Exam 1 Flashcards
Lec 1-11 (141 cards)
1
Q
Max number of hydrogen bonds per water molecule
A
4 bonds
2
Q
All of the amino acids are chiral except
a. Glycine
b. Alanine
c. Leucine
d. Tryptophan
A
a. Glycine
3
Q
Which amino acids are negatively charged at neutral pH?
A
Glutamate and aspartate
4
Q
Phosphoric acid has a pKa of 2.1. At what pH will 75% of phosphoric acid be in the conjugate base form? (HOW DO YOU FIND THIS?)
Math hints: log3=0.5 log.33=-0.5
A
The concentration of the conjugate base [A-] and weak acid [HA] in the Henderson-Hasselbach equation were flipped. When plugged into the equation, it would yield pH = 2.1 + log[.25/.75], => pH = 2.1 + log(.33) = 2.1 + (-.5) = 1.6 as the final pH answer
5
Q
Which participates in acid-base chemistry and is located in the active site of the enzyme chymotrypsin?
A
Histidine
6
Q
Why are oxyanion holes important?
A
They are commonly found in many enzyme structures. They are crucial for the stabilization of high energy oxyanion intermediates or transition states through hydrogen bonding. Typical functionalities found in enzyme oxyanion holes or chemically designed oxyanion-hole mimics are N-H and O-H groups.
7
Q
What is feedback inhibition?
A
The process by which a product of an enzymatic pathway inhibits its own synthesis by negatively regulating an enzyme in the synthesis pathway
8
Q
A series of enzymes perform a multi-step reaction pathway to produce the nucleotide cytidine triphosphate (CTP). CTP allosterically inhibits the first enzyme in the pathway. What is this an example of?
A
Feedback inhibition
9
Q
How many ionizable groups are in the following peptide? Leucine-Valine-Aspartate-Tryptophan-Lysine
A
Any peptide must have at least two ionizable groups, Aspartate and leucine both contribute ionizable groups in their side chains. (3 ionizable groups)
10
Q
What is the minimum amount of ionizable groups a peptide can have?
A
2
11
Q
What are the two ends of a peptide?
A
Amino end (NH3+) and carboxyl end (COO-)
12
Q
Why do valine and leucine not have an ionizable side chain?
A
Their side chains are non-polar.
13
Q
What is special about the side chains of aspartate and lysine?
A
They both contribute ionizable grouos in their side chains.
Aspartate contains a side chain which can be negatively charged when the carboxyl group loses its protein.
Lysine contains a side chain which can be positively charged when the amine group is fully protonated.
14
Q
Why is tryptophan unable to ionize?
A
Its side chain consists of only fused aromatic rings
15
Q
At pH 7, glycine will have an overall charge of +1. Why is this false?
A
The amino group of glycine has a pKa of about 9 and the carboxyl group has a pKa of ~2. At pH 7, the amino group will be protonated and have a positive charge, but the carboxylic group will be deprotonated and have a negative charge. These cancel each other out and make a neutral charge. Glycine has no ionizable side chains, so you only need to be concerned with the two terminal end charges.
16
Q
Energetically favorable reactions are exergonic and can be determined by (delta)G values that are….?
A. Positive
B. Negative
A
B. Negative
17
Q
What is the central dogma of biology?
A
DNA->RNA->Protein
18
Q
Between DNA, RNA, and protein, which one is a carrier of genetic information and can have catalytic properties?
A
RNA
19
Q
How to find pH from [H+] concentrations:
A
pH=-log[H+]
H+ concentration is measured in mol/L
20
Q
Which type of amino acids are most likely found buried in the interior of a protein?
A
Hydrophobic amino acids will most likely be in the interior (e.g. nonpolar amino acids like alanine,
leucine, etc. or aromatic amino acids like phenylalanine)
21
Q
Which type of amino acids are most likely found on the exterior of a protein and exposed to the cytosol?
A
Hydrophilic amino acids will most likely
be on the exterior of proteins (e.g. polar amino acids – serine, threonine, or charged amino acids –
lysine, glutamate, etc.)
