Biochem 2 CH 3

Why do amino acids, when dissolved in water, become zwitterions

an H⁺ ion is therefore transferred from one end of the molecule to the other

zwitterions

an ion that possesses both positive and negative charges

5 major grouping of amino acids

nonpolar, polar, aromatic, positive and negatively charged

non polar amino acids

do not contain a charge and hydrophobic

aromatic amino acid

contains an aromatic ring, hydrophobic

what amino acid does not have a free a-amino group

proline

structural characteristics in all amino acids found naturally occurring in proteins

an a carbon to which are attached a carboxylic acid, an amine, a hydrogen, and a variable side chain

what are the 2 amino acids that contain sulfur atoms

Methionine and cysteine

all amino acids found in protein, except for proline, contain what

Carboxyl group

Which of the following is true about aromatic amino acids

on a molar basis, tryptophan absorbs more ultraviolet light than tyrosine

Which of the following statements about cystine is correct?

Cystine forms when the —CH2—SH R group is oxidized to form a —CH2—S—S—CH2— disulfide bridge between two cysteines.

Amino acids are ampholytes because they can function as either an

acid or base

Titration of valine by a strong base, for example NaOH, reveals two pK's. The titration reaction occurring at pK2 (pK2 = 9.62) is:

—NH3+ + OH− →—NH2 + H2O

The term specific activity differs from the term activity in that specific activity:

is measured only under optimal conditions.

which of the following describes the overall three-dimensional folding of a polypeptide

tertiary structure

primary sructure

the sequence of amino acids linked together to form a polypeptide chain.

secondary structure

contains regions of amino acid chains that are stabilized by hydrogen bonds from the polypeptide backbone

quaternary structure

the interaction of two or more folded polypeptides

A polypeptide is hydrolyzed, and it is determined that there are 3 Lys residues and 2 Arg residues (as well as other residues). How many peptide fragments can be expected when the native polypeptide is incubated with the proteolytic enzyme trypsin?

Six fragments would be expected, unless the carboxyl-terminal residue is Lys or Arg; in which case there would be five.

edman reagent for protein structure analysis

directly determines the sequence of N-terminal mutated/modified proteins more accurately

protease for protein structure analysis

greatly improve the coverage of proteome sequences and PTM sites.

reducing agent for protein structure analysis (dithiothreitol or B-mercaptoethanol)

to disrupt, or reduce, disulfide bonds in peptides and proteins to view individual proteins

ion-exchange chromatography

separates proteins (or any biomolecules) based on differences in their net charge at a particular pH

size-exclusion chromatography

separates molecules based on their size by filtration through a gel

affinity chromatograghy

a separation method based on a specific binding interaction between an immobilized ligand and its binding partner

structure of gly-ala-glu in ionic form at pH 7

The amino acid histidine has three ionizable groups, with pKa values of 1.8, 6.0, and 9.2. (a) Which pKa corresponds to the histidine side chain?

6

The amino acid histidine has three ionizable groups, with pKa values of 1.8, 6.0, and 9.2. In a solution at pH 5.4, what percentage of the histidine side chains will carry a positive charge?

80%

dominant form of glycine in a basic solution

NH3+-CH2-COOH

For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have:

a net positive charge

At the isoelectric pH of a tetrapeptide:

the total net charge is zero

The average molecular weight of the 20 standard amino acids is 138, but biochemists use 110 when estimating the number of amino acids in a protein of known molecular weight. Why?

The number 110 reflects the higher proportion of small amino acids in proteins, as well as the loss of water when the peptide bond forms.

In a conjugated protein, a prosthetic group is:

a part of the protein that is not composed of amino acids.

In a mixture of the five proteins listed below, which should elute second in size-exclusion (gel-filtration) chromatography?

immunoglobulin G Mt=145,000

By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to:

determine a protein's isoelectric point