Polymers of Life

alcohols, diols, and phenols

• contains a hydroxyl group -OH

• primary- the OH is bonded to a carbon bonded to one other carbon atom

  secondary: the OH is bonded to a carbon bonded to 2 other carbon atoms

  tertiary: the OH is bonded to a carbon bonded to 3 other carbon atoms

• e.g butan-2-ol

diols

• contain 2 hydroxil groups, e.g ethane-1,2-diol

phenols

• aromatic alcohols, weak acids as the H can disocciate from the OH group, the carbon 1 is always the one bonded to the OH

carboxyllic acids, aromatic carboxylic cids dicarboxyllic acids

• contain a carboxyl group -COOH e.g ethanoic accid

• called acids bc they dissociate to relase a hydrogen ion, becoming an ion e.g sodium ethanoate. they are weak acids bc they partially dissociate(use a reversible reaction sign to show ionisation in water is partial)

• carboxyllic acid⇌carboxyllic ion -(e.g ethanoate) + H+

• or carboxyllic acid +water ⇌ carboxyl ion (e.g CH₃COO-) +H₃O-

• aromatic carboxylic acids coan contain benzene rings. If they contain another group, the carbon bonded to COOH is carbon one, e.g in 2-methyl benzoic acid

dicarboxylic acids:

• dicarboxlic acids have 2 carboxyl groups. each carboxyl group has to be at the ends of the carbon chain

• both carboxyl groups react

aldehydes and ketones

• contain a carbonyl group C=O

• aldehyde e.g ethanal

• ketone- e.g propanone, only give number if there are more than 4 carbons

acyl chlorides and acid anhydrides

acyl chlorides:

• acid chlorides, a derivative of carboxylic acid, OH is replaced with a clorine so -COCl

• replace the e in alkane name with -oly chloride e.g ethanoyl chloride

acid anhydrides:

• formed by a condensation reaction betweeen 2 carboxylic acids, eliminating a small molecule e.g water

• only need to know name of ethanoic anhydride and that it is (CH₃CO)₂O

esters

• formed from condensation reactions

• carboxylic acid +alcohol ⇌ ester+ water (needs acid catalyst)

• first part comes from alcohol and second part comes from carboxylic acid e.g ethyl butanoate

• can also be formed by acyl chlorides or acid anhydride +alcohol→ester + small molecule

• polyesters are formed by a condesation reaction between a diol and dicarboxylic acid

amines

• deriviteives of ammonia but 1 or more hydrogen is replaced with an R group

• primary amine- one hydrogen replaced with an R group, secondary- 2hydrogens replaced, tertiary, 3 huydrogens

• only need to know how to name primary amines- start w name of R group e.g methylamine, ethylamine or 1-aminopropane(name is different if 3 or more bc u need to say position of amine group)

• ‘diamino’ if 2 amine groups e.g 1,6-diaminohexane

• primary amine group is always NH₂

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amine properties

• water solube bc they form hydrogen bonds in water as N has a lone pair

• weak pd-id attractions to water ,

• more energy is required to break hydrogen bonds between water molecules than is released by forming pd-od bonds, so solubility decreases the longer the chain is

• they are weak bases bc the N has lone pairs, so acts as a proton receptor to accept a hydrogen ion from water and form a dative covalent bond forming OH- ions making the solution acidic. this is an equilibrium and there are still some undissociated amine so the smell remains in solution

• if acid is added H, the amine is neutralised but this is not an equilibrum there is no freee amine so smell disapperars

• if an alkali is added to an amine salt the amine smell returns, ph is above 7 bc hydroxide ions act as a base acceptingn protons from amine salt so free amine is regenerated

• amine salt naming is using ‘alkylammonium ion’ e.g ethylammonium chloride

amides and nylons

• derivatives of carboxyllic acids, but has an NH_x insread of OH

• primary, only one hydrogen is relaced with a carbon chain, secondary- 2 hydrogens are replaced with carbons, tertiary- 3 carbons are replaced with carbons

• formed by acyl chloride + ammonia or an amine→amide + small molecule, condensation reaction, don’t call the bond a peptide bond this is onyl for bio

• amide formation is very exothermic and steamy white fumes are produced

nylons;

• polyamides aka nylons, are fromed by diamines+diacylchloride or a dicarboxylic acid

• first number is number of carbons in the diamine, second number is number of carbons in the dicarboxylic acid or diacychloride e. nylon-6,6

hydrolysis of esters and amides in neutral, acidic and alkaline conditions

proteins

• condensation polymers of amino acids, 2-dipeptide, 3-tripeptide 4+polypetide, over 40 protein

