Chapter 3: 3.2 Protein Structure

Question 1

What are amino acids comprised of?

Answer 1

1. A basic amino group (-NH2)
2. Acidic carboxyl group (-COOH)
3. A hydrogen (H)
4. A side chain (-R) attached to an α-carbon

Question 2

How are peptide bonds formed? What type of bonds are they?

Answer 2

Created from the reaction of a carboxyl group of one amino acid to the amino group of a second amino acid
* This is a covalent bond

Question 3

There are – essential amino acids

Answer 3

1. 20

Question 4

What determines what group an amino acid belongs to?

Answer 4

The side chain (at pH 7.0)

Question 5

List

The 20 amino acids

Answer 5

1. Glycine (G) (Gly)
2. Alanine (A) (Ala)
3. Valine (V) (Val)
4. Leucine (L) (Leu)
5. Isoleucine (I) (Ile)
6. Methionine (M) (Met)
7. Phenylalanine (F) (Phe)
8. Tryptophan (W) (Trp)
9. Proline (P) (Pro)
10. Serine (S) (Ser)
11. Threonine (T) (Thr)
12. Cysteine (C) (Cys)
13. Tyrosine (Y) (Tyr)
14. Asparagine (N) (Asn)
15. Glutamine (Q) (Gln)
16. Aspartate (D) (Asp)
17. Glutamate (E) (Glu)
18. Lysine (K) (Lys)
19. Arginine (R) (Arg)
20. Histidine (H) (His)

Question 6

Which amino acids have nonpolar side chains?

Answer 6

1. Glycine
2. Alanine
3. Valine
4. Leucine
5. Isoleucine
6. Methionine
7. Phenylalanine
8. Tryptophan
9. Proline

Question 7

Which amino acids have polar side chains?

Answer 7

1. Serine
2. Threonine
3. Cysteine
4. Tyrosine
5. Asparagine
6. Glutamine

Question 8

Which amino acids have electrically charged side chains?

Answer 8

Acidic
1. Aspartate
2. Glutamate

Basic
1. Lysine
2. Arginine
3. Histidine

Question 9

The ——– group of one amino acid binds to the —– group of an adjacent amino acid forming a ——- bond

Answer 9

1. Carboxyl
2. Amino
3. Peptide

Question 10

Define:

Primary Structure

Answer 10

The sequence of amino acids in a chain

Question 11

In primary structure:

How is the protein sequence written?

Answer 11

In N to C direction
* One end has an amino group (NH2)
* One has a carboxyl group (COOH) left open

Question 12

Define:

Secondary Structure

Answer 12

Refers to the conformation of the protein as a result of hydrogen bonds between the carbonyl oxygen and the hydrogen of the amino group of amino acids within the primary structure

Question 13

What can secondary structure be like?

Answer 13

• α-helix
• β-pleated sheet

Question 14

Define:

Tertiary Structure

Answer 14

Refers to the 3-D shape of the protein as it curls and folds as a result of bonding between R-groups

Question 15

What forces contribute to the tertiary structure? (5)

Answer 15

1. Disulphide bonds between two cysteine residues
2. Ionic interactions
3. Hydrogen bonds
4. van der Waals forces
5. The Hydrophobic effect

Question 16

Define:

Quaternary Structure

Answer 16

Refers to the binding of two or more polypeptide chains together

Question 17

True or False:

Quaternary structures form by non-covalent interactions

Answer 17

True

Question 18

Compare:

Hydrophobic group vs. Hydrophilic group

Answer 18

• Hydrophobic group: Ones that don’t bind well with water
• Hydrophilic group: Bind to water well through H-bonds

Question 19

Describe:

Hydrophobic amino acids

Answer 19

• Generally non-polar (hydrocarbons)
• No electronegative molecules to create a permanent dipole needed to H-bond with water

Question 20

Describe:

Hydrophilic amino acids

Answer 20

• Generally polar
• Electronegative N or O to create permanent dipoles and H-bond with water

Question 21

Describe:

Globular proteins

Answer 21

Fold so that:
* Hydrophobic groups are buried in the interior core
* Hydrophilic groups remain on the surface where they can interact with water

Question 22

Describe:

Membrane spanning proteins

Answer 22

• Have a hydrophobic domain within membrane
• Have a hydrophilic domain on the extracellular and intracellular surfaces

Question 23

What is protein denaturation?

Answer 23

Temperatures above a certain threshold (melting temperature or Tm) cause proteins to unfold due to breaking of non-covalent bonds

Question 24

In protein denaturation:

Tertiary structure goes to what structure in denaturing?

Answer 24

Primary structure

Question 25

# In protein denaturation: What is the melting temperature (Tm) determined by?

Answer 25

Determined by the strength of the interaction

Question 26

# In primary structure: Which of the following bonds are formed? 1. Covalent bonds between backbone atoms 2. Covalent bonds betwen R groups 3. Non-covalent bonds between backbone atoms 4. Non-covalent bonds between backbone and R groups 5. Non-covalent bonds between R groups

Answer 26

1 only

Question 27

# In secondary structure: Which of the following bonds are formed? 1. Covalent bonds between backbone atoms 2. Covalent bonds betwen R groups 3. Non-covalent bonds between backbone atoms 4. Non-covalent bonds between backbone and R groups 5. Non-covalent bonds between R groups

Answer 27

1 and 3

Question 28

# In tertiary structure: Which of the following bonds are formed? 1. Covalent bonds between backbone atoms 2. Covalent bonds betwen R groups 3. Non-covalent bonds between backbone atoms 4. Non-covalent bonds between backbone and R groups 5. Non-covalent bonds between R groups

Answer 28

1, 2, 3, 4, and 5

Question 29

# In quaternary structure: Which of the following bonds are formed? 1. Covalent bonds between backbone atoms 2. Covalent bonds betwen R groups 3. Non-covalent bonds between backbone atoms 4. Non-covalent bonds between backbone and R groups 5. Non-covalent bonds between R groups

Answer 29

1, 2, 3, 4, and 5