1
Q
What are the two forms of an enzyme during a catalyzed reaction?
A
The free form (E) and the substrate-combined form (ES).
2
Q
What is the initial transient period of an enzymatic reaction called?
A
The pre-steady state.
3
Q
What builds up during the pre-steady state of an enzyme-catalyzed reaction?
A
The concentration of the ES (enzyme-substrate) complex.
4
Q
How long does the pre-steady state typically last in an enzymatic reaction?
A
Often microseconds (the time required for one enzymatic turnover).
5
Q
What is an enzymatic turnover?
A
The conversion of one molecule of substrate to product.
6
Q
What follows the pre-steady state in an enzymatic reaction?
A
The steady state.
7
Q
What characterizes the steady state of an enzymatic reaction?
A
The concentration of the ES complex remains approximately constant.
8
Q
What is the traditional analysis of reaction rates during the steady state called?
A
Steady-state kinetics.
9
Q
What equilibrium constant describes an equilibrium such as S <-> P?
A
Keq (or K).
10
Q
Under standard biochemical conditions, how is the equilibrium constant denoted?
A
K’eq.
11
Q
What equation relates the equilibrium constant to the standard free-energy change?
A
Delta G’o = -RT ln K’eq.
12
Q
In the equation Delta G’o = -RT ln K’eq, what does R represent?
A
The gas constant (8.315 J/mol K).
13
Q
What does a large negative Delta G’o indicate about a reaction?
A
A favorable reaction equilibrium (more product than substrate at equilibrium).
14
Q
Does a highly favorable reaction equilibrium guarantee a rapid reaction rate?
A
No, reaction equilibrium does not determine the rate.
15
Q
What two factors determine the rate of a chemical reaction?
A
The concentration of the reactant(s) and the rate constant (k).
16
Q
What is the rate equation for a unimolecular reaction (S -> P)?
A
V = k[S].
17
Q
In pre-steady state kinetic experiments, what does a ‘burst’ phase indicate?
A
That a step following the chemical step (such as product release) is rate-limiting.
18
Q
What graphical plot shows a pre-steady state burst phase?
A
Product concentration versus time (extrapolated to zero time).
19
Q
If the burst amplitude equals the total enzyme concentration, what does this imply?
A
One molecule of product is formed in each active site during the burst phase.
20
Q
What shorthand notation is used to describe multi-substrate enzyme reactions?
A
Cleland nomenclature.
21
Q
In Cleland nomenclature, how are substrates denoted?
A
As A, B, C, D (in the order they bind).
22
Q
In Cleland nomenclature, how are products denoted?
A
As P, Q, S, T (in the order they dissociate).
23
Q
What terms refer to enzymatic reactions with one, two, three, or four substrates?
A
Uni, bi, ter, and quad, respectively.
24
Q
In Cleland notation, what represents the progress of the reaction?
A
A horizontal line.
25
What do vertical lines represent in Cleland nomenclature?
Steps involving the binding and dissociating of substrates and products.
26
How are successive modified forms of the enzyme denoted in Cleland nomenclature?
As E, F, G, etc.
27
What is a bi bi reaction?
An enzymatic reaction with two substrates and two products.
28
What type of mechanism requires the first substrate to bind before the second can bind?
An ordered binding mechanism.
29
What type of mechanism allows substrates to bind in any sequence?
A random binding mechanism.
30
What is formed when both substrates are bound to the enzyme in a bi bi reaction?
A noncovalent ternary complex.
31
In what mechanism does the first substrate convert to product and leave before the second substrate binds?
The Ping-Pong (or double-displacement) mechanism.
32
Does a ternary complex form in a Ping-Pong mechanism?
No, no ternary complex is formed.
33
In a Ping-Pong mechanism, what usually happens to the enzyme temporarily?
It becomes covalently modified (a functional group is transferred to it).
34
What is the primary structure of a protein?
The linear sequence of amino acids linked by peptide bonds.
35
By convention, how is the sequence of a peptide or protein written?
From the N-terminus (left) to the C-terminus (right).
