Chapter 3

Question 1

what is the general structure of an amino acid?

Answer 1

alpha carbon always has 4 substituents
all except proline have an acidic carboxyl group, a basic amino group, an alpha hydrogen attached to the alpha carbon, and an R group

Question 2

what are the nonpolar, aliphatic amino acids?

Answer 2

GAPVLIM

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, and Methionine

Question 3

what are the aromatic amino acids

Answer 3

PTT

Phenylalanine, Tyrosine, Tryptophan

Question 4

What are the polar, uncharged amino acids?

Answer 4

serine, threonine, cysteine, asparagine, glutamine

Question 5

what are the polar, positively charged amino acids?

Answer 5

LAH

Lysine, Arginine, Histidine

Question 6

what are the polar, negatively charged amino acids?

Answer 6

AG

Asparate, Glutamate

Question 7

What are the uncommon amino acids in proteins?

Answer 7

carboxyglutamate, selenocysteine, 4-hydroxyproline, 5-hydroxylysine, 6-N-methylysine,

Question 8

How are amino acids ionized at acidic pH?

Answer 8

the carboxyl group is protonated and the amino acid is in the cationic form

Question 9

How are amino acids ionized at neutral pH?

Answer 9

the carboxyl group is deprotonated but the amino group is protonated. The net charge is zero; called a zwitterion

Question 10

How are amino acids ionized in alkaline pH?

Answer 10

the amino group is neutral and the amino acid is in the anionic form

Question 11

At what pH value do zwitterions dominate?

Answer 11

values between the pKa values of the amino and carboxyl group

Question 12

What happens at the isoelectric point (pI)?

Answer 12

~the net charge is zero
~the amino acid is least soluble in water
~the amino acid does not migrate in electric field

Question 13

What is the equation for pI?

Answer 13

pI = (pK1 + pK2)/ 2

Question 14

When pH is less than pI, is the cation or anion favored?

Answer 14

the cation

Question 15

When the pH is greater than the pI, is the cation or anion favored?

Answer 15

the anion is favored

Question 16

What is an essential amino acid?

Answer 16

an amino acid that cannot be synthesized in the body and therefore must be included in the diet

Question 17

What are conditionally essential amino acids?

Answer 17

amino acids that become essential under certain conditions (during early development or bc of disease)

Question 18

What are nonessential amino acids?

Answer 18

amino acids that can be synthesized in the body

Question 19

Describe Kwashiorkor

Answer 19

~malnutrition produced by a severe deficient in protein
~diet consists of mainly starchy vegetables
~the immune system and brain function are affected
~immune system is affected bc proteins are needed to make antibodies to fight disease
~treatment is typically dry milk proteins

Question 20

Describe phenylketonuria

Answer 20

~there is a mutation in PAH gene that causes phenylalanine to build up in the body bc it cannot transform phenylalanine to tyrosine (important for signal transduction, neurotransmission, pigmentation, mood stabilization)
~phenylalanine saturates LNAAT at the blood brain barrier which prevents normal brain function and causes intellectual deficiencies
~treatment: phenylalanine must be limited in the diet and tyrosine must be supplied

Question 21

What is a dipeptide?

Answer 21

peptide that has two residues (amino acids)

Question 22

Describe how peptides are formed

Answer 22

~amino acids are covalently linked through peptide bonds
~there is a reaction between the carboxyl group of one amino acid and the amino group of another (now unreactive)
~amino acids assemble into dipeptides, tripeptides, polypeptides, and proteins
~proteins have an amino terminus (N-terminus) and a carboxyl terminus (C-terminus) that stay reactive

Question 23

How are peptides named?

Answer 23

~they are named beginning with the amino terminal residue and then going down the chain
~typically done using 3-letter code abbreviations for residues
~for long peptides (like proteins) the one letter code of the residues can be used

Question 24

List the variety of functions of peptides

Answer 24

hormones and pheromones (insulin, oxytocin, sex-peptide)
neuropeptides (substance P)
antibiotics (polymyxin B, bacitracin)
protection (toxins like amanitin, conotoxin, chlorotoxin)

Question 25

Describe how column chromatography works

Answer 25

~protein mixture is loaded to a resin ~buffer is passed through ~proteins separated according to size, charge, etc. ~after separation, proteins are eluted

Question 26

Describe separation by charge in chromatrography

Answer 26

~column is coated with either positively or negatively charged resin ~for cation exchangers, the negatively charged proteins move through quickly and the positively charged proteins become attached to the resin ~ a high ionic buffer is then added to move the positively charged protein through ~vice versa for anion exchangers

Question 27

Describe separation by size in chromatography

Answer 27

~the larger proteins pass quickly through the column while the smaller proteins get caught in the pores of the column and therefore move more slowly through

Question 28

Describe separation by affinity in chromatography

Answer 28

~the proteins can be translated with "tags" (HA, GST) that recognize certain ligands ~the resin contains ligand that bind to the tag ~the unwanted proteins can then be washed away ~free ligand solution is then added which allows the specific protein to be eluted

Question 29

What are the specific properties of Glycine?

Answer 29

it is achiral and found in the flexible parts of proteins

Question 30

What are the specific properties of proline?

Answer 30

the ring structure of proline is rigid and often found at turns

Question 31

What are the specific properties of methionine?

Answer 31

it is the 1st amino acid of all proteins because the start codon of proteins in eukaryotic species encodes methionine

Question 32

What are the specific properties of amino acids with aromatic r groups?

Answer 32

ring structures absorb uv light (270nm-280nm) | can be polar or nonpolar

Question 33

what are the properties of serine and threonine?

Answer 33

amino acids are phosphorylated by serine/threonine kinsases

Question 34

what are the specific properties of cysteine?

Answer 34

it can self react to form covalent disulfide bridges making cystine

Question 35

what are the specific properties of asparagine and glutamine?

Answer 35

they are amide derivatives of Asp and Glu

Question 36

what are the properties of lysine and arginine?

Answer 36

they are positively charged at neutral pH

Question 37

what are the specific properties of histidine?

Answer 37

it has a pI near neutrality | it acts as a good proton donor/acceptor in the active site of an enzyme

Question 38

How are uncommon amino acids made?

Answer 38

they arise by post-translational modifications of proteins