SNS - Organic Chemistry - Amino Acids, Peptides and Proteins

Question 1

Amino Acids

Optical Acitivity

Answer 1

The Alpha carbon is a chiral centre (except in glycine, the simplest amino acid, where R=H)

Thus all AAs but glycine are optically active

Naturally occuring AAs are L-enantiomers with the amino group drawn on the left in the Fischer projection

Question 2

Amino Acids

Acid Base Activity

Zwitterions

Answer 2

Have an acidic -COOH and a basic -NH2 on the same molecule

Therefore, sometimes take the form of dipolar zwitterions in solution

The two halves of the molecule neutralise each other so that at neutral pH, they exist in the form of internal salts

Question 3

Amino Acids

Acid Base Activity

Amphoteric

Answer 3

May act as either acids or bases depending on environment

In acidic solutions are fully protonated

In basic soution are deprotonated

Since they have two groups that can either donate or accept o proton from or to the solution, they have two Ka and two Kb values

Question 4

Amino Acids

Acid Base Activity

Isoelectric Point

Answer 4

At low pH, AAs carry an excess positive charge and vice versa

The intermediate pH at which the AA is electrically neutral and exists as a zwitterion is called the isoelectric point of the AA

It lies between pKa1 and pKa2

Question 5

Amino Acids

Titration

Glycine

Answer 5

1. A 1M glycine solution is acidic - exists predominantly as +NH3CH2COOH. The AA is fully protonated and carries a positive charge
2. As the solution is titrated with NaOH, -COOH groups lose a proton. The AA acts as a buffer and the pH changes very slowly
3. When 0.5M base added the concentrations of +NH3CH2COOH and +NH3CH2COO- are equimolar. pH is equal to pKa
4. As more NaOH is added, all -COOHs are deprotonated. The AA loses its buffering capacity and the pH rises more rapidly
5. When 1M base added, glycine exists predominantly as +NH3CH2COO- and is electrically neutral - isoelectric point
6. Passes through a second buffering stage as continued titration begins to deprotonate -NH3+ groups
7. When 1.5M NaOH added [+NH3CH2COO-] = [NH2CH2COO-] and pH = pKa2
8. As another 0.5M NaOH added, all amino groups are deprotonated

Question 6

Amino Acids

Titration

Answer 6

• The titration of each proton occurs as a distinct step, similar to that of a simple monoprotic acid
• When adding base, the -COOH loses its proton before the -NH3+
• 2M base must be added to deprotonate most AAs: 1M for the -COOH and 1M for the -NH3+
• The buffering capacities are greatest ator near the dissociation constants Ka1 and Ka2 and minimal at the isoelectric point

Question 7

Amino Acids

Henderson Hasselbach Equation

Answer 7

Ratio of an AAs ions are dependent on pH

This equation defines the relationship between pH and ratio of conjugate acid to conjugate base and provides a mathematical expression for the dissociation constants of AAs

pH = pKa + log ([congugate base / [conjugate acid])

For example, at pH 3.3, glycine (pKa1 = 2.3) has ratio of conjugate base:acid of:

3.3 = 2.3 + log ([c. base] / [c. acid]}

log {[c. base] / [c. acid]) = 3.3-2.3 = 1

[c. base] / [c. acid] = 10/1

Question 8

Amino Acidss

Non-polar

Answer 8

Have R-groups that are saturated hydrocarbons - hydrophobic and decrease solubility in water

1. Alanine
2. Glycine
3. Isoleucine
4. Leucine
5. Phenylalanine
6. Proline
7. Tryptophan
8. Valine

Question 9

Amino Acids

Polar

Answer 9

Have polar uncharged R-groups that are hydrophilic, increasing solubility in water

1. Asparagine
2. Cysteine
3. Glutamine
4. Methionine
5. Serine
6. Threonine
7. Tyrosine

Question 10

Amino Acids

Acidic

Answer 10

R-groups contain a -COOH - have a net negative charge at physiological pH and exist as salts in the body.

Aspartic acid and glutamic acid both have three groups that must be neutralised during titration and therefore have a different titration curve from standard with three distinct dissociation constants pKa1, 2 and 3. 3M base is needed to deprotonate

1. Aspartic acid
2. Glutamic acid

Question 11

Amino Acids

Basic

Answer 11

R-gorups contain an amino group - carry a net positive charge at physiological pH

Titration curves are non-standard - additional -NH3+ must be neutralised and have three dissociation constants

1. Arginine
2. Histidine
3. Lysine

Question 12

Peptides

Reactions

Answer 12

AAs are joined by peptide bonds (amide bonds) between the -COOH of one and the -NH2 of another

Forms via condensation reaction

The reverse - hydrolysis - is catalysed by an acid or base

Question 13

Peptides

Properties

Answer 13

Terminal AA with a free alpha amino group is called the amino terminal (N- terminal)

C-terminal is the AA with a free -COOH

Amides have two resonance forms and the result is a hybrid with partial double-bond character. As a result, rotation about the C-N bond is restricted, although bonds on either side of the peptide unit have a great deal of rotational freedom

Question 14

Proteins

Structure

Answer 14

1. Primary - AA sequence
2. Secondary - local structure of neighbouring AAs into alpha helices (coils stabilised by H-bonds between C=O oxygens and amine Ns four residues away) and beta-sheets (bonds as before)
3. Tertiary - 3D shape of the protein as determined by hydrophilic and hydrophobic interactions between R-groups of AAs that are far apart in the chain and by the distribution of disulphide bonds
4. Quaternary - arrangement of subunits formed from different polypeptide chains in a protein molecule

Question 15

Proteins

Conjugated

Answer 15

Contain prosthetic groups which impart functionality

These can be organic or metal ions

Proteins with lipid, carbohydrate and nucleic acid prosthetic groups are known as lipoproteins, glycoproteins and nucleoproteins respectively

Question 16

Proteins

Denaturation

Answer 16

Process by which proteins lose their 3D structure and revert to random-coil state

Can be caused by detergent or changes in pH, solute concentration or temp as the weak intermolecular forces keeping the protein stable are disrupted