7. polymers and life

amino acids

molecules containing a basic amino group, a acidic carboxyl group and variable group

amphoteric

a molecule with both acidic and basic properties

zwitterion

a molecule that’s overall neutral with both a positive and negative charge

isoelectric point

the pH where the overall charge on the amino acid is zero so it exists as a zwitterion

both the carboxyl group and amino group are charged

acid

conditions more acidic than isoelectric point where the -NH2 group in an amino acid is protonated

base

conditions more basic than the isoelectric point where the -COOH group in amino acid loses a proton

paper chromatography

* draw pencil line and add concentrated spot
* place in beaker with solvent below pencil line, ass watch glass above to stop evaporation
* substances move up with solvent separating out
* remove paper and mark solvent front
* identify positions of amino acids by spraying ninhydrin solution (purple) or dipping paper in a jar with iodine crystals (brown), circle spots
* calculate Rf values

Rf values

= distance moved by spot ÷ distance moved by solvent

proteins

condensation polymers of amino acids, joined by peptide links

condensation reaction

reaction between the amine group of an amino acid and a carboxylic group of another, forms a dipeptide/protein with a peptide bond

polypeptide

formed when many amino acids join together to make a chain

hydrolysis

reaction to break down amino acid, requires harsh conditions hot aqueous 6 mol dm-3 hydrochloric acid and heated into reflux for 24 hours produces ammonium salts, final mixture neutralised using a base

primary structure

sequence of amino acids in the long chain that makes up the protein

secondary structure

peptide links can form hydrogen binds allowing the chain to from a alpha helix chain or beta pleated sheet

tertiary structure

extra bonds form between r groups on polypeptide chain given it a 3D shape

bonds in tertiary structure

all bonds between R groups

* instantaneous dimple-induced forces, weak attractions between non polar side groups eg CH3
* ionic interactions between charged side groups eg CO2- and NH3+
* hydrogen bonds eg -OH, -COOH, -NH2 and -CONH2
* disulphide bridge between thiol (-SH) groups

DNA deoxyribonucleic acid

polymer of nucleotides that contains all the genetic information of an organism

nucleotide

monomer of DNA made up of a phosphate group, pentose sugar (deoxyribose) and a base

adenine, cytosine, guanine and thymine

DNA bases

phosphate sugar backbone

formed when nucleotides join together to make a polynucleotide chain, bonds form between a phosphate group and sugar

RNA

polymer of nucleotides with a series of bases attached to a phosphate sugar backbone, similar to DNA but contains ribose sugar and uracil

phosphate ester link

bound formed in condensation reaction which hold phosphate sugar back bone together, between OH groups

\-NH group and -OH group

groups where a condensation reaction takes place to join DNA bases to phosphate sugar back bone

double helix

shape of DNA as it is made if 2 polynucleotide stands where the bases join them together by complementary base pairing of hydrogen bonds

2 hydrogen bonds

number of hydrogen bonds between adenine and thymine

3 hydrogen bonds

number of hydrogen bonds between guanine ad cytosine

hydrogen bonds

occur between bases where there is a polar bond with hydrogen ( H arched to anything highly electronegative like N and a lone pair of electrons is nearby to bond to like O, N or F atoms)

self replication

DNA has to be copied for cell growth

* hydrogen bonds break and DNA unzips
* free nucleotides pair up with bases by complementary base pairing
* DNA polymerase joins nucleotides together to from a polynucleotide chain
* results on 2 identical double strands DNA

base codons

a triplet of bases that code from one main acid, 64 possibilities and 20 amino acids

messenger RNA (mRNA)

single polynucleotide strand, exact reverse copy of DNA except uracil instead of thymine

transfer RNA (tRNA)

single polynucleotide strand that’s folded to a clover shape, at one end there is a sequence of 3 bases called an anticodon which attaches to mRNA, other end there is a binding site fro an amino acid

ribosomal RNA (rRNA)

polynucleotide strands attached to proteins which make things called ribosomes, largest type of RNA

transcription

process to produce mRNA

* hydrogen bonds break and DNA unzips revealing a small single stranded region
* free RNA nucleotides pair up with bases by complementary base pairing 
* RNA polymerase joins nucleotides together
* forms mRNA and DNA coils up again unaltered

translation

process to make proteins:

