Amino acids, proteins and DNA

phosphate group

A chemical group consisting of a phosphorus atom bonded to four oxygen atoms; important in energy transfer. the group is an ion because of the negative charge on one of the oxygens

polynucleotide

A polymer consisting of many nucleotide monomers in a chain; nucleotides can be those of DNA or RNA.

complement base pairing

A-T and C-G pair together because the molecules have the right structure to form hydrogen bonds with each other

DNA structure

DNA consists of two long chains of nucleotides twisted into a double helix and joined by hydrogen bonds between the complementary bases adenine and thymine or cytosine and guanine (A-T) (C-G)

Enzymes

Enzymes speed up reactions by acting as biological catalysts. Enzymes are proteins but some molecules have non protein components. The molecules that enzymes act on are known as substrates the substrate fits into the active site each enzyme only works with specific substrates

Dipeptide

Two amino acids bonded together if the 2 combining amino acids are different then 2 different dipeptides will be formed because the amino acids can join either way round

inhibitors

molecules that have a similar shape to substrates can bond to the active site and act as enzyme inhibitors

pentose sugar

a five-carbon sugar molecule found in nucleic acids All pentose sugars found in DNA are 2 deoxyribose

Zwitterion

a molecule or ion having separate positively and negatively charged groups.(a dipolar ion)

cisplatin as an anti cancer drug

a nitrogen atom in a guanine base forms a coordinate bond with cisplatin's platinum ion and this replaces one of cisplatins chloride ligands this can happen with the other chloride ion too this makes it so the strands cant unwind properly so cant be copied

hydrolysis to break down dipeptides

add 6 mol/dm-3 hydrochloric acid and then heat the mixture under reflux for 24 hours

primary structure of protein

amino acid sequence

chirality

amino acids are normally chiral molecules due to having 4 different groups attached to the central carbon

disulfide bonds

an amino acid that is part of a protein is called a residue disulfide bonds occur between residues of the amino acid cysteine. cysteine contains a thiol group (-SH) this group can lose its H and join to form a disulfide S-S bond with another thiol group. these bonds link together different parts of the chain and help stablilise a tertiary structure

peptide link

bond that forms between amino acids

DNA

deoxyribonucleic acid contains all the genetic information of an organism

Base(DNA)

each nucleotide contains one of the four bases: Adenine, Cytosine, Guanine and Thymine

Naming amino acids

find the longest carbon chain that includes the carboxylic acid group and write its name down number the carbons in the chain starting from the carboxylic acid as 1 write down the positions of NH2 groups and show there positions with amino write down the names of other functional groups and say which carbon they are on

sugar-phosphate backbone formation

formed by condensation polymerisation, a molecule of water is lost and a covalent phosphodiester is formed

Amino acid

has 2 functional groups; Amino group(NH2) and a carboxyl group (COOH) the structure of all amino acids is the same apart from the r side group. Amino acids are amphoteric(can be acid or base)

hydrogen bonds in proteins

hydrogwn bonding holds proteins in shape exists between polar groups such as -OH and -NH2

secondary structure of protein

protein structure is formed by folding and twisting of amino acid chain this is due to the peptide links forming hydrogen bonds with each other it can either be an alpha helix or a beta pleated sheet

tertiary structure of protein

protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3D structure this is due to extra bonds forming between parts of the peptide chain

proteins

proteins are condensation polymers of amino acids joined together by peptide links the chain is put together by condensation reaction and broken down by hydrolysis reactions

Nucelotide

repeating monomers in DNA and RNA; consist of a phosphate group, pentose sugar 2 deoxyribose, and a base

separating mixtures of amino acids

since different amino acids have different R groups they have different solubilities this means they can be identified easily through thin layer chromatography ninhydrin solution is sprayed on the plates as amino acids aren't coloured this gives them a purple colour you can identify the amino acid by working out the Rf value and using a table Rf = distance travelled by spot/distance travelled by solvent

use of inhibitors as drugs

some drugs are inhibitors that block the active site and stop it from working e.g. antibiotics block the active site of an enzyme in bacteria its very hard to produce drugs cause the inhibitor has to be perfect for the active site then only one enantiomer will fit in because active site are usually steriospecific

adverse effects

unfortunately cisplatin bonds to dna of normal cells too this can cause hair loss and damage the immune system

Zwitterions- Amino acids

zwitterions only exist near an amino acids isoelectric point this is the PH where where the overall charge on the amino acid is 0 an amino acid becomes a zwitterion when its amino group is protonated to NH3+ and its COOH group is de-protonated to COO- in more acidic conditions than the isoelectric point the NH2 group is likely to be protonated and vise versa with alkaline conditions (deprotonated COOH)