Introduction to molecular biology doc

Introduction to molecular
Introduction to molecular
biology…
biology…
(…in one hour!!)
(…in one hour!!)
Stephen Edwards
Stephen Edwards


Overview
Overview
Overview of the cell
Overview of the cell
Different sizes/functions
Different sizes/functions
Organised structure
Organised structure
Bacterial genetics are different
Bacterial genetics are different


Eukaryotic cell
Eukaryotic cell


DNA

DNA
Contained in the nucleus
Contained in the nucleus
Arranged in 22 chromosomes, plus two
Arranged in 22 chromosomes, plus two
sex chromosomes
sex chromosomes
Two copies of each
Two copies of each
99.9% identical to other humans, 98% to
99.9% identical to other humans, 98% to
chimp!
chimp!
Around 2m DNA, enough to travel to sun
Around 2m DNA, enough to travel to sun
and back 600 times!
and back 600 times!
Therefore, very tightly packed
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
DNA function
Carries the blueprint for life
Carries the blueprint for life

Duplication for new cells
Duplication for new cells
Make proteins for biological functions:
Make proteins for biological functions:


Gene structure
Gene structure
Genes must have:
Genes must have:
–
Exons
Exons
–
Start site
Start site
–
Control region
Control region


mRNA
mRNA
DNA is grouped into threes (codons)
DNA is grouped into threes (codons)
AGTTTTGGGCCCAAA
AGTTTTGGGCCCAAA
Start and stop codons
Start and stop codons
mRNA is then modified…

mRNA is then modified…
…
…
and travels out of the nucleus
and travels out of the nucleus


mRNA splicing
mRNA splicing


Alternative splicing
Alternative splicing


Translation
Translation
Uses mRNA as template to make proteins
Uses mRNA as template to make proteins
Occurs in ribosomes
Occurs in ribosomes
One codon corresponds to one amino acid
One codon corresponds to one amino acid


Proteins
Proteins
Huge proportion of cell (after water)
Huge proportion of cell (after water)
Many functions:

Many functions:
–
Structure (e.g. collagen in bone)
Structure (e.g. collagen in bone)
–
Enzymes
Enzymes
–
Transmembrane receptors
Transmembrane receptors
–
Hormones
Hormones
Four levels of structure
Four levels of structure


Protein structure
Protein structure


Protein interactions
Protein interactions
Proteins can form interations:
Proteins can form interations:
–
Proteins (complexes, oligomers)
Proteins (complexes, oligomers)
–
mRNA

mRNA
–
DNA
DNA
Proteins can bind to each other depending
Proteins can bind to each other depending
on their relative charges and structures
on their relative charges and structures


Gene expression regulation
Gene expression regulation


Common terminology
Common terminology
Genome/proteome
Genome/proteome
Genotype/phenotype
Genotype/phenotype
Pseudogene
Pseudogene
Novel protein/gene
Novel protein/gene
Putative gene
Putative gene
Locus/Allele/Chromosome region
Locus/Allele/Chromosome region
Dominant/Recessive
Dominant/Recessive

Homologous
Homologous
Symbol
Symbol
cDNA
cDNA
Motif
Motif
Dalton (Da or kDa)
Dalton (Da or kDa)


Common abbreviations
Common abbreviations
EST
EST
expressed sequence tag
expressed sequence tag
SNP
SNP
single nucleotide polymorphism
single nucleotide polymorphism
ORF
ORF
open reading frame
open reading frame
UTR
UTR
untranscribed region
untranscribed region

Experimental techniques
Experimental techniques
Cut, change, knockout genes
Cut, change, knockout genes
Transgenics
Transgenics
Sequence genes and proteins
Sequence genes and proteins
Over-express proteins
Over-express proteins
Microarrays
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
Future of molecular biology
Personalised medicine
Personalised medicine
Target-specific drugs (e.g. adipose tissue)
Target-specific drugs (e.g. adipose tissue)
Gene therapy
Gene therapy
Comparative genomics
Comparative genomics


References
References
Molecular biology information
Molecular biology information
–
‘
‘
Biology’, Campbell and Reece (6
Biology’, Campbell and Reece (6
th
th

Ed.), Very readable general biology textbook
Ed.), Very readable general biology textbook
–
www.ebi.ac.uk/2can, good introduction to bioinformatics and molecular biology
www.ebi.ac.uk/2can, good introduction to bioinformatics and molecular biology
–
/> /> - online biology
- online biology
book
book
–
o, good glossary/information site
o, good glossary/information site
–
/> />–
defines the nomenclature for
defines the nomenclature for
human genes
human genes
Databases
Databases
–
www.ebi.uniprot.org, excellent protein sequence database
www.ebi.uniprot.org, excellent protein sequence database
–
www.ncbi.nih.gov, numerous protein/genome databases
www.ncbi.nih.gov, numerous protein/genome databases
–
www.ensembl.org, information on genes/proteins/exons of completed genomes
www.ensembl.org, information on genes/proteins/exons of completed genomes

–
European gene sequence databank
European gene sequence databank
–
Michael Y. Galperin,
Michael Y. Galperin,
The Molecular Biology Database Collection: 2005 update, NAR
The Molecular Biology Database Collection: 2005 update, NAR
–
www.bioinfo.no/links, list of useful biological links
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
Two hybrid system