Chapter 1: Amino Acids, Peptides, and Proteins Flashcards
(136 cards)
1
Q
Amino Acid Structure
A
-Four substituents attached to central alpha carbon
- Four substituents:
1. Amino group (-NH2)
2. Carboxylic acid group (-COOH)
3. Hydrogen
4. Unique “R” or side chain group (specific to each AA) -> Determines chemical properties and their functions
2
Q
Proteinogenic Amino Acids
A
20 amino acids encoded by the human genetic code
3
Q
Are amino acids chiral or achiral?
A
Chiral: Optically active
Exception: Glycine which is achiral
4
Q
Which is amino acids are used in eukaryotes, L-amino acids or D-amino acids?
A
L-amino acids
-NH2 group is on the left side
5
Q
What is the absolute configuration of amino acids?
A
(S) configuration
Exception: Cysteine is (R) configuration
6
Q
Nonpolar Amino Acids
A
- Glycine (Gly, G)
- Alanine (Ala, A)
- Valine (Val, V)
- Leucine (Leu, L)
- Isoleucine (Ile, I)
- Methionine (Met, M)
- Proline (Pro, P) (Amino nitrogen becomes part of the
side chain) - Phenylalanine (Phe, F)
- Tryptophan (Trp, W)
Mneumonic: GAVaLIMP PT
7
Q
Polar, Uncharged Amino Acids
A
- Serine (Ser, S)
- Threonine (Thr, T)
- Cysteine (Cys, C)
- Tyrosine (Tyr, Y)
- Asparagine (Asn, N)
- Glutamine (Gln, Q)
Mneumonic: SomeTimes Cats Try A Growl
8
Q
Acidic, Negatively Charged Amino Acids
A
- Aspartic Acid (Asp, D)
- Glutamic Acid (Glu, E)
Mneumonic: A Good
9
Q
Basic, Positively Charged Amino Acids
A
- Lysine (Lys, K)
- Arginine (Arg, R)
- Histidine (His, H)
Mneumonic: Lawyer Aims High
10
Q
Aromatic Amino Acids
A
- Phenylalanine
- Tryptophan
- Tyrosine
11
Q
pKa of COOH group
A
pKa = 2
12
Q
pKa of NH2 group
A
pKa = 9-10
13
Q
Isoelectric Point (pI) of Non Polar and Polar, Uncharged Amino Acids
A
pI = 5-6
14
Q
pKa and pI for Negatively Charged Amino Acid
A
1. Aspartic Acid pKa (-NH2) = 2 pKa (-COOH) = 9-10 pKa3 = 3.7 pI = 2.8
2. Glutamic Acid pKa (-NH2) = 2 pKa (-COOH) = 9-10 pKa3 = 4.3 pI = 3.2
15
Q
pKa and pI for Positively Charged Amino Acid
A
1. Lysine pKa (-NH2) = 2 pKa (-COOH) = 9-10 pKa3 = 10.5 pI = 9.7
2. Arginine pKa (-NH2) = 2 pKa (-COOH) = 9-10 pKa3 = 12.5 pI = 10.7
3. Histidine pKa (-NH2) = 2 pKa (-COOH) = 9-10 pKa3 = 6.00 pI = 7.59
16
Q
Hydrophobic Amino Acids
A
Alanine Valine Leucine Isoleucine Phenylalanine
17
Q
Essential Amino Acids
A
Valine Histidine Methionine Isoleucine Leucine Lysine Tryptophan Threonine Phenylalanine
Mneumonic: VH MILK WTF
18
Q
Where can hydrophobic AAs be found?
A
On the interior of proteins
19
Q
Where can hydrophilic AAs be found?
A
On the surface of proteins
20
Q
Does the amino and carboxylic acid group need to be bonded to the same alpha carbon in an AA?
A
No.
Gamma-aminobutyric acid (GABA) is an AA where amino group is on gamma carbon from carboxyl group.
21
Q
Is every amino acid specified by a codon in the genetic code?
