CHEM 3438 Module 3 Quizzes

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You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 9,283 mg of total protein and 91,947 units of total activity, what is the specific activity? Report your answer in units/mg to the nearest unit/mg.

10

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 859 mg of total protein and 88,369 units of total activity, what is the purification level? Report your answer to the nearest whole number (note: it is a unitless number).

10 +/- 1

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 846 mg of total protein and 110,847 units of total activity, what is the purification level? Report your answer to the nearest whole number (note: it is a unitless number).

13 +/- 1

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 679 mg of total protein and 112,563 units of total activity, what is the purification level? Report your answer to the nearest whole number (note: it is a unitless number).

17 +/- 1

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 6,781 mg of total protein and 130,794 units of total activity, what is the specific activity? Report your answer in units/mg to the nearest unit/mg.

19

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 313 mg of total protein and 117,787 units of total activity, what is the purification level? Report your answer to the nearest whole number (note: it is a unitless number).

38 +/- 1

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 2,959 mg of total protein and 117,012 units of total activity, what is the specific activity? Report your answer in units/mg to the nearest unit/mg.

40

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 6,596 mg of total protein and 74,215 units of total activity, what is the percent yield after those two steps? Report your answer as a percentage to the nearest whole percent (56%, for example).

49%

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 1,807 mg of total protein and 88,606 units of total activity, what is the purification level? Report your answer to the nearest whole number (note: it is a unitless number).

5 +/- 1

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 3,240 mg of total protein and 20,993 units of total activity, what is the specific activity? Report your answer in units/mg to the nearest unit/mg.

6

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 1,819 mg of total protein and 114,959 units of total activity, what is the purification level? Report your answer to the nearest whole number (note: it is a unitless number).

6 +/- 1

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 9,750 mg of total protein and 68,602 units of total activity, what is the specific activity? Report your answer in units/mg to the nearest unit/mg.

7

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 1,415 mg of total protein and 102,725 units of total activity, what is the purification level? Report your answer to the nearest whole number (note: it is a unitless number).

7 +/- 1

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 2,959 mg of total protein and 117,012 units of total activity, what is the percent yield after those two steps? Report your answer as a percentage to the nearest whole percent (56%, for example).

78

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 1,259 mg of total protein and 97,823 units of total activity, what is the purification level? Report your answer to the nearest whole number (note: it is a unitless number).

8 +/- 1

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 1,413 mg of total protein and 108,702 units of total activity, what is the purification level? Report your answer to the nearest whole number (note: it is a unitless number).

8 +/- 1

You are purifying a protein that you think will win you the Nobel Prize someday. If you started with 15,000 mg of total protein in your homogenate with 150,000 units of total activity, then after two steps of purification you have 3,937 mg of total protein and 144,187 units of total activity, what is the percent yield after those two steps? Report your answer as a percentage to the nearest whole percent (56%, for example).

96%

A heptapeptide was found to have an amino acid composition of asp. leu, lys, met,phe and tyr. Trypsin has no effect on the heptapeptide. One cycle of Edman degradation renders the product whose structure is shown below. Chymotrypsin treatment yields a dipeptide and a tetrapeptide, as well as a free amino acid. The tetrapeptide is known to contain asp, leu, lys, and met. Cyanogen bromide treatment generates a dipeptide that is determined to originate from the N-terminus of the heptapetide, a tetrapeptide, and free lys. The peptide sequence in single letter amino code is ___________________.

FMYDLMK

Consider a mixture of the amino acids lysine (pI = 9.7), tyrosine (pI = 5.7), and glutamic acid (pI = 3.2) at a pH 5.7 that is subjected to an electric current. __________ will remain stationary. a. Tyrosine b. Glutamic acid c. Lysine d. All of the amino acids

a. Tyrosine

What is the one letter symbol of the amino acid below? a. W b. G c. F d. T e. Q

a. W

When the protein bands in an SDS-PAGE gel are transferred to paper and stained with antibody, it is called a a. Western Blot b. Coomassie stain c. Southern Blot d. Silver stain e. Northern Blot

a. Western Blot

To make a monoclonal antibody, as opposed to a polyclonal antibody, a. an antibody producing spleen cell is fused to a cancer cell b. the antigen is simply injected into a rabbit c. a much higher dose of antigen is injected into the rabbit d. polyclonal antibodies are purified to e. homogeneity via chromatography e. you acid digest a sample of polyclonal antibody

