Biochemistry Ch 1. Amino Acids, Peptides, and Proteins

Question 1

Amino acids

Answer 1

Have four groups attached to a central (alpha) carbon: An amino group, a carboxylic acid group, a hydrogen atom, and an R group, twenty appear in the proteins of eukaryotic organisms, amphoteric

Question 2

R group

Answer 2

Group on an amino acid that determines chemistry and function of that amino acid

Question 3

Stereochemistry of alpha carbon in amino acids

Answer 3

L for all chiral amino acids in eukaryotes, D amino acids exist in prokaryotes, all chiral have S configuration except cysteine, all chiral except glycine

Question 4

Glycine

Answer 4

H, achiral, non polar, nonaromatic

Question 5

Amino acids side chain characteristics

Answer 5

Polar or non polar, aromatic or nonromantic, charged or uncharged

Question 6

Cysteine

Answer 6

Chiral, R configuration (only one)

Question 7

Nonpolar, nonaromatic amino acids

Answer 7

Glycine, alanine, valine, leucine, isoleucine, methionine, proline

Question 8

Aromatic amino acids

Answer 8

Tryptophan, phenylalanine, tyrosine

Question 9

Polar amino acids

Answer 9

Serine, threonine, asparagine, glutamate

Question 10

Negatively charged amino acids

Answer 10

aka acidic, aspartate, glutamate, have a pI well below 6

Question 11

Positively charged amino acids

Answer 11

aka basic, lysine, Argentine, histidine, have a pI well above 6

Question 12

Amino acids and water

Answer 12

Amino acids with long alkyl chains are hydrophobic and those with charges are hydrophilic, many others fall somewhere in between

Question 13

Amphoteric

Answer 13

The ability the accept or donate protons

Question 14

pKa

Answer 14

the pH at which half of the species are deprotonated, where [HA] = [A-], titration curve flat around this point

Question 15

Low pH amino acids

Answer 15

Amino acid fully protonated

Question 16

Isoelectric point (pI)

Answer 16

The pH of an amino acid without a charged side chain, can be calculated using average of the two pKa values, titration curve vertical near this point, around 6 for amino acids without charged side chains, less than 6 for acidic amino acids, above 6 for basic amino acids

Question 17

pH near pI of an amino acid

Answer 17

Amino acid is a neural zwitterion

Question 18

Zwitterion

Answer 18

-

Question 19

High pH amino acids

Answer 19

Amino acid is fully deprotonated

Question 20

Charged amino acids

Answer 20

Amino acids with charged side chains have an additional pKa value and their pI is calculated by averaging the two pKa values that correspond to protonation and deprotonation of the zwitterion

Question 21

Peptide bond formation

Answer 21

Occurs during a condensation or dehydration reaction, nucleophilic amino group of one amino acid attacks the electrophlic carbonyl group of another amino acid

Question 22

Condensation reaction

Answer 22

aka dehydration reaction, Type of reaction where peptide bonds are formed between amino acids, water molecule is released

Question 23

Dehydration reaction

Answer 23

aka condensation reaction, Type of reaction where peptide bonds are formed between amino acids, water molecule is released

Question 24

Amide bonds

Answer 24

Rigid because of resonance??

Question 25

Hydrolysis reaction

Answer 25

Method used to break peptide bonds

Question 26

Breaking peptide bonds

Answer 26

Can be done with hydrolysis reaction

Question 27

Primary structure

Answer 27

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

Question 28

Secondary structure

Answer 28

Local structure of neighboring amino acids and is stabilized by hydrogen bonding between amino groups and nonadjacent carboxyl groups, includes alpha helices and beta pleated sheets, can be interrupted because of proline

Question 29

Alpha helices

Answer 29

Clockwise coils around a central axis, type of secondary structure

Question 30

Beta pleated sheets

Answer 30

Ripplied stands that can be parallel or antiparallel, type of secondary structure

Question 31

Proline

Answer 31

Nonpolar, nonromantic amino acid, can interrupt secondary structure because of its rigid cyclic structure

Question 32

Tertiary structure

Answer 32

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

Question 33

Hydrophobic interactions tertiary structures

Answer 33

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

Question 34

Disulfide bonds tertiary structures

Answer 34

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

Question 35

Cysteine

Answer 35

Polar amino acid, if two are oxidized, they can create a covalent bond and form cystine

Question 36

Quaternary structure

Answer 36

The interaction between peptides in proteins that contain multiple subunits

Question 37

Conjugated proteins

Answer 37

Proteins with covalently attached molecules, attached group called the prosthetic group

Question 38

Prosthetic group

Answer 38

Molecule attached to a conjugate protein, may be a metal ion, vitamin, lipid, carbohydrate, or nucleic acid

Question 39

Denaturation

Answer 39

Loss of three dimensional protein structure due to either heat or increasing solute concentration