A
No.
22
Q
Is every amino acid incorporated into proteins?
A
No.
23
Q
What is an example of an amino acid that is not specified by a codon in the genetic code, and is not incorporated in proteins?
A
Ornithine
*Ornithine is an urea cycle intermediate.
24
Q
Which amino acid is optically inactive or achiral?
A
Glycine
25
Which amino acid does NOT have a (S) configuration?
Cysteine
* The -CH2SH group takes higher priority than the carboxylic acid group.
* Cysteine has (R) configuration.
26
What is the smallest AA?
Glycine
27
What effect does proline have?
It has constraints on flexibility.
| It has limits on secondary structure.
28
Aspartate
Anion of Aspartic Acid
29
Glutamate
Anion of Glutamic Acid
30
Which amino acids have alkyl side chains?
Alanine, Valine, Leucine, and Isoleucine
31
What is the smallest aromatic side chain?
Phenylalanine
32
Which aromatic side chain is polar?
Tyrosine
33
Does the amide nitrogens in asparagine and glutamine, gain or lose protons with changes in pH?
NO
34
What is AA has a thiol (-SH) group?
Cysteine
35
Which bond is stronger, O-H or S-H?
* O-H bond is stronger
| * S-H bond is weaker and more prone to oxidation.
36
What type of bonds form between 2 cysteine AAs?
Disulfide bonds
37
What form of acidic AAs exist in cells?
The anion or deprotonated form exists in cells.
*Applies to other molecules.
38
What AAs are hydrophilic?
```
Serine
Threonine
Asparagine
Glutamine
Aspartic Acid
Glutamic Acid
Lysine
Arginine
Histidine
```
39
Glucogenic AAs
AA that can be converted into glucose via gluconeogenesis
40
Which AAs are glucogenic?
```
Alanine
Arginine
Asparagine
Aspartic Acid
Cysteine
Glutamine
Glutamic Acid
Glycine
Histidine
Methionine
Proline
Serine
Valine
```
41
Ketogenic AAs
An AA that can be degraded directly into acetyl-coA
*Acetyl-coA is a precursor of ketone bodies
42
Which AAs are ketogenic?
Leucine
| Lysine
43
Which AAs are ketogenic and glucogenic?
```
Phenylalanine
Isoleucine
Threonine
Tryptophan
Tyrosine
```
Mneumonic: PITTT
44
Amphoteric Species
* Can either accept or donate proton.
* How they react depends on the pH of the environment.
* Can act as a base or acid.
45
Bronsted-Lowry Acid
Species that donates H+
46
Bronsted-Lowry Base
Species that accepts H+
47
What happens to ionizable groups at a low pH, acidic conditions?
Groups gets protonated
48
What happens to ionizable groups at a high pH, basic conditions?
Groups gets deprotonated
49
pKa
[HA] = [A-]
[protonated version of ionizable group] = [deprotonated version of ionizable group]
*half of species deprotonated
50
Under what conditions are the majority of the species protonated?
pH < pKa
51
Under what conditions are the majority of the species deprotonated?
pH > pKa
52
What is physiological pH?
7.4
53
Zwitterion
* Dipolar ions that have a (+) and a (-) charge
| * Overall charge would be electrically neutral
54
At very acidic pH, AAs tend to be
(+) charged
55
At very basic pH, AAs tend to be
(-) charged
56
When does solution act as a buffer in terms of pH?
When pH of soln. = pKa of solute
57
Isoelectric point (pI)
pH at which all molecules are electrically neutral/exist as zwitterions
58
pI (neutral AA)
1/2 * [pKa (NH2) + pKa (COOH)]
59
pI of AA with non-ionizable chains
approximately 6
60
What are neutral molecules sensitive to?
