Ch 1 Amino acids, peptides, & proteins

amino acids have 4 groups attached to a central (α) carbon, they are

1. amino group

2. carboxylic acid group

3. hydrogen atom

4. an R group

what determines the chemistry and function of an amino acid

the R group

how many amino acids appear in the proteins of eukaryotic organism

20

the stereochemistry of the α-carbon is what for all chiral amino acids in eukaryotes

L- (D-amino acids can exist in prokaryotes)

all chiral amino acids except ___ have an (S) configuration

cysteine

all amino acids are chiral except _____, which has a hydrogen atom as its R group

glycine

Nonpolar, aromatic amino acids

1. glycine

2. alanine

3. valine

4. leucine

5. isoleucine

6. methionine

7. proline

aromatic amino acids

1. tryptophan

2. phenylalanine

3. tyrosine

polar amino acids

1. serine

2. threonine

3. asparagine

4. glutamine

5. cysteine

negatively charged (acidic) amino acids

1. aspartate

2. glutamate

positively charged (basic) amino acids

1. lysine

2. arginine

3. histidine

amino acids with long alkyl chains are ____ and those with charges are _____

hydrophobic, hydrophilic

amino acids are amphoteric, which means

they can accept or donate protons

the pK_a of a group is the

pH at which half of the species are deprotonated [HA] = [A-]

at low (acidic) pH the amino acid is

fully protonated

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

neutral zwitterion

at high (alkaline, basic) pH the amino acid is fully

deprotonated

the isoelectric point (pI) of an amino acid without a charged side chain can be calculated by averaging

the two pK_a = values

pK_a2 = 4 , pK_a2 = 2 what is pI

4+2/ 2 → 6/2 → pI is 3

what does the titration curve look like at the pK_a values of the amino acid

nearly flat

what does the titration curve look like at the pI of the amino acid

nearly vertical

amino acids with charged side chains have an additional pK_a value, and their pI is calculated by

averaging the two pK_a values that correspond to protonation and deprotonation of the zwitterion

amino acids without charged side chains have a pI around

6

acidic amino acids have a pI below

6

basic amino acids have pI above

6

how many residues do dipeptides, tripeptides, oligopeptides, and polypeptides have

• Dipeptides = 2

• tripeptides = 3

• oligopeptides = <20

• polypeptides = >20

forming a peptide bond is a ____ or ____ reaction (releasing one molecule of water)

condensation, dehydration

the _____ amino group of one amino acid attacks the ______ carbonyl group of another amino acid

nucleophilic, electrophilic

amide bonds are rigid because of

resonance

breaking a peptide bond is a _____ reaction

hydrolysis

primary structure is the linear sequence of amino acids in a peptide and is stabilized by

peptide bonds

secondary structure is the local structure of neighboring amino acids, and is stabilized by

hydrogen bonding between amino groups and nonadjacent carboxyl groups

α-helices are

clockwise coils around a central axis

β-pleated sheets are

rippled strands that can be parallel or antiparallel

which amino acid can interrupt secondary structure because of its rigid cyclic structure

proline

tertiary structure is the three-dimension shape of a single polypeptide chain, and is stabilized by

1. hydrophobic interactions

2. acid-base interactions (salt bridges)

3. hydrogen bonding

4. disulfide bonds

_____ ______ 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

hydrophobic interactions

disulfide bonds occur when

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

quaternary structure is the

interaction between peptides in proteins that contain multiple subunits

proteins with covalently attached molecules are called

conjugated proteins

the molecule attached to conjugated proteins is a ___ ___

prosthetic group

prosthetic group examples

1. metal ion

2. vitamin

3. lipid

4. carbohydrate

5. nucleic acid

what can lead to loss of three-dimensional protein structure

heat and increasing solute concentration

the loss of three-dimensional protein structure is called

denaturation