amino acids, proteins and dna Flashcards
what are the two functional groups of amino acids
NH2 and COOH
(amine and carboxylic acid)
how many naturally occurring amino acids
20
what type of amino acids are found in the body and what does this mean about their structure
a-amino acids (alpha) it means that NH2 is always on the carbon next to COOH
are a-amino acids chiral
yes, one carbon has 4 different substituents except glycine
which enantiomer do a-amino acids exist as in nature
(-) enantiomer
how can amino acids be synthesised industrially
RCHO + NH4CN –> RCH(NH2)CN via nucleophilic addition
RCH(NH2)CN + HCl + 2H2O –> RCH(NH2)COOH +NH4Cl
(hydrolysis, HCl is dilute, need to reflux the reaction mixture)
is the product from amino acids being synthesised naturally optically active
no, a 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 and what consequences does this have
zwitterions (ionic lattice) - high melting and boiling points
what colour solids are most zwitterions at room temperature
white solids
do zwitterions dissolve in water? non-polar solvents?
yes, but not in non-polar solvents
due to ionic nature/polar bonds
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 deprotonated = COO-
NH2 is protonated = NH3+
what happens to amino acids in acidic conditions
proton added to NH2 group
what happens to amino acids in alkaline conditions
loses a proton from COOH group
what is peptide linkage
-CONH-
name of chains of amino acids up to 50 amino acids
polypeptide
name of chains of amino acids over to 50 amino acids
proteins
what are polypeptides and proteins found in
enzymes
wool
hair
muscles
what is the process called by which polypeptides or proteins can be broken down into their constituent amino acids
hydrolysis
what conditions needed for hydrolysis to occur
6 moldm-3 HCl
reflux for 24 hours
what is the primary structure of a protein
sequence of amino acids along protein chain bonded by covalent bonds
how is primary structure of protein represented
sequence of 3 letter abbreviations of the amino acids
how can the primary structure of a protein be broken up
hydrolysis
6M HCl
24 hour reflux
what is the secondary structure of a protein
shape of protein chain
what are the two options for the secondary structure
alpha helix or beta pleated sheets
how is secondary structure held together
hydrogen bonding between C=O and N-H groups
what is tertiary shape of protein
a-helix or b-pleated sheet folded into complex 3D shape
how is tertiary structure held together
hydrogen bonding
ionic interactions between R groups
disulfide bridges
VdW forces
why is tertiary structure important
shape of protein molecules is vital in their function
how can amino acids bond/be attracted to each other
hydrogen bonding
ionic interactions between groups on side chains
disulfide bridges
what is wool and how is it held together
protein fibre with secondary alpha-helix structure held together by hydrogen bonds
what does wool’s 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 permanently break so garment loses its shape
what is a TLC plate made of
plastic sheet coated with silica, SiO2
this is the stationary phase
describe how you would carry out TLC
spot samples onto a pencil line a few cm above the base of the TLC plate
place this in a beaker or tank, with solvent level below the pencil line
ensure there is a lid on the breaker to keep the inside saturated with solvent vapour
wait until solvent front is almost at the top of the TLC plate; then remove from the beaker and analyse
why does TLC separate amino acids
solvent carries amino acids up the TLC plate
rate of movement depends on balance between amino acid’s affinity for the solvent (solubility in it) and affinity for the stationary phase (attraction to the silicon with hydrogen bonding)
what do you often have to do to enable the amino acids to be seen on the chromatogram
spray with ninhydrin (amino acids are colourless, ninhydrin turns spots purple)
or shine UV light on them
how do you calculate an Rf value
distance moved by that substance divided by the distance moved by the solvent front
how can Rf values verify which amino acid is which
compare experimental Rf values to known/accepted values in the same solvent
or run pure amino acids in the same solvent and compare results to identify amino acids
how can Rf values verify which amino acid is which
compare experimental Rf values to known/accepted values in the same solvent
or run pure amino acids in the same solvent and compare results to identify amino acids
what is 2D TLC
uses a square TLC plate