22
Q
What is the predominant charge state of glycine dissolved in water at pH 9.8? pK1 (of COOH) =2.34 pK2 (NH3+) =9.60
A
Negative. It will be negative because the pH is above the pKa for both the carboxylic acid group and
the amino group. The carboxylic acid group will be essentially completely deprotonated, and the
majority of the amino groups (more than 50%) will be deprotonated
23
Q
What value indicates ionizable side chains?
A
pKR value
24
Q
What is the strongest angle of hydrogen bonds?
A
180 degrees
25
Which technique separates proteins by size?
gel filtration chromography
26
What is used for protein analysis, but not purification?
SDS-PAGE
27
Which amino acid absorbs UV light?
Tryptophan
28
Which technique is used to sequence a protein?
Edman Degradation
29
How many hydrogen bonds will be found in an alpha helix that is 18 amino acids long?
14
30
Are beta sheets flat?
No, they are pleated
31
Which contributes the most to protein stability?
Hydrophobic effect
32
Does myoglobin have a quaternary structure?
No, but it does have a tertiary structure
33
What is stabilized by oxygen binding?
R-State
34
Is the T-state or R-state more stable?
The R-state is more stable at a lower pH. The T-state has a lower affinity for oxygen than the R-state.
35
What amino acid(s) in hemoglobin is(are) carbamylated at low pH?
The first amino acid of each subunit
36
What describes KM?
concentration of substrate needed to get to 1/2 Vmax
37
Do enzymes raise activation energy?
No
38
What is Le Chatelier's Principle?
If a dynamic equilibrium is disturbed by changing the conditions, the position of the equilibrium will shift in order to counteract the change and reestablish equilibrium.
39
How do you find the specific activity of an enzyme?
Activity ÷ total protein (mg) = specific activity
40
You think you have purified a protein in the laboratory. What would be a good way to check to see if the protein is indeed pure and not a mixture of proteins?
Stain an SDS-PAGE gel. This will be the cheapest and most common method. If you have to check for
the presence of a small amount of impurities, you may want to perform mass spectrometry. Isoelectric
focusing could also show purity.
41
How does the presence of a sodium dodecyl sulfate (SDS) allow all proteins to migrate towards the
positive electrode during SDS-PAGE? Explain.
Sodium Dodecyl Sulfate (SDS) contains a charged sulfate with a hydrophobic (12- carbon) tail. The
hydrophobic tail helps denature protein and make proteins rod-shaped (instead of globular). This will
allow proteins to be coated with SDS. The negative charged sulfate on each SDS molecule will make
each protein negatively charged and thus migrate towards the positive electrode and be separated by
size
42
The proteins FosB, Hemoglobin, and Myosin are added to an SDS-PAGE gel and run for 1 hour at 200 volts. The gel is stained with the dye, Coomassie blue, to visualize the proteins. Draw the order in which the proteins would travel through the gel (negative electrode at the top, positive electrode at the bottom). How many bands would be seen on the gel for hemoglobin?
Myosin (200 kDa): Top of gel
FosB (45 kDa)
Hemoglobin (16 kDa): Bottom of gel; 1 band for Hb as all monomers are same size
43
What does SDS-PAGE require?
SDS-PAGE requires that proteins are denatured and broken into their individual
subunits
44
What does protein purification require?
During a purification, you usually want your proteins to maintain their native conformation and not
unfold.
45
What kind of post-translational modification is found in keratin, the alpha-helical protein found
in hair, skin, and nails?
Disulfide bonds
46
What is the major force that stabilizes protein folding?
Hydrophobic effect. Think of
the dispersion of lipids as a primary structure of non-polar amino acids and clustering of lipids as the secondary structure of non-polar amino acids
folding into an alpha helix.
47
Does the release of ordered water molecules result in a decrease or increase in the entropy of water?
Entropy increases as a result of fewer ordered water molecules around the protein.
48
What do parallel and antiparallel mean?
