Amino acids, proteins, and intermolecular forces

Structure of an amino acid

Central/ alpha carbon has 4 different groups attached to it: the carboxylic acid group and the amino group, which make up the core backbone of the protein, there is also a hydrogen atom and the side chain or R group which is different for each amino acid, and gives each amino acid its unique biochemical properties.

Why do proteins exclusively contain L isomer amino acids

biochemical reactions and enzymes are stereospecific

Non-chiral amino acid

Glycine - its R group is a single hydrogen atom which is the same as its other hydrogen atom, so central carbon only has 3 different groups attached to it

2 main rules that govern how a protein folds

Hydrophobic residues are largely buried inside the protein away from the water

Hydrogen bonds and electrostatic interactions are maximised.

Disulphide bridge

Covalent bonding between the sulfur in the R group of cysteine residues.

How do disulphide bridges form?

Through an oxidation reaction, two sulphurs can form a covalent bond known as a disulphide bridge which can then be reversed by reduction.

Salt bridges

Electrostatic attraction between amino acids with R groups of opposite charges

Water van der waals interaction

he oxygen is permanently pulling the electrons away from the hydrogen. Electrons are not fixed in space and will move around, so you may have a transient event where by chance both electrons are by chance on one side of the atom. Making one side transiently slightly negative, and the other transiently slightly positive.

Hydrophobic effect

non-polar hydrophobic regions cluster together in the centre because they want to present the smallest area to the surrounding water they can.

What can R groups effect about an amino acid

Size, shape, Charge, bond, hydrophobicity, Chemical reactivity

Aromatic hydrophobic side chains

have benzine rings.

Polar side chain amino acids

amino acids whose side chains can interact with water. can form H bonds etc. with water.

Examples of amino acids with polar side chains

Serine (OH group), threonine (OH group), cysteine (SH group), asparagine (amide group) and glutamine (amide group).

Examples of amino acids with positively charged side chains

Lysine and Arginine, sometimes histidine (when below neutral pH).

Examples of amino acids with negatively charged side chains

aspartic acid and glutamic acid at normal physiological pH.

Peptide bond formation

The carboxylic acid end of the peptide or amino acid combines with the amino end of another amino acid and through a process called condensation they assemble into a peptide bond.

Where does a peptide bond form?

Between the carbon of the carboxylic acid of one amino acid group on the amino acid, and the nitrogen from the adjacent amino acid

Direction of the peptide bond

The start of the peptide chain is the amino end (N end) and that continues through to the C terminus of the peptide. When writing a peptide sequence you always start at the N end.

How polypeptides become proteins

They fold as a consequence of large numbers of weak interactions - intermolecular and intramolecular forces which drive and stabilise the protein structure.

Salt bridges

When there is an interaction between a carboxylate group and a positively charged group and these come into close contact with one another

Alpha helix

optimises hydrogen bonding between the C=O and the hydrogen from the N-H four amino acids away.

"helix breakers"

proline and glycine

What makes proline a helix breaker

back bonding between the amine group and alpha carbon which means that when in a peptide bond it is kinked in such a way that destabilises the regular structure of the alpha helix

Two forms of beta sheet

antiparallel beta sheet and parallel beta sheet

Difference between antiparallel beta sheet and parallel beta sheets

parallel are less stable because bonding is not as regimented and stable.

4 organic molecules of life

nucleic acids, proteins, carbohydrates and lipids

How many different R groups

20

Chrial molecules

Molecules that can not be superimposed on their mirror image. Chiral objects are mirror images of each other.

L isomer

CORN is clockwise

R isomer

CORN is anticlockwise

Order of bonds strongest to weakest

Covalent, salt bridges, hydrogen bonds, van der waals

What makes glycine a helix breaker

It is too flexible and there is too much flexibility of rotation around the bonding in glycine to stabilise the formation of an alpha helix