Biochemistry Study Set 13

Biology

Quiz 4 :

Amino Acids and Proteins

Quiz 4 :

Amino Acids and Proteins

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The amino acids can be organized in several different ways, and some appear in multiple categories. Suggest some different groupings, and identify those amino acids that can appear in more than one of these categories and in the groups presented in the text.
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The amino acids are the building blocks of proteins. These can be classified by different ways as follows:
On the basis of polarity:
1. Polar amino acids: like glutamate, arginine, lysine, tyrosine, cysteine etc
2. Non-polar amino acids: like glycine, leucine, valine, phenylalanine, proline, methionine etc.
On the basis of acid-base properties:
1. Acidic amino acids: like aspartate, glutamate
2. Basic amino acids: like arginine, histidine etc
3. Neutral amino acids: like tyrosine, asparagines, threonine, serine etc.
On the bases of -R group or side chain:
1. Alkyl chain: like alanine, glycine
2. Aromatic chain: like phenylalanine, tryptophan, tyrosine etc.
3. Branched chain: like valine, leucine, isoleucine
On the basis of functional group:
1. Hydroxyl group containing: like tyrosine, serine
2. Sulfur containing amino acids: like cysteine and methionine
From the above data, we can find many amino acids which come in more than one category as follows:
img

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Draw a titration curve for glutamate, and show the major charge forms in a manner analogous to the one for lysine in the text. What is its isoelectric point?
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Glutamic acid is an ?-amino acid, and a dicarboxylic acid. It is a polar, negatively charged amino acid. Glutamate is conjugate base of glutamic acid. The amino acid pays an important role in several metabolic functions like transamination reactions and transport of amino groups.
The titration curve for glutamate is as follows:
img pK1 = 2.2 (of carboxyl group), pK2 = 9.5 (of ammonium ion) and pK3 = 4.1 (of side chain)The various charged forms of glutamate at different pK values are as follows:
img

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A buffer is a substance that is used to ensure the pH does not change appreciably upon addition of excess acid or base. This occurs near the p K a value of a species and is effective up to about ± 1 pH unit of the p K a. Use the Henderson-Hasselbalch equation to explain why this is so.
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A buffer is a solution that contains a weak acid and its conjugate base. It resists pH change within a range of the buffer, about 1 pH unit on either side of the pKa of the conjugate acid.
The buffering capacity is otherwise defined as the pH of the equimolar solution of acid equal to its pKa. This region most effectively resists pH changes. The Henderson-Hasselbalch Equation is as follows:
img According to this equation pH is directly proportional to pK a. This means that an increase or decrease of the pK a by 1 unit, pH will also get affected by 1 unit.

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An unknown amino acid is found to contain a hydroxyl group and studies show it is immobile in an electric field if the pH is exactly 5.655. What is it?
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Polyamines are multiple amine-containing molecules derived from a non-protein amino acid (ornithine) by loss of the CO ₂ group. One of these is putrescine, which has the structure: img a. Draw its titration curve, given the p K a values of 9.35 and 10.8. b. What is its pI? c. Polyamines have at least two known functions: binding to DNA and binding to K + channels. Based on purely electrostatic effects, explain these biological activities.
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The molecular weight of an amino acid is roughly equal to 100. This allows a quick assessment of the number of amino acids in a protein given its molecular weight, or its molecule weight given the number of amino acids. What is the approximate number of amino acids in hemoglobin? Assuming a more accurate estimate of 115 for the molecular weight of an amino acid residue, how would this change your answer?
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