Deck 19: Biomolecules: Amino Acids, Peptides, and Proteins
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Deck 19: Biomolecules: Amino Acids, Peptides, and Proteins
1
Refer to the data below to answer the following question(s).
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. Draw the condensed structure for leucine, and label all chirality centers with an asterisk and identify the amine as primary, secondary or tertiary.
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. Draw the condensed structure for leucine, and label all chirality centers with an asterisk and identify the amine as primary, secondary or tertiary.
Primary 2
Draw the structure of the product of the following reaction and describe the usefulness of this type of reaction. 

Removal of a protecting group that was added to the carboxyl group. Often used in protein synthesis. 3
Refer to the data below to answer the following question(s).
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. Draw the structure of the predominant form of leucine at pH = 10.00.
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. Draw the structure of the predominant form of leucine at pH = 10.00.

4
Refer to the data below to answer the following question(s).
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. Leucine is described as an essential amino acid. What does this mean?
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. Leucine is described as an essential amino acid. What does this mean?
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5
Consider the following structure. Based on this structure answer the following question(s). 
Refer to instructions. Circle the peptide bonds.

Refer to instructions. Circle the peptide bonds.
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6
Refer to the data below to answer the following question(s).
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. How many possible stereoisomers of leucine are there?
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. How many possible stereoisomers of leucine are there?
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7
Consider the following structure. Based on this structure answer the following question(s). 
Refer to instructions. Name the peptide using both the three-letter and one-letter codes.

Refer to instructions. Name the peptide using both the three-letter and one-letter codes.
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8
Identify the aldehyde byproduct that results from the following reaction. 

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9
Refer to the data below to answer the following question(s).
Porcine dynorphin is a neuropeptide having 17 amino acid residues. Its structure is shown below.
Tyr−Gly−Gly−Phe−Leu−Arg−Arg−Ile−Arg−Pro−Lys−Leu−Lys−Trp−Asp−Asn−Gln
Refer to instructions. What fragments would result if dynorphin were cleaved by trypsin?
Porcine dynorphin is a neuropeptide having 17 amino acid residues. Its structure is shown below.
Tyr−Gly−Gly−Phe−Leu−Arg−Arg−Ile−Arg−Pro−Lys−Leu−Lys−Trp−Asp−Asn−Gln
Refer to instructions. What fragments would result if dynorphin were cleaved by trypsin?
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10
Consider the following structure. Based on this structure answer the following question(s). 
Draw and name the structure of the product of the following reaction.

Draw and name the structure of the product of the following reaction.

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11
Consider the following structure. Based on this structure answer the following question(s). 
Refer to instructions. Identify the C-terminal amino acid and the N-terminal amino acid.

