BIOCH200 Chapter Notes - Chapter 3 - 4: Heme, Hydrophile, Cooperative Binding

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goldleopard391

1 Nov 2016

School

University of Alberta

Department

Biochemistry

Course

BIOCH200

Professor

Jonathan Parrish

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Document Summary

Mcl = molecule nrg = energy fxn = function. Chapter 3 and 4 protein structure and function. The amino acids and the properties of their side chains. Draw the structure of a generic amino acid. Name and draw the 20 amino acids incorporated into proteins and use their 3-letter designations. State why all isolated amino acids bear at least one positive and one negative charge. The coo- group (c-terminus) carries a -1 and the nh3 group (n- terminus) carries a +charge. Draw each amino acid at ph 1, 7 and 14. Below their pka the aa are acidic and protonated. Above their pka they are basic and deprotonated. Explain why all of the amino acids except for glycine are chiral. All of the aa are chiral because they have 4 different groups around them. Since, glycine has a h as a r group it doesn"t have this quality.

Related Questions

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?

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=?

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pK_a Values for Ionizable Groups of Amino Acids.
Amino Acid	pK_a of Î±-COOH	pK_a of Î±-NH₃⁺	pK_a 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

Amino Acid	M.W. g/mol	pK_a for side chain
Alanine	89.1
Arginine	174.2	12.48
Asparagine	132.1
Aspartate	133.1	3.90
Cysteine	121.1	8.37
Glycine	75.0
Glutamate	147.1	4.07
Glutamine	146.1
Histidine	155.1	6.04
Isoleucine	131.2
Leucine	131.2
Lysine	146.2	10.54
Methionine	149.2
Proline	115.1
Phenylalanine	165.2
Serine	105.1
Threonine	119.1
Tryptophan	204.2
Tyrosine	181.2	10.46
Valine	117.1

Take a look at your pK_a table for the amino acids. It turns out that when these side chains are in a protein, they can have very different pK_a values. Explain the following observations:

a. In the enzyme medium chain acyl-CoA dehydrogenase (b-oxidation of fatty acids), E376 has a measured pK_a ~ 8.0. It is found in a very hydrophobic environment. What could account for it elevated pK_a?

b. For the enzyme aconitase (Krebbâs Cycle), a catalytic serine is known to have a pK_a ~ 8. What kind of factors could account for this decrease in pK_a?

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BIOCH200 Chapter Notes - Chapter 3 - 4: Heme, Hydrophile, Cooperative Binding

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