Chapter 25: Amino Acids, Peptides, and Proteins

A disulfide bond is a form of covalent bonding in which the _____ groups from two cysteine residues are _____ to form a sulfur-_____ bond

SH; oxidized; sulfue

Select all the statements that correctly describe electrophoresis

-electrophoresis may be used to separate and purify amino acids, peptides, and proteins -this method is bsaed on the movement of charged particles in an electric field

Depending on the pH of the solution, an amino acid that does not have an ionizable side chain can have an overall charge of _____, _____, or _____ when dissolved in water

+1, 0, -1

Match the specific amino acid side chain example to its functional group classification

-CH(CH3)2 : nonpolar side chain -CH2OH : polar but nonionized side chain -CH2COOH : acidic side chain --(CH2)4NH2 : basic side chain

Match each amino acid functional group with its approximate pKa in aqueous solution

-COOH : pKa ~2 -NH3+ : pKa ~ 9

Match each amino acid to its three letter abbreviation

-Glu : glutamic acid -Gly : glycine -Gln : glutamine -Asp : aspartic acid -Asn : asparagine

Which of the following functional groups can be found in the side chains of amino acids?

-OH groups and SH groups -COOH groups and NH2 groups -alkyl groups

Match each named amino acid with its side chain classification

-alanine : neutral -glutamic acid : acidic -arginine : basic

Select the features below that occur in all amino acids

-amino group -carboxyl group

Match each enzyme below with the site at which it will hydrolyze a polypeptide

-carboxypeptidase : peptide bond nearest the C-terminal amino acid -chymotrypsin : peptide bond with a carbonyl group from Phe, Tyr, or Trp -trypsin : peptide bond with a carbonyl group from Arg or Lys

Match the cofactor with the substance that it describes

-coenzyme : organic molecules not covalently bound to the enzyme (NAD+) -prosethetic group : organic molecules covalently bound to the enzyme (heme)

Which of the following are interactions that can help stabilize the tertiary structure of a protein?

-disulfide bonds -van der Waals interactions between hydrophobic groups -hydrogen bonding -electrostatic interactions between charged side chains

Select all the statements that correctly describe transamination reactions

-enzymes that catalyze transamination reactions are called transaminases or aminotransferases -transaminiation reactions provide biosynthetic pathways to amino acids -transamination is a reaction involving the transfer of an amino group from one compound to another

Select all the commonly used protecting groups to suppress the reactivity of the amino group in amino acids

-fluorenylmethoxycarbonyl -benzyloxycarbonyl -tert-butoxycarbonyl

Match each protein below with its physiological function

-hemoglobin : oxygen transport -myoglobin : oxygen storage

Which of the following are steps in the Strecker synthesis of amino acids?

-hydrolysis of an α-amino nitrile with aqueous acid to form the amino acid -treating a aldehyde with NH4Cl and NaCN to form a α-amino nitrile

Match each tertiary structural feature of an enzyme with the role it can play in the enzyme's catalytic function

-hydrophobic pocket at the active site : binding of a non-polar portion of a substrate -residues with charged side chains in the active site : binding of a metal cation cofactor -polar residues on the outside surface : allow enzymes to be water soluble

Match each group of amino acids with the pH at the isoelectric point

-neutral side chains : pH between 5 and 6 -acidic side chains : pH around 3 -basic side chains : pH above 7

Match each level of protein structure with its correct description

-primary : the amino acid sequence of the protein -secondary : localized conformation such as helices and β-strands -tertiary : the overall shape adopted by a protein molecule -quaternary : assemblies of two or more subunits into functional proteins

Match each mass spectrometry method below to its utility in determining peptide and protein sequences

-tandem mass spectrometry : sequencing by characteristic fragmentation of peptide bonds -MALDI : sequencing by ionizing large peptide/protein fragments

Select all the statements that correctly describe the differences between bovine and human insulin

-the B chain in human insulin differs in the C-terminal amino acid -the A chain in human insulin differs in two amino acids, threonine and isoleucine

Which unique chemical feature(s) allow for the N-terminal amino acid to be identified by chemical methods?

-the N-terminal amino group can act as a nucleophile -the N-termincal amino group is free; the other α-amino groups are part of amide linkages

Which of the following are physical properties of amino acids in the neutral zwitterionic form?

-they are water soluble -they have high melting points

Which of the following are characteristics of fibrous proteins?

-they tend to be insoluble in water -they are composed of long linear polypeptide chains that are bundled together -they serve structural roles in cells

Which of the following are characteristics of globular proteins?

-they tend to soluble in water -they are coiled into compact shapes -they tend to have hydrophilic outer surfaces

Which of the following are examples of stable secondary structures in proteins?

