2. Protein Structure and Function Flashcards
1
Q
What are the most abundant and functionally versatile macromolecules in living systems?
A
Proteins
2
Q
What are amino acids?
A
Monomers that make up polypeptides
3
Q
Which bonds are the alpha carbon of amino acids bonded to?
A
- carboxylic acid group
- amino group
- R group (side chain)
- hydrogen
4
Q
T/F
All amino acids are chiral except glycine
A
True
5
Q
We see the ___ isomers of amino acids in nature
A
L
6
Q
Where is the carboxylic acids groups pKa typically at?
A
3
7
Q
About what pKa do amino groups have?
A
9
8
Q
T/F A zwitterion is overal neutral and has positive and negative groups
A
True
9
Q
What is the 3 letter abbreviation for Glycine?
A
Gly
- simplest amino acid
- only amino acid that is not chiral
- nonpolar
10
Q
What is the 3 letter abbreviation for Alanine
A
Ala
nonpolar
11
Q
What is the 3 letter abbreviation for Valine?
A
Val
- forms a v in the structure
- nonpolar
12
Q
What is the 3 letter abbreviation for Leucine?
A
Leu
- nonpolar
13
Q
What is the 3 letter abbreviation for Isoleucine?
A
Ile
-nonpolar
14
Q
What is the 3 letter abbreviation for Methionine?
A
Met
- Nonpolar
15
Q
What is the 3 letter abbreviation for Proline?
A
Pro
- Nonpolar
- 1st aromatic amino acid
16
Q
What is the 3 letter abbreviation for Phenylalanine?
A
Phe
- Nonpolar
- Aromatic
17
Q
What is the 3 letter abbreviation for Tryptophan?
A
Trp
- nonpolar
- 2 aromatic rings
18
Q
What is the 3 letter abbreviation for Serine?
A
Ser
-polar uncharged
19
Q
What is the 3 letter abbreviation for Threonine?
A
Thr
-polar uncharged
20
Q
What is the 3 letter abbreviation for Tyrosine?
A
Tyr
- aromatic
- polar uncharged
21
Q
What is the 3 letter abbreviation for Cysteine?
A
Cys
- SH
- polar uncharged
22
Q
What is the 3 letter abbreviation for Asparagine?
A
Asn
-polar uncharged
23
Q
What is the 3 letter abbreviation for Glutamine?
A
Gln
-polar uncharged
24
Q
What is the 3 letter abbreviation for Lysine?
A
Lys
- positively charged amino acids
25
What is the 3 letter abbreviation for Arginine?
Arg
- positively charged amino acids
26
What is the 3 letter abbreviation for Histidine?
His
- positively charged amino acids
27
What is the 3 letter abbreviation for Aspartate
Asp
- negatively charged
28
What is the 3 letter abbreviation for Glutamate?
Glu
- Negatively charged amino acids
29
Name the typical pKa of terminal a-carboxyl group
3.1
30
Name the typical pKa of aspartic acid and glutamic acid
4.1
31
Name the typical pKa of histidine
6.0
32
Name the typical pKa of terminal a-amino group
8.0
33
Name the typical pKa of cysteine
8.3
34
Name the typical pKa of tyrosine
10.9
35
Name the typical pKa of Lysine
10.8
36
Name the typical pKa of Arginine
12.5
37
Name the amino acid: Ala
Alanine
38
Name the amino acid: Arg
Arginine
39
Name the amino acid: Asn
Asparagine
40
Name the amino acid: Asp
Aspartic acid
41
Name the amino acid: Cys
Cysteine
42
Name the amino acid: Gln
Glutamine
43
Name the amino acid: Glu
Glutamic acid
44
Name the amino acid: Gly
Glycine
45
Name the amino acid: His
Histidine
46
Name the amino acid: Ile
Isoleucine
47
Name the amino acid: Leu
Leucine
48
Name the amino acid: Lys
Lysine
49
Name the amino acid: met
Methionine
50
Name the amino acid: Phe
Phenylalanine
51
Name the amino acid:Pro
Proline
52
Name the amino acid: Ser
Serine
53
Name the amino acid: Thr
threonine
54
Name the amino acid: Trp
Tryptophan
55
Name the amino acid: Tyr
Tyrosine
56
Name the amino acid: Val
Valine
57
At pH = 2, what is the net charge on the amino acid leucine?
