Beyond the nuclear genome

Review
Summary: molecular biology
principles.
MLS210
 DNA
Contained in the nucleus
Arranged in 22 chromosomes, plus two
sex chromosomes
Two copies of each
Around 2m DNA, enough to travel to sun
and back 600 times!
Therefore, very tightly packed
DNA packaging
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'
 Gene structure
Genes must have:
– Exons
– Start site
– Control region
– Stop
 mRNA
DNA is grouped into threes (codons)
AGTTTTGGGCCCAAA
Start and stop codons
mRNA is then modified…
…and travels out of the nucleus
mRNA 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
Gene expression regulation
 Beyond the nuclear genome
The mitochondrial genome
Circulating Nucleic acids
What are the applications of circulating
DNA/RNA
 Circulating cell free DNA ( CcFDNA)

Circulating cell-free DNA (cfDNA) is released as

single-stranded DNA and double-stranded DNA
body fluids, including the blood, sputum, urine,
cerebrospinal fluid, or ascites
Origin: apoptotic and necrotic cells.

In healthy individuals, plasma cfDNA is believed to derive primarily from

apoptosis of normal cells of the hematopoietic lineage, with minimal
contributions from other tissues
How do you then differentiate martenal and fetal DNA in the blood stream?
How do you then differentiate maternal and fetal DNA
in the blood stream?
• fetal DNA is shorter than maternal DNA.
• Methylation patterns are different: fetal DNA is less methylated compared to highly
methylated maternal dna
• genes that are expressed in the placenta, but not the mother, and are therefore
specific to the fetus.

Subsequent identification of messenger RNA from these genes in maternal

circulation must therefore be fetal specific.

However, it is still not possible to extract pure fetal DNA and so currently prenatal
diagnosis using cell-free fetal DNA is limited to the detection or exclusion of genetic
sequences that are not present in the mother,
• determination of fetal sex,
• fetal rhesus D status in D-negative mothers,
• genetic conditions inherited from the father or arising de novo.
Examples of aneuploidy: trisomy 21
The mitochondrial DNA ( MtDNA)
 The mitochondrial DNA ( MtDNA)
• MtDNA in Mt matrix
• Circular, Ds, 16,569 Bp, not
packaged in chromatin
• 37 genes: 13 proteins,
22tRNA, 2rRNA
• Mt genome mode of
inheritance is martenal
• Daughter cells receive similar
but not identical copies of
MtDNA
• High mutation rates

• Classic Mitochondrial syndromes: leber hereditary optic neuropathy: loss of

vision in both eyes, postlingual deafness ( occurs after 3yrs)
• Affect tissues with high energy demands: brain,eyes,cardiac muscles
• Other syndromes: diabetes, alzhermer,parkinsons disease
Mitochondrial inheritance:
• mitochondrial inheritance does not obey the classic
rules of genetics.
• Persons with a mitochondrial disease may be male
or female but they are always related in the
maternal line.
• no male with the disease can transmit it to his
children.
 Mitochondrial inheritance
Mitochondrial DNA useful in human rights cases, as it is a great a tool for
establishing the identity of individuals who have been separated from
their families. This approach has been very successful for the following
reasons:

• A person's mitochondrial DNA sequence is shared with all of his or her

maternal relatives, allowing a genetic match even with few surviving
relatives.
• Mitochondrial DNA varies greatly between unrelated families, but it
should be nearly identical among closely related individuals.
• A given cell contains many more copies of its mitochondrial DNA than
its nuclear DNA, which allows researchers to more easily obtain and
analyze mitochondrial DNA samples from deceased relatives.
 Common terminology
Genome/proteome
Genotype/phenotype
Locus/Allele/Chromosome region
Dominant/Recessive
Homologous
cDNA
Gene sequence
Gene
ORF
 Common abbreviations

SNP single nucleotide polymorphism

ORF open reading frame
UTR untranscribed region
 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.