a. an antibody producing spleen cell is fused to a cancer cell

Which amino acid's side chain is positively charged at biological pH? a. arginine b. glutamine c. aspartic acid d. serine e. tyrosine

a. arginine

Which of the following amino acids has its isoelectric point at the highest pH? a. arginine b. aspartic acid c. glycine d. methionine e. valine

a. arginine

Which of the following amino acids has its isoelectric point at the lowest pH? a. aspartic acid b. glycine c. valine d. arginine e. methionine

a. aspartic acid

Antibodies are useful because they a. are always soluble in the presence of their antigens b. bind things c. have only one antigen binding site on each antibody molecule d. repel immune cells e. are naturally luminescent

a. bind things

In determining the following structure by NMR, the structure below would be specified by a. crosspeaks in 2D NOESY spectra between protons 2 and 5

a. crosspeaks in 2D NOESY spectra between protons 2 and 5

ELISA is a method that is used to a. detect and quantify proteins and/or small molecules b. separate proteins based on size c. separate proteins based on charge d. separate proteins based on pI e. stain cells to label specific proteins using antibodies

a. detect and quantify proteins and/or small molecules

In SDS-PAGE, the SDS serves to a. give proteins constant charge/mass b. denature proteins, so shape doesn't affect the separation c. preserve protein structure by stabilizing hydrophobic interactions d. give all proteins the same mass e. give proteins constant charge/mass and denature proteins

a. give proteins constant charge/mass and denature proteins

Which of the following amino acids has a side chain which contains a nonbasic nitrogen? a. glutamine b. lysine c. histidine d. tyrosine e. proline

a. glutamine

When centrifuging sub-cellular structures, what organelles pellet out at 10,000 x g? a. mitochondria b. microsomes c. nuclei d. endoplasmic reticulum

a. mitochondria

Which is easier to produce? a. polyclonal antibodies b. monoclonal antibodies c. other proteins successfully designed to bind an antigen and chemically synthesized

a. polyclonal antibodies

Which of the following amino acids has its α-carbon as part of a 5-membered ring? a. proline b. tryptophan c. histidine d. phenylalanine e. tyrosine

a. proline

Dialysis a. separates small molecules from large molecules b. separates molecules based on charge c. requires SDS d. is a form of electrophoresis e. is a spectroscopic technique

a. separates small molecules from large molecules

Cyanogen bromide's specificity for cleaving amide bonds after methionine residues results from the formation of a required ______________ intermediate. a. sulfonium salt b. free thiol c. aromatic d. antiaromatic e. hemiacetal

a. sulfonium salt

In the Edman Degradation, phenyl isothiocyanate reacts with ___________________. a. the N-terminal amino acid of a peptide b. Edman, dissolving him completely (poor fellow!) c. methionine residues in a peptide d. the C-terminal amion acid of a peptide e. cysteine sidechains

a. the N-terminal amino acid of a peptide

a TOF mass spec a. uses the time of transit through a flight tube as the mass selector

a. uses the time of transit through a flight tube as the mass selector

A sample of blood proteins is separated on a 2D-gel. If the patient is young enough to express significant amounts of both fetal and adult hemoglobin, and fetal hemoglobin has less positive charges than adult hemoglobin but the sizes are nearly identical, where would they be found on the gel relative to one another? a. At the same position in the isoelectric focusing dimension, but fetal hemoglobin will be found higher on the gel in the SDS-PAGE dimension b. At the same position in the SDS-PAGE dimension, but fetal hemoglobin will be found at lower pH in the isoelectric focusing dimension c. At the same position in the isoelectric focusing dimension, but fetal hemoglobin will be found lower on the gel in the SDS-PAGE dimension d. The will be in the exact same spot e. At the same position in the SDS-PAGE dimension, but fetal hemoglobin will be found at higher pH in the isoelectric focusing dimension

b. At the same position in the SDS-PAGE dimension, but fetal hemoglobin will be found at lower pH in the isoelectric focusing dimension

