Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

XX. BioChemistry > Chp 4: Protein Structure > Flashcards

Chp 4: Protein Structure Flashcards

(92 cards)

Start Studying
1
Q

What are polymers made of proteins called?

A

Amino Acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Draw the general structure of an amino acid at physiological pH

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Under what conditions can cysteine form a disulfide bond?

A

Oxidative conditions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the approximate pKa of ionizable Asp?

A

4.0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the approximate pKa of ionizable His?

A

6.0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the approximate pKa of ionizable Glu?

A

4.0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is the approximate pKa of ionizable NH3+ N-terminus?

A

9.0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is the approximate pKa of ionizable Cys?

A

8.0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the approximate pKa of ionizable Tyr?

A

10.5

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the approximate pKa of ionizable Lys?

A

10.5

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the approximate pKa of ionizable Arg?

A

12.5

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Relative abundance of amino acids in proteins

A

In nature, Leucine is the most abundant and Tryptophan is the least abundant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Average MW of an amino acid

A

110 Da when found in a protein

1 Da (Dalton) = 1 atomic mass unit (amu)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How the peptide bond is formed

A

Peptide bonds are made by condensation reactions. Amino acids in the peptide are called “amino acid residues” because only the residue atoms remain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Meaning of polypeptide chain-related terms: amino acid residue, amino- and carboxyl-terminal residues, and chain directionality

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Properties of the peptide bond

A

The peptide bond has two resonance forms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Why rotation around N-Ca-C is restricted

A

Rotation around N-Ca-C is restricted due to steric constraints

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

The four levels of protein structure

A

Primary Structure

Secondary Structure

Tertiary Structure

Quaternary Structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Definition of the secondary structure of proteins

A

The spatial arrangement of the polypeptides backbone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

How the a-helix is specifically formed, stabilized, and ways to represent it

A

There are 3.6 amino acid residues in the helix.

H-bonds along the helical axis stabilize this structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

How the b-pleated sheet is specifically formed, stabilized, and ways to represent it

A

beta-pleated sheets are antiparallel and are extended compared to the double helix. Beta strands can be connected by turns or loops.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

How the beta strands can be connected to form sheets

A

Colinear H-bonds create stability

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

How are B strands connected through H-bonds on the B sheet?

A

Beta strands can be connected by turns or loops of stabilizing H-bonds with irregular secondary structures. Antiparallel beta sheets are easily connected

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Distinguish parallel and anti-parallel b-sheets

A

Parallel beta-sheet strands run up the same way starting with carbon and ending with nitrogen. Antiparallel beta-sheet strands run opposite to each other

