A - Amino Acids

Question 1

What two functional groups do amino acids have?

Answer 1

An amino group and a carboxyl group.

Question 2

Why does an amino acid have both basic and acidic properties?

Answer 2

Because it has a basic amino group and an acidic carboxyl group, giving it the properties of both.

Question 3

What does it mean for a molecule to be amphoteric?

Answer 3

To have both acidic and basic properties.

Question 4

Why are amino acids described as chiral?

Answer 4

Because they have a carbon atom bonded to four different groups.

Question 5

What will a solution if a single amino acid enantiomer do to plane polarised light and why?

Answer 5

Rotate it because it’s a chiral molecule.

Question 6

What is a zwitterion?

Answer 6

A do polar ion - it has both a permanent positive and permanent negative charge in different parts of the molecule but with a neutral charge overall at the ion’s isoelectric point.

Question 7

What is an amino acid’s isoelectric point?

Answer 7

The pH at which the average overall charge on the amino acid is zero.

It’s different for different amino acids and dependent on their R group.

Question 8

Most amino acids have a common name, but also a systematic name. How do you find an amino acid’s systematic name?

Answer 8

1. Find the longest carbon chain that includes the carboxylic acid group and write its name.
2. Number the carbons in the chain starting with the carbon in the carboxylic acid group as number 1.
3. Write down the positions of any NH2 groups using the word ‘amino’.

Question 9

What do amino acids link together to form?

Answer 9

Peptides.

Question 10

What do two amino acids joined together make?

Answer 10

A dipeptide.

Question 11

What are proteins?

Answer 11

Sequences of amino acids joined by peptide links.

Question 12

What type of reaction makes a peptide link? What breaks it down?

Answer 12

A condensation reaction.

A hydrolysis reaction.

Question 13

How is a protein broken down into its constituent amino acids? What conditions are necessary?

Answer 13

By hydrolysis with harsh conditions. You need to add hot aqueous, 6M HCl and heat the mixture under reflux for 24 hours.

Question 14

What type of polymers are proteins?

Answer 14

Condensation polymers.

Question 15

What are the four levels of structure of proteins?

Answer 15

Primary, secondary, tertiary and quaternary.

Question 16

What is a protein’s primary structure? What type of bonding holds this structure together?

Answer 16

The sequence of amino acids in the long chain that makes up the polypeptide chain (the protein).

The structure is held together by covalent bonding.

Question 17

What is a protein’s secondary structure?

Answer 17

The peptide links of the polypeptide chain can form hydrogen bonds with each other forming either a spiral, called the alpha-helix, or a layer of protein folded like a concertina, called the beta-pleated sheet.

Question 18

Why can the secondary structure of a protein be disrupted more easily than the primary structure?

Answer 18

The secondary structure is held in place by hydrogen bonds, which are weaker than the covalent bonds present in the primary structure, so it is more easily disrupted by gentle heating or changes in pH.

Question 19

What is a protein’s tertiary structure?

Answer 19

The secondary structure can itself be folded into a 3D shape, called the tertiary structure.

It’s held together by a mixture of hydrogen bonding, ionic interactions, sulfur-sulfur bonds and van der Waals forces (vdW’s exist between all molecules).

Question 20

What is it that caused amino acid chains to fold or twist?

Answer 20

The intermolecular forces.

Question 21

Where does hydrogen bonding occur in a protein’s structure?

Answer 21

Between polar groups for example, -OH and -NH2.

Question 22

Where do sulfur-sulfur bonds occur in a protein?

Answer 22

The amino acid, cysteine, contains a thiol group (-SH).

Thiol groups on different cysteine residues can lose their H atoms and join together by forming a sulfur-sulfur bond (-S-S-).

These bonds link together different parts of the protein chain, and help to stabilise the tertiary structure.

Question 23

Why can temperature and pH change the shape of proteins?

Answer 23

Because they can affect the hydrogen bonding and the formation of sulfur-sulfur bonds.

Question 24

How can amino acids be separated and identified?

Answer 24

By thin-layer chromatography.

Question 25

Why do different amino acids have different solubilities in the same solvent?

Answer 25

Because they have different R groups.

Question 26

What is a thin-layer chromatography plate?

Answer 26

A piece of plastic or glass covered with a thin layer of silica gel or alumina powder.

Question 27

Outline the method of thin-layer chromatography, up to when amino acids need to be located/identified on a chromatogram.

Answer 27

1. Draw a pencil line near the bottom of a thin-layer chromatography plate and put a concentrated spot of the mixture of amino acids on it.
2. Dip the bottom of the plate (but not the spot) into a solvent.
3. As the solvent spreads up the plate, the different amino acids move with it, but at different rates due to their different solubilities, so they separate out.
4. When the solvent had nearly reached the top, take the plate out and mark the solvent front with a pencil.
5. Leave the plate to dry.

Question 28

What is a solvent front?

Answer 28

The distance moved by the solvent in thin-layer chromatography.

Question 29

How can you make amino acids visible in thin-layer chromatography, considering amino acids aren’t coloured?

Answer 29

You can either spray ninhydrin solution on the plate, which will turn the spots purple.

Or, you can use a plate that has a fluorescent dye added to it. The dye glows when UV light shines on it. Where there are spots of chemical on the plate, they cover the dye and appear dark. So if you put the plate under a UV lamp, you can draw around the dark patches to show where the spots are (the amino acids).

Question 30

What’s the formula for the Rf value of an amino acid?

Answer 30

Distance travelled by the spot divided by the distance travelled by the solvent.

Question 31

How do you measure how far an amino acid has travelled in thin-layer chromatography?

Answer 31

Measure the distance from the point of origin (the original spot of the mixture of amino acids on the line) to the middle of the spot of the amino acid.