* ribosomes attach to mRNA and moves along it looking for a start codon (AUG)
* a tRNA with the correct anticodon bases pairs to tRNA
* peptide bond joins the polypeptide chain together
* process continues until stop codon is reached and then the ribosome releases the polypeptide chain together

enzyme

biological catalyst for many reactions organisms, they are proteins but can have non protein parts, area called active site where substrate binds

lock and key

model which explains how enzymes are specific to one substrate

optimum conditions

the narrow range of temperature and pH which enzymes work at

to high temperature and they denature, to low and they very slow

changes in pH cause them to denature

competitive inhibitors

molecules with a similar shape to substrate they bind to enzymes and block them preventing it working

enzyme rate of reaction

increases with substrate concentration unit It plateaus due to another factor

so is first order until its zero order unlike a uncatalysed reaction that remains first order

enzymes rate experiments

can be measured using gas syringe, mass balance or titrations

eg potato (contains catalyse) and hydrogen peroxide produces a gas

receptors

sites on cells where chemicals bind to and either inhibit something or trigger a series of biochemical reactions, chemicaas have to be exactly the right shape and size to fit

molecular recognition

describes the intermolecular interaction between tow or mole molecules

medical active

allowed due to a drug having the reconnect molecular recognition with a receptor

pharmacophore

part of a the drug that fits into a receptor and makes it medically active

fit of a pharmacophore depends on

* size and shape so it can fit the receptor
* bond formation, allowing for temporary bonds with receptor, include dipole dipole interactions, hydrogen bonds and ionic interactions
* orientation, if they have E/Z optical isomers then only one will fit

modification

once the pharmacophore part has been identified other parts can be changed to make it more effective or reduce side effects, eg noradrenaline (found in body) has changed to be salbutamol and isoprenaline

optical isomers

molecules that are mirror images of each other, also called enantiomers

chiral carbon

a carbon atom which has 2 diffenert groups attached to it, so the groups have 2 possible arrangements

optically active

optical isomers rotate plane polarised light, one rotates it clockwise, the other anticlockwise the same amount

plane polarised light

light which only vibrates in one direction unlike normal light which vibrates in all directions

drawing optical isomers

identify chiral carbon, this sits in the middle of the rain then there is 2 straight lines, a dash and a wedge with the functional groups

multiple chiral centre

occurs in molecules meaning they will have multiple optical isomers

carboxylic acids

\-COOH group, CnH2nO, carboxy- / -oic acid eg ethanoic acid

weak acids as they partially dissociate in water

acid anhydride

O between C=O, CnH2n-2O3, -oic anhydride, eg ethnic anhydride

esters

O-C=O, CnH2nO2, -oate, eg methyl ethanoate

acyl chlorides

Cl-C=O, CnH2n-1OCl, -oyl chloride, eg ethanol chloride

carboxylic acid derivatives

easily lose their chlorine

amides

\-C=O-NH2, CnH2n-1ONH2, -amide, eg ethanamide

aldehydes

H-C=O, CnH2nO, -al eg ethanal

a person of a carbonyl group with it at the end and a H

Ketones

\-C=O, CnH2nO, -one, propanone

version of carbonyl group with it in the middle of the chain

alcohols

\-OH, CnH2n+1OH, -ol / hydroxyl eg ethanol

phenols

\-benzene ring with a OH, RC6H4OH, -phenol, eg 3-ethylphenol

primary amine

\-NH2 group, CnH2n+3N, -amine / amino- eg aminoethane

arenes

\-benzene ring, RC6H5, -benzene / phenyl- eg ethyl benzene

ethers

R-O-R’, CnH2n+2O, alkoxy-, eg methoxy ethane

carbonyl group

functional group C=O, found in aldehydes and ketones

diol

contain 2 -OH groups

acid anhydrides

contain a -C=OOC=O- group, R group on each end

primary amines

formed when one of the hydrogens in ammonia Is replaced with an organic group

smell fishy

basic so tested for by seeming if it runs damp red litmus paper blue

test for amides

add acyl chloride, positive result gives white fumes and HCl gas

violent reaction and produces secondary amide

dative covalent bond

formed between lone pair of electrons on nitrogen and a proton, makes it a positively charged cation