36
What genetic disease illustrates the importance of the primary structure in hemoglobin?
Sickle cell anemia.
37
What process determines the specific sequence of amino acids in a protein?
Gene translation (from an mRNA sequence).
38
Can a single amino acid substitution drastically alter protein function?
Yes, as seen in many molecular diseases.
39
What class of enzymes catalyzes the transfer of electrons (hydride ions or H atoms)?
Oxidoreductases.
40
What class of enzymes catalyzes group transfer reactions?
Transferases.
41
What class of enzymes catalyzes hydrolysis reactions?
Hydrolases.
42
What class of enzymes catalyzes the cleavage of C-C, C-O, or C-N bonds by elimination?
Lyases.
43
What class of enzymes catalyzes the transfer of groups within molecules to yield isomeric forms?
Isomerases.
44
What class of enzymes catalyzes the formation of C-C, C-S, C-O, and C-N bonds by condensation reactions?
Ligases.
45
Which protease is a classic example of covalent and general acid-base catalysis?
Chymotrypsin.
46
What three amino acids form the catalytic triad of chymotrypsin?
Serine, Histidine, and Aspartate.
47
What type of bond does chymotrypsin specifically cleave?
Peptide bonds adjacent to large hydrophobic amino acid residues.
48
What are the major storage forms of energy in most organisms?
Lipids (specifically triacylglycerols).
49
Are lipids generally soluble or insoluble in water?
Insoluble in water (hydrophobic).
50
What are the building blocks of many complex lipids?
Fatty acids.
51
What characterizes the hydrocarbon chain of a saturated fatty acid?
It contains no double bonds between carbon atoms.
52
What characterizes an unsaturated fatty acid?
It contains one or more double bonds in the hydrocarbon chain.
53
What configuration are almost all naturally occurring double bonds in fatty acids?
The cis configuration.
54
How does the presence of cis double bonds affect the melting point of fatty acids?
It significantly lowers the melting point.
55
Why do unsaturated fatty acids have lower melting points?
The cis double bond causes a kink that prevents tight packing of the chains.
56
What is a triacylglycerol composed of?
Three fatty acids esterified to a single glycerol molecule.
57
Why are triacylglycerols better for long-term energy storage than glycogen?
They are more highly reduced (yield more energy upon oxidation) and are unhydrated (weigh less).
58
What are specialized cells that store large amounts of triacylglycerols called?
Adipocytes (fat cells).
59
What are waxes chemically?
Esters of long-chain fatty acids with long-chain alcohols.
60
What are the major structural lipids found in biological membranes?
Glycerophospholipids, sphingolipids, and sterols.
61
What term describes molecules with both hydrophilic and hydrophobic regions?
Amphipathic.
62
In a glycerophospholipid, what groups are attached to the glycerol backbone?
Two fatty acids and a highly polar or charged phosphate group (often with a head-group alcohol).
63
What linkage connects the fatty acids to glycerol in most glycerophospholipids?
Ester linkages.
64
In what lipids is one fatty acid attached via an ether linkage rather than an ester linkage?
Ether lipids (like plasmalogens).
65
What lipid backbone is used in sphingolipids instead of glycerol?
Sphingosine.
66
What type of bond connects a fatty acid to sphingosine to form a ceramide?
An amide linkage.
67
What subgroup of sphingolipids contains a carbohydrate head group?
Glycosphingolipids.
68
What disease is caused by a genetic defect in the breakdown of gangliosides?
Tay-Sachs disease.
69
What is the major sterol found in animal cell membranes?
Cholesterol.
70
What is the general structure of a sterol?
A rigid core of four fused hydrocarbon rings.
71
What is the basic structural unit of biological membranes?
The lipid bilayer.
72
What forces primarily drive the formation of lipid bilayers in aqueous solutions?
The hydrophobic effect.
73
What structure forms when amphipathic molecules form a spherical droplet with hydrophobic tails inside?
A micelle.
74
What forms when a lipid bilayer folds back on itself to form a hollow sphere?
