Question 1

An _______ is a _________ monomer used in peptide synthesis. A peptide is a ____ polymer and contains _____ bonds.

Accepted Answer

A)  acid; single; homogeneous; covalent 
B)  amino acid; heterogeneous; condensation; hydrogen 
C)  amino acid; bifunctional; condensation; amide 
D)  ?-hydroxy acid; bifunctional; homogeneous; amide 
E)  none of the above 
A)  acid; single; homogeneous; covalent 
B)  amino acid; heterogeneous; condensation; hydrogen 
C)  amino acid; bifunctional; condensation; amide 
D)  ?-hydroxy acid; bifunctional; homogeneous; amide 
E)  none of the above

Question 2

The conserved folds found in proteins prove that these structures are selected by ________.

Accepted Answer

A)  evolution 
B)  scientists 
C)  random sampling 
D)  mutation 
E)  default 
A)  evolution 
B)  scientists 
C)  random sampling 
D)  mutation 
E)  default

Question 3

Engineered proteins can be studied in their natural environment in the cell. Natural proteins are engineered to contain a tag or a fusion protein in order to ____________.
I. improve protein stability at high temperatures
II. detect the localization of the natural protein in the cell
III. analyze the level of expression in the cell
IV. detect interactions with potential protein ligands in the cell
V. improve stability of the protein in the cell

Accepted Answer

A)  I and II 
B)  II, III and IV 
C)  I, III and V 
D)  II, III and V 
E)  I and IV 
A)  I and II 
B)  II, III and IV 
C)  I, III and V 
D)  II, III and V 
E)  I and IV

Question 4

Bacterial expression systems are used __________________.

Accepted Answer

A)  when single chain proteins are expressed 
B)  to produce large quantities of protein 
C)  with a variety of expression vectors 
D)  with a variety of promoters to control the expression level of the protein 
E)  all of the above 
A)  when single chain proteins are expressed 
B)  to produce large quantities of protein 
C)  with a variety of expression vectors 
D)  with a variety of promoters to control the expression level of the protein 
E)  all of the above

Question 5

The green fluorescent protein (GFP) ___________.
I. is a large protein, MW larger than 60 kDa
II. is used in chimeric protein constructs
III. is extremely useful in tagging proteins inside the cell, to visualize the localization of the expressed proteins
IV. was first isolated from the jellyfish Aequorea victoria
V. needs a substrate to exhibit fluorescence

Accepted Answer

A)  II, III, and IV 
B)  II and V 
C)  III and IV 
D)  I and II 
E)  II and IV 
A)  II, III, and IV 
B)  II and V 
C)  III and IV 
D)  I and II 
E)  II and IV

Question 6

Protecting groups used for side chains of amino acids are different than the protecting group used on the terminal amine because ___________.

Accepted Answer

A)  they can ionize. 
B)  of chemical interference. 
C)  of more activity. 
D)  they should not be deprotected during the deprotection reaction of the terminal amine 
E)  none of the above 
A)  they can ionize. 
B)  of chemical interference. 
C)  of more activity. 
D)  they should not be deprotected during the deprotection reaction of the terminal amine 
E)  none of the above

Question 7

Proteins unfold (denature) under various experimental conditions, such as heat or presence of _______ in the buffer.

Accepted Answer

A)  very low or very high pH 
B)  $\beta$-mercaptoethanol 
C)  urea 
D)  guanidinium hydrochloride 
E)  all of the above 
A)  very low or very high pH 
B)  $\beta$-mercaptoethanol 
C)  urea 
D)  guanidinium hydrochloride 
E)  all of the above

Question 8

If you would synthesize a 15-amino acid long peptide, and each cycle of the solid-phase synthesis had a 99% yield, what would be your overall yield?

Accepted Answer

A)  99% 
B)  75% 
C)  80% 
D)  86% 
E)  95% 
A)  99% 
B)  75% 
C)  80% 
D)  86% 
E)  95%

Question 9

Forming bonds _______ energy. Thus, formation of numerous _______ during protein folding contributes to the stability of the folded structure.

