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BCMB 311 Study Guide - Midterm Guide: Allosteric Regulation, Glutamic Acid, Enzyme Inhibitor

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School
UTK
Department
Biochemistry and Cellular and Molecular Biology
Course
BCMB 311
Professor
Parks, Bruce

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Ch 4 Key Concepts:
1. Each protein has a unique amino acid sequence, which determines its three-dimensional
shape and biological function.
Polar
Nonpolar
Positive
Negative
Asparaganine
Alanine
Arginine
Aspartic Acid
Glutamine
Glycine
Lysine
Glutamic Acid
Serine
Valine
Histidine
Threonine
Leucine
Tyrosine
Isoleucine
Proline
Phenylalanine
Methionine
Tryptophan
Cysteine
2. Hydrogen bonding between regions of the polypeptide sequence lead to secondary
structure patterns such as alpha-helix and beta-sheet.
- Alpha Helix: Folding pattern in which a single polypeptide chain twists around itself to
form a rigid cylinder stabilized by hydrogen bonds between every fourth amino acid
(vertical bonding)
- Beta-Sheet: folding pattern in which neighboring regions of the polypeptide chain
associate side by side with each other with hydrogen bonds to give a rigid flattened
structure (horizontal bonding); antiparallel are more stable
3. Activities of most enzymes are strictly regulated. Know some of the common methods of
regulation, such as feedback inhibition and allostery.
- Feedback inhibition: regulates the flow through biosynthetic pathways
- regulates connected metabolic pathways
- Can toggle an enzyme to be on or off
- Allostery: describes a protein that can exist in multiple conformations and binds to the
alosteric site
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Related Questions

Using the information in the table below, enter the correct pH that should be used to separate the following three amino acids by electrophoresis:

(a) Glu, Lys, and Thr: pH=?

(b) His, Lys, and Arg: pH=?

------------------------------------------------------------------------------------------------------------------------------------------------------

pKa Values for Ionizable Groups of Amino Acids.
Amino Acid pKa of α-COOH pKa of α-NH3+ pKa of Side Chain Isoelectric Point (pI)
Alanine 2.35 9.87 - 6.11
Arginine 2.01 9.04 12.48 10.76
Asparagine 2.02 8.80 - 5.41
Aspartic acid 2.10 9.82 3.86 2.98
Cysteine 2.05 10.25 8.00 5.02
Glutamic acid 2.10 9.47 4.07 3.08
Glutamine 2.17 9.13 - 5.65
Glycine 2.35 9.78 - 6.06
Histidine 1.77 9.18 6.10 7.64
Isoleucine 2.32 9.76 - 6.04
Leucine 2.33 9.74 - 6.04
Lysine 2.18 8.95 10.53 9.74
Methionine 2.28 9.21 - 5.74
Phenylalanine 2.58 9.24 - 5.91
Proline 2.00 10.60 - 6.30
Serine 2.21 9.15 - 5.68
Threonine 2.09 9.10 - 5.60
Tryptophan 2.38 9.39 - 5.88
Tyrosine 2.20 9.11 10.07 5.63
Valine 2.29 9.72 -

6.00

The peptide hormone vasopressin is used in the regulation of Na+ in many vertebrate. Porcine(pig) vasopressin has the sequence Asp-Tyr-Phe-Glu-Asn-Cys-Pro-Lys-Gly.

a) What is the pI of this peptide? Use the pKa values in the table on the last page for your calculations.

b) Could this peptide have an a helical secondary structure? Why or why not.

c) Will this peptide absorb UV light(280nm)? Why?

Type molecular weight Number in lysozyme

Alanine 89 12

Arginine 174 11

Asparagine 132 13

Aspartic acid 133 8

Cysteine 121 8

Glutamic acid 147 2

Glutamine 146 3

Glycine 75 12

Histidine 155 1

Isoleucine 131 6

Leucine 131 8

Lysine 146 6

Methionine 149 2

Phenylalanine 165 3

Proline 115 2

Serine 105 10

Threonine 119 7

Tryptophan 204 6

Tyrosine 181 3

Valine 117 6

1. The sequence of amino acids of the enzyme lysozyme is known. Below is a list of amino acids

and the number of each in the lysozyme molecule

Questions:

a. What is the average molecular weight of the 20 amino acids?

b. What is the molecular weight of lysozyme?

c. What is the average molecular weight of the amino acids in lysozome?

d. How many S-S bonds are possible in lysozyme?

(hint: look at the structures of each amino acid, and figure out which of these have sulphurs

that are FREE to form bonds).

e. Is the net charge on lysozyme positive or negative?