Amino Acids, Peptides, and Proteins Flashcards
1
Q
What are the four different roles of proteins?
A
1) Catalysis
2) Transport
3) Structure
4) Motion
2
Q
Does each cell make a similar or different repertoire of proteins?
A
Different
3
Q
Define genome.
A
Refers to all the genes encoded in a cell’s DNA.
4
Q
Define transcriptome.
A
Refers to complete RNA profile.
5
Q
Define proteome. How do proteomes vary by tissue?
A
Refers to protein complement expressed by a cell.
ex: proteome of liver not the same as heart.
6
Q
Subsets of proteins depend on what?
A
They are tissue dependant
7
Q
How many genes do we have? And proteins?
A
30 000 genes
50 000-100 000 proteins
8
Q
Define peptide.
A
Small protein containing 2-50 amino acids
9
Q
Define polypeptide.
A
More than 50 amino acids
10
Q
How many naturally occurring amino acids are there?
A
20
11
Q
Name the three classes of protein.
A
1) Soluble Proteins
2) Membrane Proteins
3) Fibrous/Structural Proteins
12
Q
What is the chemical composition of an amino acid?
A
Amino Group + Side Chain (R) + Carboxyl Group
13
Q
Name two properties of amino acids.
A
- Can function as buffers
- Capacity to polymerize
14
Q
Define a chiral molecule.
A
Non-superimposable on its mirror image; possesses an asymmetric carbon center.
15
Q
How do you achieve chirality?
A
If you attach 4 different groups to an alpha carbon
16
Q
Which amino acid is the only non-chiral one?
A
Glycine (2 hydrogens)
17
Q
Define enantiomers. Give an example of an enantiomer.
A
Non-superimposable mirror image.
Amino acids are enantiomers
18
Q
Define racemization.
A
Conversion of an enantiomerically pure mixture into a mixture with more enantiomers.
19
Q
Define a racemic mixture.
A
D and L configurations present in equal quantities.
20
Q
How does racemization between L and D isomers occur? Is it fast?
A
Spontaneously
Reaching equilibrium is a VERY slow process
21
Q
What is the most abundant configuration of amino acids?
A
CORN configuration (L configuration)
22
Q
What biological compound can back convert?
A
Enzymes but ONLY in living cells (D to L)
23
Q
How many essential amino acids are there?
A
8
24
Q
Which two amino acids are considered essential for infants?
A
Arginine and HIstidine
25
Name the 5 classes of amino acids.
1) Non-polar, aliphatic
2) Aromatic
3) Polar, uncharged
4) Positively charged
5) Negatively charged
26
Which classes of amino acids are hydrophobic?
1) Non-polar, aliphatic
| 2) Aromatic
27
Which classes of amino acids are hydrophilic?
1) Polar, uncharged
2) Positively charged
3) Negatively charged
28
Which amino acid is referred to as a secondary amine? Why?
Proline, since it cycles back and reacts with the alpha amino group
29
Which group of amino acid has a strong ultraviolet light absorption properties?
Aromatic group
30
Which amino acid in the aromatic group does not have strong ultraviolet light properties? Why?
Phenylalanine, since it does not have conjugation
31
Which amino acid can be involved with covalent disulfide bonds?
Cysteine
32
What are cysteine bonds (disulfide bonds) critical for?
Controlling the structure of proteins when they are released outside the cell
33
Where do cysteine bonds occur?
In an oxidizing environment
34
Which amino acids are always positively charged under biological systems? Why?
Arginine and Lysine
| Since they have high pKas
35
Which amino acid is not always positively charged under biological systems, but can be?
Histidine, pKa=6
| Neutral at pKa>6, Positively charged at pKa
36
If you add a proton to Histidine, what becomes positively charged?
the N will undergo protonation
37
At neutral pH, the carboxyl group is ______ but the amino group is ______. The net charge is ___.
deprotonated, protonated, 0
38
At acidic pH, the carboxyl group is ______ but the amino acid is in its ______ form. The net charge is ___.
protonated, cationic, +1
39
At alkaline pH, the amino group is ______ but the amino acid is in its ______ form. The net charge is ___.
neutral, anionic, -1
40
Define Zwitterions.
Positive and negative ions that can act as either an acid or a base
41
Define isoelectric point.
pH where the net charge on the molecule is 0.
| Occurs at 1 equivalence, no net charge
42
What is the equation to define the isoelectric point?
pI = (pK1 + pK2)/2
43
If it is an acidic amino acid, which range will the pI be in?
