1.2 - Amino Acids and Protein Primary Structure Flashcards
1
Q
what is the most abundant macromolecule in cells?
A
proteins
2
Q
how many common amino acids are found in nature?
A
20
3
Q
what makes the chemical composition of each amino acid unique?
A
R-Groups
4
Q
what structural elements are the same in all amino acids?
A
Amino groups and carboxylate groups, alpha carbon
5
Q
what influences the solubility of an amino acid in water
A
the side chain/R-group ; size, structure, electric charge
6
Q
amino group
A
H3N+
7
Q
carboxylate group
A
COO-
8
Q
chiral atom
A
carbon bonded to 4 different atoms (amino, carboxylate, hydrogen, R-group)
9
Q
which amino acid is the only one that does not have a chiral carbon center?
A
Glycine –> 2 Hydrogens
10
Q
why is chirality important in an amino acid?
A
it allows it to occupy 2 unique special arrangements (2 possible stereoisomers)
11
Q
2 stereoisomers of a chiral AA
A
L and D
12
Q
what type of stereoisomers occur in AAs?
A
enantiomers (non-superimposable)
13
Q
which stereoisomer is most commonly found in biological proteins?
A
L
14
Q
why is the _____ isomer most commonly found in proteins?
A
L ; it is able to be specifically synthesized because the active sites of the enzymes that make amino acids are asymmetric, and the active site of a ribosome is asymmetric, meaning it can only accommodate for the L isomers
15
Q
what type of reaction is the synthesis of amino acids?
A
stereospecific
16
Q
why do cells only use one of the stereoisomers in amino acids?
A
energy saving mechanism –> synthesizing proteins with mixtures of D and L isomers would be a large energy burden because 2 sets of enzymes would be required for protein synthesis
17
Q
what type of bonds hold amino acids together to create polymers?
A
covalent peptide bonds
18
Q
how are so many distinct proteins able to be made with only 20 amino acids?
A
peptide bonds link AAs in a characteristic linear sequence that creates different combinations of the same 20 amino acids
19
Q
what does the folding of a polypeptide chain determine?
A
the 3D structure of the protein, which determines the biochemical function
20
Q
what dictates how a polypeptide chain will fold?
A
the precise arrangement of amino acids
21
Q
what contributes to the diversity of biological protein functions?
A
arrangement of amino acids, number of amino acids in a chain, and the number of polypeptides that make up an entire protein
22
Q
categories of amino acids based on the properties of their R-groups
A
nonpolar/hydrophobic
positively charged
negatively charged
uncharged polar
aromatic
23
Q
what is the major force behind protein folding?
A
hydrophobic exclusion
24
Q
Nonpolar / uncharged amino acids
A
Glycine G
Alanine A
Proline P
Valine V
Leucine L
Isoleucine I
Methionine M
25
Positively charged amino acids (basic)
Lysine K
Arginine R
Histidine H
26
Negatively charged amino acids (acidic) (deprotonated / CB forms)
Aspartate D
Glutamate E
27
Aromatic amino acids
Phenylalanine F
Tyrosine Y
Tryptophan W
28
Uncharged polar amino acids
Serine S
Threonine T
Cysteine C
Asparagine N
Glutamine Q
29
what is the smallest amino acid
glycine
30
what is the only achiral amino acid
glycine
31
most chemically-neutral amino acid
glycine
32
Is alanine hydrophobic or hydrophilic?
minimally hydrophobic (one methyl group)
33
______ _______ limits the conformations that proline can adopt. In a polypeptide, the backbone nitrogen lacks a hydrogen, which limits _______ ________
cyclic ring ; hydrogen bonding
34
what amino acid is often found at the hydrophobic core of a globular protein
valine
35
most abundant amino acid in proteins
leucine
36
Leucine plays a major role in promoting ___________ ___________ in the core of globular proteins
hydrophobic interactions
37
_______ is often found in close proximity to Leucine and other hydrophobic amino acids in proteins
isoleucine
38
amino acid that codes for a start codon
methionine
39
what two amino acids contain sulfur?
