polymers of life ocr b chemistry

general structure of an amino acid

COOH-CHR-NH2

how is a protein formed from an amino acid

proteins are a condensation polymer of amjno acid monomers
-joined by peptide links
-amine group reacts with carboxyl group of another amino acid

how to hydrolise peptides

hot aqueous gmoldm^-3 Hal, under reflux for 24 hours
-produces ammonium salts of the amino acids

how to use paper chromatography to identify amino acids

-pencil line over solvent
-concentrated spot of solute
-identify with ninhydrin or iodine solution
-calculate rf values

what is primary structure of a protein

the sequence of amino acids

what is secondary structure of a protein

the folding into a beta pleated sheet or an alpha helix by hydrogen bonding between peptide links

what is tertiary structure of a protein

the interactions between atoms on r groups within the amino acids which fold the protein and give it a 3d structure

what is quarternerary structure of a protein

interactions between different subunits of proteins to form a larger protein molecule

what bonds create tertiary structure

-id-id forces between non-polar groups
-ionic interactions between charged groups
-hydrogen bonds
-disulphide bridges

chemistry definition of DNA

condensation polymer formed between nucleotides, contains deoxyribse sugar, nitrogenous bases and a phosphate group
-nucelotides form a polynucleotide chain and form a sugar-phosphate back-bone

chemistry definition of RNA

condensation polymer of nucleotides
-contains the base uracil instead of thymine
-contains ribose sugar rather than deoxyribose

how is a phosphodiester backbone formed

condensation polymerisation
ester link is formed between the sugar and phosphate group
water molecule is lost

how do bases join to sugars

condensation reaction
-OH group is eliminated from the sugar to join to an NH group of a base,
water is also lost

how does DNA form double helix

-hydrogen bonding between the bases
-sense strand runs from 5' to 3'
-A&T - 2 bonds
C&G- 3 bonds

complimentary base pair bonding

what is dna repliaction and the process

-dna unzips with dna helicase
-bases on free-floating nucleotides in the cytoplasm undergo complimentary base pairing with the now accesible bases, semiconservative replication so new strands with one old strand and new strand are formed
-dna polyermase catalyses the formation of a phosphodiester backbone on the new strand

what is a pharmacophore

a part of a molecular structure that is responsible for a particular biological or pharmacological interaction that it undergoes.

what will affect the fit of a pharmacaphore into a receptor site

-size and shape
-bond formation between the pharmacaphore and the functional groups of the receptor site
-oreintation- must be the correct e/z isomer

how to modify a pharmacaphore

adding groups onto a pharmacophore which will increase its efficacy or reduce side effects

what shape is an uncatalysed reaction for a rate vs substrate concentration graph

straight line

how does substrate concentration affect rate graphs for enzymes

-low substrate concentration = first order
-when substrate conc. is greater than enzyme conc. becomes zero order again

characteristics of enzyme function

-high specifity
-narrow range of temperatures and pH
-inhibitors

how do competitive inhibitors work

molecules with similar shape to the substrate
-block the active site
-lots of competitive inhibitor means little substrate can get to the enzyme
-amount of inhibition is affect by thr strength of bonds between inhibitor and active site

experiment with rate of enzyme reaction

-sealed conical flask attached to a gas syringe
-add pureed potato
-add hydrogen peroxide
-measure gas evolved
-trt with different hydrogen peroxide concentrations

carboxylic acid and metals

salt -oate ending and hydrogen

carboxylic acid and carbonates

salt -oate ending, water and carbon dioxide

carboxylic acid and alkali

salt and water

how are carboxylic acids weak acids

partially dissociate into carboxylate ion and hydrogen ion

what is a zwitterion

A molecule with no net charge - positive and negative charges balance each other

how do amino acids act as zwitterions

-near its isoelectric point-pH where overall chanrge is zero
-in acidic conditions the NH2 gains a H and is protonated so the N has a positive charge
-an alkaline conditions the COOH group loses a H and forms COO-
-at its isoelectric point both these things happen