* They are sensitive to pH changes.
| * Curve is nearly vertical at pI
61
What is the pI of AAs with acidic side chains?
pI < 6
62
What is the pI of AAs with basic side chains?
pI > 6
63
pI (acidic AA)
1/2 [pKa (R group) + pKa (COOH)]
64
pI (basic AA)
1/2 [pKa (NH2) + pKA (R group)]
65
Peptides
Composed of AA subunits
66
Residues
AA subunit
67
Dipeptide
Consists of 2 AA residues
68
Tripeptides
Consists of 3 AA residues
69
Oligopeptides
Relatively small peptides of up to 20 residues
70
Polypeptides
Larger peptides of more than 20 residues
71
Peptide Bonds
* An amide bond that joins 2 AA resides together
| * Forms between carboxyl group of 1 AA and amino group of another AA via loss of H2O
72
What type of rxn is peptide formation?
Dehydration or condensation rxn (removal of H2O)
73
What functional group is a peptide bond?
Amide
74
Which group is the nucleophile in peptide bond formation?
Amino group
75
Which group is the electrophile in peptide bond formation?
Carbonyl carbon of Carboxyl group
76
Can the peptide bond rotate?
Bond rotation is restricted because of partial double bond character. Has delocalizable pi e-
77
How are AAs written?
Written from N-terminus to C-terminus
78
How can amide bonds be broken?
*They can be hydrolyzed using acid or base catalysis.
OR
*Via hydrolytic enzymes
79
Hydrolysis of Peptide Bond
* Amide bond breaks apart
* Hydrogen added to amide nitrogen
* -OH group added to carbonyl carbon
80
Proteins
Polypeptides that range from a few AAs in length to up to thousands of AAs.
81
What are the levels of protein structure?
Primary
Secondary
Tertiary
Quaternary
82
Primary Structure of Protein
- Linear arrangement of amino acids
| - Written from N-terminus (amino group) to C-terminus (carboxyl group)
83
What stabilizes the primary structure of a protein?
Covalent peptide bond between adjacent AAs
84
Protein structure is energetically favorable or unfavorable?
It is most energetically favorable.
85
Sequencing
- Determines the primary structure of a protein
| - DNA or protein can be used for sequencing
86
Secondary Structure of Protein
-Local structure of neighboring AAs.
87
What bond is involved in the secondary structure of proteins?
Hydrogen bonds between nearby AAs
88
What are the 2 most common secondary structures?
1. Alpha-helix
| 2. Beta-pleated sheet
89
What stabilizes the alpha-helices and beta-pleated sheets?
-Formation of intramolecular hydrogen bonds between different residues.
90
Alpha-Helix
- Rodlike structure in which the peptide chain coils CLOCKWISE around a central axis.
- Hydrogen bonding between a carbonyl oxygen atom and an amide hydrogen atom 4 residues down the chain.
- R groups point away from the helix core
91
What protein structure does the alpha-helix play a major role in?
Keratin
92
What is keratin?
A fibrous structural protein found in human skin, hair, and fingernails.
93
Beta-Pleated Sheet
- Can be parallel or anti-parallel
- Hydrogen bonding between carbonyl oxygen of one chain and amide hydrogen of another adjacent chain
- R groups above and below plane
- Pleated or rippled shape
94
What protein structure does the beta-pleated sheet play a role in?
Fibroin
95
Fibroin
Primary protein component of silk fibers
96
What role does Proline play in secondary structure?
- Introduces a kink in the peptide chain when in the middle of an alpha-helix
- Often found in the turns between the chains of a beta-pleated sheet
- Often found as the residue at the start of an alpha-helix
97
What categories can proteins be divided into?
1. Fibrous
| 2. Globular
98
Fibrous proteins
- Structures that resemble sheets or long strands
| - Ex: collagen
99
Globular proteins
- Tend to be spherical
| - Ex: myosin
100
What factors cause the shape of fibrous and globular proteins?
Tertiary and quaternary structures of protein structures.
101
What levels of protein structure result in protein folding?
Tertiary and Quarternary Structures of Proteins
102
Tertiary Structure
-3-dimensional shape of a protein
103
What determines tertiary structure?
- Hydrophobic and hydrophilic interactions between R groups of AAs.
