Question 1

Adding restriction sites when constructing plasmids will help with _______.

Accepted Answer

A)  extraction 
B)  purification 
C)  cloning 
D)  solubility 
E)  electrophoresis 
A)  extraction 
B)  purification 
C)  cloning 
D)  solubility 
E)  electrophoresis

Question 2

Using site-directed mutagenesis, the mutation of a serine residue to an alanine residue might be used to _________.
I. decrease the solubility of a protein
II. eliminate the possibility of phosphorylation at that location
III. observe the impact of a non-polar side chain at that location
IV. prove that serine had a catalytic function in the native protein
V. promote proper folding of the protein

Accepted Answer

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

Question 3

Which statement is true about SPPS:

Accepted Answer

A)  In SPPS the carboxy terminus of the peptide is covalently linked to the resin. 
B)  The next amino acid is coupled to the N- terminus of the growing peptide. 
C)  The carboxylic group of the amino acid to be added to the growing peptide is activated by using dicyclohexylcarbodiimide (DC
C)  
D)  SPPS is used to synthesize up to 100-amino acid long peptides. 
E)  all of the above 
A)  In SPPS the carboxy terminus of the peptide is covalently linked to the resin. 
B)  The next amino acid is coupled to the N- terminus of the growing peptide. 
C)  The carboxylic group of the amino acid to be added to the growing peptide is activated by using dicyclohexylcarbodiimide (DC
C)  
D)  SPPS is used to synthesize up to 100-amino acid long peptides. 
E)  all of the above

Question 4

Unfolded (denatured) proteins can be re-folded by removing the chemicals in a process called _________.

Accepted Answer

A)  chromatography 
B)  dialysis 
C)  precipitation 
D)  nucleation 
E)  condensation 
A)  chromatography 
B)  dialysis 
C)  precipitation 
D)  nucleation 
E)  condensation

Question 5

Levinthal's conclusion was that protein folding _______, because it would take way too long to complete the folding if all randomly available rotations around the main chain bonds would be sampled to achieve the most stable structure.

Accepted Answer

The answer of Levinthal's conclusion was that protein folding _______,...

Question 6

Protein engineering is possible because of advances in biochemistry and molecular biology.
Various _______ in a protein sequence are _____ in order to determine the role they played in the protein.

Accepted Answer

A)  side chains; activated 
B)  amino acids; mutated 
C)  amino acids; activated 
D)  side chains; truncated 
E)  functional groups; replaced 
A)  side chains; activated 
B)  amino acids; mutated 
C)  amino acids; activated 
D)  side chains; truncated 
E)  functional groups; replaced

Question 7

Plasmids are _________. They can be delivered into the cell by ______ or _______.

Accepted Answer

A)  circular pieces of DNA; transfection; electroporation 
B)  pieces of DNA; translocation; transfusion 
C)  pieces of RNA; translocation; transfusion 
D)  pieces of RNA; transfection; elimination 
E)  none of the above 
A)  circular pieces of DNA; transfection; electroporation 
B)  pieces of DNA; translocation; transfusion 
C)  pieces of RNA; translocation; transfusion 
D)  pieces of RNA; transfection; elimination 
E)  none of the above

Question 8

Proteins can be denatured using $\beta$-mercaptoethanol, since this reagent will _____________.

Accepted Answer

A)  melt the protein 
B)  oxidize the amine groups 
C)  reduce the disulfide bonds 
D)  precipitate the protein 
E)  all of the above 
A)  melt the protein 
B)  oxidize the amine groups 
C)  reduce the disulfide bonds 
D)  precipitate the protein 
E)  all of the above

Question 9

During protein folding the entropy of the solvent molecules _______.

Accepted Answer

A)  does not change 
B)  decreases 
C)  increases 
D)  is zero 
E)  none of the above 
A)  does not change 
B)  decreases 
C)  increases 
D)  is zero 
E)  none of the above

Question 10

Given a peptide:  
Hydrogen bonds will form in this peptide in a buffer at pH 7 between:

Accepted Answer

A)  the amino terminus -NH3+ and Ser3 
B)  the side chain of Asp6 and Ser3 
C)  the side chains of Ser6 and His13 
D)  the side chains of Gln9 and His13 
E)  all of the above 
A)  the amino terminus -NH3+ and Ser3 
B)  the side chain of Asp6 and Ser3 
C)  the side chains of Ser6 and His13 
D)  the side chains of Gln9 and His13 
E)  all of the above

Question 11

Proteins can be synthesized in the lab by using ____________.
I. solid-phase peptide synthesis (SPPS)
II. protein overexpression in biological systems (cells)
III. esterification reactions
IV. polymerization reactions
V. hydrolysis reactions

Accepted Answer

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

Question 12

Given a peptide:  
Salt bridges will form in this peptide in a buffer at pH 7 between:
I. the amino terminus -NH3+ and the carboxy terminus -COO-
II. the side chain of Asp6 and the amino terminus -NH3+
III. the side chains of Ser6 and Gln9
IV. the side chain of His13 and the carboxy terminus -COO-
V. the side chains of Gln9 and His13

Accepted Answer

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

Question 13

What are the disadvantages of studying proteins in their purified form?

