• RNA

RNA is similar to DNA chemically. It is usually only a

DNA, RNA, and the Flow of

single strand. T(hyamine) is replaced by U(racil)

Information
”
• Several types of RNA exist for different functions in the The central dogma”
Replication
cell.

Transcription Translation

tRNA linear and 3D view: http://www.cgl.ucsf.edu/home/glasfeld/tutorial/trna/trna.gif

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Overview of DNA to RNA to Protein Proteins

• Proteins are
polypeptides (strings of

•
amino acid residues)
Represented using
strings of letters from
an alphabet of 20:

•
AEGLV…WKKLAG
Typical length
• A gene is expressed in two steps 50…1000 residues
1) Transcription: RNA synthesis
Urease enzyme from Helicobacter pylori
2) Translation: Protein synthesis
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How DNA/RNA codes for protein? How DNA/RNA codes for protein?

• DNA alphabet contains four •Three of the possible

letters but must specify triplets specify ”stop

•
protein, or polypeptide
sequence of 20 letters.
Dinucleotides are not
• translation”
Translation usually starts at
triplet AUG (this also codes

•
enough: 42 = 16 possible
dinucleotides
Trinucleotides (triplets)
• for methionine)
Most amino acids may be
specified by more than

•
allow 43 = 64 possible
trinucleotides
Triplets are also called
• triplet
How to find a gene? Look
for start and stop codons
codons (not that easy though)

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Proteins: Workhorses of the Cell 3. Where does the variation in genomes come

• • 20 different amino acids

different chemical properties cause the protein chains to fold up into
specific three-dimensional structures that define their particular
• from?
Prokaryotes are typically

•
haploid: they have a single
functions in the cell.
Proteins do all essential work for the cell
• (circular) chromosome
DNA is usually inherited
•• • build cellular structures
digest nutrients vertically (parent to

• execute metabolic functions

Mediate information flow within a cell and among cellular • daughter)
Inheritance is clonal

• communities.
Proteins work together with other proteins or nucleic acids as
•
• Descendants are faithful
copies of an ancestral DNA

• "molecular machines"
structures that fit together and function in highly specific, lock-
Variation is introduced via
mutations, transposable
and-key ways. elements, and horizontal Chromosome map of S. dysenteriae, the nine rings
describe different properties of the genome
transfer of DNA http://www.mgc.ac.cn/ShiBASE/circular_Sd197.htm

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Mitosis and meiosis Recombination and variation

• Sexual organisms are usually • Allele is a viable DNA coding
• diploid
Germline cells (gametes) contain
occupying a given locus

• N chromosomes
Somatic (body) cells have 2N • (position in the genome)
In recombination, alleles from

• chromosomes
Meiosis: reduction of
parents become suffled in
offspring individuals via

•
chromosome number from 2N to
•
N during reproductive cycle
One chromosome doubling is
chromosomal crossover over
Allele combinations in offspring

•
Major events in meiosis
followed by two cell divisions http://en.wikipedia.org/wiki/Meiosis are usually different from
Mitosis: growth and development

• of the organism
One chromosome doubling is
http://www.ncbi.nlm.nih.gov/About/Primer
• combinations found in parents
Recombination errors lead into
followed by one cell division additional variations Chromosomal crossover as described by
T. H. Morgan in 1916

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Recombination frequency and linked genes Recombination and longer time scales

• Genetic marker: some DNA sequence of interest

Conserved synteny

Chromosome i, species B
Syntenic blocks and segments

Chromosome i, species B
(e.g., gene or a part of a gene)
g2B g1B g3B g5B g4B g1B g2B g3B

• Recombination is more likely to separate two distant Chromosome j, species C

g1C g2C
syntenic block
Chromosome j, species C
g3C g4C g5C
syntenic segment

g1C g2C g3C

markers than two close ones

• Linked markers: ”tend” to be inherited together

••• Assume that species B and C are descendants of A
Conserved synteny: group of genes linked in both B and C

• ••
Conserved segment: conserved synteny with same gene order
Marker distances measured in centimorgans: 1 Syntenic segment: group of markers (!) linked in both B and C
Syntenic block: set of syntenic segments which may contain set
centimorgan corresponds to 1% chance that two
inversions and duplications
markers are separated in recombination

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Biological string manipulation References

• Errors get introduced to DNA during replication •

••
Richard C. Deonier, Simon Tavaré and Michael S. Waterman. Computational
Genome Analysis, An Introduction. Springer, 2005.
Daniel Sam, “Greedy Algorithm” presentation.
• Deletion: removal of one or more contiguous bases
••
Glenn Tesler, “Genome Rearrangements in Mammalian Evolution:

• (substring) Lessons from Human and Mouse Genomes” presentation.

•
Ernst Mayr, “What evolution is”.

•
Insertion: insertion of a substring Neil C. Jones, Pavel A. Pevzner, “An Introduction to Bioinformatics Algorithms”.

•
Alberts, Bruce, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter
Segmental duplication: insertion of a copy of a DNA region
Walter. Molecular Biology of the Cell. New York: Garland Science. 2002.

• into a different location

•
Oryx Press. 1994.
Mount, Ellis, Barbara A. List. Milestones in Science & Technology. Phoenix: The

•
Inversion: reversal of substring
•
Voet, Donald, Judith Voet, Charlotte Pratt. Fundamentals of Biochemistry. New

•
Translocation: removal and insertion of a substring Jersey: John Wiley & Sons, Inc. 2002.

•
Campbell, Neil. Biology, Third Edition. The Benjamin/Cummings Publishing
Point mutation: substitution of a base Company, Inc., 1993.
Snustad, Peter and Simmons, Michael. Principles of Genetics. John Wiley & Sons,
Inc, 2003.

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