-α-helix -β-pleated sheet

Order the steps in the Merrifield solid phase technique for synthesizing a peptide

1. attach a Boc-protected amino acid to the resin 2. remove the Boc protecting group 3. form the amide bond with DCCI 4. remove the protecting group(s) and detach the peptide from the resin

Order the steps in the synthesis of an amino acid from diethyl aceteamidomalonate

1. diethyl acetamidomalonate is deprotonated with sodium ethoxide 2. an enolate is alkylated with an unhindered alkyl halide 3. the two ethyl esters are hydrolyzed to carboxylic acids 4. the molecule is heated to induce decarboxylation

Order the steps in the synthesis of the dipeptide Val-Ala

1. protect the NH2 group of Val and the COOH group of Ala 2. form the amide bond with DCC 3. remove the protecting groups

Rank the steps involved when pyridoxal 5'-phosphate participates as a coenzyme int he racemization of amino acids

1. proton abstraction from the α carbon of the amino acid imine of PLP is the key reaction; an achiral intermediate is formed 2. proton transfer to the imine carbon of the achiral intermediate produces equal amounts of both enantiomers of the PLP imine

Order the steps in one cycle of the Edman degradation

1. the N-terminal NH2 group adds to the electrphilic carbon of phenyl isothiocyanate to form an N-phenylthiocarbamoyl (PTC) derivative 2. intramolecular cyclization followed by elimination cleaves the terminal amide bond, forming a new peptide with one fewer amino acid 3. thiazolinone rearranges to form an N-phenylthiohydantoin (PTH)

How many different levels of protein/peptide structure can be described?

4

In the Edman degradation, an amino acid is cleaved from the _____-terminal end of a peptide. The identity of the amino acid is then determined, and the process is repeated until the entire peptide sequence is known

N

In the Strecker synthesis of amino acids, a(n) _____ is treated with NH4Cl and NaCN to form an α-amino nitrile, which is then hydrolyzed with aqueous _____ to form the amino acid

aldehyde; acid

The most direct way to synthesize an α-amino acid is by a nucleophilic substitution reaction in which a(n) _____-halo carboxylic acid reacts with a large excess of _____

alpha; ammonia

Peptides and proteins are chains of amino acids joined together by ____ bonds

amide

The 20 _____ acids that occur naturally in proteins differ in the identity of the _____ group bonded to the α carbon. This group is also known as the _____ chain

amino; R; side

To determine the structure of a peptide, we must know not only what _____ _____ it is composed of, but also the _____ of the amino acids in the peptide chain

amino; acids; sequence

Naturally occuring amino acids are called α-amino acids because they have a(n) _____ group bonded to the carbon that is _____ to the carboxyl group (COOH)

amino; alpha

Two different dipeptides can be formed between two different amino acids because each amino acid has both a(n) _____ group and a(n) _____ group with which it can form amide bonds

amino; carboxyl

Which of the following alkyl halides would be used in the synthesis of phenylalanine from diethyl acetamidomalonate?

benzyl bromide

N,N'-dicyclohexylcarbodiimide (DCCI) promotes the condensation of an amine and a carboxylic acid to give an amide. In the first step, the _____ group of one amino acid adds to one of the double bonds of DCCI

carboxyl

When a G-protein-ocupled receptor binds its specific ligand, the protein undergoes a _____ change that results in the _____ of a signal across the membrane

conformational; transduction

True or false: the Boc protecting group is formed by treating an amino acid with tert-butoxycarbonyl chloride and base

false

True or false: an amino acid has an acidic functional group but not a basic functional group

false; has both an acidic and a basic functional group

Since amino acids exist as zwitterions in the neutral state, they have much _____ melting points and much _____ solubility in organic media than would be expected for uncharged molecules

higher; lower

Partial hydrolysis of a peptide with acid forms smaller fragments in a random fashion. After sequencing these fragments, which of the following is the next step in determining the sequence of the complete peptide?

identify sites of overlap in the different fragments

A neutral salt that contains both a positive and a _____ charge in the same molecule is called a _____

negative; zwitterion

Partial hydrolysis of a peptide with acid forms smaller fragments in a random fashion. Sequencing these peptides an identifying sites of _____ can be used to determine the _____ of the complete peptide

overlap; sequence

Linking the amino group of one amino acid an the carboxyl group of another amino acid forms an amide bond, which is also known as a(n) _____ bond

peptide

All of the naturally occuring amino acids are primary amines with the exception of _____, which a _____ amine

proline; secondary

The individual amino acids in peptides and proteins are called amino acid _____

residues

The peptide (amide) bond of an protein or peptide is stabilized by _____, resulting in partial double-bond character fo the C-N bond and a planar arrangement of atoms

resonance

When a peptide is heated in 6M HCl for 24h, high-performance liquid chromatography (HPLC) allows for _____

separation of the amino acids based on polarity

The primary structure of a protein is the particular _____ of amino acids that comprise it. The most important element of primary structure is the _____ bond

sequence; amide

Which of the following is a correct definition for the tertiary structure of a protein?

the 3D shape adopted by the entire protein

When synthesizing a specific dipeptide, some functional groups must be protected to prevent their participation in peptide bond formation. To synthesize His-Ile, which of the following functional groups must be protected before the amide bond is formed?

the NH2 group of His and the COOH group of Ile

Which of the following features distinguishes one amino acid from another?

the identity of the R group bonded to the α carbon

Which of the following best describes what the isoelectric point is?

the pH at which an amino acid exists primarily in its neutral form

In the second stage of pyridoxal 5'-phosphate (PLP) mediated decarboxylation of an amino acid, the pyridine ring is protonated. It can then faciliate decarboxylation because it acts as an electron-_____ group

withdrawing