In ion exhcange chromatography using diethylaminoethyl (DEAE) cellulose, which of the following amino acids would elute last? a. R b. D c. I d. C e. W

b. D

GFP is an antibody. a. True b. False

b. False

IMAC chromatography separates molecules based on size. a. True b. False

b. False

In affinity chromatography, molecules are separated based primarily on their charge. a. True b. False

b. False

NMR determination of protein structure requires that proteins be crystallized into ordered structures. a. True b. False

b. False

When a protein is 'salted-in', it precipitates and is removed form a solution. a. True b. False

b. False

Which of the following proteins will elute first (go through the fastest) in size exclusion (also called molecular exclusion) chromatography? a. Protein Y (Molecular weight 45,000 g/mol, charge -6) b. Protein X (Molecular weight 149,000 g/mol, charge +1) c. Protein F (Molecular weight 5,000 g/mol, charge +4) d. Protein B (Molecular weight 25,000 g/mol, charge +6) e. Protein Z (Molecular weight 22,000 g/mol, charge -15)

b. Protein X (Molecular weight 149,000 g/mol, charge +1)

What is the one letter symbol of the amino acid below? a. G b. Q c. M d. W e. R

b. Q

Cyanogen bromide will cleave the peptide KWNEMDAR a. after the K b. after the M c. after both the E and the D d. after the W e. actually, it won't cut it at all

b. after the M

A basic amino acid has an R group that contains a. a methyl group. b. an amine group. c. an alcohol group. d. a carboxyl group. e. a thiol group.

b. an amine group.

A quick way to start purifying a protein is to first fractionate cellular organelles and collect the one with the protein of interest. If you want to collect fractions that separately contain nuclei, mitochondria, endoplasmic reticulum, and cytosol, how is this most easily done? a. ion exchange chromatography b. centrifugation c. mass spec d. dialysis e. a good microscope and really, really small tweezers/forceps

b. centrifugation

Chymotrypsin a. degrades proteins from the N-terminus one amino acid at a time b. cleaves proteins after large hydrophobic amino acid residues c. cleaves proteins after methionine residues d. cleaves proteins after positively charged amino acid residues e. is another name for cyanogen bromide

b. cleaves proteins after large hydrophobic amino acid residues

A common reagent that activates amino acid carboxylates for solid phase protein synthesis is a. beta-mercaptoethanol b. dicyclohexylcarbodiimide c. performic acid d. trifluoroacetic acid e. cyanogen bromide

b. dicyclohexylcarbodiimide

In protein structure determination by NMR, the NMR provides a. phosphorous-chlorine coupling constants b. distance constraints c. the positions of the disulfide bonds d. the positions of the aromatic amino acids e. electron density models

b. distance constraints

Which of the following amino acids has an isoelectric pH of 3.2? a. lysine b. glutamic acid c. asparagine d. methionine e. glycine

b. glutamic acid

In normal SDS-PAGE, separation is based on a. charge b. size c. antibody affinity d. quaternary structure e. isoelectric point

b. size

Which of the following is not an application of antibodies? a. cell staining b. the Nuclear Overhauser Effect c. Western blots d. ELISA e. Immunoprecipitation

b. the Nuclear Overhauser Effect

To purify an enzyme, liver cells are homogenized in a Dounce tube and centrifuged at 500g for 10 minutes. The supernatant is centrifuged further for 10,000g for 20 minutes, then the resulting supernatant is centrifuged at 100,000g for one hour. The resulting pellet is resuspended in buffer and used for enzyme kinetics. The enzyme being studied must be found in a. the cytosol b. the endoplasmic reticulum c. the outer mitochondrial membrane d. the nucleus e. the inner mitochondrial membrane

b. the endoplasmic reticulum

Antibodies bind to antigens via a. covalent bonds b. weak interactions c. disulfide bonds d. their six tentacles e. none of the above

b. weak interactions

A mixture of five proteins are analyzed by MALDI-TOF. Their molecular weigths are 3 kD, 22 kD, 100 kD, 225 kD and 515 kD. A peak appears in the mass spectrum at 33.3 kD. Which protein most likely gave this peak? a. 3 kD b. 22 kD c. 100 kD d. 225 kD e. 515 kD

c. 100 kD

In 'Sandwich ELISA' the meat is _____________ and the bread is ______________. a. enzyme; antigen b. antibody; antigen c. antigen; antibody d. antibody; enzyme e. antigen; enzyme

c. antigen; antibody

Which amino acid has an amide group in its side chain? a. histidine b. tyrosine c. asparagine d. tryptophan e. isoleucine

c. asparagine

Dicyclohexylcarbodiimide is used to a. protect carboxylic acids b. reduce disulfide bonds c. couple amino acids (covalently bind them to each other) d. hydrolyze peptide bonds e. identify the N-terminal amino acid of a polypeptide

c. couple amino acids (covalently bind them to each other)

