Chapter 4: Amino Acids & Proteins Flashcards
1
Q
What are the two acidic amino acids?
A
Aspartic Acid & Glutamic acid ( they both have a carboxylic acid functional group (pKa about 4) (Asparate & glutamate are their depronated forms)
2
Q
What is the 3 letter abbreviation for Aspartic Acid?
A
Asp
3
Q
What is the 3 letter abbreviation for Glutamic Acid?
A
Glu
4
Q
What is the one-letter abbreviation for Aspartic Acid?
A
D
5
Q
What is the one-letter abbreviation for Glutamic Acid?
A
E
6
Q
What are the Basic Amino Acids?
A
Lysine, Arginine, & histidine
7
Q
What is the pKa for the lysine R-group side chain?
A
10
8
Q
What is the pKa for the Arginine R-group side chain?
A
12
9
Q
What is the pKa for the Histidine R-group side chain?
A
6.5
10
Q
What is special about histidine?
A
Its side chain has a pKa close to physiological pH so unlike other amino acids its either protonated or deprotonated at pH 7.4 so it can act as both an acid or base (“His goes both ways”)
11
Q
What is the 3 letter abbreviation for Lysine?
A
Lys
12
Q
What is the 3 letter abbreviation for Arginine?
A
Arg
13
Q
What is the 3 letter abbreviation for Histidine?
A
His
14
Q
What is the 1 letter abbreviation for Lysine?
A
K
15
Q
What is the 1 letter abbreviation for Arginine?
A
R
16
Q
What is the 1 letter abbreviation for Histdine?
A
H
17
Q
Nonpolar (Hydrophobic amino acids) have either ____________ or aromatic side chains
A
Aliphatic (Alkyl)
18
Q
Within the nonpolar amino acids which ones have an aliphatic (alkyl) side chain?
A
Glycine, Alanine, Valine, Leucine, & Isoleucine
19
Q
Within the nonpolar amino acids which ones have an aromatic side chain?
A
Phenylalanine, Tryptophan, & Proline
20
Q
The ______________ the hydrophobic group the greater the hydrophobic force repelling it from water
A
Larger
21
Q
What is the 3 letter abbreviation for Glycine?
A
Gly
22
Q
What is the 3 letter abbreviation for Alanine?
A
Ala
23
Q
What is the 3 letter abbreviation for Valine?
A
Val
24
Q
What is the 3 letter abbreviation for Leucine?
A
Leu
25
What is the 3 letter abbreviation for Isolecuine?
Ile
26
What is the 3 letter abbreviation for Phenylalanine?
Phe
27
What is the 3 letter abbreviation for Trypotphan?
Trp
28
What is the 1 letter abbreviation for Glycine?
G
29
What is the 1 letter abbreviation for Alanine?
A
30
What is the 1 letter abbreviation for Valine?
V
31
What is the 1 letter abbreviation for Leucine?
L
32
What is the 1 letter abbreviation for Isoleucine?
I
33
What is the 1 letter abbreviation for Phenylalanine?
F
34
What is the 1 letter abbreviation for Tryptophan?
W
35
___________ amino acids can form H bonds with water but doesn't act as an acid or base
Polar amino acids
36
What are the polar amino acids
Serine, threonine, tyrosine, Asparagine, Glutamine
37
The hydroxyl group of the polar amino acids is usually modified by the attachment of a phosphate group by a regular enzyme called ______________
kinase
38
What is the 3 letter abbreviation for Serine?
Ser
39
What is the 3 letter abbreviation for Threonine?
Thr
40
What is the 3 letter abbreviation for Tyrosine?
Tyr
41
What is the 3 letter abbreviation for Asparagine?
Asn
42
What is the 3 letter abbreviation for Glutamine?
Gln
43
What is the 1 letter abbreviation for Serine?
S
44
What is the 1 letter abbreviation for Threonine?
T
45
What is the 1 letter abbreviation for Tyrosine?
Y
46
What is the 1 letter abbreviation for Asparagine?
N
47
What is the 1 letter abbreviation for Glutamine?
Q
48
What are the amino acids that contain sulfur side chains?
