Chapter 1. Molecular Biology and Biological Chemistry

What is Bioinformatics?

Genetic Material: DNA, nucleotide bases (A, T, C, G)

DNA structure, base pairs and hydrogen bonding, orientation, reverse complement

DNA Replication: DNA polymerase

RNA role in cell

Central dogma: transcription, translation, RNA polymerase, ribosomes

Codons: amino acid encodings, read frames,

Transcription process in Prokaryotes vs. Eukaryotes

Eukaryotic genes: intron, exons, splicing, alternative splicing

Translation (elongation) process: tRNA, rRNA, mRNA, anticodon,

Regulation of protein production: regulatory region, untranslated regions, start codon, stop codon, transcription factor, regulatory factor

Protein Structure and function: primary, secondary, tertiary, quaternary

Amino acid R-groups and their properties: polar/nonpolar, hydrophobic/hydrophilic

Chemistry Review: elements, atoms, neutron, protron, electron, isotopes, ions

Quantum numbers, chemical reactivity, covalent bonding, valence

Electronegativity, polar bonds and hydrogen bonding, hydrophilic, and hydrophobic

Molecular Biology Tools: restriction enzyme digests, blunt ends and sticky ends,

gel electrophoresis, blotting, probe, hybridization, microarray (DNA chip)

cloning, PCR reaction, DNA sequencing methods

Genemoic Information content: C-value, C-value paradox, junk DNA

Chapters 2. Database searches and Pairwise Alignments

dot plots, alignment, homologs, simple alignment, gap, origination penalty, length penalty

mutation, insertions and deletions, indels

Scoring Matrices: BLAST matrix

similarity vs. distance

Amino acid scoring matrices: PAM-1, PAM-1000, PAM-250, BLOSUM-62, BLOSUM-80

Dynamic Programming: general idea

Needleman and Wunsch Algorithm for global alignment: partial alignment score table and determining optimal alignment(s)

Semiglobal alignment: partial alignment score table and determining optimal alignment(s)

Smith-Waterman Algorithm for local alignment: partial alignment score table and determining optimal alignment(s)

Database searches:

BLAST and its variations, general steps of the algorithm

FASTA algorithm, general steps of the algorithm

Search results: alignment score (S), P scores, E scores, statistical significance

Multiple sequence alignment: Problem with dynamic programming approach, CLUSTAL