chap 7- polymers and life Flashcards
why are amino acids described as amphoteric
they have a basic amino group (NH2) and an acidic carboxyl group (COOH) so has both acidic and basic properties
what is a zwitterion
an overall neutral molecule that has both positive and negative charge in different parts of the molecule. can only exist as a zwitterion near its isoelectric point
what is an isoelectric point of an amino acid
the pH where the overall charge on the amino acid is 0 (it’s different for different amino acids)
what happens to amino acids in conditions more basic (alkaline) than their isoelectric point
the COOH group is likely to lose its proton
what happens to amino acids in conditions more acidic than the isoelectric point
the NH2 group is likely to be protonated
how do amino acids bond together to form proteins
the amine group of one amino acid forms a peptide bond with the carboxylic group of another amino acid in a condensation reaction
how do you hydrolyse a protein (break it down into its original amino acids)
add hot aqueous 6moldm3 HCL and heat under reflux for 24 hours which produces ammonium salts of the amino acids which is then neutralised with a base
what is the primary structure of a protein
the sequence of amino acids that make up the polypeptide chain
what is the secondary structure of a protein
peptide links form hydrogen bonds with each other which means it forms a alpha helix chain or a beta pleated sheet
what is the tertiary structure of a protein
extra bonds form between different parts of the polypeptide chain giving the protein a 3D shape
what bonds hold together the tertiary protein structure
1) instantaneous dipole induced dipole forces: between 2 non polar side groups
2) ionic interactions: between charged side groups (CO2- and NH3+)
3) hydrogen bonds : some R group contain functional groups that can form H bonds
4) disulfide bridges: AA cysteine has a thiol group (-SH) and so different cysteine residues can bond together
what are nucleotides made up of
a phosphate group
a pentose sugar
a base
how is rna different to dna (3 ways)
1) RNA is single stranded
2) RNA nucelotides have ribose rather than deoxyribose
3) RNA has the base uracil rather than thymine
how does the phosphate-sugar backbone form in dna and rna
by condensation polymerisation produces a phosphate-ester link and produces a molecule of water.
how many hydrogen bonds do A and T and then C and G form respectively
A and T form 2
C and G form 3
why can other base pairings not pair
they would put the partially charged atoms too close together or too far apart or the bonding atoms wouldn’t line up properly
describe the process of dna self replication
1) H bonds break, double helix splits
2) free nucleotides in the cytoplasm pair up with complementary bases on nucleotides on dna because of complementary base pairing
3) dna polymerase forms the new polynucleotide chain
4) forms 2 molecules of dna identical to original
what is mRNA
- single polynucelotide strand
- an exact reverse copy of a single dna strand (U instead of T)
- amino acid codons are complementary to dna codons as they form when complementary bases pair up
what is tRNA
- single polynucleotide strand
- clover shape
- anticodon at one end
- binding site at other end where AA that corresponds to complementary mRNA codon can attach
what is rRNA (ribosomal rna)
made up of polynucleotide strands that are attached to proteins to make ribosomes (largest type of rna)
outline transcription (the process that produces mRNA)
1) dna double helix unwinds to reveal a single stranded portion
2) dna bases attract free RNA nucleotides with complementary bases
3) RNA nucleotides are joined by RNA polymerase which forms an mRNA strand
4) DNA coils up again, unaltered
mRNA then moves into cytoplasm for translation
outline process of translation (process of joining amino acids to make a polypeptide chain)
1) ribosomes are made from rRNA and proteins this attaches to the mRNA and starts to move along it looking for a start codon
2) tRNA with the correct anticodon bases pairs with the start codon
3) then moves 3 bases forwards and waits for a new tRNA to bring the next AA. a peptide bond forms between the 2 AA’S
4) first tRNA leaves the ribosome and a new tRNA brings in the 3rd AA
5) process continues until it reaches a stop codon
how are the enzyme and substrate held together
temporary hydrogen and instantaneous dipole induced dipole forces between the substrate and the R groups of the enzymes amino acids
how do enzyme catalysed reactions change order as a substrate is added
uncatalysed reaction is first order when substrate conc is low when substrate conc becomes greater than enzyme conc the rate has reached its maximum and so rate is no longer affected by conc and becomes 0 order
what is a pharmacophore
the part of a drug that fits into a receptor site and makes it medicinally active
what 3 things does the fit of a pharmacophore into a receptor site depend on
1) size and shape
2) bond formation:
- dipole-dipole interactions form between receptor and any polar functional groups
- hydrogen bonding
- ionic acidic and basic functional groups can donate or accept protons to become charged
3) orientation- only one of the E/Z isomers will fit
what is a chiral centre
a carbon atom with 4 different groups attached to it
what are enantiomers or optical isomers
the 2 different molecules that can be made by arranging the groups differently around the chiral centre (mirror images of each other that can’t be superimposed)
