Organic 13: Biochemistry

Question 1

What is a zwitterion?

Answer 1

A species that has both a positive and negative charge on different parts of the molecule

Question 2

Why are amino acids usually solids at room temperature?

Answer 2

Due to the strong ionic attraction between opposite charges on zwitterions

Question 3

Describe the general structure of an amino acid.

Answer 3

Central chiral carbon surrounded by hydrogen, carboxylic acid group, variable group, and amine group

Question 4

What is the only amino acid that isn’t optically active and why?

Answer 4

Glycine
Because glycine’s variable group is hydrogen, which means there are only three different groups around the central carbon
All other amino acids are optically active but only one enantiomer is present in nature

Question 5

How many naturally occurring amino acids are there?

Answer 5

20

Question 6

What ion is produced at low pH on an amino acid?

Answer 6

In strongly acidic conditions, the lone pair on NH2 accepts a proton to form an NH3+ ion (is protonated)

Question 7

What ion is produced at high pH on an amino acid?

Answer 7

In strongly alkaline conditions, the -OH group loses a hydrogen ion (is deprotonated) to form an OH- ion

Question 8

What is an amide linkage?

Answer 8

The bond formed after condensation reaction between two amino acids

Question 9

What is the primary structure of a protein?

Answer 9

The fixed sequence of amino acids in the polypeptide chain
It is relatively stable due to covalent bonding

Question 10

What is the secondary structure of a protein?

Answer 10

The initial folding of a polypeptide chain into either an alpha helix or a beta-pleated sheet due to hydrogen bonding
Hydrogen bonds are much weaker than covalent bonds so the secondary structure is more easily disrupted

Question 11

What is the tertiary structure of a protein?

Answer 11

Further folding into a three-dimensional shape held in place by hydrogen bonding, ionic bonding, and disulfide bridges

Question 12

How is a protein hydrolysed?

Answer 12

With hydrochloric acid of concentration 6moldm-3 for about 24 hours
This hydrolyses all peptide linkages

Question 13

How would you find the structure of proteins?

Answer 13

By refluxing the protein in 6moldm-3 hydrochloric acid to break the amide linkages (hydrolysis) resulting in a mixture of all the individual amino acids

Question 14

Describe how you would use Thin Layer Chromatography to determine which amino acids make up a protein.

Answer 14

1. Add a small spot containing the mixture of amino acids about 1cm up the plate
2. Place the plate in a tank containing a suitable solvent, and put a lid on it (this allows the solvent vapours to carry the amino acids up the stationary phase)
3. The affinity for the mobile and stationary phase depends on the intermolecular forces that act between the amino acid and each phase
4. Mark the solvent front (how far the solvent was carried up the stationary phase)
5. Spray the plate with ninhydrin, which reacts with amino acids to form a purple compound, OR shine ultra-violet light onto the plate to see how far the amino acids were carried
6. Calculate the Rf value (distance moved by spot/distance moved by solvent)

Question 15

What are enzymes?

Answer 15

Protein-based catalysts that speed up the rate of reactions
Usually globular proteins with active sites where the reaction occurs

Question 16

What is the lock and key hypothesis?

Answer 16

The reacting molecule fits precisely into the active site and is held in the precise orientation necessary to react

Question 17

What is the reality of enzyme-substrate interactions?

Answer 17

The reacting molecule must bond to the active site temporarily by intermolecular forces (i.e. van Der Waals)
These forces allow electrons to move within the substrate to lower the activation energy for the reaction

Question 18

How is the stereospecificity of enzymes important?

Answer 18

The active site of an enzyme is selective to individual enantiomers
Because the substrate molecule must have a 3D structure that can bind precisely to the active site

Question 19

How can enzymes be denatured?

Answer 19

Changes in pH
Changes in temperature
(Too much deviation from optimum)

Question 20

What is enzyme inhibition?

Answer 20

Where a molecule with a similar shape/tertiary structure to the substrate can be used to block the active site to prevent enzyme-substrate complexes from forming

Question 21

Name one drug that works by enzyme inhibition.

Answer 21

Penicillin
Inhibits the enzymes responsible for controlling the building of cell walls in bacteria

Question 22

How is computer modelling useful in drug design?

Answer 22

Computer modelling techniques can be used to predict the shape of proteins before they have been synthesised
So can therefore predict their properties

Question 23

Describe the structure of a DNA nucleotide.

Answer 23

Phosphate
2-Deoxyribose
Organic base

Question 24

What are the four organic bases?

Answer 24

Adenine, Thymine, Cytosine, Guanine

Question 25

How can two nucleotides join together?

Answer 25

In a condensation reaction
between the -OH on a phosphate and the -OH on deoxyribose
to form a phosphodiester bond

Question 26

How many hydrogen bonds do adenine-thymine and cytosine-guanine form? (and draw the bonding)

Answer 26

Adenine and thymine = 2 bonds
Cytosine and guanine = 3 bonds

Question 27

What is the function of DNA?

Answer 27

To store genetic information needed to allow organisms to develop, survive and reproduce
Needed for formation of structural material, like flesh, and also enzymes that control biochemical reactions
Contained in every cell and must be replicated precisely during cell division

Question 28

How does DNA replication occur?

Answer 28

Hydrogen bonds between bases are individually weak so can be easily broken, leaving two free template strands
Free DNA nucleotides are attracted to the parent strand via complementary base pairing (A-T, C-G) and form hydrogen bonds
Adjacent nucleotides join in condensation reactions forming phosphodiester bonds
Resulting in two new identical double-stranded molecules of DNA

Question 29

What is cancer?

Answer 29

A group of diseases caused by the uncontrolled division of cells leading to formation of a tumour

Question 30

What is cisplatin?

Answer 30

An anti-cancer drug
Square planar
Survival rates up to 90% in testicular cancer

Question 31

How does cisplatin work?

Answer 31

Ligand substitution reaction

By bonding to strands of DNA via the nitrogen atoms, which have lone pairs
They can form dative covalent bonds with the platinum
The chloride ions are displaced by water, which are then displaced by nitrogen on guanine because nitrogen is a better ligand

Question 32

What are the side effects of cisplatin use?

Answer 32

It can also form bonds to guanine on the DNA of healthy cells
However cancer cells divide more rapidly, so the effect on cancer cells is greater
Hair follicle cells divide very rapidly, so cisplatin has a greater effect on them as well
Which is why chemotherapy patients often lose their hair

Question 33

Why would transplatin not be a good anti-cancer drug?

Answer 33

Because one chloride ion would be on the opposite side of the molecule, so would be too far apart to form bonds to guanine