Parallel and antiparallel indicate the direction that the strands are orientated in relation to one another. In a parallel beta sheet the strands are in the same direction; in an antiparallel beta sheet the strands run in the opposite direction of one another.
49
What type of bonds are formed between the beta sheet strands?
Hydrogen bonds
50
What is the equation for binding a ligand to a protein and what do the variables stand for?
(Theta) = [L] / [L] + Kd
Theta = the fraction of protein bound to ligand
Kd = dissociation constant (inverse of the association constant, a measure of how tightly the protein binds to the ligand)
51
What is the hydrophobic effect due to?
The hydrophobic effect is due to a favorable increase in the entropy of water when it is
released from non-polar molecules.
52
What is a ligand?
a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein.
53
How many CO2 molecules can hemoglobin bind to in its T-state?
4 CO2
54
What is carbamylation?
Binding of CO2 (Stabilizes the T-state)
55
How is the binding of H+ and CO2 by Hb related to the binding of oxygen?
the binding of H+ and CO2 by hemoglobin (Hb) is inversely related to the binding of oxygen by Hb.
56
Explain how the protein changes from R to T states in the presence of oxygen and carbon
dioxide. (Hemoglobin)
More R state is found when oxygen is bound while more T state is found when hemoglobin is
carbamylated (CO2 is bound)
57
Explain how H+ and CO2 bind to hemoglobin.
H+ binds to certain amino acids and CO2 binds as a carbamate group to the amino-terminal
amino acid of each globin subunit via a carbamylation reaction. When the concentration of
CO2 is high (tissues), some CO2 binds to Hb and the affinity for O 2 decreases, causing its release.
58
What is the role of 2,3-bisphosphoglycerate (BPG) in hemoglobin function? Where does BPG bind hemoglobin? Does it bind both states (R and T) of hemoglobin?
BPG binds in the cavity between the four subunits of hemoglobin to decrease the affinity of hemoglobin for oxygen. R-state hemoglobin doesn’t bind BPG and cavity is closed.
59
One physiological response to high altitude is the production of more BPG. How does this help hemoglobin deliver more oxygen to the tissues?
It decreases hemoglobin's affinity for oxygen and allows the hemoglobin to deliver about the same amount from the lungs to the tissues.
60
In a typical enzyme-catalyzed reaction, which rate constant is typically ignored at the beginning of a reaction?
K2
61
Are all enzymes proteins? If not, what other type of molecule can act as an enzyme?
No; certain RNA molecules, called ribozymes (and discussed in more detail during the Genetic Information Transfer unit), can catalyze their own cleavage.
62
What is the definition of kcat?
It is the number of substrate molecules converted to product in a given unit of time on a single enzyme molecule when the enzyme is saturated with substrate. It describes the limiting rate (or rate-limiting step) for any enzyme-catalyzed
reaction at saturation
63
Describe how to calculate the catalytic efficiency of enzymes using kcat and Km?
Catalytic efficiency = kcat/Km
64
What are the 10 events (in order) that occur during the chymotrypsin?
1. Substrate binds to the hydrophobic pocket. 2. Histidine acts as a general base to activate a serine OH group. 3. A serine alkoxide ion attacks a carbonyl carbon of the substrate, forming a covalent acyl bond between enzyme and substrate. 4. A tetrahedral transition state involving an oxyanion is stabilized by the oxyanion hole. 5. Histidine acts as a general acid to protonate an amide nitrogen. The peptide
bond is broken and the first product dissociates. 6. Water enters the active site. 7. Histidine acts a general base to convert water into a hydroxide ion. 8. A hydroxide ion attacks the acyl bond between substrate and enzyme. 9. A tetrahedral transition state involving an oxyanion is stabilized by the
oxyanion hole. 10. Histidine acts as a general acid to protonate the serine oxygen group, breaking the acyl bond between enzyme and substrate. The second product dissociates.
65
The serine protease enzyme trypsin has a mechanism that is almost identical to chymotrypsin. Trypsin cleaves directly after arginine or lysine amino acids. What type of amino acids are found in the binding site of trypsin? (Hint: what is the charge of arginine and lysine? What amino acids interact with arginine and lysine?)