Refer to instructions. Identify the C-terminal amino acid and the N-terminal amino acid.
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12
Refer to the data below to answer the following question(s).
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. Draw a Fischer projection of L-leucine and label the chirality center(s) as R or S.
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. Draw a Fischer projection of L-leucine and label the chirality center(s) as R or S.
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13
Refer to the data below to answer the following question.Amino Acid
Isoelectric point
Arginine
10.76
Glutamic Acid
3.22
Tryptophan
5.89
Define isoelectric point.
Isoelectric point
Arginine
10.76
Glutamic Acid
3.22
Tryptophan
5.89
Define isoelectric point.
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14
Refer to the data below to answer the following question(s).
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. Draw the structure of the predominant form of leucine at pH = 1.50.
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. Draw the structure of the predominant form of leucine at pH = 1.50.
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15
Refer to the data below to answer the following question(s).
Porcine dynorphin is a neuropeptide having 17 amino acid residues. Its structure is shown below.
Tyr−Gly−Gly−Phe−Leu−Arg−Arg−Ile−Arg−Pro−Lys−Leu−Lys−Trp−Asp−Asn−Gln
Refer to instructions. Show the steps involved in a synthesis of F−G−I using the Merrifield procedure.
Porcine dynorphin is a neuropeptide having 17 amino acid residues. Its structure is shown below.
Tyr−Gly−Gly−Phe−Leu−Arg−Arg−Ile−Arg−Pro−Lys−Leu−Lys−Trp−Asp−Asn−Gln
Refer to instructions. Show the steps involved in a synthesis of F−G−I using the Merrifield procedure.
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16
Refer to the data below to answer the following question.Amino Acid
Isoelectric point
Arginine
10.76
Glutamic Acid
3.22
Tryptophan
5.89
Refer to instructions. At what pH would you carry out an electrophoresis experiment if you wanted to separate a mixture of lysine, aspartic acid and phenylalanine? Explain.
Isoelectric point
Arginine
10.76
Glutamic Acid
3.22
Tryptophan
5.89
Refer to instructions. At what pH would you carry out an electrophoresis experiment if you wanted to separate a mixture of lysine, aspartic acid and phenylalanine? Explain.
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17
Refer to the data below to answer the following question(s).
Porcine dynorphin is a neuropeptide having 17 amino acid residues. Its structure is shown below.
Tyr−Gly−Gly−Phe−Leu−Arg−Arg−Ile−Arg−Pro−Lys−Leu−Lys−Trp−Asp−Asn−Gln
Refer to instructions. What fragments would result if dynorphin were cleaved by chymotropsin?
Porcine dynorphin is a neuropeptide having 17 amino acid residues. Its structure is shown below.
Tyr−Gly−Gly−Phe−Leu−Arg−Arg−Ile−Arg−Pro−Lys−Leu−Lys−Trp−Asp−Asn−Gln
Refer to instructions. What fragments would result if dynorphin were cleaved by chymotropsin?
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18
Consider the following structure. Based on this structure answer the following question(s). 
Write the equation for the reaction, using methanol (CH3OH), that would render the carboxyl group of alanine unreactive.

Write the equation for the reaction, using methanol (CH3OH), that would render the carboxyl group of alanine unreactive.
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19
Refer to the data below to answer the following question(s).
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. What is the pI of leucine?
Leucine is an essential amino acid with the systematic name 2-amino-3-methylpentanoic acid. It has pKa1 = 2.36 and pKa2 = 9.60.
Refer to instructions. What is the pI of leucine?
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20
Consider the following structure. Based on this structure answer the following question(s). 
Refer to instructions. How many other peptides could be formed from this same combination of amino acids?
A) 3
B) 6
C) 9
D) 12

Refer to instructions. How many other peptides could be formed from this same combination of amino acids?
A) 3
B) 6
C) 9
D) 12
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21
Which of the following tripeptides is not hydrolysed by trypsin?
A) Glu−Arg−Ser
B) Arg−Glu−Thr
C) Glu−Ser−Arg
D) Lys−Ser−Arg
A) Glu−Arg−Ser
B) Arg−Glu−Thr
C) Glu−Ser−Arg
D) Lys−Ser−Arg
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22
Which of the following reagents can be used to cleave a tert-butoxycarbonyl (Boc) protecting group from a peptide?
A) H2/Pd
B) CF3CO2H
C) Na2CO3, H2O
D) LiAlH4
A) H2/Pd
B) CF3CO2H
C) Na2CO3, H2O
D) LiAlH4
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23
Which of the following tripeptides is not hydrolysed by chymotrypsin?
A) Phe−Lys−Glu
B) Lys−Tyr−Phe
C) Gln−Ser−Phe
D) Gln−Tyr−Ser
A) Phe−Lys−Glu
B) Lys−Tyr−Phe
C) Gln−Ser−Phe
D) Gln−Tyr−Ser
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24
How does phenyl isothiocyanate, Ph−N=C=S, react with a peptide in the Edman degradation?
A) the sp carbon acts as an electrophile in a reaction with an amino group of the peptide
B) the sulfur acts as a nucleophile and adds to the carbon of the peptide bond
C) the nitrogen acts as a nucleophile and adds to the carbon of the peptide bond
D) the sp carbon acts as an electrophile in a reaction with a carboxylate of the peptide
A) the sp carbon acts as an electrophile in a reaction with an amino group of the peptide
B) the sulfur acts as a nucleophile and adds to the carbon of the peptide bond
C) the nitrogen acts as a nucleophile and adds to the carbon of the peptide bond
D) the sp carbon acts as an electrophile in a reaction with a carboxylate of the peptide
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25
Which of the following amino acids has a non-polar side chain?
A) histidine
B) arginine
C) glutamine
D) valine
A) histidine
B) arginine
C) glutamine
D) valine
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26
To what structural feature does the term "quaternary structure" refer?
A) the sequence of amino acids in proteins
B) the overall folding pattern of proteins
C) the aggregation of polypeptides
D) the conformation of local regions of polypeptides
A) the sequence of amino acids in proteins
B) the overall folding pattern of proteins
C) the aggregation of polypeptides
D) the conformation of local regions of polypeptides
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27
Which of the following amino acids migrates to the negative electrode on paper electrophoresis at a pH of 7.0?
A) lysine
B) aspartic acid
C) asparagine
D) glutamic acid
A) lysine
B) aspartic acid
C) asparagine
D) glutamic acid
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28
Which of the following amino acids has an aromatic side chain?
A) isoleucine
B) valine
C) tyrosine
D) threonine
A) isoleucine
B) valine
C) tyrosine
D) threonine
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29
Which of the following amino acids contains two stereocenters?
A) isoleucine
B) proline
C) phenylalanine
D) glutamine
A) isoleucine
B) proline
C) phenylalanine
D) glutamine
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30
Which of the following amino acids is a secondary amine?
A) proline
B) glutamine
C) histidine
D) aspargine
A) proline
B) glutamine
C) histidine
D) aspargine
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31
To what structural feature does the term "primary structure" refer?
A) the sequence of amino acids in proteins
B) the overall folding pattern of proteins
C) the aggregation of polypeptides
D) the conformation of local regions of polypeptides
A) the sequence of amino acids in proteins
B) the overall folding pattern of proteins
C) the aggregation of polypeptides
D) the conformation of local regions of polypeptides
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32
Which of the following amino acids migrates to the positive electrode on paper electrophoresis at a pH of 7.0?
A) glutamic acid
B) arginine
C) lysine
D) histadine
A) glutamic acid
B) arginine
C) lysine
D) histadine
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33
Which of the following dipeptides is L−Ser−L−Phe?
A)

