Exam 2 Flashcards
1
Q
How are enzymes categorized
A
by their 6 major classes
2
Q
Cofactors
A
small inorganic molecules or inorganic ions bound reversibily
3
Q
Coenzymes
A
more complex organic or metallo-organic molecules bound reversibly
4
Q
Prosthetic group
A
anything bound tightly
5
Q
Apoenzyme + cofactor =
A
holoenzyme
6
Q
What is the relationship between vitamins and coenzymes
A
vitamins are precursors to enzymes
7
Q
Bind of enzyme to substrate occurs at the ________ site. This is initially facilitated by multiple ___-_________ interactions
A
active, non-covalent
8
Q
Enzymes bind to the transition site ______ than either substrates or products
A
better
9
Q
The _____________ is determined by delta G knot of the reaction
A
equilibrium
10
Q
delta G knot prime and equilibrium of a reaction are ________________ of the path of the reaction
A
independent
11
Q
What is induced fit?
A
The enzyme adjusts to fit the substrate when it binds to it
12
Q
The release of __________ ________ contributes to specificity and catalysts
A
binding energy
13
Q
Phase (1) is also known at the __________________ of reaction
A
pre ready rate
14
Q
The broad maximum of the reaction rate at phase (2) is called _____________
A
steady state
15
Q
What is V0?
A
initial rate of reaction
16
Q
What is Vmax?
A
the maximum rate of reaction – when the enzyme is saturated with substrate
17
Q
What is Km?
A
Substrate concentration at which the reaction is 1/2 Vmax
18
Q
What are the three assumptions of Michaelis-Menten equation
A
-k2 can be neglected
-there are many more molecules of substrate than of enzyme (ES can be neglected)
-very little substrate has been converted to product (P can be neglected)
19
Q
What is the steady state assumption
A
at steady state, the formation of ES (at rate K1) is equal to its breakdown
20
Q
Kcat describes the _____ of the reaction
A
speed
21
Q
Kcat/Km is also known as the
A
specificity constant or substrate preference
22
Q
If Kcat is increased the reaction is _____
If Kcat is low …
A
faster
lower substrate concentration required (higher affinity)
23
Q
When V0 = Vmax
A
the plateau at high substrate concentrations
24
Q
S with E leads to number of encounters per second which determines the _____
A
speed
25
What does diffusion-controlled mean
Determined by the speed at which substrate molecules can diffuse to the enzymes
26
Increasing the speed of diffusion-controlled reactions is only possible by increasing ______
diffusion (Circe effect)
27
What are the two reactions of ternary complexes
random-substrate binding does not matter
ordered-substrate binding matters
28
Reactions with no ternary complexes
one product is released before the 2nd substrate binds
Involve covalent modifications of enzyme
Are always ordered
29
What are the 4 reversible inhibitors
Competitive
Uncompetitive
Non-competitive
Mixed
30
Competitive Inhibition
Y-axis interception
Vmax does not change but Km increases
31
Methotrexate
competitive inhibitor
anti-cancer drug
32
Uncompetitive Inhibition
Inhibitor binds only to ES, but not to free enzyme E
Both Vmax and Km decrease
parallel lines
33
Non-competitive inhibition
Inhibitor binds to both free enzyme E and to ES complex with equal affinity
Vmax decreases, but not Km
x-axis interception
34
Mixed Inhibition
Inhibitor binds to E and ES but with two binding constants
(affinity) are different
Vmax decreases, Km increases or decreases
Intersection above or below x-axis
35
Group-specific inhibitors
React with side chains of certain amino acids in the active site or elsewhere
36
DIPF
modifies critical serine residues in acetylcholinesterase and in protease chymotrypsin
