Unit 3: Section 8 - amino acids, proteins and DNA MDY * Flashcards
amino acids proteins and enzymes DNA
what do amino acids consist of?
it has a basic amino acid group (NH2) and an acidic carboxyl group (COOH)
it is also attached to an H and an R group
what properties do amino acids have?
amphoteric - both basic and acidic properties
chiral - rotate plane polarised light (except glycine, who’s R group is just H)
what is a zwitterion?
a dipolar ion - it has a positive and a negative charge
RNH3+ and COO-
only exist near an amino acids isoelectric point
what is an amino acids isoelectric point?
the pH where the average overall charge on the amino acid is zero
how to identify the amino acids in a mixture?
thin-layer chromatography
what are proteins?
they are made up of lots of amino acids joined together by peptide links
joined via condensation between NH2 and COOH
how can proteins be broken down?
via hydrolysis
hot aqueous 6M hydrochloric acid and heat under reflux for 24 hours
what are the structures of a protein?
primary
secondary
tertiary
quarternary
what is the primary structure of a protein?
the primary structure is the sequence of amino acids in the long chain the makes up the protein
what is the secondary structure of a protein?
the peptide links can form hydrogen bonds (between C=O and NH) with each other
to form an alpha helix or beta-pleated sheet
what is the tertiary structure of a protein?
chain of amino acids coiled and folded
extra bonds form to make 3D shape
held together by various bonds between R groups of amino acids
what are types of bonds are there that hold proteins in shape in the tertiary structure?
hydrogen bonds
disulfide bonds
covalent bonds
ionic bonds
what do hydrogen bonds do in proteins?
they exist between polar groups
e.g. OH and NH2
they stabilise both secondary and tertiary structure
what do disulfide bonds do in prteins?
amino acid, cysteins, contains a thiol group (SH)
thiol groups can lose their Hs and join together to form a sulfur-sulfur bond
what factors affect hydrogen and disulfide bonds?
temperature
pH
how do enzymes speed up reactions?
biological catalysts
catalyse every metabolic reaction in the bodies of living organisms
what are enzymes?
proteins, some have non-protein parts
every enzyme has an active site, where substrate fits to interact with enzyme
active site is 3D - part of tertiary structure
how are enzymes specific?
only work with specific substrates
substrate has to fit active site (lock and key model)
active sites are stereospecific
what does it mean that active sites are stereospecific?
they’ll only work on 1 enantiomer of a substrate. the other enantiomer won’t fit properly in the active site, so the enzyme can’t work on it
what are inhibitors?
molecules that have a similar shape to the substrate
they compete with the substrate to bond to the active site, but no reaction follows. they block active site so no substrate can fit
what does the amount of inhibition depend on?
the relative concentrations of inhibitor and substrate
how strongly the inhibitor bonds to the active site
how do antibiotics kill bacteria?
they block the active site of an enzyme in bacteria that helps to make their cell wall, causing them to weaken over time, so bacteria eventually burst
why is it difficult to find a drug that works as an enzyme inhibitor?
active site is very specific
if drug is chiral only 1 enantiomer works
how are new drug molecules found?
trial and error
then adapt any that work to try and improve them, this takes a long time
how are scientist speeding up finding drugs?
using computers to model the shape of an enzymes active site and predicting how well potential drug molecules will interact with it
so hundreds can be examined before synthesising and testing in labs
what is DNA made up of?
lots of monomers called nucleotides
what are nucleotides made up of?
a phosphate group
a pentose sugar
a base
what is a pentose sugar?
a five carbon sugar
its 2-deoxyribose in DNA
what is a DNA base?
adenine
cytosine
guanine
thymine
how do nucleotides join together?
the nucleotides join together to form a polynucleotide chain
covalent bonds form between the phosphate group of 1 nucleotide and the sugar of another
forming a sugar-phosphate backbone
how is the sugar-phosphate backbone formed?
condensation reaction between OH on phosphate group and OH on sugar
water is lost
covalent phosphodiester bond formed
how is DNA formed?
made of 2 polynucleotide strands
2 strands spiral together to form double helix structure held together by hydrogen bonds between 𝛿- =O and 𝛿+ NH2 the bases
what makes 2 DNA strands complementary?
each base can only join with 1 particular partner
A-T and C-G
why does complementary base pairing happen?
the arrangement and number of atoms in the base molecules that are capable of forming hydrogen bonds
how do hydrogen bonds form between complementary bases?
between polar positive H atom and lone pair on O or N atom
A-T forms 2 hydrogen bonds
C-G form 3
why are the complementary base pairings the only possible base combinations?
other base pairings would put partially charged atoms too close or too far
DNA helix has to twist so bases are in the right alignment and at right distance apart
how does cisplatin work as an anti-cancer drug?
ligand substitution - nitrogen atom on guanine base forms coordinate bond with cisplatin’s platinum replacing Cl
2nd nitrogen from nearby gunaine replaces 2nd Cl
this causes strands to kink, so it can’t unwind and be copied properly, so cell can’t replicate
what side effects can cisplatin cause?
hair loss and suppress the immune system and kidney damage
this is because it stops replication in normal cells and has a worse affect on cells that replicate rapidly
how are side effects of cis platin reduced?
low dosages
target the tumour
why is cisplatin still used?
the balance of long term positive effects outweigh the negative short term effects
what happens to amino acids in acidic and alkaline conditions?
acidic - has RNH3+ group
alkaline - has COO- group
how can the amine group of an amino acid react?
become protonated by acids
acylation with acyl chlorides/ anhydrides
nucleophilic substitution with halogenoalkanes
how can the carboxyl group of an amino acid react?
deprotonated by bases
esterification with alcohols
what is the solid form of an amino acid?
a zwitterion
what is a dipeptide?
2 amino acids joined together by a condensation reaction to form a peptide linkage
tripeptide = 3 amino acids
polypeptide = many
what interactions do proteins have with water?
hydrophobic interactions -alkyl groups -aromatic groups -they move away from water hydrophilic interactions -acidic or basic side chains -move towards water
how do ionic attractions occur in proteins?
ionic interactions between COO- and NH3+ on side chains help stabilise the tertiary structure of a protein
how are amino acids observed in TLC?
stained using ninhydrin
can be seen under UV light
what is 2D chromatography?
after chromatography has been done with one solvent
the stationary phase is rotated 90* and chromatography is carried out again with a different solvent
different compounds have different solubilities in different solvents
if 2 compounds have the same solubility in 1 solvent they will be separated by the other one
what is cancer?
disease where some of the body’s cells grow uncontrollably. usually caused by DNA in certain genes being changed
what are the symptoms of cancer?
cancer can grow into or push on nearby organs, blood vessels and nerves - causing symptoms
fever, fatigue or weight loss - cancer cells use up much of body’s energy supply