Acidic range
44
If it is a basic amino acid, which range will the pI be in?
Alkaline range
45
How do amino acids undergo polymerization?
In a head to tail fashion.
46
How are peptides formed? What does it result in?
By condensation, results in the loss of water
47
What is the primary structure of a protein?
The linear sequence of amino acids.
48
Where does the primary structure being? End?
Begin: free amino end (or N-terminal)
End: free carboxyl end (C-terminal)
49
What does the primary structure contain?
Information that allows 2nd and 3rd structure.
50
What character do peptide bonds display? Why?
Partial double bond character due to electron delocalization
51
What does the partial double bond character cause?
Restricts rotation around the peptide bond.
52
How do single, double, and peptide bond lengths differ?
Peptide bond lengths are right in between the two
53
Which type of peptide rotations are permitted? Which aren't?
Permitted: rotation around bonds connected to the alpha carbon
Not permitted: rotation around the peptide bond
54
The phi angle refers to which bond?
Amide nitrogen bond (N-C)
55
The psi angle refers to which bond?
Carbonyl carbon bond (C-C)
56
Which configuration is conformationally favorable? Why?
Trans since atoms can't occupy the same space
57
What angles can psi and phi angles never be? Why?
0 or 180 since atoms can't occupy the same space
58
Why is Proline conformationally unique? Why?
Since it switches between cis and trans configurations (second amine)
59
What gives rise to secondary structure?
Phi and psi angles
60
Name the three secondary structures.
1. a-helix
2. B-sheets
3. B-turn
61
What defines and stabilizes the secondary structure?
- Hydrogen bonds between the main chain peptide groups
| - R-chain helps stabilize as well
62
What stabilizes the a-helix?
Intra-hellical hydrogen bonds
63
What is the pitch of the a-helix per turn?
3.6
64
What atoms are hydrogen bonded in an a-helix?
H-bond between the hydrogen atom attached to the electronegative nitrogen atom of a peptide linkage and the electronegative carbonyl oxygen atom
65
Which amino acid likes to form helices? Which don't?
Like: Alanine
| Don't like: Proline and Glycine
66
How can R-groups affect the structure of a helix.
They will either stabilize (attraction) or destabilize (repulsion)
67
How does pH influence the structure of a helix?
For ex, putting a protein into an acid will disrupt the hydrogen bonds (protonation) and cause the protein to unravel
68
What is the driving force for proteins to fold?
Hydrophobic interactions
69
Which hand is the most common helix
Right hand
70
Name a biological molecule that has a left-handed helix.
Collagen
71
Where is the - end on a helix? And _?
Carboxyl (-)
| Amino (+)
72
What's the difference between parallel and antiparallel B-sheets?
Parallel: amino groups point in the same direction
Antiparallel: amino groups point in opposite directions
73
What's critical for antiparallel B-sheets?
To have a tight-turn to allow the protein strand to do an 180o turn
74
Which type of B-sheet cannot be contiguous?
Parallel
75
What does the Ramachandran plot dictate?
Protein structure is dictated by the phi and psi angles
76
How many amino acids do B-Turns involve?
4 amino acids
77
Where are proline and glycine situated on a B-turn?
Proline (2) Glycine (3)
78
What is the function of the B-turn?
Allows the proteins to do an 180o turn
79
What are the characteristics of spider silk?
Stronger than steel, stretches
80
What is spider silk stabilized by?
Hydrogen bonds & Van der Waals interactions
81
What amino acids are in high abundance in spider silk?
Glycine and Alanine
82
What is the MAIN driving force of tertiary structure?
Bury hydrophobic interactions
83
Are B-sheets flat? Why/Why not?
B-sheets are flat, but not completely planar because of angles (tend to have a twist)
84
Name some favorable interactions in proteins.
- Hydrophobic Effect
- Hydrogen Bonds
- Van der Waals Interactions
- Electrostatic Interactions
- Disulfide Bonds
85
How is the tertiary structure of proteins held together?
Electrostatic interactions
86
How does protein structure evolve?
To accommodate the environment
87
Define homomeric.
Same subunits
88
Define heteromeric.
Different subunits
89
Define oligomeric.
More than one subunit (could be homo or hetero)
90
Provide examples of how quaternary structures bind together.
- Hydrophobic interactions
- Hydrogen bonds
- Disulfide bonds
91
Describe the function of the Allosteric effect.
