Biochemistry

Question 1

4 groups attached to an amino acid:

Answer 1

all attached to the central a-carbon
-amino group
-carboxylic acid group
-hydrogen atom
-an R group

Question 2

Point of R group on amino acid:

Answer 2

determines chemistry and function of that amino acid

Question 3

prokaryotes have —amino acids

Answer 3

d-amino acids

Question 4

Stereochemistry of a-carbon:

Answer 4

L for all chiral amino acids; only one is not chiral; glycine bc hydrogen atom as R group

Question 5

Side chains can be —– or ——, —– or——-, —– or ——-

Answer 5

polar/ non polar
aromatic/ nonaromatic
charged/uncharged

Question 6

Nonpolar, nonaromatic amino acids:

Answer 6

glycine, alanine, valine, leucine, isoleucine, methionine, proline

Question 7

aromatic amino acids:

Answer 7

tryptophan, phenylalanine, tyrosine

Question 8

polar amino acids:

Answer 8

serine, threonine, asparagine, glutamine, cysteine

Question 9

negatively charged/ acidic amino acids:

Answer 9

aspartate and glutamate

Question 10

Positively charged/ basic amino acids:

Answer 10

lysine, arginine, histidine

Question 11

what makes an amino acid hydrophobic?
what makes an amino acid hydrophilic?

Answer 11

has long alkyl side chains

has charges

Question 12

amino acids are amphoteric:

Answer 12

they can accept or donate protons

Question 13

the pka of a group is:

Answer 13

the pH at which half of the species are deprotonated

Question 14

amino acid forms at different pH values:

Answer 14

acidic- low pH, fully protonated
pH near pI- neutral, zwitterion
basic- high pH, fully deprotonated

Question 15

amino acid titration curves:

Answer 15

-curve is flat at the pka value of the amino acid
-curve is nearly vertical at the pI of the amino acid

Question 16

pI based on type of amino acid:

Answer 16

-w/o charged side chains-around 6
-acidic- well bellow 6
-basic- well above 6

Question 17

dipeptide vs tripeptide vs oligopeptides vs polypeptides

Answer 17

-2 amino acid residues
-three amino acid residues
-“few” amino acid residues (<20)
-“many” amino acid residues (>20)

Question 18

what type of reaction is forming a peptide bond?

Answer 18

condensation or dehydration reaction as it releases one molecule of water

Question 19

How does a peptide bond occur?

Answer 19

nucleophilic amino group of one amino acid attacks the electrophilic carbonyl group of another amino acid.

Question 20

why are amide bonds rigid?

Answer 20

resonance

Question 21

what type of reaction is breaking a peptide bond?

Answer 21

hydrolysis

Question 22

primary structure of a protein:

Answer 22

linear sequence of amino acids in a peptide and is stabilized by peptide bonds

Question 23

secondary structure of a protein:

Answer 23

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

Question 24

a-helices
b-pleated sheets

Answer 24

-clockwise coils around a central axis
-rippled strands that can be parallel and anti parallel

Question 25

proline in secondary structure:

Answer 25

can interrupt secondary structure because of its rigid cyclic structure

Question 26

tertiary protein structure:

Answer 26

3-D shape of a single polypeptide chain, and is stabilized by hydrophobic interactions, acid-base interactions (salt bridges), hydrogen bonding, and disulfide bonds

Question 27

hydrophobic interactions:

Answer 27

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

Question 28

Disulfide bonds

Answer 28

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

Question 29

Quaternary structure

Answer 29

interaction between peptides in proteins that contain multiple subunits

Question 30

conjugated proteins
prosthetic group

Answer 30

proteins with covalently attached molecules
the molecule attached; could be metal ion, vitamin, lipid, carbohydrate, or nucleic acid

Question 31

denaturation

Answer 31

both heat and increasing solute concentration can lead to loss of 3-D protein structure