Question 1

The lock-and-key analogy for enzymes applies to the _____.

Accepted Answer

A) specificity of enzyme primary,secondary,and tertiary structure 
B) specificity of enzyme tertiary subunits joining to form a quaternary structure 
C) specificity of enzymes binding to their substrate 
D) specificity of enzymes interacting with water 
E) specificity of enzymes interacting with ions 
A) specificity of enzyme primary,secondary,and tertiary structure 
B) specificity of enzyme tertiary subunits joining to form a quaternary structure 
C) specificity of enzymes binding to their substrate 
D) specificity of enzymes interacting with water 
E) specificity of enzymes interacting with ions C

Question 2

At the pH found in cells (about 7.0),what happens to the amino group on an amino acid?

Accepted Answer

A) It acts as a base and gains a proton,giving it a positive charge. 
B) It acts as an acid and loses a proton,giving it a negative charge. 
C) It is reduced,and tends to act as an electron donor in redox reactions. 
D) It remains neutral,like water,and does not have a charge. 
A) It acts as a base and gains a proton,giving it a positive charge. 
B) It acts as an acid and loses a proton,giving it a negative charge. 
C) It is reduced,and tends to act as an electron donor in redox reactions. 
D) It remains neutral,like water,and does not have a charge. A

Question 3

Suppose you discovered a new amino acid.Its R-group contains only hydrogen and carbon atoms.Predict the behavior of this amino acid.

Accepted Answer

A) It is hydrophobic. 
B) It is hydrophilic. 
C) Relative to the amino acids found in organisms,its interactions with water will be intermediate. 
D) Relative to the amino acids found in organisms,its interactions with water will be very high. 
A) It is hydrophobic. 
B) It is hydrophilic. 
C) Relative to the amino acids found in organisms,its interactions with water will be intermediate. 
D) Relative to the amino acids found in organisms,its interactions with water will be very high. A

Question 4

Aquaporins are proteins that control the passage of water molecules across the cell membrane.The protein forms a pore,or opening,in the membrane.You isolate what you think are two different molecules of aquaporin,and determine that one of the proteins has a larger pore diameter than the second.Which of the following do you conclude?

Accepted Answer

A) These two forms of aquaporin will have identical sequences of amino acids. 
B) These two forms of aquaporin will have different sequences of amino acids. 
C) You will have to sequence the proteins to compare their primary structure,because it should have no effect on pore diameter. 
D) These molecules both can't have aquaporin because all proteins that do the same type of job (such as catalyze a reaction)have the exact same 3-D structure. 
A) These two forms of aquaporin will have identical sequences of amino acids. 
B) These two forms of aquaporin will have different sequences of amino acids. 
C) You will have to sequence the proteins to compare their primary structure,because it should have no effect on pore diameter. 
D) These molecules both can't have aquaporin because all proteins that do the same type of job (such as catalyze a reaction)have the exact same 3-D structure.

Question 5

In cells,the activity of enzymes is often regulated by other molecules.Why is this necessary?

Accepted Answer

A) because all enzymes require some help from another molecule to function correctly 
B) because other molecules are necessary to prevent enzymes from denaturing 
C) because each enzyme has multiple functions 
D) because it is unlikely that all reaction products are required all of the time 
A) because all enzymes require some help from another molecule to function correctly 
B) because other molecules are necessary to prevent enzymes from denaturing 
C) because each enzyme has multiple functions 
D) because it is unlikely that all reaction products are required all of the time

Question 6

You collect data on the effect of pH on the function of the enzyme catalase in human cells.Which of the following graphs would you expect?

Accepted Answer

A)    
B)    
C)    
D)    
A)    
B)    
C)    
D)

Question 7

Which of the following would be an example of a cofactor?

Accepted Answer

A) an enzyme active site that contains an α-helix 
B) the nonprotein heme group in a hemoglobin molecule 
C) the disulfide bridge that forms between cysteine residues 
D) a β-pleated sheet hidden on the inside of a protein's tertiary structure 
A) an enzyme active site that contains an α-helix 
B) the nonprotein heme group in a hemoglobin molecule 
C) the disulfide bridge that forms between cysteine residues 
D) a β-pleated sheet hidden on the inside of a protein's tertiary structure

Question 8

What type of interaction is directly responsible for the formation of secondary structure?

Accepted Answer

A) peptide bonds between adjacent amino acids 
B) peptide bonds between nonadjacent amino acids 
C) hydrogen bonds between sections of the polypeptide backbone 
D) hydrogen bonds between side chains of amino acids 
A) peptide bonds between adjacent amino acids 
B) peptide bonds between nonadjacent amino acids 
C) hydrogen bonds between sections of the polypeptide backbone 
D) hydrogen bonds between side chains of amino acids

Question 9

Refer to the following paragraph and Figure 3.1 to answer the following questions.
   