spot the amino acids in one corner, then run TLC in first solvent
flip the plate through 90 degrees and repeat TLC in a second, different solvent
what are the benefits of 2D TLC
separate the spots more - it is extremely unlikely that 2 amino acids will have identical Rf values in 2 solvents
gives you 2 Rf values for each amino acids; you can be more confident in verifying the identity of the amino acids when comparing to known values, as 2 Rf values can be verified
how do you find primary structure of a protein
reflux 6M HCl and reflux 24 hours
carry out TLC to find number and type of amino acids present
how do you find the secondary and/or tertiary structure of protein
various techniques e.g. x-ray diffraction
what is an enzyme
protein based catalysts that speed up reactions in the body by factors of up to 10^10
how many reactions is each enzyme designed to catalyse
one reaction - they are very specialised
what is the structure of an enzyme
globular protein with a creft/crevice in it known as active site
very particular shape
how does its structure help the function of the enzyme
reacting molecules fit precisely into the active site and are held at exactly the right orientation to react. this is the lock and key hypothesis
how else do enzymes increase the rate of reaction
reacting molecules form temporary bonds (via intermolecular forces) to the enzyme
this weakens the bonds in the molecules, promotes movement and lowers Ea
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
what does stereospecificity mean for most naturally occurring molecules
most naturally occurring molecules only occur as one enantiomer due to stereospecific enzymes
how are enzymes denatured
change in temp or pH
how does enzyme inhibition work
molecule with a very specific shape and structure to the substrate is devised
binds to enzyme’s active site
blocks the active site (does not desorb easily)
substrate cannot adsorb to active site, so reaction cannot be catalysed
example of a drug that works through enzyme inhibition
penicillin
what are benefits of modelling new molecules on computers
now we understand factors that affect the shapes of extremely complex proteins, we can model drugs that haven’t been synthesised, predict their properties and design drugs that will treat a range of medical conditions
what does dna stand for
deoxyribonucleic acid
what does dna do
present in all cells and is a blueprint from which all organisms are made
what structure does dna take
a polymer with 4 monomers; they can be combined differently
what constitutes a nucleotide
phosphate ion
2-deoyxyribose sugar
a base (ACGT)
how does dna polymerise
OH on phosphate group and OH on number 3 carbon of 2-deoxyribose react to eliminate a molecule of H2O
what forms between bases of adjacent nucleotides
hydrogen bonding
what kind of polymer does the polymerisation of dna lead to
condensation polymer chain –> backbone of phosphate and sugar molecules, with bases attached
what defines the properties of the dna molecule
order of the bases
why does dna have double helix shape
exists as 2 strands; these 2 strands are held together by hydrogen bonding
the complementary dna molecule has bases that hydrogen bond in the same order to those on another molecule –> double helix shape formed
why is it important that DNA is exactly copied when cells divide
because it codes for proteins and makes all cells
how is dna is exactly copied when cells divide
- hydrogen bonds between base pairs break
covalent bonds in polymer chains remain intact - sequence of bases is maintained
- separate nucleotide molecules that have been created move to hydrogen bond to their relevant bases
- they polymerise
- dna replicated
how does the body use information that is stored in dna
template for arranging amino acids into protein chains –> codes for proteins
recipe for proteins that make up all living things; enzymes, flesh etc
structure of cisplatin
2 (Cl) — Pt —- 2 (NH3)
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 nitrogen atoms on 2 adjacent G bases
N atoms replace the Cl- ligand substitution reaction
why are Cl- ions able to be replaced by 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
what are the drawbacks of using cisplatin
affects healthy cells that are replicating quickly, e.g. hair follicles –> lose hair during chemotherapy
thought to damage kidneys
what happens when excess bromomethane is added to an amino acid
Ch3Br is in excess, so every H on the N atom and the lone pair on the N atom is replaced by a CH3 group –> quaternary ammonium ion (makes a salt with Br-)
