Biochemistry Flashcards
(122 cards)
1
Q
How does an enzyme change the thermodynamics of a reaction?
A
It doesn’t! Enzymes ONLY change the kinetics of a reaction, not heat, and not enthalpy.
2
Q
What are the 6 classifications of enzymes?
A
LILHOT: Ligase, Isomerase, Lyase, Hydrolase, Oxidoreductase, and Transferase
3
Q
What do oxidoreductases do?
A
Catalyze oxidation/reduction rxns
4
Q
What do transferases do?
A
Catalyze a transfer of a functional group from one molecule to another molecule
5
Q
How are transferases named?
A
trans{functional group}ase, or [functional group] transferase
6
Q
What is kinase?
A
A transferase enzyme that transfers a phosphate group from ATP
7
Q
What classification is polymerase?
A
Transferase: they transfer nuecleotides onto DNA or RNA
8
Q
What do hydrolases do?
A
Catalyze cleavage of a molecule into 2 parts by the addition of H2O and the reverse rxn of dehydration synthesis by removing H2O
9
Q
How do you name hydrolases?
A
[substrate] hydrolase, or [substrate]ase (EX: peptidase, nuclease, lipase)
10
Q
What is a proteinogenic amino acid?
A
The 20 “common” amino acids that we traditionally think of. The amino and carboxyl groups are both attached to the alpha carbon (alpha amino acids).
11
Q
What is the common optical activity of all amino acids used in eukaryotes?
A
L
12
Q
What is the common chiral configuration for amino acids?
What is the exception?
A
S, except cysteine which is R
13
Q
What are the nonpolar nonaromatic amino acids?
A
Glycine, alanine, valine, leucine, isoleucine, methionine, proline
14
Q
What is the side chain of glycine?
A
H
15
Q
What is the side chain of alanine?
A
methyl
16
Q
What is the side chain of valine?
A
isopropyl
17
Q
What is the side chain of leucine?
A
isobutyl
18
Q
What is the side chain of isoleucine?
A
sec-butyl
19
Q
What is the side chain of methionine?
A
ethyl-sulfur-methyl (in one long chain)
20
Q
What is the side chain of proline?
A
5 member ring including the alpha carbon and nitrogen
21
Q
What are the aromatic amino acids?
A
tryptophan, phenylalanine, tyrosine
22
Q
What is the side chain of tryptophan?
A
“W” double ring
23
Q
What is the side chain of phenylalanine?
A
phenyl group
24
Q
What is the side chain of tyrosine?
A
phenol group
25
What are the polar amino acids?
serine, threonine, asparagine, glutamine, cysteine
26
What is the side chain for serine?
a carbon followed by a hydroxyl
27
What is the side chain of threonine?
2 carbons w/ a hydroxyl branched off the 1st
28
What is the side chain of asparagine?
a carbon followed by an amide group
29
What is the side chain of glutamine?
2 carbons followed by an amide group
30
What is the side chain of cysteine?
a carbon followed by a thiol group
31
What are the acidic amino acids?
aspartic acid and glutamic acid
32
What are the basic amino acids?
lysine, histidine, and arganine
33
What is the side chain of aspartic acid?
a carbon followed by a carboxyl group
34
What is the side chain of glutamic acid?
2 carbons followed by a carboxyl group
35
What is the side chain of lysine?
4 cabons followed by an amino group
36
What is the side chain of histidine?
a carbon connecting an imidazole
37
What is the side chain of arganine?
3 carbons followed by a monster with 3 amino groups built in; this is the mother of basic AA's because the + is stabilized through resonance
38
What are the 5 ways that enzymes lower activation energy?
transition state stabilization, microenviroment adjustments, adjusting substrate proximity, transient covalent bonding, and reactant destabilization
39
How does an enzyme effect Gibbs free energy of a rxn?
it doesn't
40
What are the theoretical models for enzyme substrate binding? Which one is better?
Lock and Key, and Induced Fit Model
The induced fit model is better
41
What do lyases do?
They cleave a molecule without the addition of water. They can also catalyze the reverse rxn and synthesize stuff
42
How do you name a lyase?
[substrate] lyase, or [product] synthase
43
What does an isomerase do?
transfers the position of a functional group within a molec
44
How do you name an isomerase?
[substrate] isomerase, or [substrate]ase
45
What does a ligase do?
catalyse synthesizes by fusing large molecules together using ATP (MUST HAVE ATP)
46
How do you name a ligase?
