BioChem: Exam #2

"salting out," the purification method, is based on:

solubility

Which chromatography technique uses high pressure to run the protein solution through the column?

(HPLC) High pressure liquid chromatography

______ cleaves at the carboxyl side of lysine and arginine - except when either is followed by proline

Trypsin

_____________ interactions are everywhere

Van der waals

What is the overall net charge on the peptide lys-lys-ser-glu at pH 7.0? a. +2 b. +1 c. 0 d. 1 e. 2

b. +1

Hemoglobin is an alpha2, beta2 ____ whereas, glutamine synthatase from E. coli is an alpha 1,2 ____. a. -homodimer, -homomultimer b.-heteromultimer, -homomultimer c. -homomultimer, -heterodimer d. -heterodimer, -monomeric protein e. -heterodimer, -homomultimer

b. -heteromultimer, -homomultimer

Which of the following IS NOT a characteristic of a protein's overall conformation? a. The overall three-dimensional architecture of the protein. b. Achieved by breaking and reforming covalent bonds. c. Achieved by rotations about each single bond along the peptide backbone. d. The result of amino acid side-chain interactions. e. None, all are true.

b. Achieved by breaking and reforming covalent bonds.

After treating a protein with trypsin, which of the following techniques could be used to determine its identity by peptide mass fingerprinting? a. NMR b. MALDI-TOF mass spectrometer c. HPLC d. gel electrophoresis e. none of the above

b. MALDI-TOF mass spectrometer

A gene can be defined as: a. the unique function that some cells have but other cells do not have. b. a specific segment of nucleotide bases in DNA that encode for the synthesis of a particular protein. c. a single strand of DNA that is designated as the sense strand. d. a functional segment of a unique protein. e. the segment of DNA that is changed in a mutation.

b. a specific segment of nucleotide bases in DNA that encode for the synthesis of a particular protein.

Which of the following amino acids occurs most frequently in proteins? a. methionine b. alanine c. tryptophan d. tyrosine e. histidine

b. alanine

Although they have very different functions, hen egg white lysozyme and ____ share similar sequence homology and similar tertiary structure. a. trypsin b. alpha-lactalbumin c. thrombin d. hemoglobin e. chymotrypsin

b. alpha-lactalbumin

The C-terminal residue of a polypeptide can be determined by first cleaving the polypeptide with: a. chymotrypsin. b. carboxypeptidase. c. trypsin. d. CNBr. e. none of the above.

b. carboxypeptidase.

A common reaction of two cysteine residues in proteins results in the formation of ____. a. thioester bonds b. disulfide bonds c. dithiol bonds d. thioether bonds e. none of the above

b. disulfide bonds

Proteins destined for an extracellular location are characteristically: a. phosphoproteins. b. glycoproteins. c. lipoproteins. d. nucleoproteins. e. flavoproteins.

b. glycoproteins.

Which of the following reagents is correctly defined? a. iodoacetic acid: reduces disulfide bonds b. guanadinium hydrochloride: disrupts ionic interactions and hydrogen bonds c. phenylisothiocyanate: reacts with free carboxyl groups d. cyanogen bromide: reacts with internal cysteine residues e. performic acid: reacts with free cysteine residues

b. guanadinium hydrochloride: disrupts ionic interactions and hydrogen bonds

Which of the following would be a possible amino acid sequence for an oligopeptide given the experimental data below? 1. The amino acid composition is found to be [ala, lys, phe, met, cys, plus some decomposition products]. 2. The peptide has a molecular weight around 700 Da and absorbs at 280 nm. 3. Treatment with carboxypeptidase results in tryptophan and a peptide. 4. CNBr treatment yields a tetrapeptide and a dipeptide. 5. Trypsin digestion produces an amino acid and a pentapeptide with met on the amino end. 6. Chymotrypsin digestion yields a dipeptide and a tetrapeptide. a. trp-lys-met-cys-met-ala b. lys-met-cys-phe-ala-trp c. trp-ala-phe-cys-met-lys d. lys-ala-cys-phe-met-trp e. lys-met-cys-ala-phe-trp

b. lys-met-cys-phe-ala-trp

Membrane proteins differ from globular proteins in that: a. membrane associated amino acids usually have polar side chains. b. membrane proteins are much more soluble in detergents than water. c. membrane proteins usually have more hydrophobic amino acids. d. globular proteins are water insoluble. e. All are true.

b. membrane proteins are much more soluble in detergents than water.

The lac repressor is an example of a(n): a. enzyme. b. regulatory protein. c. transport protein. d. storage protein. e. structural protein.

b. regulatory protein.