A method of exchanging the buffer (and other small molecules) present in a solution of protein is to use a semipermeable membrane that lets only the small molecules through. This technique is called a. ELISA b. centrifugation c. dialysis d. gel filtration e. electrophoresis

c. dialysis

Nearly all naturally occurring amino acids: have basic side chains. a. are achiral. b. are racemic mixtures. c. have the (S) configuration at the α-carbon. d. have the (R) configuration at the α-carbon.

c. have the (S) configuration at the α-carbon.

A student is carrying out a sandwich ELISA. Their first step should be to _______________. a. mix the enzyme-linked anti-antibody antibody with its substrate before anything goes onto the plate b. immobilize some antigen in the wells of a 96-well plate c. immobilize monoclonal antibody in the wells of a 96-well plate d. immoblize enzyme-linked anti-antibody antibody in the wells of a 96-well plate e. immobilize anti-anti-anti-antibody in the wells of a 96-well plate

c. immobilize monoclonal antibody in the wells of a 96-well plate

In IMAC, proteins of interest form ___________ with the contents of the column immobilizing them until they are eluted. a. ionic interactions b. covalent bonds c. metal-ligand bonds d. hydrogen bonds

c. metal-ligand bonds

The main drawback of protein X-ray crystallography is that a. it only works well on relatively small proteins b. it only works well on very large proteins c. proteins must first be crystallized and conditions may never be found to crystallized the protein of interest d. you must first generate monoclonal antibodies to your protein, and this is very difficult and time consuming e. there are no instruments that can be used to collect data at universities, you can only collect diffraction data at synchroton sources in scenic cities like Chicago

c. proteins must first be crystallized and conditions may never be found to crystallized the protein of interest

Ion exchange chromatography a. separates molecules based on shape b. requires SDS c. separates molecules based on charge d. is a form of electrophoresis e. separates molecules based on size

c. separates molecules based on charge

Which amino acid has a phenol in its side chain? a. asparagine b. tryptophan c. tyrosine d. isoleucine e. histidine

c. tyrosine

Immobilized metal affinity chromatography (IMAC) will retain proteins a. with bound metal ions b. with a lot of alanine residues c. with 4-6 consecutive histidine residues d. smaller than 6 kD e. that immobilize metal ions

c. with 4-6 consecutive histidine residues

In the 2D gel image below, the red spot represents and unmodified version of a protein with a molecular weight of 150 kD. Which grey spot is appropriately placed to represent a version of that protein that has been phosphorylated at a serine reside (a phosphate group has been covalently attached to the serine hydroxyl group)? The SDS-PAGE portion of the gel spans from 10 kD to 2000 kD. a. 1 b. 2 c. 3 d. 4

d. 4

If a protein has an isoelectric point (pI) of 10.2, which of the following amino acids is it likely to have a lot of? a. M and W b. D and E c. C and P d. H and R e. W and Y

d. H and R

Antibodies bind to a. proteins only b. proteins or carbohydrates, but not lipids c. lipids only d. antigens e. carbohydrates only

d. antigens

Which amino acid's side chain is negatively charged at biological pH? a. arginine b. glutamine c. tyrosine d. aspartic acid e. serine

d. aspartic acid

In ion-exchange chromatography, molecules are separated based on a. affinity for metals b. hydrophobicity c. mass divided by charge d. charge e. size

d. charge

A reagent that oxidizes cystines (cysteine disulfides) into cysteic acids that can no longer form disulfide bonds is a. beta mercaptoethanol b. cyanogen bromide c. dithiothreitol (DTT) d. performic acid e. vitamin C

d. performic acid

Dialysis is carried out on a solution containing a 100 kD red protein, a 10 kD yellow protein, and a 2,000 kD blue dye by placing the mixture in the dialysis bag. If the dialysis bag has a pore size of 50 kD, what color will the solution in the bag be after several equilibrations and buffer exchanges? a. blue b. red + blue = purple c. red d. red + yellow = orange e. yellow

d. red + blue = purple

Dithiothreitol (DTT) is used to a. derivatize N-terminal amino acids during the Edman Degradation b. oxidize disulfide bonds c. derivatize C-terminal amino acids during the Edman Degradation d. reduce disulfide bonds e. hopelessly confuse undergraduate biochemistry students

d. reduce disulfide bonds

In SDS-PAGE, proteins separate based primarily on a. hydrophobicity b. ligand affinity c. charge d. size e. isoelectric point

d. size

Disulfide linkages can form between: a. two methionine residues. b. a methionine residue and a threonine residue. c. two threonine residues. d. two cysteine residues. e. a cysteine residue and a methionine residue.

d. two cysteine residues.

