3.3.13 Amino acids, proteins and DNA - Chemistry Alevel

Amino acid - simplest R group

R = H in the simplest form whereas all the others have R = an alkyl group.

When is an amino acid optically active/inactive?

All amino acids are optically active except for when R = H.

Why is an amino acid optically active?

The carbon 2 is a chiral carbon and so will rotate plane polarised light and is optically active. Therefore almost all amino acids exist as one enantiomer.

Acid properties of an amino acid

The carboxylic acid group has a tendency to lose a proton (acts as an acid) turning alcohols to esters.

Base properties of an amino acid

The amine group has a tendency to gain a proton (acts as a base) effecting acyl chlorides and halogenoalkanes.

Zwitterion charge

The zwitterion is a dipolar ion which has no net charge.

Physical properties of amino acids - list

High melting point, colourless solids at room temperature, soluble in polar but not non-polar solvents (chromatography).

Physical properties of amino acids - explanation

Amino acids are ionic in nature.

Amino acids chain name - 2 amino acids

Dipeptide

Amino acids chain name - 3 amino acids

Tripeptide

Amino acids chain name - up to 50 amino acids

Polypeptide

Protein amino acid chain - description

A folded peptide with a specific three dimensional lattice.

Reaction between amino acids forming a peptide link - type

Condensation reaction

What is the primary structure of proteins?

The sequence of amino acid units in the chain (the order).

Secondary structure of proteins - what is it determined by?

The hydrogen bonding between the atoms of the peptide links , between the O atom from the carbonyl group and H atom from the amide group.

Why are proteins stable structures?

The large number of hydrogen bonds increases the forces between the proteins and forms stable structures.

2 main types of proteins

α helices (α helix) & β plated sheets

Tertiary structure of proteins - description

The helix or sheet is folded into a characteristic 3-D shape (the tertiary structure) which is held together by various bonds between R groups in the amino acid groups.

Reaction breaking peptide link forming amino acids - type

Hydrolysis as a water is added for each link broken.

Reaction breaking peptide link forming amino acids - catalysts

An acid &/or a substrate-specific enzyme.

Metod of identifying amino acids

TLC (thin layer chromatography) and measuring their Rf values (retention factor).

How do enzymes act as specific catalysts

Enzymes are chiral (& they have a tertiary structure that gives the active site its unique shape). Therefore the active sites are stereospecific as they will only bond to one enantiomer, substrate molecule.

What bonds are in an enzyme-substrate complex?

Hydrogen bonds and ionic groups, such as -NH₃⁺ or -COO⁻, attract the substrate by electrostatic interactions. Amino acids that contain hydrocarbon side chains contribute to bonding with Van Der Waals forces as well.

How do many drugs work?

They block the active site of the enzyme of an organism such as a pathogenic bacterium. It must bond to the active site more strongly than the natural substance to be effective.

How do you design new drugs?

Computer programmes allow chemists to predict the shape of enzymes.

DNA structure - description

DNA exists as two complementary strands arranged in the form of a double helix.

DNA structure - single strand description

A polymer of nucleotides linked by covent bonds between the phosphate group of one nucleotide and the 2-deoxyribose of another nucleotide (add polynucleotide definition).

DNA structure - bases names

Adenine, guanine, cytosine and thymine.

DNA structure - base pairs

Adenine and thymine.

Guanine and cytosine.

DNA structure - sugar name

2-deoxyribose.

DNA structure - bonds between strands

Hydrogen bonds formed between the N-H and O/N on the two bases as the lone pair of electrons on the N or O bonds to the H-N.

Cisplatin - use

Used as a anticancer drug.

Cisplatin - how to prevent DNA replication

A ligand replacement reaction with DNA in which a [coordinate] bond is formed between platinum and a nitrogen atom on guanine. [One of the guanine can form a co-ordinate bond with platinum, replacing one of the ammonia or chloride ligands and then another N on another guanine can also form a co-ordinate bond with the some platinum by replacing the other ligand.] This distorts the shape of the DNA and prevents the DNA from replicating.

Cisplatin - how to minimise dangers?

Use in a very small amount.

Target application to the tumour.

Cisplatin - Benefits

Prevents increased replication of cancer cells.

Cisplatin - Dangers

Side effects, such as; nausea, hair loss, susceptibility to infection.

Kidney damage and nerve damage as enzymes in the body are effected.

How to distinguish between two stereoisomers?

Plane polarised light is rotated in opposite directions for each isomer.