Proteins that do NOT perform any obvious chemical transformation, but control the ability of other proteins to carry out their physiological functions are: a. enzymes. b. regulatory proteins. c. transport proteins. d. storage proteins. e. structural proteins.

b. regulatory proteins.

alpha-Helix and beta-strand are components of ____ structure a. primary b. secondary c. tertiary d. quaternary e. all are true

b. secondary

Homologous proteins such as hemoglobin from different organisms do NOT: a. have nearly identical lengths. b. share little sequence homology with other proteins with similar function (e.g., myoglobin). c. share a significant degree of sequence similarity. d. perform the same function in different organisms. e. have sequence identity in direct correlation to the relatedness of the species from which they were derived.

b. share little sequence homology with other proteins with similar function (e.g., myoglobin).

Alanine and leucine are both helix _________ a.) breakers b.) formers

b.) formers

To get rid of the blocking agent, make the solution slightly ________.

basic

hydrogen bonds in proteins occur:

between a backbone C=O and a backbone N-H

__________ _________ are used to control side chain reactions when synthesizing polypeptides in the lab.

blocking agents (FMOC & DIPCDI)

Ion exchange chromatography is separating molecules based on _______ _________.

net charge

different species of proteins is called:

orthologous

an alpha helix is formed if phi= ______ and psi= _______

- (-60 degrees) - (-45 to -50 degrees)

C-C bond C=O bond in Angstroms

- 1.54 A - 1.20 A

each turn of the helix is equivalent to how many amino acids?

- 3.6 amino acids (5.4 A)

A protein has a positive charge. Which matrix is best choice for its purification?

- CM-Agarose (cation)

A protein has a negative charge. Which matrix is best choice for its purification?

- DEAE-Cellulose (anion)

C(alpha)-N: C(alpha)-C:

- Phi -Psi

which type of noncovalent interaction between tightly packed amino acid side chains in the interior of the protein are a major contribution to protein structure?

- Van der waals interactions

What modified amino acid is necessary to produce collagen? - and what water soluble vitamin is this modification dependent on?

- hydroxyproline - vitamin C

the ________ bond is planar because of the partial _______ _______ character of the bond between the carboxyl carbon and the nitrogen

- peptide - double bond

types of noncovalent bonds (from weakest to strongest)

- van der waals interactions - hydrogen bonding - ionic interactions - hydrophobic interactions

If the non-amino acid part of the protein is important to its function, it is called a _________ _______.

-prosthetic group

_______ _______ and ______ _______ change the direction and the structure of secondary structures.

-tight turns -beta bulges

Which chromatography technique is often a 1-step process? -based on specific binding

Affinity chromatography

Entering a protein sequence in a data base to fine another protein with homologous sequencing

BLAST: Basic Local Alignment Search Tool

In ion exchange, what is the cation-exchanger & sugar matrix?

Carboxymethyl (CM) group with cellulose or agarose sugar matrix

In ion exchange, what is the anion-exchanger & sugar matrix?

Diethylaminoethyl (DEAE) group with cellulose or agarose sugar matrix

T/F: Dialysis is an effective technique to distinguish between small protein molecules.

False

T/F: Van der waals interaction is stronger than hydrogen bonds?

False

Which chromatography technique runs electricity through to allow the protein to separate on the gel; -separation based on size and charge

Gel electrophoresis

Which chromatography technique should be the last step, in practice, when filtering and separating molecules? -separation based on size.

Gel filtration chromatography

Which chromatography technique involves submerging the protein in a high concentration of salt?

Hydrophobic interaction chromatography

same species of proteins is called:

Paralogous

This plot represents the sterically allowed conformations of a polypeptide backbone phi and psi

Ramachandran plot

Insulin is a polypeptide hormone that contains two short polypeptide chains linked by two interstrand disulfide bonds. The most logical order of events to perform in order to sequence this protein would be: A. The peptides are reduced with mercaptoethanol. B. The peptides are sequenced using Edman chemistry. C. The peptides are separated by chromatography techniques. D. The peptides are alkylated with iodoacetamide. a. A, D, C, B b. C, A, D, B c. C, B, A, D d. A, B, C, D e. A, C, D, B

a. A, D, C, B

5. Which of the following IS NOT a characteristic of globular proteins? a. Insoluble in water. b. Roughly spherical. c. Folded so that the hydrophobic amino acids are in the interior of the molecule. d. Hydrophobic side chains are exposed to the water. e. None, all are true.

a. Insoluble in water.

