BIBC 102 Lecture Notes - Lecture 1: Metabolomics, Metabolome, Arginine

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orchidgiraffe200

16 Dec 2018

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Iterated structure: repeated, done again and again. Why study and understand metabolism: underlies every life process at some level, obesity: a world-wide problem in health, adult onset diabetes: a metabolic disease, exercise and metabolism, biofuel strategies for alternative energy. Important in ageing, cancer and many other maladies. Looking at all the metabolites in a particular sample. Amino acids: molecular tool box: there are 20 common amino acids "chemical building set, each has, an amino group, a carboxyl group, side chain (r group) Learn the one letter code for the amino acids. Isoleucine (i: glycine(g, alanine (a, valine (v) Leucine (l: methionine (m, proline (p, serine (s, threonine (t, cysteine (c, asparagine (n, glutamine (q, aspartate (d, glutamate (e, arginine (r, histidine (h, phenylalanine (f, tyrosine (y, typtophan (w) Cofactor: a covalent group that is attached to a protein to help its function, ex: vitamins, fe, molecular entity in addition to the amino acids of the polypeptide.

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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?

jadechinchilla39

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?

lilacbee20

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?

BIBC 102 Lecture Notes - Lecture 1: Metabolomics, Metabolome, Arginine

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