secondary amide

formed when nitrogen in amide has a second R group attached, have the prefix N-alkyl-

hydrolyse

process carried out to amides, either under acidic or basic conditions

dilute acid

conditions amide heated with that produces a carboxylic acid and ammonium salt

dilute alkali

conditions amide heated with to produce a carboxylate ions and ammonia gas

dicarboxylic acids

molecules containing 2 carboxylic functional groups, end in -diotic acid

more reactive metals

carboxylic acids react with them in a redox reaction forming salt and hydrogen gas

carbonates

carboxylic acids react with them to form a salt, carbon dioxide and water

neutralised

carboxylic acids with aqueous alkalies to form salta and water

esters

made by reacting an alcohol with a carboxylic acid, the name is a combination of the two

gives the molecule -C=OO- functional group

made in a condensation reaction releasing water

acid hydrolysis

reversible reaction which spilts an ester into a carboxylic acid and an alcohol, due under reflux and requires lots of water to push the equilibrium to the right

base hydrolysis

irreversible reaction with an easter which produces a carboxylate salt and an alcohol, done under reflux

acyl chloride and alcohol

a irreversible vigorous reaction that quickly produces an ester

Cl is subsituted by an oxygen, nucleophilic substitution

addition polymers

formed by alkenes joining together by the double bond breaking

produces unreactive chain

condensation polymers

usually involve 2 types of monomer with a at least 2 function groups which react together forming a link losing water in the process eg natural ones like proteins or polyester and polyamides

can be hydrolysed under acidic or basic conditions to break it down

polyamides

made form dicarboxylic acid and diamine monomers, form amide links between them when the -OH and H react releasing water

polyesters

made from dicarboxylic acid and diol monomers, ester links are formed between -OH and H releasing water

nylon

a type of polyamide, either made from one monomer or 2 monomers

2 monomers

nylon formed in condensation reaction between diamine and dicarboxylic acid

named by nylon-x,y where x and y are the number of carbon atoms in each monomer

1 monomer

nylon made from monomers coating an amide and carboxylic acid which can react with themselves

named by nylon-x where x I the number of carbon atoms in the monomer

mass spectrometry

used to identify organic compounds by mass

compounds are bombarded by electrons and break up into fragments

charged ions are detected and create a fragmentation pattern

M peak

highest peak that tells you the mr of a molecule

M+1 peak

very small peak with the highest mass due to carbon 13 isotope

lost fragments

don’t show up on mass spectrometer due to been uncharted radical or unstable so break down before detected or doens’t form a positive charge easily, can be workout however by the difference between peaks

high resolution mass spectrometers

able to give m/z values to at leats 4 decimal places, allows you to compare elements and compounds using relative atomic masses so can more accurately determine what something is

NMR spectroscopy (nuclear magnetic resonance)

analytical technique to work out structure of molecules

a sample is placed in a string magnetic field and exposed to a range of radio wave frequencies

the nuclei absorb energy, amount depends on its environment

the pattern of absorptions gives you positions of atoms in the molecule

carbon 13 NMR

tells you about the number and types if different carbon environments in a molecule

high resolution proton NMR

tells you about number of hydrogen atoms in a molecule and their environments

shielding

happens to carbon atoms due to hydrogen surrounding it, affects frequencies they absorb

chemical shift

the difference in frequencies absorbed compared to a standard substance- tetramethylsilane (TMS) has 12 hydrogens producing identical environments, produces a single peak at 0

hydrogen environments

effected by atoms up to 3 bonds away