Exam 2: Chapter 5-11.1 Flashcards
1
Q
What does the dissociation constant mean?
A
Indicates how tightly bound a molecule is. A smaller Kd value shows higher affinity
2
Q
What is myoglobin?
A
Favors oxygen moving from the blood to the muscle cell
3
Q
What is the oxygen carrier in blood?
A
Hemoglobin
4
Q
What does it mean when a ligand is cooperative?
A
The binding of one molecule will influence the binding of other molecules.
5
Q
Why is hemoglobin a cooperative ligand?
A
Oxygen binding at one subunit increases the affinity for O2 at the remaining subunits.
6
Q
What are the 2 conformational states that hemoglobin can exist in?
A
The T state has low affinity for O2 while the R state has high affinity for O2.
7
Q
Why is the T-state favored in the absence of O2?
A
Due to the formation of salt bridges involving the C-term residues of the a and b subunits.
8
Q
What is a salt bridge?
A
Connecting 2 regions using ions.
9
Q
Why does oxygenated hemoglobin favor the R-state?
A
Formation of the Fe-O2 bond is favorable and pulls the Fe2+ into the plane of the porphyrin ring, which shortens the Fe-N bond giving a lower free energy.
10
Q
Why are intermediate conformations between R-state and T-state disfavored?
A
Due to steric clashes
11
Q
What is the Bohr Effect?
A
Hemoglobin binding H+ favors unloading O2 to the tissue that needs O2 the most.
12
Q
Why does muscle metabolism favor the T-state of hemoglobin?
A
Muscle metabolism causes a pH drop in surrounding tissues, the increase [H+] protonates the hemoglobin which favors salt-bridge formation that stabilizes the T-state.
13
Q
How does the presence of BPG affect oxygen binding to hemoglobin?
A
BPG binds in the central cavity of T-state hemoglobin and contributes to further salt-bridge formation.
14
Q
What would happen to oxygenation of tissues without BPG?
A
Without BPG, hemoglobin would bind O2 too tightly to unload a significant fraction to the tissues.
15
Q
How does BPG affect oxygenation at higher altitudes?
A
An incr. in BPG decr. the affinity for O2 helps in lower O2 environments because it means hemoglobin doesn’t hold onto O2 as tight in the blood so more oxygen is releases and reach body tissue.
16
Q
What is special about fetal hemoglobin?
A
Fetal hemoglobin doesn’t have beta subunits so it binds BPG poorly and therefore has a stronger affinity for O2 and favors movement of O2 across the placental membrane.
17
Q
What is sickle cell anemia?
A
Sickle cell anemia is a mutation arising from a Glu6Val mutation on hemoglobin b. Sickled cells may block small blood vessels, limiting O2 delivery.
18
Q
What is sickling triggered by?
A
Factors that promote T-state hemoglobin. (eg. high altitude & dehydration)
19
Q
What is the biochemical basis for sickle cell anemia?
A
A hydrophobic pocket is exposed on the b-subunit when hemoglobin is in the T-state. This pocket bind the exposed Val on a neighboring hemoglobin and aggregation produces long, rigid strands of hemoglobin which deform the cell into a sickle shape.
20
Q
What are the classes of cytoskeletal fiber?
A
Actin microfilaments, Intermediate filaments, Microtubules
21
Q
What is the structure of hemoglobin?
A
Hemoglobin is composed of 2 alpha chains and 2 beta chains.
22
Q
How do actin monomers form microfilaments?
A
Actin monomers (G-actin) polymerize to form ‘F-actin’ microfilaments because the negative charges on the cleft are attracted to the positive charges of other actin monomers.
23
Q
What is the role of actin microfilaments?
A
Microfilaments help determine cell shape, allow some cells to move, and are part of the contractile apparatus in muscles.
24
Q
What are the steps of the contraction cycle?
A
- Myosin head bound to an actin subunit of the thin filament. ATP binds and myosin releases actin.
- Hydrolysis of ATP to ADP + Pi rotates the myosin lever and increases the affinity of myosin for actin.
- Myosin binds to an actin subunit farther along.
