Ch 1 - Amino Acids, Peptides, and Proteins

Question 1

What are the 4 groups attached to a central (alpha) carbon in an amino acid?

Answer 1

• an amino group (-NH2)
• a carboxylic acid group (-COOH)
• a hydrogen atom
• an R group (determines chemistry/function of AA)

Question 2

What is the stereochemistry for the alpha carbon?

Answer 2

• L is for all chiral (4 different groups attached) amino acids in eukaryotes (all except cysteine have S configuration)
• all amino acids are chiral except glycine, which has a hydrogen atom as its R group
• D amino acids can exist in prokaryotes

Question 3

Which side chains are non polar and aromatic?

Answer 3

glycine, (CH2) - Gly (G)
alanine, (CH3) - Ala (A)
valine, (CHCH3CH3) - Val (V)
leucine, (CH2CHCH3CH3) - Leu (L)
isoleucine, (CHCH3CH2CH3) - Ile (I)
methionine, (CH2CH2SCH3) - Met (M)
proline (pentagon, NH) - Pro (P)

Question 4

Which side chains are aromatic?

Answer 4

tryptophan, - Trp (W)
phenylalanine, - Phe (F)
tyrosine - Tyr (Y)

Question 5

Which side chains are polar?

Answer 5

serine, - Ser (S)
threonine, Thr (T)
asparagine, Asn (N)
glutamine, - Glu (E)
cysteine Cys (C)

Question 6

Which side chains are negatively charged (acidic)?

Answer 6

aspartate, - Asp (D)

glutamate - Gln (E)

Question 7

Which side chains are positively charged (basic)?

Answer 7

lysine, - Lys (K)
arginie, - Arg (R)
histidine - His (H)

Question 8

What determines whether amino acids are hydrophobic or hydrophilic?

Answer 8

• long alkyl chain: hydrophobic

- with charges: hydrophilic

Question 9

Amphoteric?

Answer 9

• can accept or donate protons

- ability of amino acids

Question 10

pKa?

Answer 10

• the pH at which half of the species are deprotonated

[HA] - [A-]

Question 11

How does pH level affect amino acids?

Answer 11

• at low (acidic), fully protonated
• at pH near the pI of the amino acid, neutral zwitterion
• at high (basic), fully deprotonated

Question 12

Isoelectric point?

Answer 12

• pI

- without a charged side chain can be calculated by averaging the two pKa levels

Question 13

How can amino acids be titrated?

Answer 13

• the titration curve is nearly flat at the pKa values of the amino acid
• the titration curve is nearly vertical at the pI of the amino acid

Question 14

How is pI calculated in amino acids with charged side chains?

Answer 14

• they have an additional pKa value and their pI is calculated by averaging the 2 pKa values that correspond to the protonation and deprotonation of the zwitterion
• aa without charged side chains: pI around 6
• acidic aa: pI < 6
• basic aa: pI > 6

Question 15

What is the difference between depeptides, tripeptides, oligopeptides, and polypeptides?

Answer 15

• di: have 2 aa residues
• tri: have 3 aa residues
• oligo: few aa residues (< 20)
• poly: many aa resides (>20)

Question 16

What kind of reaction is forming a peptide bond?

Answer 16

• condensation or dehydration reaction (releasing one molecule of water)
• the nucleophilic amino group of one aa attacks the electrophilic carbonyl group of another amino acid

Question 17

Why are amide bonds rigid?

Answer 17

because of resonance

Question 18

What kind of reaction is breaking a peptide bond?

Answer 18

hydrolysis

Question 19

Primary structure?

Answer 19

the linear sequence of aa in a peptide and is stabilized by peptide bonds

Question 20

Secondary structure?

Answer 20

the local structure of neighboring amino acids and is stabilized by H-bonding between amino groups and nonadjacent carboxyl groups

Question 21

What are the types of secondary structures?

Answer 21

• alpha helices: clockwise coils around a central axis

- beta pleated sheets: rippled strands that can be parallel or antiparallel

Question 22

How can Proline interrupt secondary structures?

Answer 22

because of its rigid cycle structure

Question 23

Tertiary structure?

Answer 23

• 3D shape of a single polypeptide chain, and is stabilized by hydrophobic interactions, acid-base interactions, H bonding, and disulfide bonds

Question 24

Hydrophobic interactions?

Answer 24

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

Question 25

Disulfide bonds?

Answer 25

occur when 2 cysteine molecules are oxidizes and create a covalent bond to form cystine

Question 26

Quaternary structure?

Answer 26

the interaction between peptides in proteins that contain multiple subunits

Question 27

Conjugated proteins?

Answer 27

• proteins with covalently attached molecules

- attached molecule is a prosthetic group and may be metal ion, vitamin, lipid, carbohydrate, or nucleic acid

Question 28

Denaturation?

Answer 28

when both heat and increasing solute concentration can lead t loss of 3D protein structure