[substrate] synthase (also use for lyases), or [substrate] synthetase (SPECIFIC FOR LIGASE)
47
Which class of enzymes MUST use ATP?
ligases
48
What is the Michaelis-Menten eqn?
vel = (Vmax*[S])/(Km+[S])
49
What is the definition of Km (michaelis-menten)?
Km = (sum of all K's of dissosiation)/(sum of all K's of formation)
50
How do you find Vmax and Km on a Michaelis-Menten plot?
Vmax is the y value of the horizontal assymptote, while Km is the x value that corresponds to 1/2(Vmax)
51
How do you find Vmax and Km on a Lineweaver-Burk plot?
Vmax is the reciprocal of the y-intercept, while Km is the negative of the reciprocal of the x-intercept
52
What is enzyme activity?
Same thing as enzyme rate and/or enzyme velocity
53
What happens to the Vmax and Km values during competitive inhibition? What is physically happening during competitive inhibition?
Vmax stays the same, but Km changes. A similarly shaped substance is taking the place of the substrate in the active site, but it does not react and is reversible.
54
What happens to the Vmax and Km values during noncompetitive inhibition? What is physically happening during noncompetitive inhibition?
Vmax changes, but Km stays the same. The inhibitor is attaching to an allosteric control site, changing the shape of the active site so the substrate won't fit. It is reversible and will happen to the enzyme alone, or the ES complex with equal affinity.
55
What happens to the Vmax and Km values during uncompetitive inhibition? What is physically happening during uncompetitive inhibition?
Both Vmax and Km change, and the graph lines are parallel to each other. The inhibitor is binding to the ES complex and keeping the products from being released.
56
What are the 3 letter and 1 letter abbreviations for alanine?
Ala, A
57
What are the 3 letter and 1 letter abbreviations for arginine?
Arg, R
58
What are the 3 letter and 1 letter abbreviations for asparagine?
Asn, N
59
What are the 3 letter and 1 letter abbreviations for aspartic acid?
Asp, D
60
What are the 3 letter and 1 letter abbreviations for cysteine?
Cys, C
61
What are the 3 letter and 1 letter abbreviations for glutamic acid?
Glu, E
62
What are the 3 letter and 1 letter abbreviations for glutamine?
Gln, Q
63
What are the 3 letter and 1 letter abbreviations for glycine?
Gly, G
64
What are the 3 letter and 1 letter abbreviations for histidine?
His, H
65
What are the 3 letter and 1 letter abbreviations for isoleucine?
Ile, I
66
What are the 3 letter and 1 letter abbreviations for leucine?
Leu, L
67
What are the 3 letter and 1 letter abbreviations for lysine?
Lys, K
68
What are the 3 letter and 1 letter abbreviations for methionine?
Met, M
69
What are the 3 letter and 1 letter abbreviations for phenylalanine?
Phe, F
70
What are the 3 letter and 1 letter abbreviations for proline?
Pro, P
71
What are the 3 letter and 1 letter abbreviations for serine?
Ser, S
72
What are the 3 letter and 1 letter abbreviations for threonine?
Thr, T
73
What are the 3 letter and 1 letter abbreviations for tryptophan?
Trp, W
74
What are the 3 letter and 1 letter abbreviations for tyrosine?
Tyr, Y
75
What are the 3 letter and 1 letter abbreviations for valine?
Val, V
76
How do you calculate pI for an acidic AA?
(pKa of R group + pKa of COOH group)/2
77
How do you calculate pI for a basic AA?
(pKa of R group + pKa of NH group)/2
78
Approx. how many AA are in an oligopeptide?
~ 20
79
Why is rotation around a peptide bond restricted?
Because peptide bonds experience resonance, therefor they exhibit partial double bond character.
80
Which terminus is traditionally at the "end" of a polypeptide?
The C-terminus (and it is usually shown on the right)
81
In what direction are polypeptides synthesized?
N-terminus to C-terminus; ribosomes add AA's to the C-terminus
82
What adds to the stability of the alpha helix and beta pleated sheet?
H-bonding
83
What is the main structure of keratin?
The alpha helix
84
What effect does proline have on secondary structures?
Proline will cause a kink to form in both helixes and sheets, so is normally only found in the turns of beta sheets
85
What bonds determine tertiary structure?
hydrophobic and hydrophilic effects mainly, also salt bridges, and disulfide bonds
86
What kind of rxn forms disulfide bonds?
oxidation rxn
87
What is a molten globular protein?