methionine and cysteine
40
the sulfur in _______ is unreactive
methionine
41
_______ is often the amino-terminal acid in nascent polypeptides
methionine
42
charged R-groups are side chains that are either _______ or ________
acidic ; basic
43
acids become ________ in aqueous solution
anions
44
bases become _______ in aqueous solution
cations
45
acids _________ protons
donate
46
bases _________ protons
accept
47
water can act as both a weak acid and a weak base, meaning it is _______
amphoteric
48
what does an acid dissociate into?
a conjugate base + H+
49
water has a slight tendency to _______
ionize (as an acid)
50
the equilibrium constant for the ionization of an acid
Acid Dissociation Constant (Ka)
51
strong acid = ______ dissociation = _______ Ka
high ; high
52
to get a large Ka, you need a ________ numerator and a ________ denominator --> this means products are ______ _______
large ; small ; readily formed
53
weak dissociation
occurs in weak acids where the solution ends up in equilibrium between the acid form and the base form
54
in a neutral solution, concentrations of protons and conjugate base should be _______
equal
55
basis of pH scale
1 x 10-7 M
56
pH
the measure of the total H+ in a solution
57
how to convert the concentration of protons in a solution into pH
pH = -log [H+]
58
_________ relationship between number of protons and number on pH scale
inverse
59
higher pH = ______ protons = ________ basic and _______ acidic
less ; more ; less
60
lower pH = _______ protons = _______ basic and _______ acidic
more ; less ; more
61
a measure of the relative strength of an acid or base on a log scale ; analogous to pH by logarithmic transformation of the Ka value
pKa
62
pKa = _______
pKa = -log(Ka)
63
strong acid = _____ Ka = _____ pKa
high ; low
64
what does a low pKa mean?
acid dissociates at a low pH --> strong acid
65
pKa tells us the ______ that an acid will _______, which helps to determine if a given molecule or functional group in a cell will ionize
pH ; dissociate
66
calculates the concentrations of acid vs. conjugate base and the ratio of the protonated vs. deprotonated form of the acid within a cell at a particular pH.
Henderson-Hasselbalch Equaltion
67
protonated form of an acid = ________
acidic ; [HA]
68
deprotonated form of an acid = ________
conjugate base [A-]
69
if pH = pKa, then _______
log 1 = _____
[A-] = [HA]
0
concentration of conjugate base is equal to the concentration of the protonated form
70
if we take an acid and put it in a solution that has a pH equal to the pKa, then there will be __________ of deprotonated and protonated forms
a 50/50 ratio / equal concentrations
71
if pH > pKa, then _____
log >1 = _______
[A-] > [HA]
positive number
concentration of conjugate base is greater than that of the acid
72
pH > pKa --> increased pH = _____ H+
decreased
73
if you take an acid and put it in a solution that has a pH greater than the pKa, the deprotonated form will be ________ and in ________ concentration than the protonated form.
favored ; higher
74
if the deprotonated form of an acid is higher in concentration than the protonated form, there is a ________ numerator and ________ denominator, the ratio is ________ than 1, and the log is a _______ number
large ; small ; greater ; positive
75
if pH < pKa, then _______
log < 1 = _______
[A-] < [HA]
negative number
concentration of conjugate base is less than that of the acid
76
if you take an acid and place it in a solution that has a lower pH than the pKa for that acid, it favors the _______ form
protonated
77
pH < pKa --> decreased pH = _____ H+
increased
78
if the deprotonated form of an acid is lower in concentration than the protonated form, there is a ________ numerator and ________ denominator, the ratio is ________ than 1, and the log is a _______ number
smaller ; larger ; less ; negative
79
at physiological pH, carboxylic acid groups are ________ and amino acid groups are _______
deprotonated ; protonated
80
pK1
for carboxyl group, about 2 (acidic)
81
pK2
for amino group, about 9 (basic)
82
what does the henderson hasselbalch equation tell us?
what proportion of all the phosphate groups are going to donate a proton and become charged
83
when does an acid become charged?
when it donates a proton
84
when does a base become charged?
when it accepts a proton/becomes protonated
85
if any pKa is less than the pH of a solution, the _____ version of an acid or base is favored
charged
86
pKa values can change depending on the _______
environment / surrounding amino acids in a protein
87
what form is Lysine usually found in at physiological pH of 7?