A liposome (or vesicle).
75
What model describes the membrane as a dynamic structure with proteins moving in a lipid matrix?
The fluid mosaic model.
76
Are biological membranes symmetric or asymmetric?
They are highly asymmetric (inner and outer leaflets differ).
77
What class of membrane proteins is firmly embedded in the lipid bilayer?
Integral membrane proteins.
78
What secondary structure is most common for the transmembrane segments of integral proteins?
The alpha helix.
79
How many amino acids in an alpha helix are typically needed to span the hydrophobic core of a bilayer?
About 20 hydrophobic residues.
80
What alternate structural motif can span the lipid bilayer as a pore?
A beta barrel.
81
What class of membrane proteins associates reversibly with the membrane surface?
Peripheral membrane proteins.
82
How can peripheral proteins be released from the membrane?
By relatively mild treatments like changes in pH or ionic strength.
83
What class of proteins is covalently attached to a lipid that anchors them to the membrane?
Amphitropic (or lipid-anchored) proteins.
84
What is the state of a lipid bilayer below its characteristic transition temperature?
A liquid-ordered (or gel) state.
85
What is the state of a lipid bilayer above its transition temperature?
A liquid-disordered (or fluid) state.
86
How do cells regulate membrane fluidity when temperatures change?
By altering the lipid composition (ratio of saturated to unsaturated fatty acids).
87
How does cholesterol affect membrane fluidity at physiological temperatures?
It restrains movement and reduces fluidity (but prevents tight packing to avoid freezing).
88
What type of motion within a single lipid leaflet is very fast and frequent?
Lateral diffusion.
89
What type of lipid motion between leaflets is thermodynamically unfavorable and very slow?
Transbilayer (flip-flop) movement.
90
What enzyme facilitates the movement of specific phospholipids from the outer to the inner leaflet?
Flippase.
91
What enzyme moves phospholipids from the cytosolic (inner) to the outer leaflet?
Floppase.
92
What enzyme scrambles lipids across the bilayer to equalize distribution?
Scramblase.
93
What are the microdomains in membranes enriched in cholesterol and sphingolipids called?
Lipid rafts.
94
What small integral proteins are often enriched in lipid rafts and can induce membrane curvature?
Caveolins.
95
Can polar molecules and ions easily diffuse across a pure lipid bilayer?
No, the hydrophobic core acts as a highly impermeable barrier.
96
What lowers the activation energy for the transport of polar molecules across membranes?
Transport proteins (transporters or permeases).
97
What is transport down a concentration gradient without the use of energy called?
Passive transport (or facilitated diffusion).
98
What is the process of moving a solute against its concentration gradient called?
Active transport.
99
What drives primary active transport?
Energy provided directly by a chemical reaction, such as ATP hydrolysis.
100
What drives secondary active transport?
The coupling of uphill transport of one solute to the downhill transport of another.
101
What type of transporter moves only one substrate?
A uniporter.
102
What type of transporter moves two substrates simultaneously in the same direction?
A symporter.
103
What type of transporter moves two substrates simultaneously in opposite directions?
An antiporter.
104
What class of active transporters are primarily cation transporters driven by ATP?
P-type ATPases.
105
What is a classic example of a P-type ATPase in animal cells?
The Na+K+ ATPase (sodium-potassium pump).
106
What does the Na+K+ ATPase transport per molecule of ATP hydrolyzed?
Three Na+ ions out of the cell and two K+ ions into the cell.
107
What class of ATP-driven pumps transport protons to acidify intracellular compartments?
V-type ATPases.
108
What large family of ATP-dependent transporters can pump a wide variety of molecules out of cells?
ABC transporters (ATP-binding cassette).
109
What channels allow the rapid flow of water across cell membranes?
Aquaporins.
110
Are ion channels the same as ion transporters?
No, channels allow much faster passage and are usually not saturable.
111
What triggers the opening of a voltage-gated ion channel?
A change in the transmembrane electrical potential.
112
What triggers the opening of a ligand-gated ion channel?
The binding of a specific extracellular or intracellular molecule.