- Binding to actin causes Pi + ADP to be released. The myosin lever returns to its original position. The thin filament moves (power stroke).
25
What is the structure of keratin?
Two long helices forming a coiled-coil. Each helix has a repeating 7 amino acid sequence where the 1st and 4th residues of each repeat are hydrophobic.
26
How is keratin assembled to form hair?
Disulfide bonds between dimers help strengthen keratin microfibrils.
27
How can the crosslinks between keratin fibers be manipulated in hair?
Heat can temporarily unfold proteins and allow the hair to be shaped.
28
What is activation energy?
The energy to go from the ground state to the transition state.
29
How do catalysts increase the rate of a reaction?
Catalysts increase the rate of reaction by lowering the activation energy for both the forward and reverse reaction.
30
How do enzymes bind substrates specifically?
Substrate binding occurs in a pocket or cleft on the surface of the enzyme.
31
What type of reaction is catalyzed using an Oxidoreductase enzyme?
Oxidation-reduction reactions
32
What type of reaction is catalyzed using an Transferase enzyme?
Transferases swap a functional group between substrates.
33
What type of reaction is catalyzed using an Hydrolase enzyme?
Hydrolases use water to break a bond or condense to eliminate water.
34
What type of reaction is catalyzed using an Lysase enzyme?
Lyases break bonds without the use of redox activity or water and produce an extra double bond (or ring) in the products.
35
What type of reaction is catalyzed using an Isomerase enzyme?
Isomerases rearrange functional groups within a substrate, but keep the chemical formula the same.
36
What type of reaction is catalyzed using an Ligase enzyme?
Ligases use ATP energy to connect 2 other substrates.
37
What is a coenzyme?
Coenzymes are organic cofactors.
38
What is prosthetic group?
Prosthetic groups are coenzymes that are tightly associated with the enzyme.
39
What are cosubstrates?
Cosubstrates are coenzymes that transiently associate with the enzyme.
40
What is a holoenzyme?
An active enzyme with its required cofactors.
41
What is an apoenzyme?
An inactive enzyme without its required cofactors.
42
What is a cofactor?
A cofactor is a small organic molecule or metal ion that is required for enzymatic activity.
43
What is acid-base catalysis?
In acid-base catalysis, a H+ is transferred between an enzyme and the substrate.
44
What is ionization?
Ionization requires picking up a proton or losing a proton.
45
What amino acids may participate in acid-base catalysis?
Charged amino acids, Cys, His, Ser, Tyr
46
How does RNase A hydrolyze RNA?
RNase A is an example of acid-base catalysis with histidine residues transferring H+ with the RNA substrate.
47
What is enzyme covalent catalysis?
A stable intermediate is formed when the enzyme covalently binds to the substrate.
48
What are the ways a metal ion aids catalysis?
1. Stabilize negative charges that form in the transition state
2. Shield charges that might repel the attacking group
3. Promote nucleophilic attacks through the ionization of water
4. Participate in redox reactions
49
How does the proximity and orientation of substrates affect catalysis?
An enzyme can speed up a reaction by positioning the reactants properly.
50
What is chymotrypsin?
An intestinal protease that helps you digest proteins by breaking peptide bonds.
51
How does the chymotrypsin recognize which peptide bond to break?
The specificity pocket only binds amino acids that it is complementary too, which position the peptide bond for cleavage.
52
What are zymogens?
Inactive precursors of proteases.
53
What is a protease?
An enzyme which breaks down proteins and peptides.
54
Why don't proteases destroy the small intestine where they are made?
Zymogens are secreted into the small intestine and cleaved by other proteases so that they acquire a conformation where the specificity pocket and oxyanion hole are available for catalysis. However, inhibitors in the blood stream and pancreas bind the protease to inhibit any proteases that are active outside the small intestine.
55
56
How do you know if an enzyme is more optimized for substrate or transition state binding?
The more tightly an enzyme binds to the transition state form, relative to the substrate, the greater the rate of the catalyzed reaction.
57
What is the hyperbolic shape of the rate dependence curve due to?