Figure 3.1
Since structure correlates so well with function,biochemists are constantly looking for new ways to probe the complex structure of proteins in order to understand what they do and how they do it.One of the most powerful techniques in existence today is X-ray crystallography.The main difficulty with this technique is getting the protein to crystallize.Once crystallized,the protein is bombarded with X-rays to create a pattern that can be analyzed mathematically to determine the three-dimensional structure of the protein.This analysis has been performed by Krzysztof Palczewski on the protein rhodopsin,which is a light-sensitive protein found in species ranging from ancient bacteria (archaea)to humans.The structure (schematically shown above,where each letter represents an amino acid)is characterized by a single polypeptide chain with several α-helical segments that loop back and forth across the cell membrane.Another notable feature is the disulfide bond (-S-S-)that can be seen at the bottom of the third transmembrane segment.[Figure adapted from K.Palczewski et al. ,Science 289 (2000): 739.]
-How many times does the protein in Figure 3.1 cross the cell membrane?

Accepted Answer

A) 1 
B) 3 
C) 4 
D) 7 
A) 1 
B) 3 
C) 4 
D) 7

Question 10

The functional groups of amino acids _____.

Accepted Answer

A) are always charged 
B) may be hydrophobic or hydrophilic 
C) only contain C,H,and O 
D) are identical in different types of amino acids 
A) are always charged 
B) may be hydrophobic or hydrophilic 
C) only contain C,H,and O 
D) are identical in different types of amino acids

Question 11

What is the pattern component of the theory of chemical evolution?

Accepted Answer

A) Both heat and electrical discharges are required for chemical evolution to occur. 
B) Most chemical evolution occurred at black smokers. 
C) The process occurred at black smokers,in the atmosphere and oceans,and in outer space. 
D) Increasingly complex carbon-containing molecules formed early in Earth history. 
A) Both heat and electrical discharges are required for chemical evolution to occur. 
B) Most chemical evolution occurred at black smokers. 
C) The process occurred at black smokers,in the atmosphere and oceans,and in outer space. 
D) Increasingly complex carbon-containing molecules formed early in Earth history.

Question 12

An enzyme has a total of four active sites.When you denature the molecule and study its composition,you find that each active site occurs on a different polypeptide.Which of the following hypotheses does this observation support?

Accepted Answer

A) The enzyme is subject to allosteric regulation. 
B) The enzyme requires a cofactor to function normally. 
C) The protein's structure is affected by temperature and pH. 
D) The protein has quaternary structure. 
A) The enzyme is subject to allosteric regulation. 
B) The enzyme requires a cofactor to function normally. 
C) The protein's structure is affected by temperature and pH. 
D) The protein has quaternary structure.

Question 13

At the pH found in cells (about 7.0),what happens to the carboxyl group on an amino acid?

Accepted Answer

A) It acts as a base and gains a proton,giving it a positive charge. 
B) It acts as an acid and loses a proton,giving it a negative charge. 
C) It is oxidized,and tends to act as an electron acceptor in redox reactions. 
D) It remains neutral,like water,and does not have a charge. 
A) It acts as a base and gains a proton,giving it a positive charge. 
B) It acts as an acid and loses a proton,giving it a negative charge. 
C) It is oxidized,and tends to act as an electron acceptor in redox reactions. 
D) It remains neutral,like water,and does not have a charge.

Question 14

Refer to the following paragraph and Figure 3.1 to answer the following questions.
   
Figure 3.1
Since structure correlates so well with function,biochemists are constantly looking for new ways to probe the complex structure of proteins in order to understand what they do and how they do it.One of the most powerful techniques in existence today is X-ray crystallography.The main difficulty with this technique is getting the protein to crystallize.Once crystallized,the protein is bombarded with X-rays to create a pattern that can be analyzed mathematically to determine the three-dimensional structure of the protein.This analysis has been performed by Krzysztof Palczewski on the protein rhodopsin,which is a light-sensitive protein found in species ranging from ancient bacteria (archaea)to humans.The structure (schematically shown above,where each letter represents an amino acid)is characterized by a single polypeptide chain with several α-helical segments that loop back and forth across the cell membrane.Another notable feature is the disulfide bond (-S-S-)that can be seen at the bottom of the third transmembrane segment.[Figure adapted from K.Palczewski et al. ,Science 289 (2000): 739.]
-What is the location of the C-terminus of the protein in Figure 3.1?

Accepted Answer

A) extracellular 
B) cytoplasm 
C) embedded within the membrane 
D) nucleus 
A) extracellular 
B) cytoplasm 
C) embedded within the membrane 
D) nucleus

Question 15

Which one of the following is not a component of each monomer used to make proteins?

Accepted Answer

A) a phosphorus atom,P 
B) an amino functional group,NH₂ 
C) a side chain,R 
D) a carboxyl group,COOH 
A) a phosphorus atom,P 
B) an amino functional group,NH₂ 
C) a side chain,R 
D) a carboxyl group,COOH

Question 16

A series of hydrophobic side chains will congregate together as a protein folds in an aqueous solution and be stabilized by _____.

