ORGANIC CHEMISTRY - amino acids, proteins and DNA Flashcards
what are the two functional groups of amino acids?
NH2 and COOH
how many naturally occurring amino acids are there in the body?
20
what type of amino acids are found in the body? what does this mean about their structure?
a-amino acids
NH2 ia always on the carbon next to COOH
Are a-amino acids chiral? why?
yes - one carbon has 4 different substituents
EXCEPY glycine as C is bonded to two Hs
which enantiomer do a-amino acids exist as in nature?
(-) enantiomer
how can amino acids be synthesised industrially?
via nucleophilic addition
hydrolysis (HCl is dilute) = need to reflux the reaction mixture
is the products from amino acids being synthesised naturally optically active? why?
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.
in what form do amino acids exist as solids? What consequences does this have?
Zwitterions (ionic lattice) - high Mp and Bp
what colour solids are most zwitterions at room temperature?
white solids
do zwitterions dissolve in water? Non polar solvents? why?
yes in water
no in non-polar solvents
due to ionic nature
define a zwitterion
ions which have both a permanent positive and negative charge, but are neutral overall.
How do zwitterions occur in amino acids?
COOH is deprotonated = COO-
NH2 is protonated = NH3+
what happens to amino acids in acidic conditions?
Gains a proton on the NH2 group
what happens to amino acids in alkaline conditions?
Loses a proton from COOH group
what is the peptide linkage?
-CONH-
what is the process called by which polypeptides can be broken down into amino acids?
hydrolysis
what conditions are needed for hydrolysis to occur?
6 mol dm^-3 HCl
reflux for 24 hours
how can amino acids bond to each other?
hydrogen bonding
ionic interactions between groups on side chains
disulfide bridges ( 2 S atoms oxidised to form an S-S bond )
what are the two options for the secondary structure?
alpha-helix shape or beta pleated sheet
how is the secondary structure held together?
hydrogen bonding between
C=O and N-H groups
what is the tertiary shape of a protein?
alpha helix or beta pleated sheet is folded into a complex 3D shape = this is the tertiary structure
why is the tertiary structure important?
shape of the protein molecule is vital for their function eg enzymes
What is wool? how is it held together?
protein fibre with secondary alpha-helix structure: held together by hydrogen bonds
what does wools structure and bonding mean for wool’s properties?
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
what is TLC plate made of?
plastic sheet coated with silica, SiO2.This is the stationary phase
Describe how you would carry out Thin layer chromatography?
- 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
why does TLC separate amino acids?
- 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
what do you have to do to enable the amino acid to be seen on the chromatogram?
spray with ninhydrin / shine UV light
what is an enzyme?
protein based catalyst that speeds up rate of reaction in the body
how many reactions is each enzyme designed to catalyse?
one reaction
what is the structure of an enzyme?
globular protein
has an active site
explain the lock and key hypothesis?
reacting substrates fit precisely into active site and are held at the right orientation to react
what does the stereospecificity of enzymes mean?
active sites are so selective of the shape of substrates that only reactions involving one enantiomer are catalysed
how are enzymes denatured?
change in temperature or pH
how does dna polymerise?
OH on phosphate group and OH on deoxyribose react to eliminate a molecule of H2O
what defines the properties of the DNA molecule?
the order of bases
draw the structure of cisplatin.
(Cl)2-Pt-(Nh3)2
what is cisplatin’s function? How does it do this?
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.
why are the CL- ions able to be replaced by the N on the base?
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.
drawbacks of using cisplatin?
affects healthy cells eg hair follicles so lose hair
damage kidneys