Accepted Answer

A)  increases; ionic bonds 
B)  increases; Van der Waals interactions 
C)  releases; metallic bonds 
D)  releases; hydrogen bonds 
E)  none of the above 
A)  increases; ionic bonds 
B)  increases; Van der Waals interactions 
C)  releases; metallic bonds 
D)  releases; hydrogen bonds 
E)  none of the above

Question 10

Depositing falsified protein structure data into the Protein Data Bank, PDB, is a huge disservice to the scientific community because it leads to ___________.

Accepted Answer

A)  misleading protein-drug interactions when used in drug discovery 
B)  wasted financial resources 
C)  wasted time using erroneous structures 
D)  retracted publications 
E)  all of the above 
A)  misleading protein-drug interactions when used in drug discovery 
B)  wasted financial resources 
C)  wasted time using erroneous structures 
D)  retracted publications 
E)  all of the above

Question 11

The advantages of using a yeast expression system are due to _______.

Accepted Answer

A)  a fast grow rate of yeast 
B)  the proteins being secreted into the growth media 
C)  the ability of producing large quantities of engineered protein 
D)  the lower cost than the mammalian expression systems 
E)  all of the above 
A)  a fast grow rate of yeast 
B)  the proteins being secreted into the growth media 
C)  the ability of producing large quantities of engineered protein 
D)  the lower cost than the mammalian expression systems 
E)  all of the above

Question 12

Given a peptide:   Disulfide bonds will form between the side chains of ______ in a buffer at pH 7 (under oxidizing conditions).

Accepted Answer

A)  Met1 and Cys7 
B)  Met1 and Cys12 
C)  Cys 7 and Cys12 
D)  Ser3 and Cys12 
E)  none of the above 
A)  Met1 and Cys7 
B)  Met1 and Cys12 
C)  Cys 7 and Cys12 
D)  Ser3 and Cys12 
E)  none of the above

Question 13

The 3D solution structure of a 20mer peptide could be determined by_________.

Accepted Answer

A)  electron microscopy 
B)  x-ray crystallography 
C)  multidimensional NMR 
D)  circular dichroism 
E)  none of the above 
A)  electron microscopy 
B)  x-ray crystallography 
C)  multidimensional NMR 
D)  circular dichroism 
E)  none of the above

Question 14

An insect expression system uses a baculovirus that is engineered to encode the protein of interest. The virus is used to infect ovarian cells from Spodoptera frugiperda, the fall armyworm. The advantages of using this system to produce engineered proteins are _________.

Accepted Answer

A)  correct post-translational modifications on the protein of interest 
B)  cells grow in suspension in a simple broth 
C)  cells lyse at the end of the viral life cycle releasing the protein of interest 
D)  high expression level of the engineered protein 
E)  all of the above 
A)  correct post-translational modifications on the protein of interest 
B)  cells grow in suspension in a simple broth 
C)  cells lyse at the end of the viral life cycle releasing the protein of interest 
D)  high expression level of the engineered protein 
E)  all of the above

Question 15

The most stable 3D protein structure has the ______ free energy, and is therefore assumed to be the native conformation of the protein.

Accepted Answer

A)  highest 
B)  lowest 
C)  widest 
D)  most defined 
E)  least defined 
A)  highest 
B)  lowest 
C)  widest 
D)  most defined 
E)  least defined

Question 16

During solid-phase protein synthesis (SPPS) it is common to link the first amino acid to the resin by a(n) ___________.

Accepted Answer

A)  hydrogen bond 
B)  ionic bond 
C)  ester bond 
D)  amide bond 
E)  none of the above 
A)  hydrogen bond 
B)  ionic bond 
C)  ester bond 
D)  amide bond 
E)  none of the above

Question 17

His6-tagged proteins are often overexpressed in E. coli cells and purified by _______ chromatography.