- Easier to load and unload oxygen
| - Allows to more tightly regulate the activity of an enzyme
92
If there is a change in amino acid, which protein structure would it affect the most?
Quaternary
93
Describe briefly the 4 levels of protein structure.
Primary: amino acid residues (important order of polymerization)
Secondary: a-Helix
Tertiary: polypeptide chains
Quaternary: assembled subunits
94
For a generic amino acid, NH2CRHCOOH (uncharged), what would be the predominant form at:
a) pH=1
b) pH=7
c) pH=11
a) +NH2CRHCOOH
b) +NH2CRHCOOH-
c) NH2CRHCOOH-
95
What determines how curly a human's hair is?
Disulfide bonds
96
What do disulfide bonds create?
Loops in the protein chain
97
Do all proteins have quaternary structure? In what case?
No, exist for proteins that contain more than one polypeptide chain
98
In a neutral solution, most amino acids exist as ____?
Zwitterions
99
At pH 7, what is the charge on a glutamic acid molecule?
2x negative because of 2x carboxyl
1x positive because of amino
so -1
100
What holds up tertiary structure?
Disulfide bridges and hydrophobic effects
101
Which amino acids would be likely to be found in a transmembrane portion of the a-helix?
Amino acids with a hydrophobic side chain
102
Which amino acid is likely to be found in high concentration in collagen?
Glycine, reduce steric hindrance
103
Why can amino acids ionize?
Since both the carboxyl and amino groups (sometimes side chains as well) can ionize
104
Why is glycine not optically active?
It does not have a D and L isomer, not chiral
105
Which amino acid allows the most structural flexibility (least amount of steric hindrance)? Which the least?
Most: Glycine
Least: Proline
106
What happens to an R-group when pH < pka? When pH pka?
pH smaller than pka: protonation
| pH higher than pka: deprotonation
107
Name the amino acids that are positively charged at physiological pH.
Lysine and arginine
| Histidine (possibly, but low pKa)
108
Name the amino acids that are part of the aromatic R group, hydrophobic and neutral at any pH
Phenylalanine and tryptophan
| not tyrosine since it has an OH
109
Name the amino acids that have saturated hydrocarbon R groups.
Alanine, valine, leucine, isoleucine
110
Name the only amino acid having an R group with a pKa near 7.
Histidine
111
Name the only amino acid with a substituted a-amino group.
Proline
112
Why are all individual amino acids soluble in water but not all peptides are soluble?
Individual amino acids are zwitterions at physiological pHs
113
What do the amino acids threonine and tyrosine have in common?
Both have an OH group (contributes to polarity and hydrogen bonding)
114
What makes amino acid cysteine so important? Can methionine perform the same function?
Cysteine can form disulfide bridges to stabilize the structures of proteins, methionine cannot
115
Are protein structures static?
No, they undergo changes in conformation
116
Where do phi and psi angles occur?
In the peptide backbone
117
How many residues per turn does an alpha helix have?
3.6 residues/turn
118
The rise along the helical axis for each amino acid residue is ____?
Rise: 5.4/3.6 residues per turn = 1.5
119
Where are the amino acid sidechains on an a-helix?
The amino-acid side-chains are on the outside of the helix, and point roughly "downward"
120
Where are the R groups located in a B-sheet?
Opposite directions, either below or above the peptide chain (alternating)
121
What noncovalent forces stabilize B-sheet structures?
Hydrogen bonds
122
What is unusual about peptide bonds involving the nitrogen of proline in B turns?
It readily assumes the cis configuration, a form that is particularly amenable to a tight turn.
123
How can we permanently wave someones hair?
1) Reduce disulfide bonds to seperate cysteines
2) Curl the hair with heat
3) Oxidize the hair to form new disulfide bonds with the curled formation
124
What are the roles of soluble proteins (globular)?
Antibodies, enzymes, structural
125
What are the roles of membrane proteins?
Hydrophobic proteins, transporters, receptors
126
What are the roles of fibrous/structural proteins?
Keratin, muscles (myosin), spider webs (silk)
127
How many pKa values does glycine have? It can act as a buffer in how many regions?
- Two pKa values (carboxyl and amino group)
| - Buffer in two regions
128
What is the most likely charge of tyrosine at pH 7?
Neutral
129
What is the probability of histidine to have a positive charge at ph=7? ph=6?
pH7: 10%
pH6: 50%
Very sensitive to pH change in the physiological range
130
What is the phi angle between? Psi? Peptide bond?
Phi: N-Ca
Psi: Ca-C
Peptide bond: C-N