Trypsin likely has aspartate and/or glutamate amino acids (which have negatively charged side-chains or R-groups) where the hydrophobic pocket is located in chymotrypsin.
66
For the Lineweaver-Burke plots, indicate what the X and Y intercepts represent.
X intercept = -1/KM
Y intercept = 1/Vmax
67
How are the KM and the Vmax affected in a competitive plot?
Vmax stays the same while KM increases. It takes more substrate to 'outcompete’ the inhibitor for the active site. The same Vmax will be achieved but you will need more substrate to achieve it.
68
How are the KM and Vmax affected in an uncompetitive plot?
Both Vmax and KM will decrease. If KM goes down, it is reasonable to think that the enzyme is more efficient. How I approach uncompetitive inhibitors with students is that I tell them that because Vmax has decreased, you “have a new but unimproved Vmax , and to achieve that new Vmax you actually need less substrate"
69
How are the KM and Vmax affected in an mixed plot?
Vmax will decrease while KM will increase
70
Why does Vmax have to go down for both uncompetitive and mixed inhibitors?
because they bind to a region other than the active site. These inhibitors cannot be outcompeted
71
Does the inhibitor is binding to the enzyme (E) or the enzyme-substrate complex (ES) for competitive, uncompetitive, and mixed inhibitors?
Competitive: binds to E
Uncompetitive: binds to ES
Mixed: binds to both E and ES
72
An unknown inhibitor X of an enzyme is tested to see if it is competitive, uncompetitive, or mixed.
What type of inhibitor is X if V max is the same in the presence or absence of inhibitor X? What type
of inhibitor could X be if V max is lower in the presence of inhibitor X?
When V max is the same, it is competitive,
When Vmax decreases, it can be either uncompetitive or mixed
73
Which molecule is not found in biological membranes?
a. triglycerol
b. phosphatidylcholine
c. ceramide
a. triglycerol
74
Which lipid will have the highest melting point?
a. 13:0 b. 15:0 c. 17:1 d. 17:2
b. 15:0
Longer carbon chain + higher number of cis double bonds = higher melting point
75
How many fatty acids attached to ...
a. triglycerol
b. phosphatidylcholine (a glycerophospholipid)
c. ceramide (a sphingolipid)
a. 3
b. 2
c. 1
76
What kind of lipid is used to make prostaglandins?
Glycerophospholipids
77
Which fatty acid is cleaved from the lipid to make a prostaglandin?
Lipases cleave arachidonic acid from a glycerophospholipid
78
What biological responses are controlled by prostaglandins?
Variety of functions: 1. contraction of smooth muscle of the uterus during labor and menstruation, 2. blood flow to certain organs, 3. the wake-sleep cycle, and most notably 4. they produce fever and cause inflammation and pain.
79
Which vitamin can cholesterol be converted to?
Vitamin D
80
What is the steroid nucleus, alkyl tail and polar head group of cholesterol?
The steroid nucleus is the four fused rings. The
alkyl tail is on the right and the polar head is at the bottom left (the OH group). Hydroxyl group is in the cytoplasm or outside and the hydrophobic tail will be in the lipid bilayer
81
What is the function of this vitamin once it is converted into a hormone?
Regulate calcium uptake in the bone
82
How do bacterial cells maintain a balance in the fluidity of their membranes?
They vary the lengths and degrees of unsaturation of the fatty acids in the glycerophospholipids.
83
Which one, when present in a cell membrane, increases membrane fluidity?
Unsaturated fatty acids within the phospholipid tail regions increase membrane fluidity because they cannot pack as tightly together as saturated fatty acids within the phospholipid tail region. The double bonds within the unsaturated fatty acids of
the phospholipid cause a kink (see above) in the hydrocarbon chain that prevents them from assembling tightly together in the membrane
84
Which type of phospholipid (saturated or unsaturated) is present in the cellular membrane at higher concentrations when cells are grown at low temperatures?
