pH, Acids, Bases, Buffers, Protein Structure, and Folding Activity

Question 1

Are polypeptide bonds in a trans- or cis-configuration

Answer 1

They can be both but are usually found in the trans-configuration

Question 2

What forces contribute to protein folding?

Answer 2

• Hydrogen bonding between neutral groups and between peptide bonds
• Ionic interactions (attraction and repulsion)
• Hydrophobic interactions

Question 3

What amino acids have polar and uncharged R groups?

Answer 3

• Glutamine
• Cysteine
• Asparagine
• Threonine
• Serine

The uncharged R groups on these amino acids can participate in Hydrogen Bonding

Question 4

What amino acid does di-sulfide bonds form between

Answer 4

Cystein

Question 5

What amino acids have ionic interactions?

Which are positively charged and which are negatively charged?

Answer 5

Positively charged R groups:

• Histidine
• Arginine
• Lysine

Negatively charged R groups:

• Aspartate
• Glutamate

Question 6

What amino acids form hydrophobic interactions?

Answer 6

Aromatic R Groups:

• Phenylalanine
• Tyrosine
• Tryptophan

Nonpolar, aliphatic R groups:

• Glycine
• Alanine
• Proline
• Valine
• Leucine
• Isoleucine
• Methionine
• Form hydrophobic interactions and tend to cluster together inside of proteins or interact with hydrophobic portions of ligands

Question 7

Primary Structure

Answer 7

Linear sequence of amino acids

Question 8

Secondary Structure

Answer 8

Alpha Helixes
Beta Sheets
Beta Turns

Result of hydrogen bonding between the amide hydrogens and carbonyl oxygens of the polypeptide backbone

Question 9

Tertiary Structure

Answer 9

Overall three dimensional arrangement of a protein

Maximizes hydrogen bonding and ionic interactions. Clusters hydrophobic amino acids in the interior of the protein

Question 10

Quaternary Structure

Answer 10

Three dimensional arrangement of subunits (multiple proteins) assembled together

Question 11

What is an acidic and basic pH?

Answer 11

Acidic solutions: pH < 7

Basic solutions: pH > 7

Question 12

Why is pH in the human body important?

Answer 12

• pH values of different body fluids are related to physiological function. Ex: Stomach acid pH 1.5, Ileum pH of 8.0, Blood has a normal pH of 7.35-7.45
• pH is important in medicine and drug absorption
• pH is important for enzyme function
• pH influences the binding of oxygen to hemoglobin

Question 13

Strong acids and basis

Answer 13

Ionize completely in water

Question 14

Weak acids and bases

Answer 14

Ionize only partially in water

Question 15

What does a buffer consist of?

Answer 15

A weak acid and its conjugate base

Question 16

Acidosis

Answer 16

• Blood pH less than 7.35

- Can be fatal if pH is less than 6.8

Question 17

Alkalosis

Answer 17

• Blood pH greater than 7.45

- Can be fatal if pH is greater than 7.8

Question 18

Plasma bicarbonate buffer system

Answer 18

Maintains pH of the blood around 7.4

CO2 CO2 + H20 H2CO3 H+ + HCO3-

CO2 produced by metabolsim (mainly TCA cycle) and eliminate through respiration

H2CO3 is carbonic acid

HCO3 - is bicaronate ion (conjugate base)