Amino Acids & Proteins

Question 1

What are the three aromatic amino acids?

Answer 1

1. Phenylalanine (nonpolar)
2. Tryptophan (nonpolar)
3. Tyrosine

Question 2

What are the acidic amino acids?

Answer 2

1. Glutamic Acid

2. Aspartic Acid

Question 3

What are the basic amino acids?

Answer 3

Histidine
Arginine
Lysine

Question 4

What is the molecular weight of a single amino acid?

Answer 4

110 Daltons (Da)

Question 5

If a protein has 450 amino acids, what is it’s molecular weight?

Answer 5

450 x 110 = 49,500 = ~ 50

Question 6

What is a “residue?”

Answer 6

an amino acid within a polypeptide

Question 7

What types of bonds make up amino acids?

Answer 7

peptide bonds

Question 8

What residues are most prone to phosphorylation and why?

Answer 8

Serine, Tyrosine, Threonine

they all have a hydroxyl group (O attacks P)

Question 9

What is “phosphorylation?”

Answer 9

addition of a phosphate group

causes a protein to become more negative ( - )

Question 10

What amino acid can form disulfide bridges?

Answer 10

Cysteine

Question 11

What bonds are found within the primary structure of a protein?

Answer 11

peptide bonds

Question 12

What is the “primary” structure of a protein?

Answer 12

the linear order of amino acids

Question 13

What is the “secondary” structure of a protein?

Answer 13

the folding of amino acids (alpha helix, beta sheet)

Question 14

What are the primary bonds found within the secondary structure of a protein?

Answer 14

Hydrogen bonds

Question 15

What type of interactions are found within the tertiary structure of a protein?

Answer 15

distant interactions

• Hydrogen bonds
• van der walls forces
• disulfide bridge formation

Question 16

What are the main methods of protein denaturation?

Answer 16

• temperature
• pH
• chemicals
• enzymes

Question 17

Temperature can disrupt what levels of protein structure?

Answer 17

2, 3, 4

Question 18

pH can disrupt what levels of protein structure?

Answer 18

3, 4

Question 19

Chemicals can disrupt what levels of protein structure?

Answer 19

2, 3, 4

Question 20

Enzymes can disrupt what levels of protein structure?

Answer 20

1 - which prevents the formation of 2-4

Question 21

Amino acids uniformly have what configuration?

Answer 21

L

Question 22

What is the “isoelectric point” for a polypeptide?

Answer 22

this is the pH at which the molecule does not have a net charge

Question 23

What is a zwitterion?

Answer 23

a molecule with both a positive and negative charge

Question 24

What are the only amino acids with branched alkyl side chains?

Answer 24

Leucine, Isoleucine and Valine

*any “L” / “I” / “V” would count as a cleavage point

Question 25

What is the function of proteases?

Answer 25

they cleave peptide bonds at specific points, either at the N-terminus side or the C-terminus side

Question 26

What are protein domains?

Answer 26

distinct regions in a polypeptide that fold independently

Question 27

When will an ionizable amino acid become “protonated?”

Answer 27

protonated = pick up H+

at LOW pH

Question 28

When will an ionizable amino acid become “deprotonated?”

Answer 28

deprotonated = lose H+

at HIGH pH

Question 29

When does steric hindrance occur?

Answer 29

when 2 electron clouds in close proximity repel each other

“the milk freeway” are the a.a with large side chains

M, I, L, K, F, R, W, Y

Question 30

Folding to unfolding proteins

Answer 30

negative to positive

Question 31

What 2 amino acids contain sulfur?

Answer 31

Cysteine and Methionine

Smoke: Crystal Meth

Question 32

What amino acid is associated with radiolabeling?

Answer 32

Methionine

Question 33

What is the only amino acid with an amine in its side chain?

Answer 33

Lysine (K)

Question 34

What is the result of acetylation?

Answer 34

brings in a ( - ) charge to neutralize the (+ ) charge on the histones

-looser structure creates euchromatin

Question 35

What is the result of de-acetylation?

Answer 35

returns ( + ) charge to histones

-denser chromatin = decreased transcription / gene expression

Question 36

What is the driving force of tertiary structure (ie protein folding)?

Answer 36

the hydrophobic effect

Question 37

What is the “hydrophobic effect?”

Answer 37

hydrophobic / water hating molecules are buried on the interior of proteins, preventing water from forming solvation layers

Question 38

When will a protein gain protons to become positively charged?

Answer 38

if the ambient pH is lower than the protein’s isoelectric point (pl)

Question 39

When will a protein lose protons to become negatively charged?

Answer 39

if the ambient pH is higher than the protein

s isoelectric point (pl)

Question 40

Are phosphates positively or negatively charged?

Answer 40

negatively charged ( - )