Accepted Answer

A)  The natural regulators and molecular interactors are missing from the assay, which can lead to missing out on the actual function of the protein. 
B)  The protein may not be soluble. 
C)  The protein may not be stable. 
D)  The protein may aggregate. 
E)  none of the above 
A)  The natural regulators and molecular interactors are missing from the assay, which can lead to missing out on the actual function of the protein. 
B)  The protein may not be soluble. 
C)  The protein may not be stable. 
D)  The protein may aggregate. 
E)  none of the above

Question 14

The origin of replication enables the plasmid to ______________.

Accepted Answer

A)  fuse with the call wall 
B)  replicate within the cell 
C)  fold properly 
D)  react to antibiotics 
E)  all of the above 
A)  fuse with the call wall 
B)  replicate within the cell 
C)  fold properly 
D)  react to antibiotics 
E)  all of the above

Question 15

__________ suppression is used to incorporate unnatural amino acids into a protein using cellular expression.

Accepted Answer

The answer of __________ suppression is used to incorporate unnatural...

Question 16

Engineered proteins can be expressed in a variety of host cells (mammalian, bacterial, etc). Choosing the host cell depends on ___________.

Accepted Answer

A)  how fast the cells grow 
B)  the post-translational modifications that are required for the expressed protein to be biologically active 
C)  the type of single-domain or multi-domain protein that is expressed 
D)  amount of protein that needs to be produced 
E)  all of the above 
A)  how fast the cells grow 
B)  the post-translational modifications that are required for the expressed protein to be biologically active 
C)  the type of single-domain or multi-domain protein that is expressed 
D)  amount of protein that needs to be produced 
E)  all of the above

Question 17

Molecular dynamics simulations can be used to model the sequence in which the _____ structure of a protein forms during protein folding.

Accepted Answer

The answer of Molecular dynamics simulations can be used to...

Question 18

Whistleblowers are in general protected from being fired from the job by __________.

Accepted Answer

A)  federal and state laws 
B)  regulations 
C)  internal guidelines 
D)  company policy 
E)  all of the above 
A)  federal and state laws 
B)  regulations 
C)  internal guidelines 
D)  company policy 
E)  all of the above

Question 19

The ___________ sequence is needed to predict the 3D structure of a relatively small protein using de novo structure prediction software.

Accepted Answer

A)  base 
B)  amino acid 
C)  side chain 
D)  ionization 
E)  propagation 
A)  base 
B)  amino acid 
C)  side chain 
D)  ionization 
E)  propagation

Question 20

The amine group of the amino acid monomers used in SPPS can be protected by a ____________.
I. phosphate group
II. tert-butoxycarbonyl group (t-Boc)
III. fluoprenylmethyloxycarbonyl group (Fmoc)
IV. sulfonamide group

Accepted Answer

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

Exam 20: Designer Proteins and Protein Folding

Adding restriction sites when constructing plasmids will help with _______.

Which statement is true about SPPS:

Unfolded (denatured) proteins can be re-folded by removing the chemicals in a process called _________.

Levinthal's conclusion was that protein folding _______, because it would take way too long to complete the folding if all randomly available rotations around the main chain bonds would be sampled to achieve the most stable structure.

Protein engineering is possible because of advances in biochemistry and molecular biology. Various _______ in a protein sequence are _____ in order to determine the role they played in the protein.

Plasmids are _________. They can be delivered into the cell by ______ or _______.

Proteins can be denatured using β\betaβ -mercaptoethanol, since this reagent will _____________.

During protein folding the entropy of the solvent molecules _______.

Given a peptide: Hydrogen bonds will form in this peptide in a buffer at pH 7 between:

Proteins can be synthesized in the lab by using ____________. I. solid-phase peptide synthesis (SPPS) II. protein overexpression in biological systems (cells) III. esterification reactions IV. polymerization reactions V. hydrolysis reactions

What are the disadvantages of studying proteins in their purified form?

The origin of replication enables the plasmid to ______________.

__________ suppression is used to incorporate unnatural amino acids into a protein using cellular expression.

Engineered proteins can be expressed in a variety of host cells (mammalian, bacterial, etc). Choosing the host cell depends on ___________.

Molecular dynamics simulations can be used to model the sequence in which the _____ structure of a protein forms during protein folding.

Whistleblowers are in general protected from being fired from the job by __________.

The ___________ sequence is needed to predict the 3D structure of a relatively small protein using de novo structure prediction software.

The amine group of the amino acid monomers used in SPPS can be protected by a ____________. I. phosphate group II. tert-butoxycarbonyl group (t-Boc) III. fluoprenylmethyloxycarbonyl group (Fmoc) IV. sulfonamide group

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

Protein engineering is possible because of advances in biochemistry and molecular biology. Various ___ in a protein sequence are _ in order to determine the role they played in the protein.

Plasmids are _. They can be delivered into the cell by or _.

Proteins can be denatured using $\beta$ -mercaptoethanol, since this reagent will _____________.