113
What allows the K+ channel to be highly specific for potassium over sodium?
The selectivity filter (carbonyl oxygens perfectly positioned to dehydrate K+).
114
What dictates the native 3D structure of a protein?
Its primary amino acid sequence.
115
What does an enzyme do to the activation energy of a reaction?
It lowers it.
116
What are enzymes that have both active sites and regulatory sites called?
Allosteric enzymes.
117
What defines the specificity of an enzyme?
Its active site's geometric and chemical complementarity to the transition state.
118
What is a competitive inhibitor?
An inhibitor that binds to the active site, competing with the substrate.
119
How does a competitive inhibitor affect Vmax and Km?
Vmax is unchanged; apparent Km increases.
120
What is an uncompetitive inhibitor?
An inhibitor that binds only to the enzyme-substrate (ES) complex.
121
How does an uncompetitive inhibitor affect Vmax and Km?
Both apparent Vmax and apparent Km decrease.
122
What is a mixed inhibitor?
An inhibitor that can bind to both the free enzyme and the ES complex.
123
What is the mechanism of suicide inhibitors (mechanism-based inactivators)?
They are converted by the enzyme into a reactive species that irreversibly inactivates the enzyme.
124
What is an isozyme?
Multiple forms of an enzyme that catalyze the same reaction but differ in amino acid sequence.
125
What form of energy storage do plants utilize in seeds instead of fat?
Oils (liquid triacylglycerols).
126
Are triacylglycerols components of biological membranes?
No, they are strictly for energy storage.
127
Why is cholesterol considered a precursor?
It is the metabolic precursor of steroid hormones and bile acids.
128
What is the main function of bile acids?
They act as biological detergents in the intestine to emulsify dietary fats.
129
What group of lipids serves as potent intracellular signals and local hormones?
Eicosanoids.
130
What are the three classes of eicosanoids?
Prostaglandins, thromboxanes, and leukotrienes.
131
What precursor fatty acid is used to synthesize eicosanoids?
Arachidonic acid.
132
What class of drugs inhibits the synthesis of prostaglandins and thromboxanes?
NSAIDs (like aspirin and ibuprofen).
133
What lipid-soluble vitamins are derived from isoprene units?
Vitamins A, D, E, and K.
134
What vitamin is a hormone precursor involved in calcium regulation?
Vitamin D.
135
What vitamin is necessary for visual pigments?
Vitamin A (retinol).
136
What lipid-soluble vitamins act primarily as biological antioxidants?
Vitamin E (tocopherols).
137
What vitamin is essential for blood clotting?
Vitamin K.
138
What technique is commonly used to separate complex mixtures of lipids?
Chromatography (like TLC or HPLC).
139
What is the common structure of membrane-spanning alpha helices?
They are composed mostly of hydrophobic amino acids.
140
What is a hydropathy plot used for?
To predict transmembrane domains from an amino acid sequence.
141
What defines simple diffusion?
Movement of nonpolar solutes down their concentration gradient without a transporter.
142
What characterizes an electrogenic transport process?
It results in a net transfer of charge across the membrane.
143
Is the Na+K+ ATPase electrogenic?
Yes, it creates a net separation of charge across the membrane.
144
What is the resting membrane potential of a typical animal cell?
Between -50 and -70 millivolts (inside negative).
145
What toxins specifically target ion channels to block nerve function?
Neurotoxins (like tetrodotoxin from pufferfish).
146
What type of membrane protein is the acetylcholine receptor?
A ligand-gated ion channel.
147
What happens when acetylcholine binds to its receptor?
The channel opens, allowing Na+ and Ca2+ to flow into the cell.
148
How does glucose enter erythrocytes?
Through passive transport via the GLUT1 transporter (a uniporter).
149
What ion gradient is often used in animal cells for secondary active transport?
The Na+ gradient.
150
What ion gradient is often used in plant and fungal cells for secondary active transport?
The H+ (proton) gradient.
151
BIOMG 3300
flashcards
Decks in class (4)
# Cards