The formation of an enzyme-substrate complex.
58
What are the criteria for the Michaelias-Menten kinetics being valid?
1. Measurements are made before much product has formed.
2. There is only one substrate.
3. The reaction occurs in a single step.
4. Binding is non-cooperative.
59
What is V0?
The initial velocity of a reaction.
60
What is an irreversible inhibitor?
A molecule that permanently binds to an enzyme and prevents it from working.
61
What is pure competitive inhibition?
A pure competitive inhibitor can only bind to an enzyme if the substrate isn't there because it competes with the substrate at the enzyme's active site.
62
What is the KI?
The inhibitor constant, a low KI indicates a good inhibitor that binds tightly.
63
How does a competitive inhibitor affect a reciprocal plot?
Competitive inhibition:
-Vmax stays the same
-KM increases by a factor of a
64
What are the best competitive inhibitors?
The best competitive inhibitors mimic the transition state of the reaction.
65
What is pure uncompetitive inhibtion?
Pure uncompetitive inhibitors only bind to enzymes when the substrate is present.
66
How does an uncompetitive inhibitor affect the reciprocal plot?
Lowers the Km and the Vmax by the same factor of a'
67
What is mixed inhibition?
A mixture of competitive and uncompetitive inhibition affects both Vmax and Km.
68
What is Km?
A measure of affinity, a smaller Km indicates that the substrate is more tightly bound.
69
What is divergent evolution?
Common ancestor but leads to different structures
70
What is convergent evolution?
Different ancestors leads to different structures, but converge to find same solutions
71
What is pure noncompetitive inhibition?
A pure noncompetitive inhibitor binds away from the enzyme active site and does not affect the substrate binding.
72
What is allosteric regulation?
Allosteric regulators affect the activity of multisubunit enzymes by stabilizing the R-state or T-state
73
How do allosteric inhibitors affect the relative activity curve?
Shift the sigmodial curve to the right
74
How can we regulate enzyme activity without using inhibitors?
1. Rate of synthesis and/or degradation
2. Localization
3. Release of co-activators such as Ca2+
4. Covalent modification (phosphorylation)
75
How does HIV infect cells?
The virus attaches to the CD4 cell and uses reverse transcription to imbed itself in the DNA.
76
How do we design an inhibitor for the HIV reverse transciptase?
The error-prone nature of HIV reverse transcriptase means it may incorporate chain-terminator nucleotide drugs.
77
What are the common features of fatty acids?
78
What is the difference between saturated and unsaturated fatty acids?
Unsaturated fatty acids have at least one double bond in the hydrocarbon tail.
79
What happens to the melting point of fatty acids as the chain length increases?
The melting point increases because temperature must increase to overcome the greater van der Waals interactions.
80
Why is the melting point of saturated fatty acids higher?
The packing of fatty acid chains is disrupted by the presence of cis double bonds which lowers the VDW forces and decreases melting point.
81
How are fatty acids stored?
Fatty acids are usually carried as tricylglycerols rather than free fatty acids.
82
What is the role of Vitamin A? What does a deficiency result in?
A fat soluble vitamin that is important for visual perception. A deficiency results in night blindness.
83
What is cholesterol?
Cholesterol is a major component of animal membranes that helps maintain fluidity and integrity. Cholesterol also serves as a precursor for steroid hormones, Vitamin D, and bile salts.
84
What is the role of Vitamin D? What does a deficiency result in?
A fat soluble vitamin that is important for calcium homeostasis. A deficiency results in rickets, a disease characterized by deformed bones and stunted growth.
85
What is the role of Vitamin E?
A fat soluble vitamin that has antioxidant activity.
86
What is the role of Vitamin K?
A fat soluble vitamin that is a cofactor for an enzyme that modifies glutamate residues on blood clotting proteins. A deficiency results in excessive bleeding.
87
What is the main component of lipid bilayers?
Glycerophospholipids
88
What is the advantage of two-tailed amphipathic lipids in membrane formation?
A two-tailed lipid gives the correct geometry to stack correctly without forming voids.
89
What are integral membrane proteins?
