Protein Structure

Question 1

What determines the 3D shape of a protein?

Answer 1

The AA sequence

Question 2

What forces stabilize the shape?

Answer 2

Non covalent interactions

Question 3

What mediates interactions between proteins and other substances?

Answer 3

Non covalent interactions

Question 4

What is a zwitterion?

Answer 4

A positive charge and negative charge on different atoms in a molecule

Question 5

When the pH is greater than the pKa, the acid exists predominantly as…

Answer 5

the conjugate base form (DEprotonated)

Question 6

When the pH is less than the pKa, the acid exists predominantly as…

Answer 6

the acid form (protonated)

Question 7

Define a polypeptide.

Answer 7

Long chain of amino acids (protein)

Question 8

The sequence of amino acids is the _______ structure.

Answer 8

primary

Question 9

List the properties of peptide bonds.

Answer 9

• the electrons in peptide bonds are somewhat delocalized generating two resonance forms
• therefore exhibit partial double bond character with no rotation around the C-N bond
• the functional groups in peptide bonds are potential H-bond acceptors or donors
• polar

Question 10

What two key words describe secondary structure?

Answer 10

Local and backbone

Question 11

Describe secondary structure.

Answer 11

• local folding of the polypeptide backbone
• allows for H-bonding of the groups in the polypeptide backbone (C=O, N-H)
• “regular” secondary structures occur when each amino acid adopts the same geometry
• alpha helix and beta sheet

Question 12

Is a loop a part of secondary structure?

Answer 12

Yes

Question 13

Is a loop a part of regular secondary structure?

Answer 13

No

Question 14

How does an alpha helix form H-bonds?

Answer 14

The carbonyl oxygen of each residue forms an H-bond with the backbone -NH groups FOUR residues down. (C1…N5)

Question 15

What forces stabilize alpha helices and beta sheets?

Answer 15

H-bonds between the backbone residues

Question 16

What is tertiary structure?

Answer 16

Arrangements of all atoms in a single polypeptide (arrangements of secondary structures in relation to one another)

Question 17

What are the two main protein classes?

Answer 17

Fibrous and globular

Question 18

Describe globular proteins.

Answer 18

• essentially soluble in aq solutions

- fold into compact structures with non polar cores and polar surfaces

Question 19

In a globular protein, hydrophobic amino acids are most likely to be found in the ________.

Answer 19

Interior

Question 20

What is the main stabilizing force for tertiary structure?

Answer 20

Hydrophobic effect

Question 21

What forces “fine tune” tertiary structure of a protein?

Answer 21

H-bonds

Question 22

Where will you find disulphide bridges (cys-cys)?

Answer 22

extracellular (reducing conditions)

Question 23

Define domain.

Answer 23

A polypeptide segment that has folded into a single structural unit with a hydrophobic core. Proteins may encode more than one domain.

Question 24

Define motif.

Answer 24

A short region of polypeptide with a recognizable 3D shape. A common grouping of secondary structural elements.

Question 25

Describe a zinc finger.

Answer 25

A single Zn2+ ion is COORDINATED by 2Cys and 2His residues.

Question 26

What is a coordination bond?

Answer 26

1 atom getting 2 electrons from a single atom.

Question 27

Define prosthetic group.

Answer 27

A nonprotein component that is permanently incorporated into a protein. These provide structure and reactive groups.

Question 28

What is quaternary structure?

Answer 28

Proteins composed of more than one polypeptide chain (subunit)

Question 29

What is the main stabilizing force of quaternary structure?

Answer 29

Hydrophobic effect