B)

C)

D)

A)

B)

C)

D)

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34
Which of the following dipeptides is L−Cys−L−Ala?
A)

B)

C)

D)

A)

B)

C)

D)

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35
Which of the following amino acids has a sulfur-containing side chain?
A) serine
B) cysteine
C) lysine
D) methionine
E) both b and d
A) serine
B) cysteine
C) lysine
D) methionine
E) both b and d
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36
What are the R/S designations of the two stereocenters of L-threonine? 
A) 2R,3R
B) 2R,3S
C) 2S,3R
D) 2S,3S

A) 2R,3R
B) 2R,3S
C) 2S,3R
D) 2S,3S
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37
Which amino acid results from the following sequence of transformations? 

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38
To what structural feature does the term "secondary structure" refer?
A) the sequence of amino acids in proteins
B) the overall folding pattern of proteins
C) the aggregation of polypeptides
D) the conformation of local regions of polypeptides
A) the sequence of amino acids in proteins
B) the overall folding pattern of proteins
C) the aggregation of polypeptides
D) the conformation of local regions of polypeptides
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39
Which of the following amino acids would contain the highest concentration of zwitterions at pH 5.90?
A) aspartic acid (pI 2.77)
B) alanine (pI 6.01)
C) lysine (pI 9.74)
D) glutamic acid (pI 3.22)
E) all of these contain approximately equal concentrations of zwitterions
A) aspartic acid (pI 2.77)
B) alanine (pI 6.01)
C) lysine (pI 9.74)
D) glutamic acid (pI 3.22)
E) all of these contain approximately equal concentrations of zwitterions
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40
To what structural feature does the term "tertiary structure" refer?
A) the sequence of amino acids in proteins
B) the overall folding pattern of proteins
C) the aggregation of polypeptides
D) the conformation of local regions of polypeptides
A) the sequence of amino acids in proteins
B) the overall folding pattern of proteins
C) the aggregation of polypeptides
D) the conformation of local regions of polypeptides
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41
Match a structure from the list below to each of the following terms.
An amino acid with a protected carboxyl group.
A)
B)
C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)
E)
F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)
I)
J)
K)
L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
An amino acid with a protected carboxyl group.
A)

B)

C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)

E)

F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)

I)

J)