how does the amine group act basic

accepts a proton
lone pair of electrons on NH2 forms dative covalent bond

test for amine

-fishy smell
-damp red litmus paper turns blue
- reacting with acyl chloride gives off white HCl gas fumes

reaction of an amine and an acid

ammonium salt

naming carboxylic acid

-oic acid

naming acid anhydride

-oic anhydride

naming ester

alcohol group- oate ending is from carboxylic acid

naming acyl chloride

-oyl chloride

naming amide

-amide suffix

naming aldehyde

-al ending

naming ketone

-one ending

naming alcohol

-ol ending

naming phenol

-phenol ending

naming primary and diamines

-amine ending or amino- start
-diamine or diamino-

naming arenes

-benzene, phenol-

naming ethers

alkoxy-

nylon 6,6 structure

nylon 6,10 structure

nylon 6 structure

how are esters hydrolysed

acid or base hydrolysis

how to do acid hydrolysis on an ester

reflux with a dilute acid and water to get carboxylic acid and alcohol
reversible

how to do base hydrolysis on an ester

ester and dilute alkali under reflux
makes carboxylate salt and alcohol
not reversible

how to hydrolyse an amide

acid hydrolysis- heat with dilute acid to get carboxylic acid and ammonium salt
alkali hydrolysis- dilute alkali to carboxylate ion and ammonium gas

acyl chloride and alcohol reaction

at RTP, ester and HCl

acyl chloride and amine reaction

RTP, secondary amide and HCl

what is addition polymerisation

when two monomers with carbon-carbon double bonds react together to form a polymer

what is condensation polymerisation

Where monomers with two functional groups join together, usually losing small molecules such as water (which is why they are called condensation reactions)

carboxyl and amino group condensation polymer

-water molecule is lost, amide link forms

carboxyl group and hydroxyl group condensation polymer

-water molecule lost, ester link forms

types of stereoisomers isomerism

-optical isomers
-e/z isomerism

what is an optical isomer

a carbon has 4 different groups attached to it, meaning the molecule can be arranged in 2 different ways.
they are mirror images but cannot be superimposed

how are optical isomers optically active

they rotate plane-polarised light. one optical isomer will rotate it clockwise and the other anticlockwise

what is mass spectrometry used for

to find the relative masses of fragments of a molecule

steps of a mass spectrometry

vaporisation, ionisation, acceleration, deflection, and detection

why does a molecule split into fragments in mass spectrometry

-when it is bombarded with electrons when the molecule is turned into a positive ion this causes it to split

what fragments are not detected by a mass spectrometer

-if an uncharged radical is made
-charged fragments that are so unstable they break down before they are detected

how to tell where a lost peak is in mass spectrometry

the difference in between peaks
-eg 44-29= 15
-CH3 uncharged radical was lost

why are high resolution mass spectrometers good

-can measure to 4 decimal places
-accurate
-allow you to compare elements and compounds using relative isotopic masses

what does carbon nmr do

gives information about the number and types od carbon environments

how does nmr work

sample of a compound is placed in a strong magnetic field and exposed to a range of frequencies of radio waves
-the nuclei absorb energy at each frequency depending on the environment that its in
-the pattern it gives u reveals information on the position and environment of some atoms within the molecule

what does proton nmr look at

-information on the number of hydrogen atoms within a molecule and the environments theyre in

what do the peaks in carbon nmr tell you

number of peaks- not counting at 0, are the number of different carbon environments
-chemical shift shows what carbon environment each peak represents

what do the peaks in h-nmr reveal

-one peak represents a hydrogen environment
-chemical shift can identify the environment type
-split peaks show many hydrogens there are on the adjacent carbon (n+1 rule- splits=4, 3 hydrogens on adjacent carbon)
-realtive area under a peak can tell you the relative number of hydrogens in each environment