Amino Acids & Protein Structure

Question 1

What is the stereochemistry of the alpha carbon for all chiral amino acids in eukaryotes?

Answer 1

L

Question 2

where are D-amino acids found?

Answer 2

prokaryotes

Question 3

what is the configuration of all chiral amino acids & what are the two exceptions?

Answer 3

• configuration is (S)

- glycine is non-chiral and cysteine has (R) configuration

Question 4

amphoteric

Answer 4

can either accept or donate protons

Question 5

the pKa of a group is:

Answer 5

the pH at whic half of the species is deprotonated

[HA] = [A-]

Question 6

at the pH near the pI of the amino acid, the amino acid is

Answer 6

a neutral zwitterion

Question 7

pH > pKa

Answer 7

amino acid is deprotonated

Question 8

pH < pKa

Answer 8

amino acid protonated

Question 9

pH = pKa

Answer 9

amino acid is neutral (no net charge)

Question 10

amino acids without charged side chains have a pI around

Answer 10

6

Question 11

acidic amino acids have a pI around

Answer 11

well below 6

Question 12

basic amino acids have a pI around

Answer 12

well above 6

Question 13

formation of a peptide bond

Answer 13

• condensation/dehydration reaction (releases H20)

- nucleophilic amino group of one aa attacks the electrophilic carbonyl carbon of another aa

Question 14

breaking of a dipeptide bond

Answer 14

hydrolysis reaction; addition of water cleaves peptide bond

Question 15

why are amide bonds rigid?

Answer 15

because of resonance

Question 16

primary protein structure

Answer 16

• linear sequence of amino acids

- stabilized by peptide bonds

Question 17

secondary protein structure

Answer 17

• local interactions/folding of neighboring amino acids in regions within the polypeptide chain
• stabilized by hydrogen bonding (between amino groups and nonadjacent carboxyl groups)
• includes alpha helices and beta pleated sheets
• secondary structure can be interrupted by Pro and Gly

Question 18

tertiary protein structure

Answer 18

• 3D arrangement of all the amino acids within a polypeptide chain
• stabilized by hydrophobic interactions, acid-base interactions (salt-bridges), and disulfide bonds

Question 19

quaternary protein structure

Answer 19

• interaction between peptides in proteins that contain multiple subunits
• this refers to the spatial arrangement of the polypeptide subunits and the interactions between them
• a protein must contain more than one subunit in order to possess quaternary structure

Question 20

hydrophobic interactions

Answer 20

push the R groups to the interior of a protein, which increases entropy of surrounding water molecules and creates a negative Gibbs free energy

Question 21

disulfide bonds

Answer 21

occur when two cysteine molecules are oxidized and create a covalent bond to form cystine

Question 22

are disulfide bonds found intra- or extracellularly? Why?

Answer 22

disulfide bonds are found extracellularly
this is because extracellular = oxidizing environment and intracellular = reducing environment which would break the disulfide bond and revert cysteine back to its original protonated -SH state

Question 23

what formula would one use to figure out the number of possible peptide arrangements that could be formed containing one of each “n” amino acids?

Answer 23

n! (n factorial)

ex: n! = 3! = 3 x 2 x 1 = 6 possible peptides