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Exam 2 questions

front 1

A polypeptide of unknown sequence was digested with staphylococcal protease in bicarbonate buffer (pH 10), and separately with chymotrypsin. Based on these results, what is the sequence of this polypeptide?

1. Staphylococcal protease digest (pH 10):

-GNFLIME

-TD

-DKAYE

2. Chymotrypsin digest:

-LIMETD

-DKAY

-EGNF

back 1

DKAYEGNFLIMETD

front 2

In which of the following techniques is the protein denatured?

back 2

2-D Gel Electrophoresis

front 3

What result would you expect, for the polypeptide, PRKLPR, treated with carboxypeptidase A?

A)PRK + LPR

B) PRKL + PR

C) P+ RKLPR

D) PRKLP + R

E) none

back 3

E) none

front 4

Which amino acid has a side chain that forms a covalent bond with its own α-amino group, creating a ring structure?

back 4

P, proline

front 5

Which of these following tripeptides is most positively charged at pH 4?

A)Tyr-Ser-Thr

B) Asn-His-Met

C)Tyr-Cys-Ala

D)Gly-Glu-Gln

E) Thr-Trp-Phe

back 5

B) Asn-His-Met

front 6

How does fetal hemoglobin (Hb-F) ensure the fetus gets oxygen from the adult's hemoglobin (Hb-A)?

back 6

Hb-F has a higher affinity for oxygen due to the replacement of β with γ subunits, resulting in reduced BPG binding.

front 7

What is the function of iodoacetate (IOAc)?

back 7

To prevent disulfide bonds from reforming

front 8

Which of the following forces best describes stabilization of a protein's quaternary structure?

back 8

Burial of non-polar sidechains between subunits

front 9

Which of the following best describes protein folding inside a cell?

A) Protein folding is driven by primary structure and may be assisted by molecular chaperones

B) Protein folding depends only on hydrogen bonding

C) Protein folding depends only on side-chain interactions

D) Proteins fold randomly until they reach their native structure

E) Proteins remain unfolded until they form quaternary structures

back 9

A) Protein folding is driven by primary structure and may be assisted by molecular chaperones

front 10

Which cleavage reagent could have produced the peptide INWARD as an internal fragment?

Note: "Internal" means the last amino acid shown is not the C-terminal amino acid of the full-length polypeptide.

back 10

Staphylococcal Protease at pH 7

front 11

What key product results from using Edman's reagent?

back 11

Amino acid-PTH derivative

front 12

All of the following describe the β-sheet, EXCEPT:

A) Amino acid side chains alternate above and below the sheet.

B) β sheets have a pleated, edge-on appearance.

C) Strands align either in parallel or anti-parallel, within a sheet.

D) No exceptions. All of these are true.

E) Parallel β sheets contain as few as two strands.

back 12

E) Parallel β sheets contain as few as two strands.

front 13

What best describes a protein's tertiary structure?

back 13

The overall three-dimensional shape of a single polypeptide chain

front 14

All of the following statements describe the amino acid glycine, EXCEPT:

A) Its hydrogen sidechain allows it to pack inside a collagen triple helix.

B) It is not found in alpha helices or beta sheets.

C) It is the only achiral amino acid.

D) It has a pI of 5.5.

E) Its permissive phi and si bond angles make it more flexible.

back 14

B) It is not found in alpha helices or beta sheets.

front 15

Which of the following correctly matches a scientist with their contribution?

A) Ramachandran: change in free energy accounts for the change in enthalpy and entropy, as a function of temperature.

B) Anfinsen: phi-psi dihedrals of structured proteins fall into clusters of secondary structure.

C) Bohr: a protein's tertiary structure is directed by its primary structure.

D) Levinthal: protein folding must follow a pathway.

E) Gibbs: metabolic CO2 stabilizes hemoglobin in the T-state.

back 15

D) Levinthal: protein folding must follow a pathway.

front 16

If the red curve (3) is Hb-A, which of the following indicates cooperative oxygen binding by Hb-F, the fetal hemoglobin?

back 16

2

front 17

What structural consequence arises from the hydrophobic patch formed by the sickle-cell (Hb-S) mutation?

back 17

Hb-S molecules aggregate into insoluble fibers under low oxygen conditions.

front 18

How many amino acids make an α-helix 99 Å in length?

back 18

66

front 19

What was the key conclusion of Anfinsen’s experiment with ribonuclease A?

back 19

Protein structure is determined by its amino acid sequence

front 20

Which of the following statements is true about the Bohr effect?

A) Hemoglobin binding to oxygen is unaffected by pH

B) Hemoglobin binds oxygen more tightly at lower pH

C) Hemoglobin’s affinity for oxygen increases at higher [H+]

D) Myoglobin shows a Bohr effect similar to hemoglobin

E) Hemoglobin releases oxygen more efficiently at lower pH

back 20

E) Hemoglobin releases oxygen more efficiently at lower pH

front 21

What is the overall charge of histidine at pH 1?

back 21

+2

front 22

What explains cooperative binding in hemoglobin?

back 22

The binding of one oxygen molecule increases the affinity for additional oxygen molecules.

front 23

All of the following statements can describe SDS-PAGE, EXCEPT:

A) It uses an electrical current.

