Medicinal and Biological Chemistry

Question 1

Components of an Amino Acid

Answer 1

An amino acid has:

• a basic amino group
• and acidic carboxyl group
• a hydrogen atom
• a side chain (R)

Question 2

Aliphatic Non-Polar Amino Acids

Answer 2

They have a saturated hydrocarbon side chain e.g. alanine

Question 3

Aromatic Non-Polar

Answer 3

They are cyclic and hydrophobic e.g. tryptophan

Question 4

Neutral Polar

Answer 4

OH or CONH2 reactive groups found at active sites in proteins e.g. serine

Question 5

Acidic

Answer 5

Negative charge at pH 7 e.g. glutamate

Question 6

Basic

Answer 6

Postitive charge at pH 7 e.g. histidine

Question 7

Sulfur Containing

Answer 7

Contain sulfur e.g. cystine, methionine

Question 8

Imino Acid

Answer 8

Has -NH group instead of NH2 in amino acids.

e.g. proline which forces ‘bends’ in proteins

Question 9

Zwitterions

Answer 9

Amphoteric molecules have both acidic and basic groups (carboxylic acid and amine, respectively). At pH 7 most amino acids exist as zwitterions in solution (meaning they have one positively charged group and one negatively charged group giving a neutral net charge).
At acidic pH, the amino acids would be predominantly positively charged, while at basic pH the they would be predominantly negatively charged.

Question 10

Buffering capacity of amino acids

Answer 10

Histidine is the amino acid which has a buffering capacity in the physiological range.

Question 11

Peptide Bonds

Answer 11

Two amino acids react to form a peptide bond (-NH-C=O).

When two react, we get a dipeptide, three give a tripeptide etc).

Question 12

Primary Structure of Proteins

Answer 12

The primary structure of a protein is the sequence of amino acids.

Question 13

Proteins as Buffers

Answer 13

As proteins have many ionisable functional groups (they are amphoteric) they are good buffers. Haemoglobin is an example of this.

Question 14

Hydrogen Bonding

Answer 14

Because they are polarised, two H2O molecules can form a linkage known as hydrogen bonding. This is strongest when the three atoms lie in a straight line and has about 1/20 the strength of a covalent bond.

Question 15

Polar Molecules

Answer 15

Because of the polar nature of water molecules they will cluster around ions and other polar molecules. They can be accommodated in water hydrogen bonded structures and are hydrophilic and relatively water soluble.

Question 16

Non-Polar Molecules

Answer 16

As water is polar, non-polar molecules interupt the hydrogen bonding that occurs in water without forming favourable interactions with water molecules. Therefore they are hydrophobic and are insoluble in water.

Question 17

Secondary Structure of Proteins

Answer 17

This is sub structures of proteins and consists of alpha helices and beta sheets. Beta sheets can be parallel or antiparallel to each other.

Question 18

Tertiary Structure of Proteins

Answer 18

This is the folding of proteins and it is driven by hydrophobic interactions (certain areas trying to avoid water will be on the centre of the structure). It is driven by disulphide bonds, hydrophobic interactions, hydrogen bonding and salt bridges.

Question 19

Quaternary Structure

Answer 19

This consists of the aggregation of two or more individual proteins which operate as a single unit. If it contains two proteins is a dimer, three is a trimer, four is a tetramer etc.

Question 20

Prosthetic groups

Answer 20

A prosthetic group is a non-polypeptide moiety that forms a functional part of a protein.
An apoprotein is a protein without its prosthetic group.
A holoprotein is a protein with its prosthetic group.

Question 21

Metabolism

Answer 21

Metabolism is the sum of all the enzyme-catalysed reactions that take place in cells.

Question 22

Catabolism

Answer 22

This is the degradation phase of metabolism in which complex molecules are degraded to small molecules. It is an oxidative process which is accompanied by the release of free energy which is conserved in a form useful for cellular work, usually ATP.

Question 23

Anabolism

Answer 23

A biosynthetic phase of metabolism in which simple precursor molecules are enzymatically converted into the molecular components of cells such as nucleic acids, proteins, lipids and polysaccharides These pathways require an input of chemical energy.

Question 24

What does life need?

Answer 24

• Energy which it must know how to extract, transform and utilise.
• Simple molecules which is must know how to convert, polymerise and degrade.
• chemical mechanisms, to harness energy, drive sequential chemical reactions, synthesis and degrade macromolecules, maintain a dynamic steady state, self-assemble complex structures, replicate accurately and efficiently and maintain biochemical “order” vs outside.

Question 25

Enzymes

Answer 25

• Enzymes are catalytic proteins.
• They catalyse chemical proteins
• They change the rate of reactions without

Question 26

How are enzymes different from chemical catalysts?

Answer 26

• Enzymes increase a reaction rate between 10^6 and 10^12 times compared to no catalyst and reaction rates are several orders of magnitudes larger than chemically catalysed reactions.
• They have milder reaction conditions (temp, pressure etc)
• They have a greater reaction specificity, no side products.
• They have the capacity to regulate - their activity varies in response to concentrations of substances other than substrates and products.

Question 27

Enzymes and Temperature

Answer 27

• As temperature increases, the rate of the enzymatic reaction increases as the substance collides with the enzyme more frequently.
• The optimum temperature is where the reaction rate is fastest, beyond this temperature the proteins denature.

Question 28

Enzymes and pH

Answer 28

• The optimal pH range for most enzymes is between 6-8 with pH 7.4 being optimal for the majority.
• As pH increases beyond 8 or less than 6, the enzymes denature as electrostatic forces hoping to stabilise the 3D protein structure breakdown.
• Pepsin is a digestive enzyme found in the stomach and has an optimum pH of ~2.