K)

L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
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42
Match a structure from the list below to each of the following terms.
The product of an Edman degradation.
A)
B)
C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)
E)
F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)
I)
J)
K)
L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
The product of an Edman degradation.
A)

B)

C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)

E)

F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)

I)

J)

K)

L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
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43
An enzyme classified as a ligase would be associated with a reaction than involves the:
A) introduction of a double bond.
B) loss of water.
C) loss of carbon dioxide.
D) transfer of an amino group.
E) hydrolysis of an ester.
A) introduction of a double bond.
B) loss of water.
C) loss of carbon dioxide.
D) transfer of an amino group.
E) hydrolysis of an ester.
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44
Match a structure from the list below to each of the following terms.
A peptide coupling reagent.
A)
B)
C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)
E)
F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)
I)
J)
K)
L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
A peptide coupling reagent.
A)

B)

C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)

E)

F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)

I)

J)

K)

L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
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45
Match a structure from the list below to each of the following terms.
Source from which many coenzymes are derived.
A)
B)
C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)
E)
F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)
I)
J)
K)
L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
Source from which many coenzymes are derived.
A)

B)

C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)

E)

F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)

I)

J)

K)

L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
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46
Match a structure from the list below to each of the following terms.
A polypeptide which gives four fragments on treatment with chymotrypsin.
A)
B)
C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)
E)
F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)
I)
J)
K)
L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
A polypeptide which gives four fragments on treatment with chymotrypsin.
A)

B)

C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)

E)

F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)

I)

J)

K)

L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
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47
Match a structure from the list below to each of the following terms.
An amino acid in its zwitterionic form.
A)
B)
C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)
E)
F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)
I)
J)
K)
L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
An amino acid in its zwitterionic form.
A)

B)

C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)

E)

F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)

I)

J)

K)

L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
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48
Match a term from the list below to each definition.
Proteins which are tough and insoluble in water.
A)Ligases
B)Fibrous proteins
C)Conjugated protein
D)Hydrolases
E)Simple protein
F)Globular proteins
G)Kinases
Proteins which are tough and insoluble in water.
A)Ligases
B)Fibrous proteins
C)Conjugated protein
D)Hydrolases
E)Simple protein
F)Globular proteins
G)Kinases
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49
Match a structure from the list below to each of the following terms.
A peptide containing eight amino acid residues with a C-terminal valine.
A)
B)
C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)
E)
F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)
I)
J)
K)
L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
A peptide containing eight amino acid residues with a C-terminal valine.
A)

B)

C) Val−Phe−Leu−Met−Tyr−Pro−Gly−Trp−Cys−Glu
D)

E)

F) Asp−Tyr−Ile−His−Pro−Phe−Arg−Val
G) apoenzyme
H)

I)

J)

K)

L)Val−Lys−Phe−Gly−Arg−Met−Arg−Phe
M)vitamins
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50
Match a term from the list below to each definition.
Enzymes which catalyze the bonding together of two substrates.
A)Ligases
B)Fibrous proteins
C)Conjugated protein
D)Hydrolases
E)Simple protein
F)Globular proteins
G)Kinases
Enzymes which catalyze the bonding together of two substrates.
A)Ligases
B)Fibrous proteins
C)Conjugated protein
D)Hydrolases
E)Simple protein
F)Globular proteins
G)Kinases
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51
Match a term from the list below to each definition.
Proteins which coil into compact shapes.
A)Ligases
B)Fibrous proteins
C)Conjugated protein
D)Hydrolases
E)Simple protein
F)Globular proteins
G)Kinases
Proteins which coil into compact shapes.
A)Ligases
B)Fibrous proteins
C)Conjugated protein
D)Hydrolases
E)Simple protein
F)Globular proteins
G)Kinases
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52
Match a term from the list below to each definition.
Enzymes which catalyze the transfer of a phosphate group.
A)Ligases
B)Fibrous proteins
C)Conjugated protein
D)Hydrolases
E)Simple protein
F)Globular proteins
G)Kinases
Enzymes which catalyze the transfer of a phosphate group.
A)Ligases
B)Fibrous proteins
C)Conjugated protein
D)Hydrolases
E)Simple protein
F)Globular proteins
G)Kinases
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