Molecular Genetics

Molecular genetics


03/10/2019

 Denaturation – disruption of bonds and structures in DNA and protein e.g. turning liquid gelatine
into solid jelly. Caused by environment alterations like pH, salt, temp).
 Renaturation – Proteins return to normal when normal environment is set
 Structure of protein dictates function, and amino acid order determines conformation of
protein.
 Monomers are amino acids; proteins are the polymers.
 Amino acids contain amino group, carboxyl group, hydrogen atom, variable R group (side chain)
 PRIMARY STRUCTURE
 R chains differentiate 20 different amino acids – 4 categories are polar (hydrophobic), non-polar
(hydrophilic), acidic, and basic.
 Nonpolar (glycine, proline), polar (serine, tyrosine, glutamine),
 Acidic (carboxyl acid, negative charge) and basic (hydrogen, positively charged) are electrically
charged
 Amino acids exist as stereoisomers (L or D mirror image forms)
 mammalian proteins made of L-isomers
 Residue or moiety – component amino acid in a polypeptide chain
 1⁴ can mean the 4th amino acid etc. etc. with any other number.
 Carboxyl group and amine cause condensation reaction
 Peptides – links between amino acids.
 SECONDARY STRUCTURE
 Alpha helix (tight coiled polypeptide backbone core)
 Beta pleated sheet formed when two or more polypeptides come side by side
 TERTIERY STRUCTURE
 3-D conformation. Reveals about function and evolution.
 R groups and R groups interact, and R groups and backbones.
 Bonds: hydrogen , ionic, covalent (disulphide bridges), hydrophobic (interior of protein)
 Proline’s R group connects to amino group and forms natural kink in polypeptide. Tertiary
structure, good for making drugs and vaccines.
 X-ray crystallographic studies last years, nuclear magnetic resonance is shorter.
 QUATERNARY STRUCTURE
 4 tertiary structures coming together (e.g. insulin)
 Forms globular and fibrous proteins. not in all proteins.
 Globular – water soluble, compact
 People with anaemia can struggle with these structures
 Fibrous – water insoluble e.g. collagen
 Protein binding examples : antibodies, enzymes, neurotransmitters
 Protein folding occurs spontaneously and are aided by chaperone proteins (chaperonins),
providing ideal environment for folding.
 Conformational change – change in shape once bound to something

 Structural layers in the formation of a protein – primary, secondary, tertiary, quaternary
structures. All build up from amino acids in a condensation reaction to form peptide bonds. Each
amino acid could be polar, nonpolar, acidic, or basic in their R groups. Alpha helices and beta

, pleated sheets join in secondary structure. Tertiary 3-D structure are secondary structures joined
by covalent bonds (disulphide bridges), ionic bonds, hydrophobic bonds (interior), and hydrogen
bonds.



10/10/2019

 Mobile phase – liquid or gas, a transporter
 Stationary phase – impedes different components of the solution to different degrees
 Ion exchange chromatography is separation based on charge. Charged molecules are large
proteins, small nucleotides, amino acids. Relies on charge-charge interactions between the
proteins, the two types are: anion exchangers, cation exchangers
 Ions – the same charged molecules
 Cation exchange chromatography – positively charged molecules are attracted to a
negatively charged solid support. Commonly used resins are: S-resin, sulphonyl group
derivatives,
 Anion exchange chromatography – negatively charged molecules are attached to a positively
charged solid support. Common resins are: Q-resin, a quaternary amine.
 Oligonucleotide – a big stretch of DNA
 Disadvantages of gel flowmetry – proteolysis (the breakdown of proteins) occurs , large size
columns mean large volumes of eluent and higher cost, non-ideal flow around beads
 HIS (X6), GST, FLAG TAGs are all specific unique sequences that do not exist in any human
genomes but, when attached to a protein, it allows us to see where the protein is going.
 Epitope – short sequence of peptides
 Polyclonal antibodies – derived from B cell clones; recognises only a single epitope on an
antigen.
 Affinity chromatography has 3 components; matrix, ligands, spacer or covalent link. Has the
highest costs due to the components being so expensive i.e. antibodies cost lots.



17/10/2019

 Restriction enzymes – cleaves certain DNA sequences at a particular point.
 Dyes to stain DNA will bind to the specific DNA sequences in order to find certain genetic
makeup.
 Southern blotting (DNA) – Detection of DNA molecules with transfer. DNA is cut using Res ->
DNA is denatured -> needs to be separated onto an agarose gel or polyacrylamide gel ->
transferred onto a solid support etc. Uses UV light for detection.
 Northern blotting (RNA)– Detection of RNA (transcript) molecules for blotting and probing.
RNA extracted from cells fractionated on an agarose gel -> transferred to a nylon (or similar)
membrane -> hybridized to a solution of a radiolabelled cDNA probe corresponding to the
mRNA of interest. Measurement in base pairs.
 Western blotting (Proteins) – Detecting proteins following transfer to membranes after
polyacrylamide gel electrophoresis. Proteins extracted through cell lysis, and the proteins
are denatured. Blocking is used to avoid membrane cross-reactions.
 KDAs – kilodalton (atomic mass unit)