Computational Molecular Biology and Genomics:
      Molecular Biology Concepts

Familiarity with the following concepts is a prerequisite for this course.   While some of this material will be reviewed in class, students are ultimately responsible for acquiring any background knowledge they may be lacking. 

Resources

• The Cartoon Guide to Genetics by  Larry Gonick  and Mark Wheelis.
• Introduction to Computational Molecular Biology, J.C. Setubal and J. Meidanis, Chapter 1.
• Computational Biology , P. Clote and R. Backofen, Chapter 1.
• Genetic Code
• Genetic Code
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• Amino acid nomenclature, structures and properties
• Glossaries
• Flash Tutorials for Biological Sciences
  W.E. Brown, W. McClure, G. Rule, Dept of Biological Sciences, CMU
• Jon Minden's faculty to faculty biology course
  Quicktime format

Tree of life

• Prokaryotes, Eukaryotes
• Eubacteria, Archaebacteria, Eukaryotes

Proteins

• Amino acids
• Properties: hydrophobic, polar, charge, size, acidic, basic
• Protein sequence:
• Orientation: C and N terminals
• Backbone, side chains
• Primary, secondary , tertiary structure

(Modified) Central Dogma

DNA

• Nucleotides:
• Basic structure: sugar, phosphate, base
• adenine, thymine, guanine, cytosine
• purines and pyrimidines
• Watson-crick pairing
• Double helix structure
• DNA replication
• Genomic versus complementary DNA (cDNA)

RNA

• Differs from DNA: ribose, uracil, single stranded
• Secondary and tertiary structure

Genes

• Genetic code
• Transcription
• Translation
• Regulation
• Differences between prokaryotes and eukaryotes
• Intron/exon structure
• mRNA, tRNA
• Ribosomes
• Alternative splicing

Cell organization

• Mitosis and Meiosis

• Prokaryotes :
• Typically, one circular chromosome
• No nucleus, no organelles
• Eukaryotes:
• Typically, more than one diploid chromosome
• Nucleus, organelles (esp mitochondria, chloroplasts).
• Diploid versus haploid cells.

Genetics

• Haploid versus diploid (and polyploid) organisms
• Alleles
• Recombination (crossing over)