Question 1

Arrange the following in order of increasing complexity: secondary structure,tertiary structure,motif,and domain.

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Question 2

Use the theoretical Ramachandran plot at the top to evaluate the two experimental plots on the bottom.Describe the likely secondary structures found in each experimental plot.

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Question 3

Would a nonsense mutation in a gene encoding a protein be expected to result in a gain-of-function or a loss-of-function protein folding disease?

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Question 4

Describe the proposed model of globular protein folding called the nucleation model.

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Question 5

Draw the resonance structures that stabilize the peptide bonds found in proteins.

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Question 6

Identify the four images below,which represent the four classes of protein structures commonly identified across MOST structures found in the Protein Data Bank.

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Question 7

In the famous experiment where Christian Anfinsen unfolded and refolded the protein RNaseA,in what order was the denaturant and reductant removed to give an inactive protein? Why was the protein inactive?

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Question 8

Draw the reaction by which a protein disulfide bond forms.

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Question 9

Collagen is an important structural protein in biological systems.It is formed by a repeating unit containing glycine,proline,and 4-hydroxyproline (4HyP).The synthesis of 4HyP from proline requires vitamin C.Draw the structure of 4HyP.

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Question 10

Why is the amino acid proline not commonly found in  
-helices or  
-sheets? In what secondary structure might proline be commonly found?

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Question 11

Describe generally how a gain-of-function protein folding disease can lead to cell death.

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Question 12

List the levels of protein structure and give a brief description of each.

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Question 13

Use the table below and write out the amino acid sequence coded by the following RNA sequence: AUG_CAC_AGG_UGA.

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Question 14

List reagents and conditions that denature proteins.

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Question 15

What specific reagents or conditions might be found on the X-axis label of the following figure?

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Question 16

After analyzing all the structures of proteins found in the Protein Data Bank,scientists have found that four general classes of protein structures exist,based on their secondary structure themes.Name the four classes of general protein structures.

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Question 17

Draw the structure of the amino acid cysteine showing the predominant form found at pH = 12.0 (assume NH₃₊ pKa 9.0; Cys pK_R 8.0; COOH pKa 2.0).

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Question 18

In the multi-subunit protein family called immunoglobulins,the different subunits are held together by both covalent and noncovalent forces.What are the covalent forces that hold subunits together in immunoglobulins?

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Question 19

Use the two-stranded antiparallel  
-sheet below and drawn in a  
-turn.

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-sheet below...

Question 20

Use the table below and the following RNA sequence to determine which reading frame would give rise to the shortest peptide,or which reading frame gives rise to the first stop codon.
Frame: 1 2 3
RNA: GCG CCC CCU AAC AGG UAG CUG CGG UUC CUG

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Quiz 4: Protein Structure