(group-specific inhibitor)
37
Iodoacetamide
reacts with the sulfhydryl group of critical cysteines
(group-specific inhibitor)
38
Affinity labels
React only with active side groups
39
TPCK
Binds to the active site of chymotrypsin and modifies an essential histidine residue
(affinity label)
40
Suicide Inhibitors
metabolized by the enzyme to create an inhibitor that inactivates the enzyme
41
5-fluorouracil
Anti-cancer drug
(suicide inhibitor)
42
Deprenyl
suicide inhibitor of monoamine oxidase
used for Parkinson's disease
43
Penicillin
Suicide inhibitor of an enzyme that catalyzes a critical step in bacterial cell wall synthesis
44
General acid/base catalysts
an AA side chain donates or accepts a proton which may facilitate the formation of a transition state or a reaction intermediate
45
Covalent catalysts
During the enzymatic reaction, an intermediate becomes covalently attached to the enzyme
46
Metal Ion catalysts
may interact with a transition state and stabilize it
generate nucleophile
orient it in the active site
47
What are the 6 strategies used by enzymes
genreal acid-base catalysts
covalent catalysts
metal ion catalysts
electrostatic catalyst
entropy reduction
straining the substrate
48
Which of the 6 strategies used by enzymes are usually combined to elucidate an enzyme's catalytic mechanism
all of them
49
Proteases cleave specific ________ _______ in proteins and have a wide variety of roles in digestion, protein recycling, enzyme activation, virus maturation
peptide bonds
50
What do the different types of proteases depend on
whether a critical AA or metal is used in the active site
51
What are the three serine proteases
Chymotrypsin
Trypsin
Elastase
52
Chymotrypsin
-cuts the polypeptide chain next to bulky hydrophobic residues
-pocket is deep and hydrophobic -> bulky AA fit
53
Trypsin
-cuts next to positively charged residues
-negatively charge Asp at bottom of pocket -> attracts positively charged AAs
54
Elastase
-cuts next to small neutral AAs
-small pocket is filled with valine residues -> only small AA will fit
55
What is the first part of covalent mechanisms
Serine OH attacks the carbonyl carbon of the peptide bond
first fragment is released
56
The negative charge of the short-lived intermediate in covalent first step mechanism causes the intermediate to become
unstable and start to decay
57
The ester bonds in acyl enzyme does what to the product of the first step of covalent mechanism
stabilizes it
58
What is the second part of covalent mechanisms
water attacks the acylated enzyme
covalent bond with the enzymes is cleaved
second fragment is released, free enzyme is regenerated
59
Catalytic triad
Serine
Histidine
Aspartate
60
Cysteine proteases use ______ made more active by histidine
Cysteine
61
Aspartyl proteases use _______ activated by _______
Water
Aspartate
62
Metalloproteases use _____ activated by a _____ and a base
Water
Metal
63
HIV protease is a _________
Homodimer
64
Inhibitors have been designed that resemble the __________ __________ of the reaction but cannot be cleaved
Tetrahedral Intermediate
65
HIV protease inhibitors mimic the negatively charged _________ of the tetrahedral intermediate
Oxygen
66
What are the four principle ways of regulation of enzyme activity
allosteric regulation
reversible covalent modification
proteolytic activation
regulation of enzyme levels
67
What regulation pathway is reversible? Which one is irreversible?
reversible: covalent modification
irreversible: proteolytic activation
68
Which regulation of enzyme activity pathway is multimeric
allosteric regulation
69
Allosteric regulators can be...