You start a protein purification with 15 g of a crude mixture of mitochondrial protein and measure the enzyme activity and get 150,000 units of activity. You then do several rounds of chromatography, and end up at 150 mg of protein that assays to give 100,000 units of activity. The percent yield of the enzyme you are trying to purify is a. 0.67% b. 6.7% c. 10% d. 33% e. 67%

e. 67%

The N-terminal sequence of a peptide can be determined by a. complete hydrolysis of the protein b. treatment with cyanogen bromide c. trypsin digestion d. treatment with dicyclohexylcarbodiimide e. Edman degradation

e. Edman degradation

The Edman Degradation a. is how proteins are hydrolyzed completely for amino acid analysis b. is an unavoidable denaturing of protein when we try to purify it c. has to do with disulfide bonds d. is a method for sequencing proteins from the C-terminus e. is a method for sequencing proteins from the N-terminus

e. is a method for sequencing proteins from the N-terminus

Which of the following amino acids has a nonpolar side chain? a. threonine b. serine c. aspartic acid d. asparagine e. leucine

e. leucine

Which of the following amino acids has its isoelectric point at the highest pH? a. histidine b. glutamic acid c. serine d. cysteine e. lysine

e. lysine

Which of the following amino acids does not contain an aromatic R-group? a. Histidine b. Phenylalanine c. Tryptophan d. Tyrosine e. none of the above

e. none of the above

Which of the following terms best describes the side chain of valine? a. uncharged, polar b. acidic c. basic d. charged, polar e. nonpolar

e. nonpolar

Which of the following proteins would elute first from a size exclusion chromatography column? a. protein X (MW 50,000 g/mol; charge +8) b. protein C (MW 75,000 g/mol; charge +31) c. protein M (MW 2,500 g/mol; charge -7) d. protein K (MW 50,000 g/mol; charge -5) e. protein Z (MW 250,000 g/mol; charge +3)

e. protein Z (MW 250,000 g/mol; charge +3)

Gel-filtration chromatography largely separates proteins (or other molecules) based upon a. isoelectric point b. flexibility c. charge d. hydrophobic surface area e. size

e. size

Advances in computers have increased our ability to image proteins in cells at very high resolution. a. True b. False

a. True

Advances in techniques for the determination of protein structures by Cryo Electron Microscopy won the Nobel Prize in 2017. a. True b. False

a. True

Denatures protein will usually not bind to an affinity column as well as normal, folded protein. a. True b. False

a. True

Mass spec can be used to detect cancer cells. a. True b. False

a. True

Peptides can be synthesized using the techniques of Organic Chemistry. a. True b. False

a. True

Salting-out means adding the right amount of salt to cause a protein to precipitate. a. True b. False

a. True

Some nuclear hormone receptors wait in the cytosol for their hormone to arrive. a. True b. False

a. True

We can now follow movement of proteins in live cells using advances in microscopy, antibody methods, and fluorescent proteins. a. True b. False

a. True

When we purify protein, we are going against the natural tendency toward disorder (we are fighting against entropy). a. True b. False

a. True

You can sequence a protein using mass spec (along with some other tools, like enzymes to cut the protein into smaller pieces). a. True b. False

a. True

A tetrapeptide contains alanine, lysine, glutamate, and methionine. If cyanogen bromide cleaves the tetrapeptide into a tripeptide and free glutamate, and trypsin cleaves the tetrapeptide into two dipeptides, what is the sequence of the tetrapeptide? a. AKME b. AKEM c. MAKE d. KAME e. EMAK

a. AKME

In this mass spectrum, click on the peak that represents lactoglobulin in a state whose m/z value is approximately one half of its molecular weight.

Top Left Coordinates(264, 190)Bottom Right Coordinates(384, 394)


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