Proteins, amino acids and DNA

Describe the optical activity of amino acids

All, expect glycine mare chiral as there are 4 different groups around the C - will rotate plane-polarised light

Give the general structure of amino acids

NH2 - CHR - COOH

Describe the structure of acidic amino acids

Have an extra carboxylic acid group on R group

Describe the structure of basic amino acids

Have an extra amine group on R group

Define zwitterion

The form amino acids exist as even in solid state

Describe the structure of zwitterions

Compounds with no overall electrical charge, but which contain separate parts which are positively and negatively charged

Explain the relatively high melting points of amino acids

due to ionic interactions between zwitterions as opposed to the weaker hydrogen bonding that would occur in the no-charge form

Describe what happens when you add an alkaline to a solution of amino acid

The hydrogen ion is removed from the -NH3+ group and reacts with OH- ions to produce water - the amino acid is now a negative ion, not a zwitterion

Describe what happens when you add acid to a solution of amino acid

The COO- part of the zwitterion picks up a hydrogen ion to form -COOH - the amino acid is now a positive ion, not a zwitterion

Describe the structure of a DNA nucleotide

A phosphate ion bonded to 2-deoxyribose which in turn is bonded to one of 4 nitrogenous bases

What molecule is removed when 2 nucleotides are joined?

Water

Describe the structure of a single strand of DNA

A polymer of nucleotides linked by covalent bonds between the inorganic phosphate group of one and the sugar of another nucleotide

How does DNA exist as 2 complementary strands?

Due to hydrogen bonding between complementary base pairs, arranging the strands in a double helix

How many hydrogen bonds form between adenine and thymine?

2

How many hydrogen bonds form between cytosine and guanine?

3

Give a use of cisplatin

Anti cancer drug

Draw the structure of cisplatin

Why does only cisplatin and not transplatin work at preventing DNA replication?

As two chloride ions are displaced and the molecule joins onto the DNA - stops the replication of cancerous cells

How does cisplatin prevent DNA replication in cancerous cells?

By ligand replacement reaction with DNA in which a dative covalent bond is formed between platinum and a nitrogen atom on guanine

Why can cisplatin have adverse effects?

Can also prevent the replication of healthy cells by bonding on to healthy DNA (can be minimised by giving cis-platin in small doses)

Why can a stereo specific active site only bond to one enantiomer of a substrate or drug?

The substrate molecule must bond to the amino acid side chains through a variety of interactions, which are highly specific

How do drugs act as enzyme inhibitors?

Block the active site (often binding strongly so stopping the substrate attaching to the enzyme)

What can be used to design enzyme inhibiting drugs?

Computers

Describe the structure of a protein

A polymer/sequence of amino acids joined by peptide links

Describe the primary structure of proteins

The sequence of amino acids joined by condensation reactions with peptide links

Describe the secondary structure of a protein

The basic 3D arrangement of amino acids

Describe an alpha helix structure in proteins

The polypeptide chains coils into a corkscrew shape and is held in place by hydrogen bonds between the H on N-H and O of C=O

Describe the beta pleated sheet structure in proteins

The protein chain folds into parallel strands side by side - held in shape by hydrogen bonds between the H on N-H and O of C=O on the amino acid much further along the chain but in the parallel region

Describe the tertiary structure of a protein

The folding of the secondary structure into more complex shapes

How is the tertiary structure of a protein held together?

By interactions between the R side groups in more distant amino acids eg, hydrogen bonding, Sulfur-sulfur bonds, ionic interactions

Between which amino acids do Sulfur bridges form?

Cysteine

What type of bond are Sulfur bridges?

Covalent