Lecture 2: Protein

Question 1

can you draw an amino acid and label every group?

Answer 1

• see notes

Question 2

What makes negatively charged /acidic side chains different? List all the negatively charged amino acids (2)

Answer 2

• side chains can form H bonds or ionic bonds
• aspartate
• glutamate

Question 3

List the polar amino acids (5) and their property

Answer 3

• serine
• threonine
• tyrosine (also aromatic)
• asparagine
• glutamine
• can form H bonds

Question 4

peptide bonds

Answer 4

chemical bonds formed between 2 molecules when the carboxyl group of one molecule reacts with the amino group of another; the process of creating this bond creates an H2O molecule

Question 5

condensation vs dehydration

Answer 5

forward vs backward reaction of A+B–> AB + H2O

Question 6

residue

Answer 6

specific monomer within polymeric chain

Question 7

Explain protein sequences through 3 properties

Answer 7

• sequence always goes N - C
• N terminus is considered residue 1
• only side chains are charged except terminals

Question 8

List the positively charged/ basic side chains (3)

Answer 8

• lysine
• arginine
• histidine

Question 9

List the amides of aspartate and glutamate

Answer 9

• asparagine and glutamine

Question 10

List the non polar amino acids (10)

Answer 10

• glycine
• leucine
• alanine
• methionine
• valine
• isoleucine
• proline
• phenylaline
• tryptophan
• cysteine

Question 11

List the aromatic side chains (2)

Answer 11

• phenylaline

- tryptophan

Question 12

condensation vs dehydration

Answer 12

• condensation: forwards synthesis and remove water

- dehydration: backwards synthesis add water

Question 13

how many residues in an oligopeptide

Answer 13

• 3-50 amino acid residues

Question 14

polypetide; aka?

Answer 14

• protein

Question 15

explain the secondary, tertiary, and quaternary structure of proteins

Answer 15

• secondary: alpha helix or B- pleated sheet (H bonds every 3 residues); see notes for picture
• tertiary: side chains interact and form bonds (H bonds, ionic bonds, disulfide bonds)
• quaternary: protein with more than one subunit (dimer2 vs tetramer4)

Question 16

native protein

Answer 16

• correctly folded protein/ protein strucutre how it occurs naturally

Question 17

• denatured protein

Answer 17

• non functional/ unfolded protein; bonds are broken and thats how it becomes unfolded
• heat or an irregular pH environment can cause it to become denatured

Question 18

the protein backbone is flexible and can freely rotate except around which bond?

Answer 18

• peptide bond