• amino acids are the monomers and they are known as residues when part of a polymer

• the order in which the residues are joined-primary structure of protien

• say peptide bond isntead of amide bond between COOH and NH₂

zwitterions

• proteins are bifunctional bc they have an acidic group that donates a proton (amine group) and a basic group that accepts a protein

• this forms zwitterions which have a positive charged group and a engative charged group with no overal charge but lots of ionic attractions between zwitterions

• this can happen with amino acids, they are solunble in qater bc zwitter ions form ion dipole attractiosn w polar water molecules

• amino acids can react with OH- or H+ ions to buffer solutions

hydrolysis of peptides and chromatography

• amide bond can be hydrolysed using enzymes in roganisms or heating under reflux with moderated conc HCL in a lab

• then you can do chromatography and compare Rf values with known amino acids to identify an unknown one

amino acids ened to know: functional group,

the carbon bonded to R is the alpha carbon

glycine R group is just H
alanine functional group is CH₃

secondary and tertiary bonding in proteins

secondary structure:

• coil into helix or fold into a sheet due to hydrogen bonds between the NH and CO of neighboruing parts of the same chain

tertiary structure:

• 3d strucute held together by bonds and attractions between r groups of amino acid residues e.g ionic, covalent(disulfide bridges), hydrogen bonding, id-id forces

• structural proteins e.g collagen are fibrous whilst chemical proteins are globular

enzymes and competitive inhibtors

• globular tertiary structure proteins.

• a substrate fits the active site and forms attractions to the R groups of the protein structre to be broken down or joined into new products

• R groups on the residues of the enzymes interact with substrate froming weak bonds, forcing other bonds within the substrate to weaken or change shape forcing the areas to come close enough to react

• weak bonds are broken when reaction is complete leaving active site unchanged and free for another substrate molecule to enter

• often only one enantiomer of an optical isomer will fit into the active site

competitiev inhibitors(4)

• competitive inhibitors similar shape to the substrate so can fit into the same active sites and

• form same interactions/bonds w active sites.

• however it does not form any new products

• remains bonded to the active site preventing anuy more substrates from entering and being catalysed. (model answer)

define pharmacophore, molecular recognition

molecular recognition- how molecules interact in terms of intermolecular and covalent bonds

pharmacophore- the part of a drug molecule that gives the medicine its particular pharmocological properties
they can fit into receptor sites, interact w receptor sites to form weak intermolecular attractions, be modifided to reduce side effects by changing side groups

optical isomerism

• all molecules have a mirror image

• non-superimposable mirror image- mirror image is a different molecule (left hand is a nonsuperimposable mirrr image of right hand bc if you pick up the mirror image and put it over it wont fit the original

• this happens when a molecule has a chiral centre- carbon with 4 different groups bonded 2 it. So molecules with a chiral carbon have optical isomerism

• enantiomers- non-superimposable mirror images

• they usuallly have the same physical and chemical properties, but react differently with other chiral molecules e.g left hand doesnt fit a right handed glove. most amino acids are chiral so most enzymes only interact wirtha. specific enantiomer of a chiral molecule

DNA structure and bonding

• each side of the sugar phosphate backbone is anti-parrallel

• condensation reactions to form phosphodiester bonds betweeen phosphates and sugars insugar phosphate backbone

• hydrogen bonds between A and T (2) and C and G(3)complementary nitrogenous base pairing

transcription and translation

transcriptipon- the DNA is unzipped by DNA helicase and RNA neuclotides organise to form a complementary mRNA strand, small enough to enter ribosomes

translation- trna runs along mrna strand and has anticodons that complement mRNA codons

in RNA there is U instead T

NMR spectrocoscopy

nuclear magentic resonance

• if some nuclei are exc ited they emit radiation as radio frequency to drop down to grown state

• nuclei needs to have an odd number of nucleons(protons and neurons) to do this

• each enviornment what surrounds carbon/hydrogen gives one peak

• position of peak tells us what the environment is but not how many there are for carbon, only hydrogen

• ‘we will find x peaks with a chemicl shift between a and b ppm’

• for hydrogen nmr there is a splitting pattern which is the number of H on the neighbouring carbons +1. = singlet(1), doublet(2), triplet(3) quartet, or mulitiplet

• this can be combined with infrared spectroscopy to identify molecules

• if recap: OH for alcohol produces a smooth broad peak betwen(3200-2600 given), if jagged then the OH is likely of a carboxyllic acid