Protein Structure

Question 1

In all cases, how is a protein’s function determined?

Answer 1

By its structure.

Question 2

What is a zwitterion?

Answer 2

A neutral ion with an equal number of positive and negative charges.

Question 3

What is pKA?

Answer 3

The strength of the weak acid; as pKA becomes smaller, the conjugate strong acid becomes stronger (more likely to be present in a solution).

Question 4

What happens when pKA is less than pH

Answer 4

The base form of the ion is more present in a solution. The molecule will be deprotonated.

Question 5

What happens when pKA>pH?

Answer 5

The acid form of the ion is more present in a solution.

Question 6

What is the pKA of COO-?

Answer 6

pKA = 2

Question 7

What is the pKA of NH3+?

Answer 7

pKA = 9.5

Question 8

Why are amino acids chiral? Which amino acid is the exception? Why is it important that amino acids are chiral?

Answer 8

1. They are chiral because the alpha carbon always has 4 different substituents.
2. Glycine is achiral.
3. Amino acids occur in L- and D- conformations based on their chirality (enantiomers). While L-isomers are present in living organisms and are the most common isomer, D- conformations are present in pharmacological substances and have vastly different functions from their L-type conformers.

Question 9

Which amino acids are nonpolar?

Answer 9

[A] Alanine
[V] Valine
[L] Leucine
[F] Phenylalanine
[W] Tryptophan
[P] Proline
[I] Isoleucine
[M] Methionine

Question 10

Which amino acids are polar uncharged?

Answer 10

[G] Glycine
[S] Serine
[T] Threonine
[C] Cysteine
[N] Asparagine
[Q] Glutamine
[Y] Tyrosine

Question 11

Which amino acids are polar charged?

Answer 11

[D] Aspartate
[E] Glutamate
[K] Lysine
[R] Arginine
[H] Histidine

Question 12

What is the pKA of cysteine?

Answer 12

8.5

Question 13

What is unique about cysteine?

Answer 13

It is able to form disulphide bonds with other cysteine molecules in oxidizing environments.

Question 14

What is the pKA of Tyrosine?

Answer 14

10.5

Question 15

What is the pKA of Histidine?

Answer 15

6

Question 16

What is the pKA of Aspartate?

Answer 16

4

Question 17

What is the pKA of Glutamate?

Answer 17

4

Question 18

What is the pKA of Lysine?

Answer 18

10

Question 19

What is the pKA of Arginine?

Answer 19

12.5

Question 20

Where are polar side chains typically found within a protein? Why?

Answer 20

On the surface; these groups can interact with water.

Question 21

Where are nonpolar side chains typically found within a protein? Why? What is the exception?

Answer 21

In the core to minimize interaction with water. Alanine is the exception.

Question 22

How are peptide bonds formed?

Answer 22

Peptide bonds are formed when two hydrogens from the N-terminus are accepted by an oxygen atom at the C-terminus. The result is an amide bond at the expense of a water molecule.

Question 23

What are peptides/oligopeptides?

Answer 23

A general term for a larger number of amino acids that are generally synthetically synthesized.

Question 24

What is a polypeptide?

Answer 24

A long chain of amino acids that is usually produced naturally.

Question 25

What is a protein?

Answer 25

A large polypeptide or group of polypeptides with a biological function.

Question 26

What is the primary structure of a protein? What interactions are present?

Answer 26

The basic sequence of amino acids in a polypeptide. Peptide/amide bonds between amino acids.

Question 27

What is the secondary structure of a protein? What interactions are present?

Answer 27

The local folding of the polypeptide backbone driven by hydrogen bonding between carbonyl and amino groups.

Question 28

What are the two most regular patterns of secondary structure in a protein?

Answer 28

Alpha-helix and Beta-sheet.

Question 29

How many residues downstream can carbonyl and amino groups interact in an alpha-helix?

Answer 29

4 residues downstream.

Question 30

What forces stabilize beta-sheets?

Answer 30

Hydrogen bonds between backbone CO and NH groups of neighbouring strands.

Question 31

What forces stabilize alpha-helices?

Answer 31

Hydrogen bonds between backbone CO and NH groups in the same helices.

Question 32

What is an irregular structure?

Answer 32

Polypeptide loops of varying sizes that link together regular secondary structures.

Question 33

What is the tertiary structure of a protein? What interactions are present?

Answer 33

The arrangement of all atoms in a single polypeptide; the arrangement of secondary structures in relation to one another. The structure is determined by non-covalent interactions between amino acid R-groups, as well as interactions with prosthetic groups. In some cases, salt bridges form between ionizable amino acid chains.

Question 34

What are the two classifications of tertiary structures?

Answer 34

Fibrous and Globular.

Question 35

What are fibrous proteins?

Answer 35

Insoluble in aqueous, long-filament proteins that contain limited residues with many repeats. Their primary function is structure or connectivity.

Question 36

What are globular proteins?

Answer 36

Soluble in aqueous solutions, folded into compact structures with nonpolar cores and polar surfaces.

Question 37

How is the hydrophobic effect relative in protein folding?

Answer 37

The hydrophobic effect drives soluble globular proteins to maintain a tertiary structure in which their hydrophobic cores remain compacted in the internalized structure.

Question 38

What are salt bridges?

Answer 38

Ionic interactions that form between closely-positioned charged amino acids that stabilize secondary and tertiary structure.

Question 39

What is a domain?

Answer 39

A polypeptide segment that has folded into a single structural unit with a hydrophobic core. There may be more than one present in a protein.

Question 40

What is a motif?

Answer 40

A short region of polypeptide with a recognizable 3D shape (Zinc fingers).

Question 41

What is a prosthetic group?

Answer 41

A non-peptide component in a protein that is permanently incorporated.

Question 42

What is the function of a prosthetic group?

Answer 42

To provide structure and function in different proteins.

Question 43

How are globular proteins stabilized? Are they easily denatured?

Answer 43

1. Weak noncovalent forces. | 2. Easily denatured.

Question 44

What can disrupt a disulphide bond?

Answer 44

Reducing agents (DTT)

Question 45

What is the quaternary structure of a protein?

Answer 45

The association of multiple polypeptides, stabilized by same forces as in tertiary.