Cysteine & Methionine
49
Cysteine is fairly ___________ whereas methionine is fairly ___________
Polar, nonpolar
50
Proline is what type of amino acid?
Nonpolar amino acid & has a ring structure
51
What is the 3 letter abbreviation for Proline?
Pro
52
What is the 1 letter abbreviation for Proline?
P
53
What equation is used to used related to acid-base reactions?
Henderson -Hasselbalch equation (pH= pKa + log [A-/HA]
54
When the pH of the solution is ________ than the pKa of an acidic group the acidic group will mostly be in its protonated form
Less
55
When the Ph of the solution is __________ than the pKa of an acidic group the acidic group will mostly be in its deprotonated form
Greater
56
The alpha-amino group of amino acids have a pka of what?
9-10
57
The alpha-carboxyl group of amino acids have a pKa of what?
2
58
When an amino has no net charge (both groups cancel each other out) its called what?
The Zwiterion (dipolar)
59
The zwitterion is referred to as what?
Isoelectric point (pI)
60
What is the point of calculating the pI
To figure out the pH value at which the (+) & (-) charges balance (cancel out)
61
What are the two types of covalent bonds in proteins?
1. Peptide bonds that link amino acids together into polypeptides
2. Disulfides bridges between cysteine R - groups
62
Why can't you use proline residues to form an alpha helix?
1. The formation of a peptide bond with proline eliminates the only hydrogen atom on the nitrogen of proline. The absence of the N-H bond disrupts the backbone hydrgen bonding in the polypeptide chain
2. The unique structureof proline forces it to kink the polypeptide chain
63
Thermodynamically unfavorable reactions that take place in the cell are driven by what?
Reaction coupling
64
In _______________ one very favorable reaction is used to drive an unfavorable one
Reaction coupling (since free energy changes are additive)
65
___________ is a type of reaction coupling that drives unfavorable reactions
ATP hydrolysis
66
The active site model
Known as "The lock & Key model" which states that the substrate and active site are perfectly complementary
67
Induced fit model
States that the substrate and active site differ slightly in structure and that the binding of the substrate induces a conformational change in the enzyme
68
Cofactors
Are metal ions or small molecules that are used in enzyme activity
69
Coenzyme
Often bind to the substrate during the catalyzed reaction (ex. Coenzyme A (CoA)
70
The activity of enzymes are regulated in metabolic pathwaysin what ways?
1. Covalent modifications
2. Proteolytic Cleavage
3. Association with other polypeptides
4. Allosteric regulation
71
Covalent Modifications
Proteins can have several different groups covalently attached to them which can regulate their activity
72
Proteolytic cleavage
Enzymes that are synthesized in inactive forms that are activated by cleavage by a protease
73
Association with other polypeptides
Some enzymes have catalytic activity in one poly peptide subunit that is regulated with a separate regulatory subunit.
74
Constitutive activity ( continuous or unregulated)
When proteins have a continuous rapid catlysis if their their regulatory subunit is removed
75
Allosteric Regulation
The modification of active site activity through the interaction of molecules with other specific sites on the enzyme
76
When bound the ____________ regulator can alter the conformation of the enzyme to increase or decrease catalysis even though it may be bound to the enzyme at a site distant from the active site or even on a separate polypeptide
allosteric
77
___________________ (feedback inhibition, feedback regulation) is used in the regulation of substrates & involves enzymes
Negative feedback
78
Enzyme kinetics
Is the study of the rate of formation of products from substrates in the presence of an enzyme
79
The reaction rate (V (mol/s))
Is the amount of product formed per unit of time & it depends on [S] & enzyme
80
If there is only a little substrate then the rate V is ___________ proportional to the amount of substrate added
directly (double the amount of substrate & the reaction doubles)
81
Vmax
Is when the enzyme is saturated so, therefore, adding more substrate won't increase the reaction at all
82
Km (Michaelis constant)
A low Km means that the enzyme has a high affinity for the substrate
83
Km is found how?
1/2 Vmax
84
Cooperativity (related to enzymes)
The binding of substrate to one subunit modulates the affinity of other subunitsfor substances
85
What is the main type of Cooperativity related to enzymes?