second messengers (cAMP, Ca2+)
indicators of available metabolic energy (ATP)
70
Which step in an activity pathway is usually regulated
the first step
71
What kind of regulators are carbamoyl phosphate ad aspartate
homotropic regulators
72
Does the response to substrate concentration sigmoid follow michaelis-menten kinetics
no
73
ATPase is a multimeric protein with two _______ ______ and three ________ ________
catalytic trimers
regulatory dimers
74
CTP and ATP are _________ regulators
Heterotropic
75
Binding if CTP shifts the equilibrium to the __ state
T state (less active)
76
Binding of ATP shift equilibrium to the __ state
R state (more active)
77
Most common covalent modifications
R-OH at Ser, Tyr or Thr residues or of His
78
What does glucagon do to the liver
Increase phosphorylation b kinase
79
What does epinephrine (increase ca2+, AMP) do to the muscle
Increase phosphorylase b kinase
80
Glycogen phosphorylase is made more active by __________ which is catalyzed by what
Phosphorylation
Phosphorylase kinase
81
Phosphorylation can be reversed by what
Insulin (decreases glucose levels)
Phosphoprotein phosphatase 1 causes this
82
Two examples of zymogens
Insulin
Proteases
83
What are zymogens
Inactive substance which is converted into an enzyme when activated by another enzyme
84
How is regulation of glycogen phosphorylase by covalent modifications turned off
Destruction of the enzyme/hormone
Specific binding of an inhibitor
85
By making zymogens rather than active enzymes the pancreas protects itself from what
Auto digestion
86
What are two examples of proteolytic cascades
-Blood clotting factors are activated by a cascade of proteolysjs events
-Complement cascade utilized by the immune system to destroy pathogens consists of a series of proteolytic events
87
How are carbohydrates defined
They have the formula Cn(H2O)n
88
How to name basic carbohydrates
Number of carbon atoms in the carbohydrate +
“ose”
Ex: triose
89
Difference between aldose and ketose
Aldose = aldehyde
Ketose = ketone
90
Difference between D and L amino acids
They are chiral centers where D is right and L is left
91
Constitutional isomer
Molecules with same formula but connected differently
92
Stereoisomers
Molecules with same formula and same connectivity but different 3D arrangement
93
Diastereomers
Stereoisomers that are not mirror images of each other they have different physical properties
94
Epimers
Stereoisomers that differ at only one chiral center
95
Enantiomers
Are mirror images of one another
96
Hemiacetals and hemiketals are produced by being attacked by what molecule
Alcohols
97
When linear glucose cyclones what species is formed
Hemiacetal carbon (is has two isomers: alpha and beta)
98
Upon cyclization the former carbonyl carbon becomes a new chiral center called the
Anomeric Carbon
99
Trans is ____
Cis is ____
Trans is alpha
Cis is beta
100
Sugars with free anomeric carbon are ______
Reducing (can be oxidized)
101
Which functional group in a sugar is reducing
Ester
102
Difference between homo and hetero polysaccharides
Homo: one monomer
Hetero: two or more sugars
103
Polysaccharides do not have a defined _________ _________
Molecular weight
104
Glycogen and starch are composed of which sugar
Homopolysaccharides
105
What are glycosaminoglycans
Linear polymers of repeating disaccharide units
106
What are the 4 glycoaminoglycans
Hyaluronate (GLcNAc)
Chondroitin 4-sulfate (GalNAc45)
Keratan Sulfate (GlcNAc6s)
Heparin (GlcNS3S6S)
107
Heparin sulfate is heparin like ___________ but attached to ________
Polysaccharide
Proteins
108
Why is heparin therapeutic
Bind to virus and bacteria and decrease virulence
Form blood vessels
109
Glycoproteins are proteins with small ___________________ attached
Oligosaccharides
110
Proteoglycans consist of sulfated ________________ which are attached to a large rod shaped protein
Glucoseaminoglycans
111
Syndecans and glypicans
syndecans: protein has a single transmembrane domain
Glypicans: protein is anchored to a lipid membrane
112
What part of LPS causes septic shock? Which part determines the serotype
Endotoxin
O-specific chain
113
What is the function of hyaluronan in proteoglycan aggregates and what are their functions
Hyaluronan and aggrecan form huge noncovalent aggregates
-hold water
-provide lubrication
-low friction
-covers joint surfaces
114
Which membrane proteins mediate the interaction of cells with the extracellular matrix