Which of the following is not a commonly used technique for protein isolation and purification? a. gas-liquid chromatography. b. ion exchange chromatography. c. electrophoresis. d. solubility ("salting in" and "salting out"). e. affinity chromatography.

a. gas-liquid chromatography.

All of the information necessary for a protein to achieve its intricate architecture is contained within its ____ structure. a. primary b. secondary c. tertiary d. quaternary e. all are true

a. primary

The amino acid sequence is defined as ____ structure. a. primary b. secondary c. tertiary d. quaternary e. all are true

a. primary

Which of the following amino acids is likely to be found on the inside of a water soluble protein? a.) Valine b.) Histidine c.) Aspartic acid d.) Arginine

a.) Valine it contains a hydrophobic R group

the primary backbone is only: a.) covalent b.) noncovalent

a.) covalent

Which of the following would not be a useful procedure for dissociating the subunits of a multimeric protein in order to sequence the individual subunits? a. Exposure to pH extremes (ie, pH 1 or pH 13). b. High salt concentrations. c. 6 N HCl at 110C for 24 hours. d. 8 M urea. e. 6 M guanidinium chloride.

c. 6 N HCl at 110C for 24 hours.

All of the statements about the peptide val-asp-trp-asn-ser are correct EXCEPT: a. This peptide would show a strong absorption band at 280 nm. b. Reaction with chymotrypsin would yield two peptides. c. To synthesize this peptide using the solid phase method of Merrifield, the amino acid directly attached to the resin would be valine. d. After the second round of Edman degradation using the reagent PITC, the PTH-amino acid residue released would be PTH-asp. e. The peptide would be converted to a dipeptide and a tripeptide by chymotrypsin.

c. To synthesize this peptide using the solid phase method of Merrifield, the amino acid directly attached to the resin would be valine.

____ is specific in hydrolyzing only peptide bonds in which the carboxyl function is contributed by an arginine or a lysine residue. a. Chymotrypsin b. Carboxypeptidase c. Trypsin d. CNBr e. None of the above.

c. Trypsin

Molecules of a given protein have all EXCEPT: a. a fixed amino acid composition. b. a defined amino acid sequence. c. a sequence read from C-terminal end to N-terminal end. d. an invariant molecular weight. e. a nucleotide sequence from which they are encoded.

c. a sequence read from C-terminal end to N-terminal end.

What is the product formed from the acid hydrolysis of a simple amide? a. acid & base b. aldehyde & alcohol c. acid & amine d. ester & alcohol e. amine & aldehyde

c. acid & amine

The diversity in hemoglobin mutants indicates that: a. any amino acid change is relatively important. b. any amino acid change is lethal to the organism. c. specific amino acid changes drastically alter one or more functions of a protein. d. any amino acid change will have the same effect on the protein function. e. All are true.

c. specific amino acid changes drastically alter one or more functions of a protein.

Which of the following protease enzymes is correctly identified with its specificity? a. trypsin: cleaves on C-side of acidic amino acids b. chymotrypsin: cleaves on C-side of aliphatic amino acids c. staphylococcal protease: cleaves on C-side of acidic amino acids d. clostripain: cleaves on C-side of lysine e. none of the above are correct

c. staphylococcal protease: cleaves on C-side of acidic amino acids

Which of the following levels of protein structure is correctly defined? a. primary: interaction between subunits of a protein b. secondary: hydrogen bond arrangement of polar R-groups c. tertiary: three dimensional arrangement of all atoms in a single peptide d. quaternary: order of amino acid residues in the peptide chain e. none of the above are correct

c. tertiary: three dimensional arrangement of all atoms in a single peptide

Hemoglobin is an example of a(n): a. enzyme. b. regulatory protein. c. transport protein. d. storage protein. e. structural protein.

c. transport protein.

If the R group is ________ or _________, it will be blocked

charged polar

_________ cleaves at the carboxyl side of aromatic and bulky amino acids (Phenylalanine, tryptophan, tyrosine)

chymotrypsin

These proteins "need some help: to function properly

conjugated proteins

The B-pleated sheet in proteins are mostly stabilized by:

covalent disulfide bonds

_________ ________ hydrolyzes peptide bonds at the C-terminus of methionine residues. This reaction is used to reduce the size of polypeptide segments for identification and sequencing.

cyanogen bromide

The following five proteins are separated by SDS/PAGE. Give the order of their migration from the top to the bottom of the gel. a.) alpha-antitrypsin (45'000 Dalton) b.) cytochrome c (13'400 Dalton) c.) myoglobin ( 17'000 Dalton) d.) serum albumin (69'000 Dalton)

d, a, c, b

Reaction of the peptide, ala-met-lys-ser, with phenylisothiocyanate (PITC) at pH 8.0 followed by mild acidification (first cycle of Edman method) would release: a. the labeled peptide ala-met-lys-ser-PTH. b. PTH-ala, PTH-ser, PTH-lys and PTH-met. c. PTH-ser and the peptide ala-met-lys. d. PTH-ala and the peptide met-lys-ser. e. All of the above.

d. PTH-ala and the peptide met-lys-ser.