Positive Cooperativity
86
In _____________ cooperativity the binding of a substrate to one subunit increases the affinity of other subunits for the substrate
Positive ( Usually referred to as "tense" for the conformation of enzyme prior to substrate binding & referred as "relaxed" for the conformation of enzyme with increased affinity
87
A _________ curve results from positive cooperactive binding
Sigmodial
88
Describe the sigmodial curve
The beginning flat part of the curve means at low [S] the enzyme complex has low affinity for substrate (its in the tense state) & as you add more substrate it increase the rate so the steep part of the middle curve represents the part where adding more substrate increases the rate (in the relaxed state) & the top level part represent the Vmax part
89
Cooperativity is a special kind of _________ interaction, one active site acts like an allosteric regulatory site for the other active sites & cooperative enzyme complexes are often allosterically regulated also
Allosteric
90
Enzyme inhibitors can reduce enzyme activity by what mechanisms?
1. Competitive inhibition
2. Noncompetitive inhibition
3. Uncompetitive inhibition
4. Mixed-type inhibition inhibition
91
Competitive Inhibitors
Are molecules that compete with the substrate for binding at the active sites
92
How can competitive Inhibitors inhibition be overcome?
By adding more substrate, where if the [S] is high enough it can outcompete the inhibitor (Vmax is not affected)
93
When you are dealing with competitive inhibitor what happens to Km?
The Km increases, Vmax doesnt change
94
When dealing with a noncompetitive inhibitor
The Vmax decreases & the Km doesnt change
95
Noncompeptive inhibitors bind at an ___________ site
Allosteric site (another site) so an "allosteric inhibitor"
96
Uncompetitive inhibitors also bind to __________ sites
Allosteric
97
How does uncompetitive inhibitors affect Vmax & Km
It decreases Vmax & decrease Km
98
Mixed type inhibitors bind to __________ sites but additional substrates cant overcome inhibition
Allosteric
99
How does mixed type inhibition affect Vmax & Km
It decrease Vmax but varies with Km where if the enzyme has lower affinity for the substrate then the Km increases & if the enzyme has a greater affinity for the substrate then Km decreases
100
When dealing with the double reciprocal plot (Lineweaver plot) how do you interpret it?
1. The slope of the graph is Km/ Vmax
2. The y-intercept of the graph is 1/Vmax
3. The x-intercept of the graph is -1/Km
101
What is the 3 letter abbreviation for Cysteine?
Cys
102
What is the 1 letter abbreviation for Cysteine?
C
103
What is the 3 letter abbreviation for Methionine?
Met
104
What is the 1 letter abbreviation for Methionine?
M
105
What is the common structure of all 20 amino acids?
They have the N-C-C backbone & have an amino group, carboxyl group, & a side chain (side chain is what makes them different)
106
Hydrophobic residues tend to be found in the ___________ of the globular protein ( the larger the hydrophobic group the greater the hydrophobic force repelling it from water)
Interior
107
When the amino group is protonated its called an _______________________ group
Ammonium group
108
Isoelectric point (pI)
The pH which a molecule is uncharged
109
When a molecule just has 2 functional groups (no side that is acidic or basic) then the pI can be calculated by just ________________ the 2 functional groups
Averaging
110
In a pI If the pH is higher than the pKa the site is mostly __________________________
Deprotonated
111
In a pI If the pH is lower than the pKa the site is mostly ____________________
protonated
112
Peptide bonds
Link amino acids together into polypeptide chains (by a loss of water)
113
Disulfides bonds
Bonds between cysteine R groups
114
How is a peptide bond formed?
Its formed between the carboxyl group of one amino acids & the amino groups of the other amino acids & a loss of water in the process
115
In a polypeptide chain what is its backbone pattern?
N-C-C-N-C-C
116
The ____________________ residue side is always written first floor a polypeptide or just a peptide bond
Amino- terminal
117
Denatured proteins are __________________
Non-functional
118
Denaturation
The disruption of a protein shape without breaking the peptide bond
119
Primary sequence
The linear sequence of amino acids residues (determined by the peptide bond)
120
The secondary structure is stabilized by what?
Hydrogen bonds between the backbone