Integral membrane proteins have hydrophobic regions embedded in the lipid bilayer and these proteins require strong detergents to isolate.
90
What are peripheral membrane proteins?
Peripheral membrane proteins associate with the polar head groups of membrane lipids. These proteins may be isolated with mild salt solutions.
91
What is a lipid-linked protein?
Lipid-linked proteins insert a hydrophobic anchor into the membrane.
92
What kind of anchor is this lipid-linked protein using?
A myristoyl group attached to an N-term Gly via an amide linkage
93
What kind of anchor is this lipid-linked protein using?
A palmitoyl group reversibly attached to a Cys side chain via a thioester linkage
94
What kind of anchor is this lipid-linked protein using?
An isoprenoid group linked to a C-term Cys via thioether linkage.
95
What kind of anchor is this lipid-linked protein using?
A GPI group linked to the C-term of the protein
96
What is the fluid mosaic model?
Proposes that lipids and proteins may freely move laterally but cannot flip-flop through the layer by themselves.
97
Are both sides of a membrane the same?
Membranes have a polarity. The inside of a membrane is different, in both lipid and protein composition, from the outside.
98
What are translocases?
Proteins that move membrane lipids from one side of the membrane to the other.
99
Draw the first step of the Chymotrypsin mechanism.
100
Draw the second step of the Chymotrypsin mechanism.
101
Draw the third step of the Chymotrypsin mechanism.
102
Draw the fourth step of the Chymotrypsin mechanism.
103
Draw the fifth step of the Chymotrypsin mechanism.
104
Does sodium have a higher concentration inside or outside of the cell?
Outside
105
Does potassium have a higher concentration inside or outside of the cell?
Inside
106
When does K+ reach equilibrium?
With a high concentration inside the cell (favoring K+ efflux) and a negative membrane potential (favoring K+ influx)
107
What are the steps of the action potential?
1. Stimulus opens Na+ channels in the membrane
2. Influx of Na+ causes depolarization, which triggers the opening of the VGPC.
3. Efflux of K+ restores resting membrane potential.
4. Initial depolarization also triggers opening of additional Na+ channels farther down the axon.
108
What are porins?
Porins are proteins that form an open channel in the membrane of bacteria and certain organelles to allow the passage of small solutes.
109
How does the Potassium channel select only for K+?
K+ channels have a selectivity filter that is too narrow for large ions and too wide for smaller ions such as Na+.
110
What happens when K+ moves into the selectivity filter?
When K+ moves into the filter, it loses favorable interactions with water, but gains favorable interactions with the residues lining the filter.
111
What can a gated channel change in response too?
1. changes in membrane potential
2. changes in pH
3. binding of a specific ligand
4. phosphorylation
5. temperature
6. mechanical pressure
112
What is an aquaporin?
A channel that allows water to pass through, but not H+ because the size of the channel is optimized for a single chain of H2O and a positively charged Arg residue disfavors entry of H3O+.
113
What is an antiporter?
Antiporters move two different substances across the membrane in opposite directions.
114
What kind of transporter is the Na+/K+ ATPase pump? What does it do?
An antiporter that uses the energy of ATP to move 3 Na+ out of the cell and 2 K+ into the cell against their concentration gradients.
115
What is a symporter?
Move two different substances across the membrane in the same direction.
116
What is primary active transport?
The use of ATP to drive transport
117
What does the Na+-glucose transporter do? What kind of transporter is it?
The Na+ glucose transporter uses the energy of Na+ moving down its concentration gradient into the cell to drive glucose import into the cell against its gradient. It is a symporter.
118
What is secondary active transport?
Using the favorable movement of an ion down its gradient to move another substance across the membrane.
119
What is a uniporter?
Uniporters move a single substance across the membrane.
120
What is facilitated diffusion?
Using a protein to bind and move a molecule or ion across the membrane.
121
How does the glucose transporter work?
Glucose binding changes the conformation, so that the transporter opens on the opposite side of the membrane.
122
How does exocytosis work?