Integrins
115
Which sugar targets proteins to lysosomes
mannose 6-phosphate receptor/lectin of the trans Golgi complex binds to the oligosaccharide of lysosomal enzymes, targeting them for transfer into the lysosome
116
What is a key feature of a lipid
insoluble in water
117
Which functional groups are part of fatty acids
carboxylic acids with hydrocarbon chains
118
Structure of 18:1 cis-9-octadecenoic acid
cen = double bond
18 carbons
1 double bond
119
What is an omega three fatty acid
3rd carbon from end
120
What are the two essential fatty acids
Linoleate and Linolenate
121
What is the effect of chain length and unsaturation on the melting point of fatty acids
More double bonds = lower melting point
Longer chain = higher melting point
122
Saturated FA are more _______ and can pack closer
linear this leads to a higher melting point
123
What are three triglycerols
ester, glycerol, fatty acids
124
Most natural triglycerols are ______, containing different fatty acids
mixed
125
Often the fatty acid attached at the what carbon is unsaturated
C2
126
In glycerophospholipids, the backbone is what and what is the hydrophilic head joined by
glycerol
phosphodiester linkage
127
Glycerophospholipids are both fatty acids, forming hydrophobic tails, are joined to C1 and C2 by what kind of bonds
ester bonds
128
Ether lipids are joined by what bonds
ether bonds
129
The ______ is particularly rich in plasamalogens
heart
130
What is the sphingolipid called with no head group
ceramide
131
Sphingolipids can be classified as phospholipids or glycolipids, what are the linakes of each
phospholipids: phosphodiester
glycolipids: beta-glycosidic
132
Glycolipids with one uncharged sugar are called
cerebroside
133
If 2 or more uncharged sugars are attached, these lipids are called
globosides
134
More complex glycolipids with at least one sialic acid are called
gangliosides
135
Cholesterol spans only one ________ of a lipid bilayer
leaflet
136
Three types of lipids can self-assemble in aqueous solution to form a ______ which can close to form _______. This driving force is caused by what
bilayer
vesicle
hydrophobic interactions
137
Micelle = __ fatty acid
Bilayer = __ fatty acid
Lipid Droplet = __ fatty acid
1
2
3
138
What are the three types of membrane proteins
peripheral, integral, lipid-anchored
139
Proteins and lipids can move _______
laterally
140
Proteins can not _______ while lipids use enzymes to _____
flip-flop
(flippase-inside, flopade-outside)
141
Lipids are asymmetric what is found on the outside and what is found in the inside
outside: sphingomyelin and phosphatidylcholine
inside: phosphatidyl ethanolamine and phosphatidyl serine
142
How are peripheral membrane proteins attached
attachment to membrane can be disrupted by concentrated salt solutions, low pH, Ca2+ chelators, or urea
143
Integral membrane protein's membrane must be dissolved by what
detergent or organic solvent
144
Membrane spanning integral proteins are _________ and _______. They can be predicted by plotting the __________ of amino acids
alpha-helical and beta-conformation
hydrophobicity (hydropathy plot)
145
What are the three common lipid anchors of proteins found inside, what is the one common lipid anchor found outside
inside: palmitoyl group, myristoyl group, farnesyl group
outside: GPI
146
Where are GPI proteins concentrated
lipid rafts
147
Lipid rafts play an important role in ________ ___________
single transduction
148
Caveolae
Inward curved rafts
induced by caveolin
membrane traffic and signaling
149
What is the major differences of gram positive and gram negative
positive: 1 membrane, more proteoglycan complex
negative: 2 membrane, LPS
150
What are the special characteristics of transporters
sterospecific
saturable (michaelis-menten)
transport rates below the limit of unhindered diffusion
151
What are the 4 classes of transport ATPase
P-type
V-type
F-type
ABC-type
152
Which class of transport ATPase has sodium/potassium
P-type
153
Which class of transport ATPase has cystic fibrosis chloride channel and MDR
ABC-type
154
What are the special characteristics of channels
greater rate of diffusion
not saturable
not stereospecific
155
Why can the channel open for K+ instead of Na+ when Na+ is smaller
there is minimal energy difference because the K+ shape is the same as the active site making it ideal for it to pass causing an influx of K+