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Which beta sheet type is more stable and why
Antiparallel because the colinear H bonds create stability and are easily connected
26
How proteins differ in their composition
Proteins differ in their composition by the number of amino acid residues. The normal range of the number of amino acid residues is 153 (myoglobin) - 416 (phosphorylase kinase (yeast)). (#AA residues)(110)=Molar mass
27
Definition of 3o structure of proteins, ways to represent it, and their advantages
The tertiary structure is the overall three-dimensional structure of a polypeptide made of interactions between the R-groups of the amino acids that make up the protein. **Tertiary structures have hydrophobic interactions**, in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules. There’s one special type of covalent bond that can contribute to tertiary structure: the disulfide bond. **Disulfide bonds**, covalent linkages between the sulfur-containing side chains of cysteines, are much stronger than the other types of bonds that contribute to tertiary structure. They act like molecular "safety pins," keeping parts of the polypeptide firmly attached to one another.
28
Recognize protein types: all-alpha, all-beta, alpha/beta
29
How to identify layers in proteins and the location of non-polar residues
polar molecules are exterior and nonpolar molecules are on the interior or the proteins
30
Major stabilizing force of the tertiary structure
*The largest force governing protein structure is the hydrophobic effect* which causes nonpolar groups to aggregate in order to minimize their contact with water.
31
Meaning of a protein domain
Domain: a polypeptide segment that has folded into a single structural unit with a hydrophobic core
32
General principles of globular proteins
* Typically at least 2 layers of secondary structure * Hydrophobic core * Typically rich in secondary structure * H-bonds minimize hydrophilicity of the polar backbone groups * Hydrophilic surface * Typically with irregular structure * Polar backbone groups of loops can form H-bonds with water
33
Correlation of residue’s hydrophobicity with location
The greater the residue's hydrophobicity is, the more likely it is found in the interior of the protein
34
Role of ions pairs, disulfide bonds, and metals in the stabilization of proteins
Some proteins are stabilized by electrostatic or ionic interactions.
35
Characteristics of protein folding *in vivo* vs *in vitro*
In Vivo: a newly synthesized polypeptide begins to fold as it leaves the ribosome 1. may require molecular chaperones 2. post-translation process In Vitro: full-length polypeptide is denatured and then allowed to renature. 1. Not a random process 2. Afinsen found that primary structure determines tertiary structure
36
Molecular chaperones: what they are and what they do
In the laboratory, certain small proteins can be repeatedly denatured and renatured, but in the cell, protein folding is more complicated and may require the assistance of other proteins. Some of these are known as **molecular chaperones**
37
Anfinsen’s postulate
The structure of a small globular protein is determined by the protein's amino acid sequence
38
What is the driving force of protein folding
hydrophobic effect
39
The largest stabilizing force in proteins
Hydrophobic effect. H-bonding is NOT a major determinant of protein stability
40
How to interpret the folding funnel
When the protein is in the unfolded state there are many forms and increased entropy. When the protein is in the folded state it has one conformation and decreased entropy.
41
Definition of quaternary structure
The spatial arrangement of polypeptides is known as the protein’s quaternary structure. Most proteins, especially those with molecular masses greater than 100 kD, consist of more than one polypeptide chain. The individual chains, called **subunits,** may all be identical, in which case the protein is known as a **homodimer, homotetramer,** and so on. If the chains are not all identical, the prefix ***hetero-*** is used. *The forces that hold subunits together are similar to those that determine the tertiary structures of the individual polypeptides.*
42
Meaning of a subunit
individual polypeptide chains and two or more are quarternary structures
43
Nomenclature used to distinguish the different types of quaternary structure
The individual polypeptide chains, called **subunits,** may all be identical, in which case the protein is known as a **homodimer, homotetramer,** and so on. If the chains are not all identical, the prefix ***hetero-*** is used.
44
Techniques used to separate proteins
Chromatography
45
Separation bases of size-exclusion chromatography
Separation based on size. Also called gel filtration
46
Other name of size-exclusion chromatography
gel filtration
47
Separation bases of ion-exchange chromatography
Protein separation based on differences in net charge. (-) charged proteins bind to (+) charged solid supports and (+) charges proteins bind to (-) charges sold supports
48
Components of SDS-PAGE
Used to verify purification of a protein. Separation is based on mass and size
49
Separation bases of SDS-PAGE
BetaME is added to reduce disulfide bonds. SDS is added to denature protein and add a (-) charge. 1 SDS bonds uniformly along the chain every 2 amino acid residues and the protein is separated on the basis of mass or size.
50
D. Asp
51
B
52
D. Asp
53
B. His
54
D. Polar Neutral
55
B. Acidic
56
C. Tyr
57
C. T N Y
58
B. +1
59
D. Cys
60
E. W, Y, F
61
E. W
62
C. Glu
63
E. His
64
E. L & W
65
B. b
66
C. A pentapeptide with 4 peptide bonds
67
E. 5
68
B. -1
69
E. +2
70
71
A. a
72
C. 5 18/3.6=5
73
C. It is not stabilized by the H-bonds
74
A. Alpha helix
75
D. An anitparallel Beta sheet
76
C. Parallel beta sheets are more stable than anti-parallel ones
77
C. The protein's amino acid sequence (primary structure)
78
B. Disulfide bond
79
E. Hydrophobic interactions
80
B. The tendency of non-polar molecules to avoid interaction with water and thus aggregate
81
C. Leu; Ser
82
C. Glu (-) - Asn - Ser - Thr - Arg (+)
83
C. E (glutamate)
84
B. His; H-bond Ser is polar nuetral
85
What is the abbreviated form of hemoglobin?
alpha2beta2
86
What are the 3 most commonly used types of chromatography?
1. Ion-exchange chromatography 2. Gel-filtration chromatography 3. Affinity chromatography
87
D. Gel-filtration chromatography
88
E. All of the above
89
B. Largest
90
B. Size
91
E. Lysozyme, hemoglobin, TPI
92
D. Hemoglobin, TPI, myoglobin, lysozyme

XX. BioChemistry (15 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions