygen is bound to the heme...
the iron is pulled within the plane of the porphyrin ring
83
when oxygen is release, this causes
a shift so the iron moves below the plane of the porphyrin ring towards the histidine, cuasing a conformational change to break the salt bridges and facilitate the offloading of oxygen from the other subunits
84
what serves as an oxygen carrier in the blood?
hemoglobin
85
the task for hemoglobin is
to become completely loaded with oxygen in the lungs and to off load that in low oxygen environments such as active tissues
86
hemoglobin displays what type of binding curve
sigmoidal - oxygen saturation changes rapidly over a very short range of partial pressures of oxygen and hemoglobin can rapidly unload oxygen
87
to perform its job, myoglobin must
effectively bind the oxygen released by hemoglobin so must have a higher oxygen affinity
88
cooperativity
initial binding of oxygen is difficult as requires initial breaking of salt bridges, however this becomes easier with each additional oxygen binding until finally all bonds broken and in relaxed state and the reverse is true - as each oxygen is released and new salt bridges form, it is easier for the next oxygen to be released until back in tense state
89
the on and offloading of oxygen can be modified through
allosteric regulation
90
allosteric regulation is
regulation of enzyme kinetics by a compound biding at a site unique from the active site
91
common stabilizers of hemoglobins tense state
- 2,3 bisphosphoglycerate
- protons/decreased pH
- carbon dioxide
92
oxidoreductases
- catalyze oxidation and reduction reactions
| - coupled with NADH and FADH2 to allow a reaction to move forward or capture energy
93
transferases
catalyze the transfer of moieties such as glycosyl, methyl, or phosphoryl group and may allow the recycling of a cofactor
94
hydrolases
catalyze the cleave of C-C, C-O, C-N bonds
95
phosphatases are one of the most common...
hydrolases
96
phosphorylation by
kinases
97
dephosphorylation by
regulatory phosphatase
98
ligases
catalyze the joining together of 2 molecules coupled with the hydrolysis of ATP
99
isomerases
catalyze geometric or structural rearrangements within a molecule
100
are isomerases regulated
no
101
lyases
catalyze cleavage of common bonds by an elimination reaction which therefore generates a double bond
102
major groups that change enzyme activity or are required for it to function
prosthetic groups
cofactors
coenzymes
103
tightly bound to the enzyme and remain associated during the reaction
prosthetic groups
| ex. heme group
104
common prosthetic groups
FAD
thiamine pyrophosphate
pyridoxal phosphate
transition metals
105
thiamine phosphate is a
prosthetic group commonly used by dehydrogenases
106
pyridoxal phosphate is a
prosthetic group used in transferase reaction
107
transition metals are commonly used
as prosthetic groups for ETC enzymes
108
reversibly associate with the enzyme or substrates
coenzymes and cofactors
109
which must be in the environment in order for catalysis to occur - prosthetic groups or cofactors/coenzymes
cofactors/coenzymes
110
made up of inorganic compounds
cofactors
111
organic in nature
coenzymes
112
enzymes increase the local concentrations by binding substrates within the active site which orients the substrates in a position to chemically interact
catalysis by proximity
113
enzymes participate in reactions by breaking covalent bonds, lytic reactions, typically bind their substrates in a conformation that is somewhat unfavorable for the bond targeted for cleavage
catalysis by strain
114
ionizable functional groups of individual amino acids can also contribute to the reaction by acting as acids or bases
acid-base catlysis
115
the formation of a covalent bond between the enzyme and one or more substrates. The modified enzyme becomes a reactant
covalent catalysis
116
what type of catalysis produces something that mimics the transition state of the intermediate
catalysis by strain
117
pyridoxal phosphate in transamination reactions is an example of
covalent catalysis
118
catalyze group transfer reactions - the transfer of a functional group from one molecule to another
transferase
119
catalyze oxidation reduction reactions
at least one substrate becomes oxidized and one reduced
oxidoreductase
120
C-O, C-N, and C-S bonds are cleaved by the addition of H2O in the form of h- and H+ to the atoms forming the bond
hydrolase
121
cleave C-C, C-O, C-N, and C-S bonds by means other than hydrolysis or oxidation
lyase
122
rearrange the existing atoms of a molecule
isomerase
123
synthesize C-C, C-S, C-O, and C-N bonds in reactions boupled ot the cleavage of high energy phosphate bonds in ATP or some other nucleotide
ligase
124
involved in CHO digestion
amylase
125
amylase dx
acute pancreatitis
126
use to transfer amino groups from amino acid to ketoacid
ALT
127
ALT dx
viral hepatitis
128
anaerobic glycolysis to convert glucose ot lactase
lactate dehydrogenase
129
lactate dehydrogenase dx
liver diseases
130
located on endothelial cells and hydrolyzes TAG into free FA to be stored in adipose
lipase
131
lipase dx
acute pancreatitis
132
involved in complex lipid metabolism
beta-glucocerebrosidase
133
beta-glucocerebrosidase dx
gaucher diease
134
participates in the nonoxidative portion of the PPP
transketolase
135
transketolase requires what as cofactor
thiamin
136
transketolase dx
reduced activity indicates thiamine deficiency
137
NAD/FAD necessary for
redox rxns
138
pantothenic acid necessary for
acyl group carriers
139
thiamin necessary for
decarboxylation rxns
140
pyridoxal phosphate necessary for
transamination
141
biotin necessary for
carboxylation rxns
142
cobalamin necessary for
carbon transfers
143
heme necessary for
oxygen carrying
144
bohr effect
decrease in pH decreases hemoglobin saturation
145
mechanism of bohr effect
Carbon dioxide generated in peripheral tissues combines with water to form carbonic acid, which dissociates into protons and bicarbonate ions. Deoxyhemoglobin acts as a buffer by binding protons and enhances quantity of CO2 absorbed by RBCS thus enhancing delivery of O2 to respiring tissues by stabilizing the T state.
146
2,3-bisphosphoglycerate and hemoglobin
CO2 induced decreases in RBC pH promotes synth of 2,3-BPG in erythrocytes which binds in central cavity of t-state hemoglobin, forming salt bridges and stabilizing the deoxygenated, t-state hemoglobin and increasing the quantity of O2 released in peripheral tissues
147
Cleavage of fructose 1, 6-bisphosphate to dihydroxyacetone and glyceraldehyde 3-phosphate is achieved by what class of enzymes?
lyase
148
Movement of ammonia from an amino acid to an α-keto acid involves a family of enzymes best categorized as?
transferases
149
ping-pong method
covalent catalysis
150
amino transferases use what type of catalysis
covalent catalysis
151
Chymotrypsin is a protease that cleaves peptide bonds. It is characterized as which class of enzymes?
hydrolases
152
Prosthetic groups are complex nonprotein molecules that participate in catalysis by providing functional groups that form a covalent intermediate between the enzyme and the substrate. What is an example of a coenzyme or cofactor that participates in a covalent catalysis reaction?
pyridoxal phosphate
153
Hemoglobin bound to heme is termed a holoprotein. The heme or porphyrin ring is required for oxygen binding and it is defined as?
prosthetic group
154
Covalent catalysis is used by many enzymes to cleave peptide bonds. Which amino acids would not facilitate this type of catalysis?
valine
155
which amino acids most commonly participate in covalent catlysis
cysteine
serine
histidine
156
Hemoglobin has the ability to display cooperative binding while myoglobin does not display this binding kinetic pattern. Which difference between the two proteins accounts for this difference in binding kinetics?
the presence of quaternary structure in hemoglobin
