1. (Really) Basic Molecular Biology
James A. Foster
U. Idaho, IBEST

2. Overview Intro to subject and course Problems being addressed
Translation: turning DNA into living things
DNA to RNA to proteins
Regulating expression
Types of DNA
Proteins
Evolution: changing living things
Errors
Phylogeny

3. Bioinformatics & Comp. Bio.
Bioinformatics: developing tools and techniques for storing and analyzing data from molecular biology
Computational biology: bioinorganic plus simulations and modeling
This course covers a narrow slice of bioinformatics (despite the course title)

4. Pop Quiz!! (5 minutes)
Please write a paragraph on each of the following:
What you hope to get out of this class
What you know that you can contribute
What you don’t know that you wish you did

5. Course Details
Web page has assignments, readings, discussions, extra materials—refer to it often:
Syllabus, office hours, notes on webpage 3 exams, regular homework, discussion, presentations (grads)
Books: why these, what about others?
The Web: use it
You will want Unix accounts

6. What Problem Are We Solving?
Biology:
Polymers
In space
Interact
For life
Data:
Sequences
Structures
Graphs

7. Examples of Questions
What known data (sequences, structures, graphs) are similar to mine?
What biological purpose do my molecules have?
How do my molecules work?
Where did my molecules come from?

8. The Central Dogma
Copyright 1999 Access the National Health Museum.

9. DNA, RNA and proteins See page 162 of BCS Backbone
Nucleotides: A, C, G, T
Base pairing: A-T, G-C
Two strands, connected by base pairing and listed 5’ to 3’ in double helix
Then wadded into tight little balls
Sometimes grouped into chromosomes

10. DNA: Illustration
Copyright 1999 Access the National Health Museum.

11. DNA Replication

12. DNA, RNA and proteins Just like DNA, except:
Slighly different backbone
U instead of T
only one strand, which folds in on itself

13. DNA, RNA and proteins Backbone
Side chain of amino acids (aka residues)
20 available
Different chemical properties
Structures: alpha coils, beta sheets
Where the action is: interact with other molecules (DNA, RNA, proteins)

14. Protein Structure
Copyright 1999 Access the National Health Museum.

15. Binding sites
Copyright 1999 Access the National Health Museum.

16. Cells: where it all happens
Copyright 1999 Access the National Health Museum.

17. DNA to RNA Enzymes (e.g. relaxase) unwind DNA
Enzymes (e.g. rna synthetase) makes complementary pre-mRNA (AU, CG, G  C, T  A)
Enzymes edit pre-mRNA to get mRNA: removing introns, rearranging exons, correcting errors, etc.

18. RNA to proteins
Ribosome (a protein) binds to RNA at start codon (usually AUG)
Reads 3-nucleotide codon in appropriate Open Reading Frame (ORF)
Binds to tRNA, which is linked to amino acid (determined by genetic code)
Transfers tRNA residue to growing protein
Moves to next codon
Detaches at stop codon (UAA, UAG, or UGA)

19. The genetic code
Copyright 1999 Access the National Health Museum.

20. Steps during translation
Copyright 1999 Access the National Health Museum.

21. Protein Synthesis
Copyright 1999 Access the National Health Museum.

22. Proteins to Life The new protein Folds as determined by chemystery
Is transported to appropriate place (in, on, or outside of cell membrane or equivalent)
Binds to its target
Changes conformation
And the magic continues…

23. Types of DNA Genomic Non-genomic
Genic: codes for proteins for the host (30K in humans, 100K proteins)
Non-Genic (95% of humans)
RNA coding
Regulatory
Mobile elements (over 40% of humans)
Endogenous retroviruses
Non-genomic
Organelles (mitochondria, chloroplasts)
Plasmids

24. Evolution Errors happen: Isolated populations get different errors
While transcribing: misreads, slipping, breaks, exon duplication, gene duplication
While sitting in the cell: rearrangements, chromosomal duplication
From the outside: viruses, mobile elements
Isolated populations get different errors
We observe only those differences that persist
Because they actually help (selection)
Or just because (neutral evolution)