3.13 Amino Acids

Question 1

What are amino acids?

Answer 1

Organic compounds that contain an amino group (NH2) and a carboxylic acid group (COOH)

Question 2

How does the structure of an amino acid change in acidic conditions?

Answer 2

The lone pair of electrons on N accepts a proton, forming +NH3

Question 3

How does the structure of an amino acid change in alkaline conditions?

Answer 3

The Carboxylic acid group loses its hydrogen, forming COO:-

Question 4

At specific pHs, what happens to the structure of amino acids?

Answer 4

They both lose a proton from the carboxylic acid group and gains a proton on the amine group, forming a zwitter ion

Question 5

How are alpha helices formed?

Answer 5

The alpha helix is held together by hydrogen bonds, with the R group pointed towards the outside of the helix.

Question 6

How are beta pleated sheets formed?

Answer 6

In a beta pleated sheet two or more parallel regions of the protein can line up so that hydrogen bonds form between the N-H group from one peptide link and the C=O from another one.

Question 7

What are disulfide bridges?

Answer 7

Cysteine contains -SH on their side chain, meaning if these groups come close together they can react to from a strong S-S disulfide bridge, fixing the tertiary structure of a protein.

Question 8

What are ionic interactions in a protein?

Answer 8

A protonated lysine side chain can interact via electrostatic ionic interaction with a deprotonated glutamic acid side chain close to it in space. If the pH changes this interaction could be broken

Question 9

How can the peptide link in polypeptides be broken?

Answer 9

Through enzymes (proteases) hydrolysing this bond, heating proteins with 6moldm-3 HCl for 24hours

Question 10

Which are the H-bonding sites to base pair (yellow) and to deoxyribose (red) in guanine?

Answer 10

Question 11

Which are the H-bonding sites to base pair (yellow) and to deoxyribose (red) in cytosine?

Answer 11

Question 12

Which are the H-bonding sites to base pair (yellow) and to deoxyribose (red) in adenine?

Answer 12

Question 13

Which are the H-bonding sites to base pair (yellow) and to deoxyribose (red) in thymine?

Answer 13

Question 14

Draw the cytosine-guanine bond.

Answer 14

Question 15

Draw the adenine-thymine bond.

Answer 15

Question 16

Draw and describe cisplatin

Answer 16

Cisplatin is an anti cancer drug, and is the cis isomer of a square planar platinum complex

Question 17

Describe how cisplatin works.

Answer 17

Cells in the natural world are chiral so only z-isomer of the drug is effective and will be the correct orientation to “fit” the cells. It has to be able to bond to two adjacent guanine bases. Cancer spreads by replicating corrupted DNA, and cisplatin bonds to strands of this DNA to prevent it from replicating via ligand replacement with guanine.