net positive charge
88
what form is Arginine usually found in at physiological pH of 7?
net positive charge
89
what form is Histidine usually found in at physiological pH of 7?
neutral / mix of protonated and deprotonated form --> can be positive or negative depending on environment
90
why is histidine able to facilitate many enzyme catalyzed reactions?
it can serve as both a proton donor and acceptor due to its' ability to switch based on the surrounding environment
91
aspartate is the _______ ______ version of aspartic acid
conjugate base
92
the ________ form of aspartate is called aspartic acid
protonated
93
glutamate is the _______ ______ version of glutamic acid
conjugate base
94
the ________ form of glutamate is called glutamic acid
protonated
95
both aspartate and glutamate give up a _______ at physiological pH and become _____ charged because they both have a carboxyl group at the end of their side chains
_____ pKas
proton ; negatively ; low
96
5 amino acids with charged R groups
Aspartate
Glutamate
Lysine
Arginine
Histidine
97
charged R groups are important in protein folding because they are able to form _____ interactions with each other to _______ a protein structure and with other molecules to facilitate interactions
ionic ; stabilize
98
what type of R group is able to absorb UV light?
aromatic
99
what amino acid is COMPLETELY hydrophobic?
phenylalanine
100
what makes Tyrosine more polar than Phenylalanine?
the OH group
101
the ionizable __________ group on Tyrosine forms __________ bonds, making Tyr an amphipathic amino acid having both hydrophobic and hydrophilic properties
hydroxyl ; hydrogen
102
Tyrosine only donates protons in a very _____ environment due to its ______ pKa value. It is very rare to dissociate and become charged.
basic ; low
103
Largest amino acid
Tryptophan
104
The ring nitrogen in Trp forms weak _______ bonds, which makes the Trp indole amphipathic.
hydrogen
105
what amino acids are amphipathic? Why?
Trp and Tyr ; due to the hydrophobic ring and hydrophilic portion of it
106
amphipathic amino acids _______ protein folding. why?
influence ; they require a specific position within a protein that shields the ring from water while also providing H-bond partners for the Hydrophilic portion
107
phosphorylation
hydroxyl group on the end can be used to attach a phosphate functional group to the R-group
108
phosphorylation can _____ or ______ a protein
activate ; inactivate
109
what type of modifications are important in regulation?
transient
110
what transient modification is important in regulation?
phosphorylation
111
what catalyzes a phosphorylation reaction? what does it create?
tyrosine kinase ; phosphotyrosine
112
_______ is a regulatory mark that can help control a protein function
phosphotyrosine
113
uncharged, polar R-groups are _______ soluble in water because they have functional groups that ________
more ; form H bonds with water
114
Serine and Threonine are polar due to their ______ groups
hydroxyl
115
Serine can be a substrate in proteins for _______-________ __________
kinase-mediated phosphorylation
116
Threonine can be ________ by kinases
phosphorylated
117
Cysteine gets its modest polarity from the _______ group
sulfhydryl
118
Asparagine and Glutamine are polar due to their ________ groups
amine
119
Asparagine and Glutamine are often found on the ________ of a folded protein
exterior
120
peptide bonds
covalently-linked amino acids
121
peptide bonds are very ______ and are formed by ________ reactions
stable ; condensation
122
condensation reactions are formed by the ______ of a water molecule from the ______ group of the first amino acid and the _____ group of the other
removal ; carboxyl ; amino
123
hydrolysis reactions use a ________ molecule to ________ peptide bonds and _______ amino acids
water ; break ; separate
124
the amino terminus is also called the ______ terminus
N
125
the carboxyl terminus is also called the ______ terminus
C
126
directionality of peptides: the 2 ends have different free-functional groups
_____ terminus on the left
_____ terminus on the right
read L to R
N ; C
127
under standard conditions, the equilibrium of a condensation reaction favors the ______ over the dipeptide.
amino acids
128
input of _______ is required to build proteins in a cell
energy
129
building proteins by creating peptide bonds is done with a _______ reaction
condensation / dehydration
130
hydrolysis is an ______ process because it _______ energy
exergonic ; releases
