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)