ORGANIC CHEMISTRY - amino acids, proteins and DNA

Question 1

what are the two functional groups of amino acids?

Answer 1

NH2 and COOH

Question 2

how many naturally occurring amino acids are there in the body?

Answer 2

20

Question 3

what type of amino acids are found in the body? what does this mean about their structure?

Answer 3

a-amino acids

NH2 ia always on the carbon next to COOH

Question 4

Are a-amino acids chiral? why?

Answer 4

yes - one carbon has 4 different substituents

EXCEPY glycine as C is bonded to two Hs

Question 5

which enantiomer do a-amino acids exist as in nature?

Answer 5

(-) enantiomer

Question 6

how can amino acids be synthesised industrially?

Answer 6

via nucleophilic addition
hydrolysis (HCl is dilute) = need to reflux the reaction mixture

Question 7

is the products from amino acids being synthesised naturally optically active? why?

Answer 7

No - racemic mixture is formed as the CN- ion can attack from above or below the planar C=O bond with equal likelihood. An equal amount of each enantiomer is formed, so no net effect on plane polarised light.

Question 8

in what form do amino acids exist as solids? What consequences does this have?

Answer 8

Zwitterions (ionic lattice) - high Mp and Bp

Question 9

what colour solids are most zwitterions at room temperature?

Answer 9

white solids

Question 10

do zwitterions dissolve in water? Non polar solvents? why?

Answer 10

yes in water
no in non-polar solvents
due to ionic nature

Question 11

define a zwitterion

Answer 11

ions which have both a permanent positive and negative charge, but are neutral overall.

Question 12

How do zwitterions occur in amino acids?

Answer 12

COOH is deprotonated = COO-
NH2 is protonated = NH3+

Question 13

what happens to amino acids in acidic conditions?

Answer 13

Gains a proton on the NH2 group

Question 14

what happens to amino acids in alkaline conditions?

Answer 14

Loses a proton from COOH group

Question 15

what is the peptide linkage?

Answer 15

-CONH-

Question 16

what is the process called by which polypeptides can be broken down into amino acids?

Answer 16

hydrolysis

Question 17

what conditions are needed for hydrolysis to occur?

Answer 17

6 mol dm^-3 HCl
reflux for 24 hours

Question 18

how can amino acids bond to each other?

Answer 18

hydrogen bonding
ionic interactions between groups on side chains
disulfide bridges ( 2 S atoms oxidised to form an S-S bond )

Question 19

what are the two options for the secondary structure?

Answer 19

alpha-helix shape or beta pleated sheet

Question 20

how is the secondary structure held together?

Answer 20

hydrogen bonding between
C=O and N-H groups

Question 21

what is the tertiary shape of a protein?

Answer 21

alpha helix or beta pleated sheet is folded into a complex 3D shape = this is the tertiary structure

Question 22

why is the tertiary structure important?

Answer 22

shape of the protein molecule is vital for their function eg enzymes

Question 23

What is wool? how is it held together?

Answer 23

protein fibre with secondary alpha-helix structure: held together by hydrogen bonds

Question 24

what does wools structure and bonding mean for wool’s properties?

Answer 24

can be stretched, H bonds extend
release it and returns to original shape
wash too hot and h-bonds break permanently, garment loses its shape

Question 25

what is TLC plate made of?

Answer 25

plastic sheet coated with silica, SiO2.This is the stationary phase

Question 26

Describe how you would carry out Thin layer chromatography?

Answer 26

• spot samples onto pencil lines
• place in beaker with solvent level below pencil line
• wait until solvent front is almost at the top of the TLC plate, remove from the beaker and analyse

Question 27

why does TLC separate amino acids?

Answer 27

• solvent carries A.A up the TLC plate
• rate of movement depends on the amino acids affinity for the solvent and affinity for the stationary phase

Question 28

what do you have to do to enable the amino acid to be seen on the chromatogram?

Answer 28

spray with ninhydrin / shine UV light

Question 29

what is an enzyme?

Answer 29

protein based catalyst that speeds up rate of reaction in the body

Question 30

how many reactions is each enzyme designed to catalyse?

Answer 30

one reaction

Question 31

what is the structure of an enzyme?

Answer 31

globular protein
has an active site

Question 32

explain the lock and key hypothesis?

Answer 32

reacting substrates fit precisely into active site and are held at the right orientation to react

Question 33

what does the stereospecificity of enzymes mean?

Answer 33

active sites are so selective of the shape of substrates that only reactions involving one enantiomer are catalysed

Question 34

how are enzymes denatured?

Answer 34

change in temperature or pH

Question 35

how does dna polymerise?

Answer 35

OH on phosphate group and OH on deoxyribose react to eliminate a molecule of H2O

Question 36

what defines the properties of the DNA molecule?

Answer 36

the order of bases

Question 37

draw the structure of cisplatin.

Answer 37

(Cl)2-Pt-(Nh3)2

Question 38

what is cisplatin’s function? How does it do this?

Answer 38

anti-cancer drug
bonds to strands of DNA to distort shape and prevent cell replication. Bonds to N atoms on 2 adjacent G bases. The N atoms replace Cl- ligands in a ligand substitution reaction.

Question 39

why are the CL- ions able to be replaced by the N on the base?

Answer 39

N atoms on the G base have lone pairs of electrons that can co-ordinately bond to the Pt ion. N atoms are better ligands than CL- so replace them.

Question 40

drawbacks of using cisplatin?

Answer 40

affects healthy cells eg hair follicles so lose hair
damage kidneys