Accepted Answer

A) disulfide bonds 
B) van der Waals interaction 
C) hydrogen bonds 
D) quaternary structure bonds 
A) disulfide bonds 
B) van der Waals interaction 
C) hydrogen bonds 
D) quaternary structure bonds

Question 17

HIV is the virus that causes AIDS.In the mid-1990s,researchers discovered an enzyme in HIV called protease.Once the enzyme's structure was known,researchers began looking for drugs that would fit into the active site and block it.If this strategy for stopping HIV infections were successful,it would be an example of what phenomenon?

Accepted Answer

A) vaccination 
B) poisoning 
C) allosteric regulation 
D) competitive inhibition 
A) vaccination 
B) poisoning 
C) allosteric regulation 
D) competitive inhibition

Question 18

You've just sequenced a new protein found in mice and observe that sulfur-containing cysteine residues occur at regular intervals.What is the significance of this finding?

Accepted Answer

A) Cysteine residues are required for the formation of α-helices and β-pleated sheets. 
B) It will be important to include cysteine in the diet of the mice. 
C) Cysteine residues are involved in disulfide bridges that help form tertiary structure. 
D) Cysteine causes bends,or angles,to occur in the tertiary structure of proteins. 
A) Cysteine residues are required for the formation of α-helices and β-pleated sheets. 
B) It will be important to include cysteine in the diet of the mice. 
C) Cysteine residues are involved in disulfide bridges that help form tertiary structure. 
D) Cysteine causes bends,or angles,to occur in the tertiary structure of proteins.

Question 19

Which of the following observations is the strongest argument in favor of the hypothesis that protein structure and function are correlated?

Accepted Answer

A) Proteins function best at certain temperatures. 
B) Proteins have four distinct levels of structure and many functions. 
C) Enzymes tend to be globular in shape. 
D) Denatured (unfolded)proteins do not function normally. 
A) Proteins function best at certain temperatures. 
B) Proteins have four distinct levels of structure and many functions. 
C) Enzymes tend to be globular in shape. 
D) Denatured (unfolded)proteins do not function normally.

Question 20

You disrupt all hydrogen bonds in a protein.What level of structure will be preserved?

Accepted Answer

A) primary structure 
B) secondary structure 
C) tertiary structure 
D) quaternary structure 
A) primary structure 
B) secondary structure 
C) tertiary structure 
D) quaternary structure

Exam 3: Protein Structure and Function

The lock-and-key analogy for enzymes applies to the _____.

At the pH found in cells (about 7.0),what happens to the amino group on an amino acid?

Suppose you discovered a new amino acid.Its R-group contains only hydrogen and carbon atoms.Predict the behavior of this amino acid.

In cells,the activity of enzymes is often regulated by other molecules.Why is this necessary?

You collect data on the effect of pH on the function of the enzyme catalase in human cells.Which of the following graphs would you expect?

Which of the following would be an example of a cofactor?

What type of interaction is directly responsible for the formation of secondary structure?

The functional groups of amino acids _____.

What is the pattern component of the theory of chemical evolution?

An enzyme has a total of four active sites.When you denature the molecule and study its composition,you find that each active site occurs on a different polypeptide.Which of the following hypotheses does this observation support?

At the pH found in cells (about 7.0),what happens to the carboxyl group on an amino acid?

Which one of the following is not a component of each monomer used to make proteins?

A series of hydrophobic side chains will congregate together as a protein folds in an aqueous solution and be stabilized by _____.

You've just sequenced a new protein found in mice and observe that sulfur-containing cysteine residues occur at regular intervals.What is the significance of this finding?

Which of the following observations is the strongest argument in favor of the hypothesis that protein structure and function are correlated?

You disrupt all hydrogen bonds in a protein.What level of structure will be preserved?

Biology and the Tree of Life

Water and Carbon: the Chemical Basis of Life

Nucleic Acids and the Rna World

An Introduction to Carbohydrates

Lipids, membranes, and the First Cells

Inside the Cell

Cell-Cell Interactions

Cellular Respiration and Fermentation

Photosynthesis

The Cell Cycle

Meiosis

Mendel and the Gene

Dna and the Gene: Synthesis and Repair

How Genes Work

Transcription and Translation

Control of Gene Expression in Bacteria

Control of Gene Expression in Eukaryotes

Analyzing and Engineering Genes

Genomics

Principles of Development

An Introduction to Animal Development

An Introduction to Plant Development

Evolution by Natural Selection

Evolutionary Processes

Speciation

Phylogenies and the History of Life

Bacteria and Archaea

Protists

Green Plants

Fungi

An Introduction to Animals

Protostome Animals

Deuterostome Animals

Viruses

Plant Form and Function

Water and Sugar Transport in Plants

Plant Nutrition

Plant Sensory Systems, signals, and Responses

Plant Reproduction

Animal Form and Function

Water and Electrolyte Balance in Animals

Animal Nutrition

Gas Exchange and Circulation

Electrical Signals in Animals

Animal Sensory Systems and Movement

Chemical Signals in Animals

Animal Reproduction

The Immune System in Animals

An Introduction to Ecology

Behavioral Ecology

Population Ecology

Community Ecology

Ecosystems

Biodiversity and Conservation Biology

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