Accepted Answer

A)  ion exchange 
B)  size exclusion 
C)  nickel-affinity 
D)  high pressure 
E)  reverse phase 
A)  ion exchange 
B)  size exclusion 
C)  nickel-affinity 
D)  high pressure 
E)  reverse phase

Question 18

Proteins containing ________ residues may not re-fold properly.

Accepted Answer

A)  few cysteine 
B)  multiple serine 
C)  few serine 
D)  numerous cysteine 
E)  multiple lysine 
A)  few cysteine 
B)  multiple serine 
C)  few serine 
D)  numerous cysteine 
E)  multiple lysine

Question 19

A solid-phase protein synthesis reaction cycle includes_______________.

Accepted Answer

A)  washing steps 
B)  deprotection of the peptide amino terminus using piperidine 
C)  activation of the carboxy group on the amino acid monomer to be added to the growing peptide 
D)  coupling of the activated amino acid with the amino group of the growing peptide polymer 
E)  all of the above 
A)  washing steps 
B)  deprotection of the peptide amino terminus using piperidine 
C)  activation of the carboxy group on the amino acid monomer to be added to the growing peptide 
D)  coupling of the activated amino acid with the amino group of the growing peptide polymer 
E)  all of the above

Exam 20: Designer Proteins and Protein Folding

An _______ is a _________ monomer used in peptide synthesis. A peptide is a ____ polymer and contains _____ bonds.

The conserved folds found in proteins prove that these structures are selected by ________.

Bacterial expression systems are used __________________.

Protecting groups used for side chains of amino acids are different than the protecting group used on the terminal amine because ___________.

Proteins unfold (denature) under various experimental conditions, such as heat or presence of _______ in the buffer.

If you would synthesize a 15-amino acid long peptide, and each cycle of the solid-phase synthesis had a 99% yield, what would be your overall yield?

Forming bonds _______ energy. Thus, formation of numerous _______ during protein folding contributes to the stability of the folded structure.

Depositing falsified protein structure data into the Protein Data Bank, PDB, is a huge disservice to the scientific community because it leads to ___________.

The advantages of using a yeast expression system are due to _______.

Given a peptide: Disulfide bonds will form between the side chains of ______ in a buffer at pH 7 (under oxidizing conditions).

The 3D solution structure of a 20mer peptide could be determined by_________.

An insect expression system uses a baculovirus that is engineered to encode the protein of interest. The virus is used to infect ovarian cells from Spodoptera frugiperda, the fall armyworm. The advantages of using this system to produce engineered proteins are _________.

The most stable 3D protein structure has the ______ free energy, and is therefore assumed to be the native conformation of the protein.

During solid-phase protein synthesis (SPPS) it is common to link the first amino acid to the resin by a(n) ___________.

His6-tagged proteins are often overexpressed in E. coli cells and purified by _______ chromatography.

Proteins containing ________ residues may not re-fold properly.

A solid-phase protein synthesis reaction cycle includes_______________.

The Chemical Foundations of Biochemistry

Nucleic Acids

Proteins I

Proteins Iienzymes

Membranes and an Introduction to Signal Transduction

Carbohydrates I

The Common Catabolic Pathway

Carbohydrates II

Lipids I

Lipids II

Amine Metabolism

Metabolism Integration

Nucleotide Deoxynucleotide Metabolism

Dna Replication, Damage and Repair

Rna Synthesis

Protein

Control of Gene

Determination of Macromolecular Structure

Allosterism and Receptor-Ligand

Biomolecule Purification

Bioinformatics and Omics

Signal

Protein Trafficking

Photosynthesis Nitrogen

Filters

An ___ is a _ monomer used in peptide synthesis. A peptide is a polymer and contains _ bonds.

Forming bonds _ energy. Thus, formation of numerous _ during protein folding contributes to the stability of the folded structure.