Unsaturated fatty acids within the phospholipid tail region will be present in relatively
higher amounts because they are necessary to increase membrane fluidity at low
temperatures. Think about putting butter (full of saturated fat) in the freezer and how
hard it would become. If cellular membranes contained phospholipid bilayers with a
higher concentration of saturated fatty acids then the membrane would become
nearly solid
85
Which of the following treatments could be used to remove an integral membrane protein from a membrane?
A. High salt treatment
B. Change in pH
C. Addition of detergents
C. Addition of detergents
86
What kind of amino acids are found in the transmembrane region of a
transmembrane spanning alpha helix?
Nonpolar amino acids
87
How to calculate the [OH-] concentration from the pH?
Find pOH using: pH + pOH = 14
Once you know the pOH, you can find the [OH-] using the following formula:
[OH−]=10^(−pOH) M
example: Find [OH-] for a solution with a pH of 3.5.
pOH=14–3.5=10.5
[OH−] = 10^(−10.5)≈3.16×10^(−11) M
88
What does a hydropathy plot indicate? What can it predict?
Reveals segments of protein sequence that are hydrophobic. Can predict membrane proteins bases on hydrophobicity profile.
89
Give an example of simple diffusion across a membrane that is important for hemoglobin function.
Diffusion of oxygen across a plasma membrane (lipid bilayer)
90
What is the difference between simple and facilitated diffusion?
Simple diffusion is directly across a membrane (phospholipid bilayer)
Facilitated diffusion requires the participation of protein carrier to allow polar molecules to cross the membrane.
For example, glucose requires a glucose transport protein embedded within the membrane lipid bilayer for glucose to enter and exit a cell.
91
What is the difference between passive and active transport? Which one transports against an existing gradient?
Passive transport is along (or down) a gradient (high to low) and energy is not required.
Active transport if against (or up) a gradient (low to high) and energy is required (directly [primary] or indirectly [secondary]), usually in the form of
the ATP hydrolysis.
92
What kind of transporter is the Na+/K+ pump?
Primary active transport. Transport of Na + out of the cell and K + into the cell against their concentration gradients requires ATP hydrolysis.
93
At what pH would a 1 L solution of 1 M histidine (side chain pKa = 6) have 80% of its side chains in the protonated form?
5.4
94
Calculate the pI of glutamate given its pKa values of 2.2, 9.2, and 4.2 (side chain).
3.2
95
What does the SARS coronavirus-2 do to infect a host cell?
SARS coronavirus-2 must fuse its lipid bilayer with the host cell bilayer and this process depends on the viral
spike protein binding to receptors on the host cell surface.
96
What is an example of Post-translational modification?
The activity of enzyme A is regulated by enzyme B, which covalently attaches a phosphate group to enzyme A.
97
Which method could be used to determine the primary structure or sequence of a protein?
Tandem mass spectrometry
98
Which amino acid is capable of occupying more regions of the Ramachandran Plot than any other amino acid?
Glycine
99
How is vitamin D made? (When it is not derived from cholesterol)
Made in the skin upon exposure to UV light.
100
What is cholesterol's steroid nucleus used for?
Cholesterol's steroid nucleus that is used to synthesize hormones
101
Where is cholesterol found?
found in the plasma membrane of animal cells because it has a polar head group
102
What type of fatty acids can glycerophospholipids contain?
Glycerophospholipids can contain either saturated or unsaturated fatty acids.
103
Which type of lipid is an immunogenic determinant in the blood
Sphingolipids
104
What are triacylglycerols used for?
Energy storage
105
Which fatty acid has a high melting point?
Stearic acid (18:0)
106
How are allosteric enzymes' initial velocity and [S] plots related?
Their initial velocity vs. [S] plots are sigmoidal
107
When chymotrypsin catalyzes the cleavage of a single peptide bond, which step occurs twice?
A tetrahedral transition state with an oxyanion becomes stabilized by the oxyanion hole
108
In the chymotrypsin mechanism, what does the serine oxygen form?
A covalent bond to the substrate carbonyl carbon
109
In the chymotrypsin mechanism, why does the histidine act as a general acid?
To donate a proton to an amide nitrogen and serine oxygen
110
What are enzyme activities dependent upon?
Enzyme activities are dependent upon pH and temperature
111
What assumptions are made in the Michaelis-
Menten equation?
The rate of k-2 is negligible, and the concentration of the enzyme-substrate complex remains constant during the experiment
112
How does fetal and adult hemoglobin's bonding affinity to hemoglobin differ?
BPG binds with lower affinity to fetal hemoglobin than to adult hemoglobin
113
What are 4 characteristics of myoglobin?
1. It has an oxygen binding curve that is hyperbolic.
2. It binds heme, which consists of a porphyrin ring and an iron atom
3. The iron atom in the heme ring is in the +2 state (Fe2+)
4. It is an oxygen storage protein, but not a good transporter
114
What is the difference between hemoglobin and myoglobin?
Hemoglobin is a heterotetrameric oxygen transport protein found in red blood cells (erythrocytes), whereas myoglobin is a monomeric protein found mainly in muscle tissue where it serves as an intracellular storage site for oxygen
115
Which method could be used to separate a mixture of proteins by size?
SDS polyacrylamide gel electrophoresis
116
How many hydrogen bonds would be found in a 100 amino acid alpha helix?
96
117
The folding of a globular, soluble protein is thermodynamically favorable due to:
The hydrophobic effect
118
What does the peptide bond hold between the carbonyl carbon and the amide nitrogen?
The peptide bond has partial double bond character between the carbonyl carbon and the
amide nitrogen
119
What are important buffers in blood?
Bicarbonate, phosphate
120
How is the pKa related to the pH?
The pKa is the pH where there are equal amounts of conjugate acid and conjugate base
121
How is the pI related to the pH?
The pI is the pH where the net charge is equal to 0
122
Do disulfide bonds happen pre or post translationally?
Disulfide bonds are a type of post-translational modification
123
How do alpha helices' number of amino acids compare to the number of H bonds?
Alpha helices have an n, n+4 hydrogen bonding pattern
124
Which amino acids are likely to be found on the inside of a protein structure?
The nonpolar (hydrophobic) side chains in a protein—belonging to such amino acids as phenylalanine, leucine, valine, and tryptophan—tend to cluster in the interior of the molecule
125
What is a post-translational modification found in collagen?
Hydroxyproline is a post-translational modification found in collagen.
126
What is the most abundant protein found in humans?
Collagen
127
What is a fibrous protein found in hair and skin?
Keratin
128
What are two characteristics of fibrous proteins?
Fibrous proteins are
1. highly extended with
2. repeating helical or beta sheet structure.
129
How many oxygen molecules can myoglobin bind to at once?
Myoglobin can only bind to 1 oxygen molecule at a time
130
What does heme consist of?
Heme consists of a porphyrin ring bound to a central iron atom
131
What does the T state of hemoglobin do?
The T state of hemoglobin binds CO2 and hydrogen ions
132
What are 4 true things about enzymes?
1. Enzymes work by lowering the activation energy of a reaction.
2. Some enzymes are limited by the rate of diffusion.
3. Enzymes bind more tightly to their transition states than to either substrate or products.
4. Enzymes can be regulated by allosteric modulators.
133
What does histidine do in the chymotrypsin mechanism?
In the chymotrypsin mechanism, histidine acts as a general base to:
A. Remove a proton from a serine hydroxyl group and a water molecule
134
E. coli cells were grown at different temperatures. At which temperature (O C) do the cells produce membranes with the highest ratio of unsaturated/ saturated fatty acids?
5 degrees C
135
What are two structural lipids found in membranes?
1. Sphingolipids
2. Glycerophospholipids
136
What are prostaglandins?
Prostaglandins are signaling molecules derived from arachidonic acid
137
Which method would denature (unfold) a protein while leaving the primary structure intact?
SDS polyacrylamide gel electrophoresis
138
What kind of chemical reaction forms a peptide bond?
Condensation
139
Which amino acid does not have a chiral alpha carbon center?
Glycine
140
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