Basic Biology for Bioinformatics: genes as information The central dogma of molecular genetics DNA to RNA to protein to phenotype Protein functions, synthesis

Basic Biology for Bioinformatics:genes as information

The central dogma of molecular geneticsDNA to RNA to protein to phenotype

Protein functions, synthesis and structureRNA synthesis and processingDNA replicationBasics of transmission genetics

Note: many of the figures used in this presentation are copyrighted. Most are taken from "Genetics: From Genes to Genomes" by Hartwell and colleagues (McGraw Hill)

Biology for bioinformatics:

Alignment of pairs of sequencesMultiple sequence alignmentPrediction of RNA secondary structurePhylogenetic predictionDatabase searching for sequencesGene predictionAnalysis of microarray expression dataProtein classificationProtein folding / structure predictionGenome analysis / databasesGenetic variation (haplotypes and allelic association)

What is it about DNA that allows it to carry information?

DNA polymeraseAlberts et al. Fig. 6-36

Molecular genetics: genes as information

DNA -> RNA -> protein.

DNA is digital information.Each nucleotide carries 2 bits of information.

ImplicationsLow-error propagation.Complete representation in digital databases.

Aquisition of genetic information is the raw fuel behind the explosion of bioinformatics

Clelland et al. Nature 399:533. Hiding messages in DNA microdots.

"For it is not cell nuclei, not even individual chromosomes, but certain parts of certain chromsomes from certain cells that must be isolated and collected in enormous quantities for analysis; that would be the precondition for placing the chemist in such a position as would allow him to analyze [the hereditary material] more minutely than the morphologists."

- Theodor Boveri 1904

If the information in DNA is contained in single molecules, how can we know about it?

We reduce the complexity of the DNA by amplification and use the power of complementarity to detect specific sequences by hybridization.

Determination of the chromosomal location of TGx in the human genome by fluorescent in situ hybridization.(from Daniel Aeschlimann's web site (Univ. of Wales)http://www.uwcm.ac.uk/study/dentistry/bds/staff/aeschlimann.htm

from Konstantin V. Krutovskii and David B. Neale 2001"Forest Genomics for Conserving Adaptive Genetic Diversity"

Microarrays

ArrayScanVisualizeAnalyze

Photolithographic arrays(Affymetrix)

from www.affymetrix.com

Each spot has an oligo with a distinct sequence

Homologous proteins conserve elements of genetic information (sequence).

New gene functions can arise from pre-existing gene functions

Related genes retain sequence similarity.

DNA to RNA to protein to phenotype

Proteins:enzymes alkaptonuria

phenylketonuriaphenylalanine buildup in the brain can cause mental retardation


Proteins:regulators


Structural proteins

Ehlers-Danlos syndrome (joint hypermobility) is one of the phenotypes associated with mutations in genes encoding collagen.


Proteins

What do they do?

see http://www.ncbi.nlm.nih.gov/cgi-bin/COG/palox?fun=all


DNA to RNA to protein





protein

Hydrogen bonds within the protein and the rigidity of the peptide bond are critical determinants of protein structure.


Molecular Biology of the Cell.1994. Figure 3-30 -helix


Molecular Biology of the Cell.1994. Figure 3-29

ß-sheet

NCBI provides information about proteins

GenBank flat file format for HA oxidase

GenBank fasta file format for HA oxidase

Links to other information about HA oxidase

The HA oxidase gene and its flanking region on chromosome 3q21

OMIM: Alkaptonuria is caused by mutations in HA oxidase

Conserved Domains

Three-dimensionalstructure of the protein, if known, can be viewed.

Lectures 8 and 35 will cover types of mutation in detail

Gene density in selected genomesSpecies Genome size Gene # Ave. Size

(Mb.)

Eschericia coli 4.7 4,300 1.1 kb.

Saccharomyces cerevisiae 12.1 6,000 2.0 kb.

C. elegans 97 16,000 6.0 kb.

Arabidopsis 115 25,500 4.5 kb.

Drosophila melanogaster 120 13,600 8.8 kb.

Homo sapiens 3,200 75,000 ? 40.0 kb.30,000 100.0 kb.

CDS (coding sequence) sizes do not vary much at all, between 1.3 and 1.5 kb.

What's in the genome besides genes:

introns

What's in the genome besides genes:

remote regulatory DNA


Lecture 14 will cover transcription in detail



DNA to RNA





DNA must be maintained. Natural processes can degrade the information in the DNA

Molecular Biology of the Cell, third edition, panel 1-1

Cells and organelles

4C 46 chromosomes

each with 2 duplexes

4C 92 chromosomes

2C 46 chromosomes

per cell

Mitosis: heterozygosity is maintained

Meiosis results in new combinations of alleles

Mendel's laws of segregation and independent assortment come from meiosis

A

Aa

a

a

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a

a

A

A

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B

Bb

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B

Recombination

A

Aa

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bB

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Measuring rates of recombination.

Formal definition of linkage disequilibrium

If two loci have alleles A1, A2 with frequencies p1, p2 and B1, B2 with frequencies q1, q2, there are four possible haplotypes (A1B1, A1B2, A2B1, and A2B2). Let these frequencies be f1,1, f1,2, f2,1, f2.2.

If there is no linkage disequilibrium, then f1,1 = p1 q1 , f1,2 = p1 q2 , and so on.

There are a number of measures of linkage disequilibrium. One of them is D = f1,1f2.2 - f1,2f2.1.

Interpreting allelic associationThe general case is described by an isolated population that has high frequencies (p and r respectively) of both a disease-causing allele D1 and an unlinked marker M1. The descendents of people who move from that population to a second population with different frequencies will show association between D1 and M1 even though they are not linked.

p = .02, r = .5p = .0001r = .1

The disease-causing allele is at a high frequency in a small village.

Affected people in a nearby city are more likely to have other alleles, such as M1, that are found in elevated frequencies in that village merely because they have ancestors from that village.

Biology for bioinformatics:

Alignment of pairs of sequencesMultiple sequence alignmentPrediction of RNA secondary structurePhylogenetic predictionDatabase searching for sequencesGene predictionAnalysis of microarray expression dataProtein classificationProtein folding / structure predictionGenome analysis / databasesGenetic variation (haplotypes and allelic association)

Next time:more about the status of those problems and current state of the art methods.

Tutorial II: Monday, May 10, 2118 CSIC, 2:00 - 3:45

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Basic Biology for Bioinformatics: genes as information The central dogma of molecular genetics DNA to RNA to protein to phenotype Protein functions, synthesis