Chapter 6 Flashcards

1
Q

What is conformation?

A

Every functional 3D structure from the same organism is exactly the same.

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

Why do proteins assume a certain conformation?

A

Because it’s thermodynamically favorable (lowest Gibbs free energy).

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

What are the four levels of protein organization?

A

A protein’s primary structure is defined as the amino acid sequence of its polypeptide chain; the secondary structure is the local spatial arrangement of a polypeptide’s backbone (main chain) atoms; tertiary structure refers to the three-dimensional structure of an entire polypeptide chain; and quaternary structure is the three-dimensional arrangement of the subunits in a multisubunit protein.

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

What are the two principles to remember?

A

1)Hydrophobic residues are buried within a protein’s core.
2)The number of hydrogen bonds and ionic interactions within a protein is maximized.

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

The stability of a protein’s structure is maintained through what?

A

Weak interactions (hydrogen bonds, hydrophobic/hydrophilic interactions, ionic interactions, van der Waals interactions, disulfide bonds).

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

What is the primary structure of proteins?

A

Amino acids joined together in a linear way by peptide bond; with no folding.
The primary covalent bond in proteins is the peptide bond, which constrains the conformation of the polypeptide.

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

What configuration do almost all peptide bonds in proteins occur in?

A

Trans configuration.

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

What are the three dihedral angles peptide conformations are defined by?

A

phi, psi, omega

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

What bonds does phi involve?

A

C-N-C(alpha)-C bonds, with rotation occurring about the N-C(alpha) bond.

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

What bonds does psi involve?

A

The N-C(alpha)-C-N bonds

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

What bonds does omega involve?

A

The peptide bond C(alpha)-C-N-C(alpha), where rotation is constrained.

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

Which dihedral angle is not often considered? Also, think about what happens to it regarding trans and cis configurations.

A

The omega angle, because peptide bonds are almost always trans, which constrains omega to be + or - 180 degrees. When the peptide bond is cis, omega = 0 degrees.

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

What degree are phi and psi when the first and fourth atoms are furthest apart and the peptide is fully extended and all the peptide groups are in the same plane?

A

180 or -180 degrees

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

When omega is 0 degrees, what configuration is it? What about 180 degrees?

A

0- cis
180- trans

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

What is the secondary structure of proteins?

A

The simplest secondary structure that a peptide can assume is the alpha helix. With the “R” group protruding from the helical structure of the peptide.

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

How many protein structures are alpha helices?

A

1/4th of all protein structures.

17
Q

Why is there a predominance of alpha helices as secondary structures?

A

Due to their stability from extensive internal hydrogen bonding.

18
Q

What conformation do alpha helices have in nature?

A

The right-handed conformation. The left-handed conformation has never been observed in nature.

19
Q

What types of amino acids can form right-handed alpha helices, and how do they have to do it?

A

D-amino acids and L-amino acids. In order to do so, the alpha helix must be a homogenous mix of either stereoisomer.

20
Q

Because of the shape of an alpha helix, the R group of amino acids 3 or 4 residues apart must be what?

A

Compatible.

21
Q

What does Proline cause in alpha helices?

A

A kink

22
Q

What is flexible, and a major component of alpha helices, though by themselves, don’t form an alpha helices?

A

Glycine

23
Q

Every alpha helix has what on the N and C - terminals?

A

A dipole.

24
Q

In beta-pleated sheets, what conformation are the peptide bonds in and what amino acid do they involve?

A

Cis conformation and proline.

25
Q

What are fibrous proteins?

A

Linear proteins with polypeptide chains arranged in long sheets or strands. Insoluble proteins, that give strength and flexibility to the biological structures they make up.

26
Q

What are globular proteins?

A

Spherical proteins with polypeptide chains arranged in a spherical or globular shape.

27
Q

What is scurvy?

A

A disease caused by the lack of Vitamin C (L - ascorbic acid), which causes a degeneration of connective tissue.

28
Q

What is Vitamine C inadvertently necessary for?

A

The hydroxylation of proline makes 4-hydroxyproline because it restores prolyl 4- 4-hydroxylase.

29
Q

What are some symptoms of scurvy?

A

Loss of teeth, pale skin, sunken eyes

30
Q

What is fibroin the main component of?

A

Silk. Produced by spiders and insects, the polypeptide chains are made up of layers of antiparallel beta-sheets.

31
Q

What is a motif?

A

A recognizable folding pattern involving 2 or more elements of secondary structure and the connections between them.

32
Q

What is a supersecondary structure and a fold?

A

The same as a motif.

33
Q

What is a domain?

A

Part of a polypeptide chain that is independently stable or could undergo movements as a single entity with respect to the entire protein.

34
Q

What is X-ray crystallography?

A

X-ray diffraction patterns are generated from a crystal of a protein, and the diffraction pattern is used to calculate the 3D electron-density map. The electron density map shows the atomic nuclei, so a structure can be pieced together. The diffraction pattern is for the heme in myoglobin.

35
Q

When molecules get complicated, what can resolve their structure and how?

A

2D NMR can resolve their structure by overlapping two different NMR frequencies.

36
Q

What are the different types of structural motifs?

A

Beta-alpha-beta loop, Beta - barrel, alpha/beta barrel

37
Q

What is denaturation?

A

The loss of 3D structure sufficient enough to cause a loss in function.

38
Q

What can proteins be denatured by?

A

heat, pH, organic solvents (alcohol or acetone), solutes (urea, guanidine, hydrochloride), and detergents (SDS).

39
Q

What is Tm (melting temp)?

A

The point at which half of the
protein is denatured.