Final Exam Flashcards
1
Q
Equation for K of Water
A
K = [H+][OH-]/[H2O]
2
Q
pH =
A
pH = -log[H+]
3
Q
Equation for Ka
A
Ka = K[H2O] = [H+][A-]/[HA]
4
Q
pH at titration midpoint =
A
pK
5
Q
At titration midpoint, [HA] = ?
A
[A-]
6
Q
Carbonic anhydrase equation
A
CO2 + H2O <–> H2CO3 <–>HCO3- + H+
7
Q
Purines
A
Adenine & guanine
8
Q
Pyrimidines
A
Cytosine, uracil, & thymine
9
Q
How does deoxyribose differ from ribose?
A
Deoxyribose lacks the 2’ -OH group
10
Q
What is the effect of ribose’s 2’ -OH group on RNA?
A
Decreases stability
Discourages double helix formation
Allows RNA to undergo chemical rxns
11
Q
Nucleoside
A
A nitrogenous base bound to a sugar
12
Q
Phosphodiester bonds are formed via ________ reactions.
A
Condensation
13
Q
How many hydrogen bonds does A-T form?
A
2
14
Q
How many hydrogen bonds does G-C form?
A
3
15
Q
The DNA double helix is ______-handed.
A
right-handed
16
Q
How do bacteria use restriction endonucleases?
A
They methylate their own DNA, then purge bacteriophages by having restriction endonucleases cleave any unmethylated DNA.
17
Q
Hydrophobic AAs
A
Cys, Leu, Ala, Met, Ile, Val (CLAMIV)
18
Q
Aromatic AAs
A
Tyr, Phe, Try (TPT)
19
Q
Basic AAs
A
His, Arg, Lys (HAL)
20
Q
Acidic AAs
A
Asp, Glu (AG)
21
Q
Neutral AAs
A
Thr, Asn, Gln, Ser (TAGS)
22
Q
What are unique properties of Pro?
A
Conformationally restricted
No NH
23
Q
What are unique properties of Gly?
A
Smallest
Achiral
Conformationally most free
24
Q
AAS are ______, with ______-handedness being more common.
A
Chiral, with left-handedness being more common
25
Peptide bond formation is a _________ reaction
condensation
26
Is the cis or trans form preferred in peptide bonds?
Trans
27
Phi describes the __ bond
CO bond
28
Psi describes the __ bond
CN
29
Torsion angles are ____ when the polypeptide backbone is fully extended.
180*
30
Secondary structure
Encompasses backbone, but not side chains.
31
Tertiary Structure
Encompasses the 3D shape of the polypeptide
32
The alpha helix is _____-handed.
right-handed
33
Where do side chains project in the alpha helix?
Outwards and downwards from the helix
34
Where does H bonding occur in beta sheets?
Between the peptide strands
35
How many peptide strands are contained within a beta sheet?
2-22 (average of 6)
36
How many residues per strand in a beta sheet?
Up to 15 (average 6)
37
Supersecondary structures
Groupings of secondary structural elements.
38
Beta-Alpha-Beta Motif
Alpha helix connects two parallel beta sheets
39
Beta hairpin motif
Antiparallel beta strands connected by tight reverse turns
40
Alpha-Alpha motif
Two alpha helices, connected and inclined towards one another (side chains can intermesh)
41
Greek Key motif
A beta hairpin is folded over to form a 4-stranded antiparallel beta sheet
42
Structure of collagen
Right-handed triple helix
43
Structure of keratin
2 alpha helices coiled around one another (coiled coil)
44
Structure of myoglobin
8 alpha helices arranged into a globular protein
45
Where is myoglobin's heme complex manufactured?
The mitochondria
46
p50 of myoglobin
2.8 Torr (fully saturated at physiological pO2)
47
Myoglobin has a ________ binding curve.
Hyperbolic
48
What role does His64 play in myoglobin?
It sterically blocks the linear arrangement, preventing CO from binding
49
Structure of hemoglobin
Alpha-beta tetramer (dimer of dimers)
50
p50 of hemoglobin
26 Torr (10x that of myoglobin)
51
Which protein has T and R states?
Hemoglobin
52
T state
"Tense" state, low O2 affinity (better for release of O2 in the muscles)
53
R state
"Relaxed" state, high O2 affinity (better for O2 pickup in the lungs)
54
The Bohr effect
Hemoglobin binds more O2 at a higher pH
55
Hemoglobin has a _______ binding curve.
sigmoidal
56
Function of molecular chaperones
Lift folding polypeptides out of false minima in the folding funnel, prevent misfolding and aggregation
57
Which protein does BPG interact with?
Hemoglobin
58
How does BPG impact hemoglobin?
Stabilizes the T state, promoting oxygen release
59
What is the relationship between fetal hemoglobin and BPG?
Fetal hemoglobin has a low affinity for BPG
60
What molecule is impacted by altitude adaptation?
BPG - increased BPG at altitude helps with release of O2 in the body
61
What is modified in the hemoglobin of an SCA patient?
A residue is converted to a hydrophobic valine
62
How does hydroxyurea impact the body?
It increases the quantity of cells containing fetal hemoglobin
63
Fatty acids
Carboxylic acids with long-chain hydrocarbon side groups.
64
__ and __ are the two most common fatty acid types in higher plants and animals.
C16 & C18
65
Where does the first double bond of an unsaturated fatty acid occur?
Between C9 and C10
66
Do bacteria have polyunsaturated fatty acids?
No
67
Triglycerides
Fatty acid triesters of glycerol.
68
What suffix is used for fatty acids in a triglyceride?
-oyl
69
Phospholipids
Molecules of glycerol-3-phosphate whose C1 and C2 have been esterified with fatty acids.
70
Simplest form of phospholipid
Phosphatidic acids
71
C1 of a phospholipid is typically __________.
saturated
72
C2 of a phospholipid is typically __________.
Unsaturated
73
What do phospholipases do?
They excise the C2 fatty acid residue of phospholipids, leaving a lysophospholipid.
74
Sphingolipids
Fatty acid derivatives of sphingosines; major membrane components.
75
What is notable about the structure of sphingosine?
Its alkene is trans
76
Ceramides
N-acyl fatty acid derivatives of sphingosines. A sphingosine with an attached fatty acid.
77
What is unique about the properties of cholesterol?
Weakly amphiphilic
Greater rigidity than other membrane lipids
78
Do plants have cholesterol?
They have little cholesterol, and synthesize other sterols.
79
Do yeast and fungi have cholesterol?
No, they synthesize their own unique sterols.
80
Do prokaryotes contain cholesterol?
Very rarely
81
How many residues in the hydrophobic regions of integral membrane proteins?
18-23
82
Which molecules carry out passive-mediated transport?
Ionophores, porins, ion channels, aquaporins, & transport proteins
83
Valinomycin
A carrier ionophore that transports K across the membrane.
84
What coordinates K within valinomycin?
Carbonyl groups of its six Val residues (can only coordinate K)
85
What makes valinomycin lipid-soluble?
Projecting methyl and isopropyl side chains
86
KcsA K+ Channel
A channel ionophore that moves K and water.
87
Which transport component is known for its selectivity filter?
The KcsA K+ channel
88
What is a prominent example of a voltage-gated channel? What kind of transport does it facilitate?
The Kv channel; voltage-gated channels facilitate passive transport
89
GLUT1
A uniport that moves glucose across the membrane.
90
SGLT
A symport that moves glucose and Na+ simultaneously.
91
What does the Na+-K+ ATPase move across the membrane?
3 Na+ ions out of the cell, 2 K+ into the cell
92
E1 of Na-K ATPase
High Na affinity, dephosphorylated
93
E2 of Na-K ATPase
Low Na affinity, phosphorylated
94
What direction do Na and glucose move in the SGLT transporter?
Na+ moves with its gradient
Glucose moves against its gradient
95
Why are SGL2 inhibitors used to treat diabetes?
They prevent glucose uptake in the kidneys.
96
Process of glucose-induced signal transduction in pancreatic beta cell insulin secretion
* Glucose enters the cell, and is metabolized to ATP.
* High intracellular ATP triggers closing of ATP-dependent K channels.
*Buildup of K causes depolarization, opening up Ca2+ channels.
*Rise in intracellular Ca2+ triggers release of secretory vesicles & insulin.
97
How do sulfonylureas work?
They bind to ATP-dependent K channels and inhibit them, triggering a rise in intracellular Ca2+ and subsequent insulin release.
98
What does the cardiac ATPase/Ca2+ exchanger do?
It swaps Na+ for Ca2+, getting rid of extra Ca2+ in the cell.
99
How does digoxin work?
It inhibits the Na-K ATPase, which causes the NCX to not have enough energy to swap Na and Ca2+. The rise in intracellular Ca2+ improves cardiac function.
100
What do aldehydes and ketones react with to form hemiacetals and hemiketals?
Alcohols
101
D sugars have the same absolute configuration as _________.
D-glyceraldehyde
102
The ________ points to the right in D sugars.
C5 -OH
103
Alpha anomer
The anomeric -OH is on the opposite side of the ring as the CH2OH
104
Beta anomer
The anomeric -OH is on the same side of the ring as the CH2OH
105
Mutarotation
Carbohydrate anomers freely interconvert in aqueous solution.