1. When an action potential reached the axon terminus, it causes VGCC to open
2. An incr. in Ca2+ triggers the fusion of synaptic vesicles with the plasma membrane and release NT into the synaptic cleft
123
How do SNARE proteins help mediate exocytosis?
The favorable formation of a four-helix coiled-coil pulls the vesicle into the target membrane
124
What is the structure of G-protein coupled receptors?
GPCRS have 7 transmembrane helices with a ligand binding region on the extracellular face and a G protein binding region on the intracellular face.
125
What are the steps of GPCR transmitting the ligand binding signal?
1. Ligand binds
2. Conformation change in GPCR
3. Ga releases GDP and binds GTP
4. Ga-GTP dissociates from the Gby subunits
5. Ga has intrinsic GTPase activity and hydrolyzes GTP back to GDP to turn off
6. Ga-GDP reassociates with the Gby subunits
126
How does the hormone epinephrine initiate the fight or flight response?
Epinephrine is an agonist for a GPCR which activates adenyly cyclase to produce cAMP. cAMP activates PKA which phosphorylates multiple proteins involved in fuel metabolism.
127
How are signaling pathways turned off?
-Phosphatases hydrolyze (turn off) the phosphate group from proteins that have been modified by kinases
-Phosphodiesterases hydrolyze cAMP to turn off PKA
-Ga converts GTP to GDP
-Arrestin binds the GPCR and prevents further activation
128
How do receptor tyrosine kinases transmit a ligand binding signal?
Ligand binding to the extracellular domain of RTK induces a conformation change so that the cytosolic domain of one monomer moves close enough to the cytosolic domain of other monomer to phosphorylate Tyr residues and turn the receptor on. RTK activation induces a kinase cascade.
129
How do Ras proteins mediate growth factor signaling?
1. Ras is a G-protein that is activated by adapter proteins once RTK is auto-phosphoylated with a growth factor ligand bound.
2. Ras exchanges GDP for GTP and initiates a kinase cascade that regulates the expression of genes that are important for cell growth and division.
130
Are cell surface receptors required for all hormones?
No, many lipid hormones (ie cortisol) move inside the cell to activate intracellular receptors.
131
How does the body initiate the pain and inflammation response?
1. Phospholipases cleave a 20-carbon fatty acid (arachidonated) from the membrane
2. Cyclooxygenase enzymes the convert the arachidonate to prostaglandins that promote a pain and inflammatio response
132
How do certain drugs like Aspirin and Ibuprofen limit pain and inflammation?
Aspirin and ibuprofen inhibit both COX-1 and COX-2
133
What is the anomeric carbon?
The anomeric carbon has 2 bonds with an electronegative element such as oxygen or nitrogen. The anomeric carbon is assigned the lowest possible number.
134
What are epimers?
Differ in stereochemistry of a single carbon center
135
How do you distinguish an L from a D enantiomer?
A D-sugar has the -OH group to the right of the furthest carbon
An L-Sugar has the -OH group to the left of the furthest carbon
136
What is an a-anomer in a D-sugar?
Anomeric hydroxyl below the ring
137
What is a b-anomer in a D-sugar?
Anomeric hydroxyl above the ring
138
What is an a-anomer in a L-sugar?
Anomeric hydroxyl above the ring
139
What is an b-anomer in a L-sugar?
Anomeric hydroxyl below the ring
140
How do you determine Vmax from a Lineweaver-Burk plot?
Vmax = 1 / y-int
141
How do you determine Km from a Lineweaver-Burk plot?
Km = slope x Vmax
142
What is an inhibitor that covalently attaches to the active site of an enzyme?
An irreversible inhibitor
143
Which class of protein associates with the membrane through noncovalent binding of either the polar head groups of lipids or the water-soluable domains of transmembrane proteins?
Peripheral membrane proteins
144
The ______ side of the plasma membrane frequently has glycosylated ______?
Extracellular; lipids & proteins
145
How does a noncompetitive inhibitor affect the Lineweaver-Burk plot?
Meets at same X-intercept, but with steeper slope
146
How does an uncompetitive inhibitor affect the Lineweaver-Burk plot?
Same slope, but increase y-int.
