Introduction to molecular

biology

(in one hour!!)

Stephen Edwards
 Overview
Overview of the cell
Different sizes/functions
Organised structure
Bacterial genetics are different
Eukaryotic cell
 DNA
Contained in the nucleus
Arranged in 22 chromosomes, plus two
sex chromosomes
Two copies of each
99.9% identical to other humans, 98% to
chimp!
Around 2m DNA, enough to travel to sun
and back 600 times!
Therefore, very tightly packed
5' C-G-A-T-T-G-C-A-A-C-G-A-T-G-C 3'
| | | | | | | | | | | | | | |
3' G-C-T-A-A-C-G-T-T-G-C-T-A-C-G 5'
 DNA function
Carries the blueprint for life
Duplication for new cells
Make proteins for biological functions:
 Gene structure
Genes must have:
Exons
Start site
Control region
 mRNA
DNA is grouped into threes (codons)
AGTTTTGGGCCCAAA
Start and stop codons
mRNA is then modified
and travels out of the nucleus
mRNA splicing
Alternative splicing
 Translation
Uses mRNA as template to make proteins
Occurs in ribosomes
One codon corresponds to one amino acid
 Proteins
Huge proportion of cell (after water)
Many functions:
Structure (e.g. collagen in bone)
Enzymes
Transmembrane receptors
Hormones
Four levels of structure
Protein structure
 Protein interactions
Proteins can form interations:
Proteins (complexes, oligomers)
mRNA
DNA
Proteins can bind to each other depending
on their relative charges and structures
Gene expression regulation
 Common terminology
Genome/proteome
Genotype/phenotype
Pseudogene
Novel protein/gene
Putative gene
Locus/Allele/Chromosome region
Dominant/Recessive
Homologous
Symbol
cDNA
Motif
Dalton (Da or kDa)
 Common abbreviations
EST expressed sequence tag
SNP single nucleotide polymorphism
ORF open reading frame
UTR untranscribed region
 Experimental techniques
Cut, change, knockout genes
Transgenics
Sequence genes and proteins
Over-express proteins
Microarrays
We have used the yeast two-hybrid system to identify proteins that interact with the
intracellular portion of the hepatocyte growth factor (HGF) receptor (Met). We isolated a
human cDNA encoding a novel protein of 68 kDa, which we termed FAP68. This protein is
homologous to a previously described FK506-binding protein-associated protein, FAP48,
which derives from an alternative spliced form of the same cDNA, lacking an 85-nucleotide
exon and leading to an early stop codon. Here we show that epithelial cells, in which the
HGF receptor is naturally expressed, contain FAP68 and not FAP48 proteins. FAP68 binding
to Met requires the last 30 amino acids of the C-terminal tail, which are unique to the HGF
receptor. Indeed, FAP68 does not interact with related tyrosine kinases of the Met and
insulin receptor families. FAP68 interacts specifically with the inactive form of HGF receptor,
such as a kinase-defective receptor or a dephosphorylated wild type receptor.

Evidence

In vivo, endogenous FAP68 can be coimmunoprecipitated with the HGF receptor in the
absence of stimuli and not upon HGF stimulation. Thus, FAP68 represents a novel type of
effector that interacts with the inactive HGF receptor and is released upon receptor
phosphorylation. Free FAP68 exerts a specific stimulatory activity toward the downstream
target p70 S6 protein kinase (p70S6K). Significantly, nonphosphorylated HGF receptor
prevents FAP68 from stimulating p70S6K. These data suggest a role for FAP68 in coupling
HGF receptor signaling to the p70S6K pathway.
 Future of molecular biology
Personalised medicine
Target-specific drugs (e.g. adipose tissue)
Gene therapy
Comparative genomics
 References
Molecular biology information
Biology, Campbell and Reece (6th Ed.), Very readable general biology textbook
www.ebi.ac.uk/2can, good introduction to bioinformatics and molecular biology
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.html - online biology book
http://biology-pages.info, good glossary/information site
http://www.genomicglossaries.com/
http://www.gene.ucl.ac.uk/nomenclature/guidelines.html, defines the nomenclature for human
genes
Databases
www.ebi.uniprot.org, excellent protein sequence database
www.ncbi.nih.gov, numerous protein/genome databases
www.ensembl.org, information on genes/proteins/exons of completed genomes
http://www.ebi.ac.uk/embl/, European gene sequence databank
Michael Y. Galperin, The Molecular Biology Database Collection: 2005 update, NAR
www.bioinfo.no/links, list of useful biological links
Gene/Protein naming conventions
Bioinformatics. 2005 Jan 15;21(2):248-56. Epub 2004 Aug 27. Gene name ambiguity of
eukaryotic nomenclatures.Chen L, Liu H, Friedman C.
Two hybrid system