106
Formation of a glycosidic bond is a ________ reaction.
Condensation
107
Lactose
Galactose + Glucose
108
Sucrose
Glucose + Fructose
109
Structure of cellulose
Up to 15,000 glucose residues connected via B(1-->4) bonds
110
Amylose structure
A linear polymer of several thousand glucose residues connected via A(1--->4) bonds
111
_________ is an isomer of cellulose
Amylose
112
Amylopectin structure
A(1-->4) linked glucose residues with A(1-->6) branch points every 24-30 residues
113
Glycogen structure
Resembles a more branched form of amylopectin (branching every 8-10 residues)
114
What does glycogen phosphorylase do?
Cleaves A(1-->4) bonds sequentially from nonreducing ends
115
What does glycogen debranching enzyme do?
Cleaves A(1-->6) bonds
116
Heparin activates ________, which inhibits __________.
Activates anti-thrombin, which inhibits thrombin.
117
N-linked glycosylation
Oligosaccharides are linked to Asn (Asn-X-Ser or Asn-X-Thr)
118
Where does N-linked glycosylation occur?
Endoplasmic reticulum
119
O-Linked Glycosylation
Oligosaccharides are attached to Ser or Thr
120
Which form of glycosylation occurs cotranslationally?
N-linked glycosylation
121
Where does O-linked glycosylation occur?
Golgi
122
What is the size range of O-linked glycosylation additives?
1 galactose up to 1,000 disaccharides
123
Which levels of protein structure dictate glycosylation sites?
Secondary and tertiary
124
Proteoglycan structure
"Bristles" noncovalently attached to a hyaluronate backbone. A highly hydrated gel forms within the bristles.
125
Which part of the body notably contains proteoglycans?
Cartilage (collagen fibrils are filled in with proteoglycans)
126
Hyaluronate is a prominent _____________.
Glycosaminoglycan
127
Where in the body is hyaluronate found?
Synovial fluid, vitreous humor, connective tissue
128
Which molecule fulfills the function of hyaluronate in plants?
Pectin
129
What are the 5 mechanisms of enzyme catalysis?
Acid-base catalysis
Covalent catalysis
Metal ion cofactors
Orientation and proximity effects
Preferential binding of transition state
130
Acid catalysis
Proton transfer from an acid lowers the free energy of a reaction's transition state.
131
Covalent catalysis
Transient formation of a catalyst-substrate covalent bond.
132
During covalent catalysis, the enzyme acts as a _________, and the substrate as a _________.
The enzyme acts as a nucleophile, and the substrate as an electrophile.
133
What are the three ways that metal ion cofactors catalyze reactions?
- Bind to substrates and orient them
- Mediate redox reactions (by changing their own oxidation states)
- Electrostatically stabilizing or shielding negative charges
134
What metal ion does carbonic anhydrase use in mediating blood pH?
Zn2+
135
What are the four ways that proximity and orientation effects catalyze reactions?
- Bring substrates in contact with catalytic groups
- Bind substrate at proper orientations
- Charged groups stabilize TSs
- Freeze out relative translational and rotational movement
136
The Michaelis-Menten equation describes a ___________.
rectangular hyperbola
137
Vmax
The maximum reaction velocity
138
Km
The substrate concentration when the reaction velocity is half of its maximum.
139
Lower Km indicates _____ substrate affinity.
Lower Km = Higher affinity
140
What enzyme is associated with competitive inhibition?
Succinate dehydrogenase/fumarate
141
How are Km and Vmax impacted by competitive inhibition?
Km increases, Vmax stays constant
142
How are Km and Vmax impacted by noncompetitive inhibition?
Km stays constant, Vmax decreases
143
What is the rate-determining step of glycolysis?
Phosphorylation of F6P to F1,6BP by phosphofructose kinase
144
What are the two high-energy intermediates seen in glycolysis?
2,3-BPG and PEP
145
How does ATP impact PFK?
It is an allosteric inhibitor - it preferentially binds to the T state, reducing binding of F6P
146
Substrate cycling
F6P and FBP are both active in resting muscle (cycling); PFK activity is dominant in active muscle, increasing GADP/DHAP output.
147
Where do animals use substrate cycling and for what purpose?
They use substrate cycling in the muscles and liver to generate heat (nonshivering thermogenesis).
148
In the ___ state of hemoglobin, the Fe is out of the heme plane.
T state
149
When oxygen binds to heme, the oxygen forms a hydrogen bond with ____.
His E7
150
What is indicated by the pKa of an amino acid?
The pH at which the side chain will be 50% protonated and 50% deprotonated.
151
What does Kcat represent?
The number of substrate molecules converted to product per enzyme molecule per second at Vmax (rate constant for conversion of substrate to product).
152