- Hydrogen bonding
- Acid-Base Interactions
104
Where are the hydrophobic residues mostly located?
- They are located on the interior of proteins.
| - It reduces its proximity to H2O.
105
Where are the hydrophilic residues mostly located?
-They are located on the surface of proteins
106
What further stabilizes the interior of proteins?
- Electrostatic interactions between hydrophilic N-H + C=O bonds and the hydrophobic residues
- Hydrogen bonding
107
What is created as a result of acid-base interactions between R groups in tertiary structure of proteins?
Salt Bridges
108
What is an example of a component involved in tertiary structures?
Disulfide Bonds
109
Disulfide Bonds
- Bond that forms between 2 cysteine molecules that are oxidized to form cystine.
- Involves the loss of 2 protons and 2 electrons
110
Molten globules
Intermediate states in tertiary structures
111
Denaturation
- When a protein loses its tertiary structure or three-dimensional structure
- Loss of function results
112
Why do hydrophobic residues reside on the interior and hydrophilic residues on the surface?
Entropy
113
Would hydrophobic residues in aqueous solutions be energetically favorable or unfavorable?
Energetically unfavorable
delta S < 0 : increasing order, decreasing order
114
Would hydrophilic residues in aqueous solutions be energetically favorable or unfavorable?
- Energetically favorable
- Allows H2O molecules more latitude in their positioning
delta S > 0: decreasing order, increasing entropy
115
What would happen if hydrophobic residues are placed in an aqueous solution?
Solvation layer forms
116
What position of residues provides maximum stability?
Hydrophilic: toward H2O
Hydrophobic: away H2O
117
Does all proteins have primary structure?
Yes
118
Does all proteins have secondary structure?
Yes
119
Does all proteins have tertiary structure?
Yes
120
Does all proteins have quaternary structure?
No
121
Quarternary Structures
-Only in proteins with multiple polypeptide
chains
-Is an aggregate of smaller globular peptides, or subunits
-Represents the functional form of the protein
122
What examples of proteins have quaternary structures?
Hemoglobin and immunoglobulins
123
How many subunits does hemoglobin have?
4 subunits
124
What purposes do quarternary structures serve?
1. Provides more stability by further reducing the surface area of the protein complex
2. Can reduce the amount of DNA needed to encode the protein complex
3. Can bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction
4. Can induce cooperativity and allosteric effects
125
Cooperativity
- Involves multiple subunits
- When one subunit undergoes conformational or structural changes, it can either enhance or reduce the activity of the other subunits
126
Can denatured proteins catalyze reactions?
No, they CAN NOT,
127
What are the 2 main causes of denaturation?
Heat and solutes
128
How does increase in temperature or heat cause denaturation?
- Temperature increases, average KE increases
- Increase in average KE allows overcoming of hydrophobic interactions that hold protein together.
- This causes protein to unfold
129
What is an example of a solute that unfolds protein?
Urea and SDS (sodium dodecyl sulfate or sodium lauryl sulfate)
130
How does urea cause proteins to denature?
- They directly interfere with the forces that hold the protein together.
- They break disulfide bridges in which cystine is reduced to 2 cysteine residues.
- They can also overcome hydrogen bonds and other side chain interactions that hold alpha-helices and beta-pleated sheets intact.
131
Conjugated Proteins
Derives part of their function from prosthetic groups.
132
Prosthetic groups
- Covalently attached molecules to proteins
- Can be organic molecules (i.e. vitamins) or metal ions (i.e. iron)
- Major role in determining function of their respective proteins
133
Heme
- A prosthetic group for each hemoglobin subunit.
- Contains an iron atom in the core
- Binds to and carries oxygen
134
Denaturation
* Protein loses its three-dimensional structure
| * Thus loses its function
135
Is denaturation reversible or irreversible?
* Often it is irreversible
| * Sometimes it is reversible
136
How does SDS denature proteins?
Can solubilize proteins by disrupting non-covalent bonds
