On this page you will find copies of the handouts and summary
information for each lecture. You will also find the question of the day and
a listing of any assignments handed out during that lecture. Notes for each
lecture are not provided--you must take your own. While sample lecture notes
are given at the textbook website,
exams will also include additional topics discussed only in class.
Summary |
An introduction to the course and to basic molecular biology. |
QOTD |
What are some advantages to having RNA as an intermediary
between the genetic source (DNA) and the functional element (protein)
in the cell?
|
Handouts |
Computational Questionnaire (Due Feb. 3)
Room 122 Access Application (Due Feb. 3)
Nucleic Acid Structures
|
Summary |
Accessing information through the NCBI website. |
Reading |
Chapters 1, 2
|
Optional Reading |
Brenner, S.E. (1999)
“Errors in Genome Annotation.” Trends in
Genetics 15 (4): 132-3.
[PDF]
|
QOTD |
What is the protein sequence of the human gene p53?
Why is this gene relevant?
|
Summary |
Pairwise sequence alignment. |
Reading |
Chapter 3
|
QOTD |
In a PAM matrix, the cell for a mutation from Val
to Ile has a value of 0.15. What does this number mean?
|
Summary |
Pairwise sequence alignment. |
Reading |
Chapter 3
|
QOTD |
What are the key differences between global and
local sequence alignment?
|
Handouts |
Worked Needleman-Wunsch Example
|
Summary |
BLAST Searching |
Reading |
Chapter 4
|
QOTD |
What factors affect the number of results returned
by a BLAST search?
|
Summary |
Advanced BLAST Searching |
Reading |
Chapter 5
|
QOTD |
What are the differences between PHI- and PSI-
BLAST?
|
Summary |
Gene Expression and Microarrays |
Reading |
Chapter 6
|
QOTD |
How would you design an experiment to determine
the effects of a particular drug on tumor cells grown in
culture? To what aspects of the gene expression setup would
you have to pay particular attention?
|
Summary |
Protein Structure |
Reading |
Chapter 9
|
QOTD |
How many possible backbone conformations
exist for a peptide chain of length 10?
|
Summary |
Proteomics |
Reading |
Chapter 8
|
QOTD |
Why might the predictions made from a hydropathy
plot be inaccurate?
|
Summary |
Multiple Sequence Alignment |
Reading |
Chapter 10
|
QOTD |
What aspects of ClustalW might cause your seqeunce
alignment to be sub-optimal?
|
Summary |
Protein Structure Prediction (George Rose) |
Reading |
Bradley, P., Misura, K. S. M., and Baker, D. (2005)
“Toward High-Resolution de Novo Structure Prediction for
Small Proteins.” Science 309 (5742):
1868-1871. [PDF]
|
Summary |
Molecular Evolution and Genome Analysis |
Reading |
Chapters 11, 12
|
Optional Reading |
Sanger Dideoxynucleotide Sequencing
|
QOTD |
When might a distance-based tree be better than a maximum
parsimony tree?
|
Summary |
The Human Genome |
Reading |
Chapter 17
|
QOTD |
What limitations currently exist on the full potential
of knowing the human genome?
|
Summary |
Bioinformatics and Human Disease |
Reading |
Chapter 18
|
QOTD |
How would you determine whether a single-nucleotide
polymorphism was responsible for a specific disorder?
|