what is the difference between an aldehyde and a ketone
an aldehyde has it carbonyl group (C=O) at the end of its carbon chain and its name ends in -al. ketones have their carbonyl group in the middle of the chain and the name ends in -one
what is an amine
derivative of ammonia if one of the hydrogens from ammonia (NH3) is replaced with an organic group
test for amines
if it turns damp red litmus paper blue. and if you react it with a small amount of acyl chloride, white fumes of hcl gas are given off
what is a base
something that can accept protons and form a cation also can be neutralised with an acid
what is an amide
carboxylic acid derivative (func group -CONH2)
why do amides behave differently to amines
the carbonyl group pulls electrons away from the rest of the -CONH2 group so amides behave differently
what are the 2 ways of hydrolysing amides
under acidic conditions: heat with dilute acid to get carboxylic acid and ammonium salt
under basic conditions: heat with dilute alkali to get carboxylate ion and ammonia gas
how are esters made
reacting an alcohol with a carboxylic acid (or derivative)
what are the 2 ways of hydrolysing esters to produce alcohols
acid hydrolysis: splits the ester into carboxylic acid and alcohol (reflux with a dilute acid)
base hydrolysis: reflux with dilute alkali to get carboxylate salt and alcohol
what are acyl chlorides
carboxylic acid derivatives (func group -COCl) general formula = CnH2n-1OCl
what is addition polymerisation
double bond in an alkene breaks to form a long chain (addition polymer)
what is condensation polymerisation
involves 2 different types of monomers each with 2 different functional groups each time a link is formed between 2 func groups a small molecule (usually water) is lost
how do polyamides form
from dicarboxylic acids and diamine molecules (carboxyl group reacts with amino group to form amide links)
how are polyesters formed
dicarboxylic acids and diol molecules (COOH reacts with OH to form ester links -COO) in a condensation reaction
how is nylon-x,y named
x= no of carbon atoms in the diamine y= number of carbon atoms in the dicarboxylic acid
how are the nylons made from one type of monomer formed
some molecules contain both an amine and a carboxylic acid group that can react with themselves in condensation polymerisation to form polyamides
how does a mass spectrometer work
an organic compound is bombarded with electrons, breaks up into different fragments (some of which are charged ions ) these are then detected by a mass spectrometer and create a fragmentation pattern
what kind of fragments wont be shown on a mass spectrometer
any fragments that only form as radicals rather than charged or any fragments that are unstable and so break down before they have time to be detected
what is high resolution mass spectrometry
measures m/z values to at least 4 decimal places which allows comparison of elements and compounds using relative isotopic masses
outline the way in which NMR works
- sample of compound placed in strong magnetic field exposed to range of freq of radio waves
- nuclei absorb energy from the radio waves
- amount of energy absorbed at each freq depends on the environment of that nuclei
- pattern of these absorptions gives you info about position of certain atoms and how many there are
- this helps you work out structure of the molecule
what is the difference between 13C NMR and high resolution proton NMR
13C NMR gives info about the number and types of different carbon environments in that molecule but high resolution proton NMR gives info about the number of hydrogen atoms in the molecule and their environments
why do nuclei in different environments absorb different frequencies and amounts of energy
they are partly shielded by the effects of external magnetic fields by surrounding electrons
how are 2 atoms classed as being in the same environment
they have to be joined to exactly the same things
what is the significance of tetramethylsilane in NMR spectroscopy
NMR measures difference in absorption (chemical shift) relative to a standard substance (tetramethylsilane) Si(CH3)4 it has 12 hydrogen atoms in identical environments so produces a single absorption peak
on NMR what does the number of peaks mean
number of peaks = number of carbon environments or number of hydrogen environments
what does the area under each peak in H NMR tell us (can be shown with numbers or with an integration trace)
the number of H atoms in each environment eg if the areas under 2 peaks is in the ratio 2:1 then there will be 2 H atoms in the first environment for every one in the second
why can proton NMR have split peaks
because of the influence of hydrogen atoms that are bonded to neighbouring carbons
what is the idea of spin-spin coupling
the idea that only hydrogen nuclei on adjacent carbon atoms and in different environments can affect each other
how can you work out the number of neighbouring hydrogens
n+1 rule- if a peak has 2 splits then there’s one neighbouring hydrogen
what is elemental analysis
when experiments determine the masses or percentage compositions of different elements in a compound which means you can then work out the empirical or molecular formulae of a compound
what do you have to do after paper chromatography of amino acids
spray with ninhydrin solution as amino acids are colourless and ninhydrin will turn them purple or dip the paper into a jar of iodine crystals which will turn the spots brown