Question 32

How do you identify amino acids using thin-layer chromatography?

Answer 32

Work out the amino acid’s Rf value and then use a table of known amino acid Rf values to identify them.

Question 33

What are enzymes?

Answer 33

Proteins that act as biological catalysts.

Question 34

What are substrates?

Answer 34

The molecules that enzymes act on to speed up reactions.

Question 35

What reactions do enzymes catalyse?

Answer 35

Every metabolic reaction in the bodies of living organisms.

Question 36

What is an enzyme’s active site?

Answer 36

The part of the enzyme that the substrate fits into so it can interact with the enzyme.

The active site is three-dimensional. It’s part of the tertiary structure of the enzyme protein.

Question 37

An enzyme has a stereospecific active site. What does this mean?

Answer 37

Enzymes are made up of amino acids, so they contain chiral centres.

Enzymes are specific and so will only work on one enantiomer of a substrate (this is called stereospecificity).

Question 38

What is an enzyme inhibitor?

Answer 38

A molecule with a similar shape to an enzyme’s substrate molecule.

Question 39

How do enzyme inhibitors work?

Answer 39

They compete with the substrate to bond to the active site, but no reaction follows. Instead, they block the active site so that no substrate can fit into it.

Question 40

What affects the amount of enzyme inhibition?

Answer 40

It depends on the relative concentrations of inhibitor and substrate, and is also affected by how strongly the inhibitor bonds to the active site.

Question 41

Some drugs work as enzyme inhibitors. Why does it take such a long time to find a drug that will fit into an enzyme’s active site?

Answer 41

Because the enzyme’s active site is specific. What makes it even harder, is if the drug molecule is chiral, because the active site is stereospecific, so will only work with one enantiomer of the molecule.

So scientists find new drug molecules, often by trial and error. They carry out experiments using lots of compounds to see if they work as inhibitors for a certain enzyme. This process takes a long time.

Question 42

How a computers helping to find new drugs which act as enzyme inhibitors?

Answer 42

They use computers to model the shape of an enzyme’s active site and predict how well potential drug molecules will interact with it.

This means they can quickly examine hundreds of molecules to look for ones that might be the right shape before they start synthesising and testing molecules in the lab.

Question 43

What is DNA made up from?

Answer 43

Deoxyribonucleic acid is made up from lots of monomers called nucleotides (it’s a polymer).

Question 44

What are nucleotides made up of?

Answer 44

A phosphate ion bonded to 2-deoxyribose (a pentose sugar), which is in turn bonded to one of the four bases, adenine, thymine, cytosine or guanine.

Question 45

What does a single strand of DNA consist of?

Answer 45

A polymer of nucleotides linked by covalent bonds between the phosphate group of one nucleotide and the 2-deoxyribose of another nucleotide.

This results in a sugar-phosphate backbone with bases attached to the sugars in the chain.

Question 46

What type of reaction forms the sugar-phosphate backbone of DNA?

Answer 46

Condensation polymerisation reaction.

Question 47

Explain how the double helix of DNA is formed and how it is held together.

Answer 47

DNA is made up if two polynucleotide strands which spiral together to form a double helix structure, which is held together by hydrogen bonds between bases.

Question 48

Explain why the two strands of DNA are complementary.

Answer 48

Each base will only bond with a specific base. This is due to the arrangement and number of atoms in the base molecules.

A hydrogen bond forms between a polar positive H atom (an H attached to anything highly electronegative) and a lone pair of electrons on a nearby O or N atom. To bind, the two atoms have to be the correct distance apart.

Adenine - thymine (form two H bonds).
Guanine - cytosine (form three H bonds).

These are the only possible base combinations. Other base pairings would put the partially charged atoms too close together (they’d repel each other), or too far apart, or the bonding atoms wouldn’t line up properly.

Question 49

Why does the DNA helix have to twist?

Answer 49

So that the bases are in the right alignment and at the right distance apart for the complementary base pairs to form.

Question 50

What is cisplatin and what is it used for?

Answer 50

It’s a complex of platinum(II) with two chloride ion ligands and two ammonia ligands in a square planar shape.

Used as an anti-cancer drug.

Question 51

Briefly explain how cisplatin works as an anti-cancer drug.

Answer 51

Cancer is caused by cells in the body dividing uncontrollably and forming tumours. In order for a cell to divide, it had to replicate its DNA.

Cisplatin binds to DNA, causing kinks in the helix which stop the proteins that replicate the DNA from copying it properly. This stops tumour cells reproducing.

Question 52

Explain exactly how cisplatin binds to DNA.

Answer 52

A nitrogen atom on a guanine base in DNA forms a co-ordinate bond with cisplatin’s platinum ion, replacing one of the chloride ion ligands (this is a ligand substitution reaction).

A second nitrogen atom from a nearby guanine (either on the same strand or opposite strand of DNA) can bond to the platinum and replace the second chloride ion.

The presence of the cisplatin complex bound to the DNA strands causes the strands to link. This means the DNA strands can’t unwind and be copied properly, so the cell can’t replicate.

Question 53

What are the side effects of cisplatin and why?

Answer 53

Cisplatin can bind to DNA in normal cells as well as cancer cells. This stops the healthy cells that replicate frequently, such as hair cells and blood cells, from replicating.

So it can cause hair loss and suppress the immune system (which is controlled by white blood cells). It can also cause kidney damage.

Question 54

How can the side effects of cisplatin be lessened?

Answer 54

By using very low dosages of cisplatin.

Or, to target the tumour directly (a method which involves delivering the drug only to the cancer cells, so it doesn’t get a chance to attack healthy cells).

Question 55

Why is cisplatin used as an anti-cancer drug despite its side effects? What

Answer 55

The balance if the long term positive effects of curing cancer outweighs the negative short term effects.