A protein that is in an intermediate state of folding.
88
What is the mathematical cause of hydrophobicity?
a decrease in entropy of the system
89
What is a conjugated protein?
A protein that needs a prosthetic group to be added for function
90
What are some examples of prosthetic groups?
metal ions, vitamins, and other macromolecules like lipids, nucleic acids, and carbohydrates
91
Not necessary, but: What is the name for vitamin B1?
thiamine
92
Not necessary, but: What is the name for vitamin B2?
riboflavin
93
Not necessary, but: What is the name for vitamin B3?
niacin
94
Not necessary, but: What is the name for vitamin B5?
pantothenic acid
95
Not necessary, but: What is the name for vitamin B6?
pyridoxal phosphate
96
Not necessary, but: What is the name for vitamin B7?
biotin
97
Not necessary, but: What is the name for vitamin B9?
folic acid
98
Not necessary, but: What is the name for vitamin B12?
cyanocobalamin
99
What happens to the Vmax and Km values during mixed inhibition? What is physically happening during mixed inhibition?
Vmax decreases, but Km increases if the inhibitor has higher affinity for the enzyme only, and Km decreases if the it has a higher affinity for the ES complex. The inhibitor binds to an allosteric site preventing the enzyme from either binding or releasing substrate. Each of these inhibitors has a higher affinity for EITHER the enzyme OR the ES complex, depending on the inhibitor.
100
What is the general structure of collagen? Where is it found?
Three left-handed helixes wrapped into a right-hand super helix. Found in extracellular matrix of connective tissues
101
What is the function of the protein elastin?
to make connective tissue have elastic recoil
102
Where is keratin found?
Primary structure in hair and nails; also the intermediate filament that provides structure to epithelial cells
103
Where is actin found? What is unique about it's structure?
Microfilaments in cells and the thin filaments in myofibrils. It has a positive side and a negative side, which allows for motor proteins to travel along it's length.
104
What is the most abundant protein in eukaryotic cells?
Actin
105
Where is tubulin found? What is special about the structure?
Microtubules that provide cell structure, act in mitosis/meiosis, and provides transport within the cell. Each strand has 2 polarities, with the positive end usually near the plasma membrane and the negative end attached to the nucleus.
106
What is myosin? Where is it found?
The main motor protein that interacts with actin. It makes up the thick filament of sarcomeres and is involved with intracellular transport.
107
What are the 2 motor proteins associated with microtubules?
Kinesins and dyneins
108
What is the general structure of kinesins and dyneins?
globular protein with 2 heads, attached so that one or both heads remain stuck to tubulin at all times
109
What do kinesins transport and where?
They transport chromosomes during metaphase and they transport vesicles towards the positive ends of tubulin (for exocytosis)
110
What do dyneins transport and where?
They transport vesicles toward the negative ends of tubulin (inner cell). They also move cilia and flagella
111
What are CAM's?
cell adhesion molecules; integral membrane proteins
112
What are the 3 main groups of CAM's?
cadherins, integrins, and selectins
113
What are cadherins?
Glycoprotein CAM's that mediate calcium dependent cell adhesion btw like cells
114
What are integrins?
CAM's w/ 2 membrane spanning chains called alpha and beta; binds cell to extracellular matrix and important for cellular signaling.
115
What are selectins?
CAM's that are on endothelial cells and WBC's which bind to carbohydrates on other cells for cell defense
116
What cells make immunoglobulins?
B-cells
117
What is the structure of an immunoglobulin?
"Y" shape, made of 2 heavy chains and and 2 lights chains w/ the variable regions at the ends of the "Y" and the constant region at the base of the "Y"; all 4 subunits held in place by disulfide bonds.
118
What are the 3 responses induced by antibodies aka immunoglobulins?
- Neutralizing the antigen
- Opsonization (marking for death by WBC's)
- Agglutination (clumping together into complexes that can be eaten by macrophages)
119
What are 3 kinds of ion channel proteins?
ungated channels, voltage-gated channels, and ligand-gated channels
120
How do enzyme-linked receptors operate?
A ligand-binding domain on one side of the membrane binds to a ligand and causes a conformational change in the catalytic domain on the other side of the membrane, which can then catalyze a rxn (usually second a messenger)
121
What are GPCR's? What is their main function?
G-protein coupled receptors; integral membrane proteins for signal transduction
122
What is the key structural trait of G-
k