Fibrous proteins, such as collagen, have which one of the following properties? a. Highly soluble in water. b. Their hydrophilic residues are directed into the interior of the protein. c. Exhibit enzymatic activity. d. Serve structural roles in the cell. e. Monomeric.

d. Serve structural roles in the cell.

Which of the following mutations would probably be least likely to impact the function of the protein? a. Lys to Ser b. Ala to Asp c. His to Pro d. Val to Ile e. Phe to Tyr

d. Val to Ile

Edman degradation will: a. determine the C-terminal amino acid by using a carboxypeptidase. b. cleave the protein into a multitude of smaller peptides. c. compare overlapping sets of peptide fragments. d. determine the N-terminal amino acid. e. generate two different, but overlapping sets of peptide fragments.

d. determine the N-terminal amino acid.

The advantage of treating separate samples of a protein with two or more enzymes when sequencing a protein is that the products are: a. more homogeneous. b. sequenceable without further chromatography. c. fragments with the same N- and C-terminal amino acids. d. fragments with sequence overlaps. e. all are true.

d. fragments with sequence overlaps.

Proteins with two different polypeptide chains are: a. monomeric proteins. b. trimeric proteins. c. homodimeric proteins. d. heterodimeric proteins. e. none of the above.

d. heterodimeric proteins.

Amino acid analysis of a protein gives: a. the sequence of the protein. b. the number of residues of each amino acid in the protein. c. the molecular weight of the protein. d. the percentage or ratio of the various amino acids in the protein. e. an identification of the N-terminal and C-terminal amino acids.

d. the percentage or ratio of the various amino acids in the protein.

The preponderance of protein sequence information is now derived from: a. chemical sequencing (Edman method). b. mass spectrometry. c. mass spectrometry-mass spectrometry. d. translating the nucleotide sequence of genes into codons, and thus amino acid sequence. e. none of the above.

d. translating the nucleotide sequence of genes into codons, and thus amino acid sequence.

Secondary and higher orders of structures are determined by all EXCEPT: a.) hydrophobic interactions b.) ionic bonds c.) van der waals forces d.) hydrogen bonds e.) peptide bonds

d.) hydrogen bonds

Even though acid hydrolysis of proteins is favored over basic hydrolysis, with acid hydrolysis ____ is destroyed and must be estimated by other means. a. Lys b. Leu c. Asp d. Cys e. Trp

e. Trp

The formation of a disulfide bond would be an example of what level of protein structure? a. primary b. secondary c. tertiary d. quaternary e. both c and d are correct

e. both c and d are correct

The amino acid sequence is NOT: a. a distinctive characteristic of a polypeptide. b. encoded by the nucleotide sequence of DNA. c. a form of genetic information. d. read from N-terminal end to C-terminal end. e. constant for proteins with the same function from different organisms.

e. constant for proteins with the same function from different organisms.

Collagen is an example of a(n): a. enzyme. b. regulatory protein. c. transport protein. d. storage protein. e. structural protein.

e. structural protein.

alpha-Keratin beta-Keratin and Collagen are all types of _______ proteins

fibrous

what is the prosthetic group for myoglobin?

heme group

____________ interactions drive protein folding

hydrophobic

Which chromatography technique is based on charge only?

ion exchange chromatography

_______ interactions usually occur on the protein surface.

ionic

In 2 dimensional gel electophoresis, isoelectric focusing is combined with a thin layer chromatography to isolate protein of different _______ _______.

isoelectric points

In isoelectric focusing, the pH gradient in the gel is formed by _________ _________.

multicharged polymers

in protein cleavage, what cleaves at the C-terminal side of aromatic amino acids such as phenylalanine, tryptophan, and tyrosine

pepsin

Which amino acid may alter the direction of the polypeptide chain and interrupt a-helix?

proline

These amino acids fold and function on their own

simple proteins

Gel filtration chromatography os a technique that separates molecules according to _____.

size

ultracentrifugation is based on:

size

T/F: fibrous proteins have highly repetitive primary structures

true

globular proteins are soluble in:

water acids bases

fibrous proteins are insoluble in:

water weak acids weak bases