3.8 amino acids, proteins and DNA

Question 1

what is the structure of an amino acid?

Answer 1

NH2 group and COOH group
all same structure apart from R group

Question 2

amino acids are amphoteric. what does this mean?

Answer 2

they have acidic and basic properties
COOH = COO- + H+
NH2 + H+ = NH3+

Question 3

why are amino acids chiral molecules?
what does this mean happens?

Answer 3

c has 4 diff groups attached
so solution of single amino acid enantiomer rotates polarised light

Question 4

what is a zwitterion?

Answer 4

a dipolar ion- both + and - charge in diff parts of the molecule

Question 5

what is an isoelectric point?

Answer 5

where zwitterions exist on an amino acid
the pH where the overall charge is 0- depends on R group

Question 6

when does an amino acid become a zwitterion?

Answer 6

when its amino group is protonated to NH3+ and its COOH group is deprotonated to COO-

Question 7

what happens to an amino acid in conditions more acidic than its isoelectric point?

Answer 7

Nh2 group is likely to be protonated but COOH stays same so amino acid has + charge

Question 8

what happens to an amino acid in conditions more basic than its isoelectric point?

Answer 8

COOH point likely to lose proton but NH2 unchanged so amino acid has - charge

Question 9

what happens on/ near isoelectric point?

Answer 9

COOH and NH2 likely to be ionised, forming a zwitterion

Question 10

how can you separate amino acids?

Answer 10

diff r groups have diff solubilities in same solvent so can use thin-layer chromatography

Question 11

amino acids arent coloured so how can we see them on TLC plates?

Answer 11

use plate with fluorescent dye and UV lamp

Question 12

how can you identify amino acids?

Answer 12

rf value (distance travelled by spot/ distance travelled by solvent)

Question 13

what are proteins?

Answer 13

condensation polymers of amino acids
lots of amino acids joined by peptide links

Question 14

what happens if the 2 amino acids that are joining are different?

Answer 14

2 diff dipeptides are produced as they can join either way round

Question 15

how do you split protein into its amino acids?

Answer 15

hydrolysis using harsh conditions
(eg HCl and heat under reflux)

Question 16

what is the primary structure of a protein?

Answer 16

sequence of amino acids

Question 17

what is the secondary structure of a protein?

Answer 17

peptide links form H bonds with each other so the chain isnt straight
alpha-helix or beta- pleated sheet

Question 18

what is the tertiary structure of a protein?

Answer 18

chain of amino acids coiled and folded in characteristic way- extra bonds form

Question 19

what intermolecular forces are present in proteins?

Answer 19

hydrogen bonding- between polar groups that contain electronegative atoms which induce + charge on H atom which is then attracted to lp on adjacent polar groups

disulphide bridges- occurs between cysteines. cysteine contains thiol group (SH) which can lose its H and join to form -S-S- with another thiol

Question 20

what are enzymes?

Answer 20

proteins that are biological catalysts and act upon substrates

Question 21

what is specificity?
what is stereospecific?

Answer 21

enzymes can be explained by lock and key- only work if active site and substrate are complimentary

active sites are stereospecific so only work on 1 enantiomer of a substrate

Question 22

what are inhibitors?

Answer 22

molecules with a similar shape to the substrate
they bind to active site so no substrate can fit
amount of inhibition depends on relative conc of inhibitor and substrate/ how strongly the inhibitor binds

Question 23

eg of inhibitors as drugs
problems

Answer 23

antibiotics can block active site of enzyme in bacteria that helps them make cell wall so cell wall weakens and bacteria burst

hard to find drug that fits- very specific- found by trial and error/ using computers to model active site

Question 24

what are nucleotides made up off?

Answer 24

phosphate group (ion)
pentose sugar- 2 deoxyribose
base- A,C,T,G

Question 25

see data sheet for how nucleotides are put together

Question 26

what are the structures of the nucleotides?

Answer 26

see poster

Question 27

what are polynucleotides?

Answer 27

nucleotides joined by condensation reaction that forms covalent phosphodiester bonds between phosphate group of one and sugar of another

Question 28

what is complimentary base pairing due to?

Answer 28

arrangement of atoms in base molecules that are capable of forming h bonds
atoms have to be right distance apart for h bonds to form
A and T can each form 2 H bonds and C and G can each form 3 so these are the base pairings- others would put them at diff distances so can form h bonds

double helix has to twist so bases are in correct alignment

Question 29

what is cisplatin?

Answer 29

complex of platinum II with 2 chloride ion ligands and 2 ammonia ligands in a square planar shape
the 2 chloride ions are next to each other making it cisplatin not transplatin

Question 30

how is cisplatin an anticancer drug?

Answer 30

1) N atom on G base form coordinate bond with cisplatins pt ion, replacing one of the cl ion ligands
2) 2nd N from nearby G can bond and replace 2nd chloride ion
3) presence of cisplatin complex bound to DNA causes strands to kink so DNA cant unwind and be copied properly so cant replicate properly

Question 31

adverse effects of cisplatin
how can you lessen the side effects?
why is it still used?

Answer 31

can bind to DNA in normal cells too so problem for any healthy cells that replicate frequently such as hair and blood cells- leads to hair loss and poor immune system and kidney damage

give patients low dosages, target tumour directly

long term positive effects outweigh negative short term effects

Question 32

draw the structure of cisplatin

Answer 32

make/ see poster