AMINO ACIDS PROTEINS N DNA

AMINO ACIDS HAVE 2 FUNCTIONAL GROUPS

amide -NH2 and carboxylic acid -COOH

amino acids are amphoteric

can act as an acid OR base

amino acids can donate protons

-COOH ⇄ -COO^- + H⁺

amino acids can accept protons

-NH₂ + H⁺ ⇄ -NH₃⁺

amino acids are chiral molecules

the carbon is attached to 4 different groups

a solution of a single amino acid enantiomer

rotates polarised light

naming amino acids

• find longest carbon chain w COOH

• number the carbon starting w 1COOH

• write down the position of -NH2 followed by AMINO

• write the name of any other functional group w its position on the carbon chain

amino acids can exist as zwitterions

dipolar ions with both positive and negative parts

zwitterions only exist near an amino acids isoelectric point

when the pH gives the amino acid an overall charge of 0

amino acids becom zwiterions when the amino group is protonated -NH₃⁺

and the COOH group is deprotonated -COO^-

in acidic conditions

the NH2 group is likely to be protonated while the COOH remains the same so the amino acid molecules carried a positive charge

in basic conditions

the COOH is likely to be deprotonated and the -NH2 remains unchanged so the amino acid molecules carries a negative charge

only at or NEAR the isoelectric point are BOTH the carboxyl group and the amino group likely to be ionised forming a zwitterion

different amino acids have different R groups

therefroe they will have different solubilities to the same solvent

you can easily seperate and identify differemt amino acids in a mixture using

Thin layer chromatography

amino acids are colourless

you make them visible by spraying ninhydrin solution on the plate which causes amino acids to turn purple

you can use a special plate with added flourescent dye on it

the dye glows in UV light so wherever theres an amino acid the spot will appear darker

you can identify amino acids by comparing their Rf value to the databook Rf value

Rf= distance travel by spot ÷ distance traveled by solvent

protein

condensation polymers of amino acids joined in peptide links

amino acid 1-COOH+HHN-amino acid 2 → protein + H₂O

if 2 different amino acids compine then 2 different products can be formed because of chiral carbon

protein hydrolysis conditions

• 6 mol dm-3 HCL

• heat mixture in reflux for 24hours

peptide bond

-CONH

PRIMARY STRUCTURE

sequence of amino acids in long chain held together by peptide bonds

SECONDARY STRUCTURE

• peptide links can form hydrogen bonds with each other so the chain is NOT straight

• in fact the chain can spiral into an alpha helix structure OR fold into a beta pleated sheet structure

TERTIARY STRUCTURE

chain of amino acids itself coil and fold in characteristic ways that identifies the protein

extra bonds form between different parts of the polypeptide chain which gives is 3D shape

secondary and tertiary structures of proteins are formed by intermolecular forces

causing the amino acid chain to fold and twist

hydrogen bonding exists between polar groups like OH and NH2

these groups contain electronegative atoms which induce partial positive charges on hydrogen atoms which are attracted to lone pairs of electrons on adjacent polar groups to form hydrogen bonds

cystine

an amino acid with the thiol group -SH

the thiol group can lose its H atom and join together to form a disulphide bridge

-S-S-

these disulfide bonds link together different part of the protein chain

to help stabalise the tertiary structure

factors that affect intermolecular forces in amino acids

• temperature

• pH

enzymes

speed up chemical reactions by acting as biological catalysts

enzymes catalyst every metabolic reaction in the bodies of living organisms

they are proteins but have non protein components

substrates

molecules that enzymes bind to

enzyme active sites

has a specific tertiary structure for the substrate to fit into so it can interact with the enzyme

enzymes only work with specific substrates

for enzymes to work the substrates has to fit into the active site for the reaction to be catalysed

enzyme active siets are stereospecific

the active sites only work for one enantimer of a substrate (enantiomers are non superimposible so wont fit in properly)

inhibitors

molecuels with a similar shape to substrates

inhibitors compete with substrates to bind with the active site

when an inhibitor binds to the active site to reaction takes place

if there are more inhibitors to substrates

they will take up more active sites drastically decreasing the rate of reaction

the amount of inhibition is also affected by how strongly the inhibitor bonds

to the active site

some drugs are inhibitors that block the active site of an enzyme

to stop it from working

antibiotics block the active site of bacteria that helps make their cell wall

this causes theri cell wall to weaken till it bursts

active sites of enzymes are VERY specific

so its difficult to findd a drug molecule that will fit into the active site

DNA stands for

Deoxyribonucleic acid

DNA monomer

nucleotide

nucleotides are made up of 3 components

• a phosphate group

• pentose sugar, 2-deoxyribose

• base

phosphate group is an ion with a negative charge

PO₂(OH)₂^-

pentose sugar, sugars with 5 carbons

2-deoxyribose

bases

ADENINE N THYMINE, CYTOSIN N GUANINE

NUCEOTIDE STRUCTURE

nucleotide examples

nucleotides join together to form polynucleotide chains

via sugar-phosphate backbone

a covalent bond is formed between the phosphate group of one nucleotide and the sugar of another

this forms the sugar-phosphate backbone

the sugar-phosphate backbone of DNA is formed via condensation polymerisation

a water molecule is lost and a covalent phosphodiester bond is formed

DNA is formed from 2 polynucleotide strands

they spiral together to form a double helix structure held by hydrogen bonds between bases

Adenine always COMPLIMENTARY to thymine A-T

guanine always COMPLIMENTARY to cytosine C-G

complimentary base pairing is due to the arrangement of atoms in the base molecules

which are capable of forming hydrogen bonds

hydrogen bonds

form between partial positive hydrogen atoms and partially negative oxygen/nitrogen/fluorine atoms which are the right distance apart

adenine and thymine can form 2 hydrogen bonds

guanine and cytosine can form 3 hydrogen bonds

non complimentary base parings would put partialy charged atoms too close together making them repel

OR too far apart OR the bonding wouldnt line up properly

the double helix structure of DNA is important

as it twists so that the bases are in the right alignment and the right distance apart for the complementary base pairs to form

cisplatin

A platinum complex with 2 chloride ligands and 2 ammonia ligands

cisplatin is square planar, there are only 2 types of molecules attached ot Platinum making it CIS/TRANS

chloride ions are on the same plane to its a CIS molecule

cancer

caused when cells mutate and there is uncontrolled cell division forming tumours

inorder for cells to divide

Their DNA needs to replicate

2 strands of the DNA double helix must unwind

so they can be used as templates for DNA replication

Cisplantin stops DNA replication

thus halting uncontrolled cell division

how cisplatin works PART 1:

• a nitrogen atom on guanine base forms a coordinate bond with cisplatin’s platinum ion

• the guanine base replaces a chloride ion ligand

• this process is called ligand replacement reaction

how cisplatin works PART 2:

• a second nitrogen atom on a different guanine base (from the same/opposite strand) replaces the second chloride ion in ligand substitution

the presence of the cisplatin complex bound to the DNA strands cause the strand to kink

this means the DNA strands can’t unwind and be copied properly so cannot replicate

UNFORTUNATELY cisplatin binds to the DNA of healthy cells aswell and tumour cells

this is a problem for healthy cells that undergo replication frequently like hair cells and blood cells

cisplatin stops healthy cells from replicating the same wat is stops tumour cells

this means cisplatin can cause hair loss and supress the immune system, which is controlled by white blood cells and cause kidney damage

these side effects can be lessened by giving patients LOW dosages of Cisplatin

they can also be reduced by targeting the tumour cells directly so healthy cells aren’t attacked

cisplatin is still used as chemotherapy

because the long term advantages outweight the short term disadvantages