pH and Protein Folding

Question 1

What forces / bonds hold a protein together at each of these levels of structure?

Answer 1

PRIMARY: Covalent peptide bonds
SECONDARY: Hydrogen bonds
TERTIARY: Ionic bond, Disulfide bridge, Hydrogen bond (Hydrophobic interactions)
QUATERNARY: Ionic bond, Disulfide bridge, Hydrogen bond (Hydrophobic interactions)

Question 2

How does each level of structure contribute to the overall shape of a protein?

Answer 2

• Primary structure puts together the unique sequence of amino acids
• Secondary coils or folds the polypeptide (R groups not involved) with H bonds
• Tertiary gives the protein its 3D shape by R group interactions
• Quaternary bonds two or more polypeptide chains through disulfide bridges and H bonds

Question 3

How are alpha helices and beta pleated sheets formed?

Answer 3

• In the secondary structure the polypeptide chain sometimes coils to form an alpha helix or folds to form a pleated sheet using H bonds
• Form between the carbonyl O of one amino acid and the amino H of another (NH to CO coming off of backbone) (never between R groups)

Question 4

What does it mean for a protein to have fibrous shape? (ex)

Answer 4

Formed when polypeptides with helical subunits form long chains running parallel to each other linked by disulfide bridges, and have structural functions

• Construct connective tissues, tendons, bone and muscle fiber
• Keratins, collagens and elastins

Question 5

What does it mean for a protein to have a globular shape? (ex)

Answer 5

Results from the compact combination of an alpha helix and several pleated sheet regions and have roles in metabolic reactions
-Haemoglobin, insulin and many enzymes in the body

Question 6

What factors affect the shape of a protein?

Answer 6

Different types of bonds at different levels of structure, such as H-bonds, ionic bonds, hydrophobic interactions, and disulfide bridges

Question 7

Given a polypeptide with certain properties and amino acid R groups, in a given environment (water, oil, vacuum) can you predict how this protein might behave / fold?

Answer 7

-

Question 8

What kinds of forces may cause a protein to denature?

Answer 8

• Heat and changes in pH, changes in salt concentration

- pH affects the charge of the amino groups and carboxyl groups on an amino acid

Question 9

What is the pH scale and what is it a measure of?

Answer 9

• It measures how acidic or basic a solution is, which is based on the amount of Hydrogen in a solution
• A pH of 0 has more Hydrogen atoms than 14, which has less

Question 10

What does it mean for a solution to be at pH 7?

Answer 10

A pH of 7 is neutral, meaning it has an equal concentration of H+ and OH- ions

Question 11

Acid (define, ex)

Answer 11

• A compound that donates Hydrogen atoms to solutions.

- Battery acid, lemon juice, vinegar

Question 12

Base (define, ex)

Answer 12

• A compound that accept Hydrogen atoms and removes them from a solution.
• Oven cleaner, bleach, milk

Question 13

Buffer (define, ex)

Answer 13

• A substance that minimizes the changes in pH by either accepting or donating hydrogens to keep the pH the same.
• Tricine, bicine, cacodylate
• Weak acid + corresponding base
• Carbonic acid in human blood (H2CO3)

Question 14

How does a change in pH potentially affect protein structure?

Answer 14

-If a change in pH is too great, a protein may denature causing it to lose its shape and function. Secondary and up are affected.

Question 15

Primary

Answer 15

-The unique sequence in which Amino Acids bond to each other through peptide bonds to create a polypeptide.

Question 16

Secondary

Answer 16

-Parts of the polypeptide fold coil or fold into local patterns such as an alpha helix or pleated sheet.

Question 17

Tertiary

Answer 17

-The 3D shape of a polypeptide due to the interactions of the R groups.

Question 18

Quaternary

Answer 18

-Exists in some proteins where two or more polypeptide chains bond together through various types of bonding.

Question 19

Covalent

Answer 19

-The sharing of electron pairs between two atoms.

Question 20

Ionic

Answer 20

-Two ions with opposite charges attract to each other.

Question 21

Hydrogen Bond

Answer 21

-Opposite ends of polar molecules stick together weakly.

Question 22

Hydrophobic Interactions

Answer 22

-The tendency of nonpolar molecules in a polar solvent to interact with one another by avoiding the solvent.

Question 23

Disulfide Bridge

Answer 23

-A covalent bond connected with two sulfur atoms connecting tertiary or quaternary structures.

Question 24

Denature / Denaturation

Answer 24

-The process in which proteins unfold due to changes in temperature or pH. Secondary structure and up are affected.

Question 25

pH

Answer 25

• The measure of how basic or acidic a solution is (Potential of Hydrogen)
• 0 is most acidic and 14 is least acidic.

Question 26

Solution

Answer 26

-A liquid consisting of a uniform mixture of two or more substances.

Question 27

Solvent

Answer 27

-The dissolving agent.

Question 28

Solute

Answer 28

-The substance being dissolved.

Question 29

Examples of proteins denaturing

Answer 29

• Irreversible - egg is fried, the albumin protein in the liquid egg white is denatured when placed in a hot pan
• Bacteria that survive in hot springs have proteins that function at temperatures close to boiling
• The stomach is also very acidic, has a low pH, and denatures proteins as part of the digestion process; however, the digestive enzymes of the stomach retain their activity under these conditions.

Question 30

How do pH changes affect amino acid structure?

Answer 30

• Affects the charge of amino and carboxyl groups (and amino acid R groups)
• Ex: carboxyl (acid) group will be uncharged at a low pH (COOH), but charged at a high pH (COO - )

Question 31

How do pH changes affect protein structure?

Answer 31

• In an aqueous solution, an equilibrium (balance) exists between the dipolar ion and the anionic and cationic forms of the amino acid
• These changes will affect bonding and weak attractions within the protein and between the protein and other molecules

Question 32

Carboxyl group

Answer 32

Acts as an acid by contributing an H+ to a solution and becoming ionized

Question 33

Amino group

Answer 33

Acts as a base by picking up an H+ from a solution