+1
58
At pH = 1, what is the net charge on the amino acid aspartic acid?
+1
59
At pH = 7, what is the net charge on the amino acid aspartic acid?
-1
60
At pH = 11, what is the net charge on the amino acid aspartic acid (aspartate)?
-2
61
What is the primary structure of amino acids?
The sequence of amino acids linked by peptide bonds
62
Which bonds are present in primary amino acid structure?
peptide bonds
63
What is the term for two amino acids linked together?
Dipeptide
64
Is there rotation about the peptide bond?
No they are planar, no rotation around the bond
65
What is the directionality of a polypeptide chain?
N-terminus to C-terminus
66
T/F there are steric interactions that have to be taken into consideration in primary protein structure
True
67
T/F
| Polypeptides have directionality
True
68
What is the net charge at pH = 5 on the tripeptide Tyr-His-Ala?
+1
69
What is the net charge at pH = 12 on the tripeptide Cys-Val-Glu?
-3
70
Almost all peptide bonds are _____ this prevents steric clashes between R groups
trans
71
The bond between the alpha carbon and the amino group is the ____-
phi bond
72
The bond between the alpha carbon and the carbonyl bond is the _____
psi bond
73
What does a ramachandran plot show?
The favorable combination of phi and psi bonds. Dark green shows the most favorable
74
How are protein structures determined?
- x-ray crystallography
- cryo-electron microscopy
- AI --> alpha fold 2, a computer algorithm
75
What is alpha fold 2?
A computer algorithm that can help determine protein structures
76
What type of bonds/interactions contribute to the primary structure of a protein?
covalent bonds
77
Define protein secondary structure:
Local folded protein structure that is due to interactions between atoms in the protein backbone (main chain)
78
Who discovered the alpha helix?
Linus pauling
79
What are the characteristics of alpha helices?
- tightly coiled backbone
- side chains extend outward
- stabilized by hydrogen bonds between N-H group on one amino acid and C=O group (4 amino acid residues ahead)
- 3.6 amino acid residues per turn
- right handed helices in nature
80
How many amino acid residues per turn in alpha helices?
3.6
81
What are the characteristics of beta sheets?
- links of beta strands running parallel or anti parallel
- direction indicated by arrows in ribbon diagrams
- most adopt a somewhat twisted shape
- strands don't need to be neighbors in amino acid sequence
82
In the protein antiparallel beta sheet, which of the following is true?
A. The beta sheet is stabilized by hydrogen bonds between R groups
B. One strand can hydrogen bond to two other strands
C. One strand can hydrogen bond to one other strand
D. Hydrogen bonds are formed between and amino acid and the fourth amino acid ahead
One strand can hydrogen bond to two other strands
83
What is the main type of bond/interaction that stabilizes protein structure?
Hydrogen bonds
84
Define tertiary structure of proteins:
the overall 3d structure resulting from folding and covalent cross-linking of a polypeptide
85
What are the characteristics of 3d protein structure?
- result of the interaction between r groups
- generally the interior consists almost entirely of nonpolar residues with polar residues on the outside
- motifs
- domains
86
what are motifs?
combination of secondary structure with a particular role
* **Super secondary structure
ex. helix turn helix
87
What are domains?
Compact globular units connected by a short polypeptide strand
ex. CD4 domains, same polypeptide but look like 4 globular units
88
Cysteine residues each have a _____ group and these link to form _______ bonds
thiol
disulfide
This is how you get a perm, the solution put on the hair links covalent disulfide bonds
89
Define quaternary structure:
multiple polypeptide chains (subunits) that assemble into a functional protein
- subunits can be the same or different
- nomenclature: alpha, beta, gamma
Hemoglobin: alpha 2 beta 2 (tetramer)
90
Define protein denaturation:
loss of secondary, tertiary, or quaternary structure of a protein
91
What are the 3 ways proteins can be denatured?
- heat
- pH
- kinetic energy
92
```
An enzyme is found to consists of two identical subunits. Which of the following would be an appropriate representation of the quaternary structure?
a2
ab
b2
ay
```
a2
93
Disulfide bonds are formed between pairs of which amino acid?
Cysteine