B) It does not involve protein denaturation.

C) It is following by Coomassie Brilliant Blue staining to visualize the protein bands.

D) It is an analytical technique.

E) It does not require DTT or β-ME.

back 23

B) It does not involve protein denaturation.

front 24

Which of the following defines the chirality of naturally occurring amino acids?

A) L configuration, based on glyceraldehyde

B) D configuration, based on glyceraldehyde

C) S configuration, based on glyceraldehyde

D) Naturally occurring amino acids are not chiral.

E) R configuration, based on glyceraldehyde

back 24

A) L configuration, based on glyceraldehyde

front 25

Which of the following amino acids can form a disulfide linkage?

A) C

B) S

C)Y

D) M

E) M and C

back 25

A) C

front 26

The oxygen-binding curve of myoglobin is

back 26

hyperbolic

front 27

What are the amino acid side chains that are always charged at physiological pH?

back 27

Glu, Asp, Lys, and Arg

front 28

What is the pI for the peptide, LATCH?

back 28

7.2

front 29

Which amino acid contains a sulfur atom in its side chain?

A) Lys

B) Try

C) Trp

D) Ser

E)Met

back 29

E) Met

front 30

Consider the schematic of the heterotrimeric protein below, where the dash, "-" indicates an intermolecular disulfide bond.

BO-X

What is/are the products of separation by SDS-PAGE, WITHOUT reducing agent?

back 30

B + O-X

front 31

Which of the following amino acids contains a non-polar, aromatic side chain?

A) N

B) R

C) S

D) E

E) F

back 31

F

front 32

Which of the proteins in this table can be purified BEST by anion-exchange chromatography at pH 7.4?

back 32

Insulin

front 33

Which statement about protein denaturation is true?

A) Denatured proteins lose their primary structure

B) Denatured proteins lose their native function

C) Denaturation breaks peptide bonds

D) Denaturation affects only tertiary and quaternary structures

E) Denaturation is another term for hydrolysis

back 33

B) Denatured proteins lose their native function

front 34

Can two different amino acids with the same side-chain pKa have different net charges, when the solution pH > side-chain pKa ?

back 34

Yes, because one side chain may be neutral when deprotonated, while the other has a negative charge when deprotonated.

front 35

What type of secondary structure is most prominent in myoglobin?

back 35

α-helices

front 36

What bond is primarily responsible for the primary structure of a protein?

back 36

peptide bonds

front 37

The______ sidechain of arginine is______when the solution pH is above its pKa of______.

back 37

guanidino, neutral, 12.5

front 38

What is the primary role of myoglobin in muscle tissue?

back 38

Binding and storage of oxygen in muscle cells

front 39

What mutation is responsible for sickle-cell anemia?

back 39

Valine instead of glutamate in the β subunit of hemoglobin

front 40

What type of secondary structure is characterized by hydrogen bonds forming between the carbonyl oxygen of one amino acid and the amide hydrogen of another amino acid four residues away?

back 40

α-helix

front 41

All of the following statements describe the peptide bond, EXCEPT:

A) The correct order for atoms in the peptide bond plane is Cα1, CO, NH, Cα2.

B) Peptide bonds are formed from a condensation reaction between two amino acids.

C) The partial charges of the amide NH and carbonyl O allow for hydrogen bonds within the polypeptide backbone.

D) The rigid peptide bond plane allows for no rotation of the side chains.

E) The peptide bond stays in a trans configuration due to its partial double-bond character.

back 41

D) The rigid peptide bond plane allows for no rotation of the side chains.

front 42

Which two amino acids act as helix breakers due to their ϕ and ψ angle flexibility?

back 42

Proline and Glycine

front 43

Which molecule stabilizes the T state of hemoglobin, reducing its affinity for oxygen?

back 43

2,3-bisphosphoglycerate

front 44

Which state of hemoglobin has a higher affinity for oxygen?

back 44

R (relaxed) state

front 45

Which of the following amino acids is most likely to be found in a protein’s interior, away from water?

A) K

B) R

C) V

D) E

E) S

back 45

C) V

front 46

What is the main characteristic of fibrous proteins?

back 46

Serve structural roles in cells and tissues

front 47

How does the coiled-coil structure in viral spike proteins facilitate fusion with host cells?

back 47

By undergoing a conformational change that brings viral and host membranes closer

front 48

Which of the following sequences could be found in α-keratin?

A) LMIWAFMVLFIIVILMFWAALIVALW

B) GPPGPPGPPGPPGPPGPPGPP

C) VSKINRSMKQFHEDVEELKNR

D) YSTDQRHDYSTDQRHDYSTDQRHD

E) GSGAGSGSGAGAGSGAGSGAGSGA

back 48

C) VSKINRSMKQFHEDVEELKNR

front 49

In affinity chromatography of a mixture of 3 proteins, the protein with no affinity for the ligand elutes ____, low Kd for the ligand elutes _____, and high Kd for the ligand elutes ____.

back 49

first; last; second

front 50

Which of the following functional groups is common to all standard amino acids?

A) Phosphate

B) Sulfhydryl

C) Amide

D) Carboxyl

E) Methyl

back 50

D) Carboxyl