A respite from the "Python Firehose," we'll be starting our journey into applying the tools and techniques we've covered over the past couple weeks to answer biological questions. Here, we'll cover a basic introduction to molecular biology and the types of problems that crop up. By the end of this lecture, you should be able to:
Cells are the smallest functional unit of life; consequently, most cells share common structures...
...and functions.
What are some of the main differences between prokaryotic and eukaryotic cells?
Prokaryotes
Eukaryotes
Signaling pathways allow cells to coordinate complex behaviors and make decisions between them that would otherwise be impossible. Some of these decisions may include
DNA
RNA
Proteins
Gregor Mendel discovered this effect in the 1860s while experimenting with pea plants. He was trying to answer the question: Do traits come from a blend of both parents' traits, or from only one?
Mendel discovered that genes were passed on to offspring by both parents in the form of either dominant or recessive traits.
The dominant gene determined the phenotype of the offspring; unless it wasn't present, in which case the recessive gene would determine the phenotype. The gene itself is the genotype.
DNA and its building blocks were later discovered in the 1950s.
DNA is a sequence of nucleotides (A, G, T, and C). When one of these bases in the sequence change, this is known as a mutation.
Mutations can have one of three possible effects:
DNA -> RNA -> Protein
Ribonucleic acid
Several "types" of RNA exist that are understood to perform specific functions.
This is the process through which genes in the DNA are "converted" to RNA (specifically, mRNA).
Analyze a genome in four easy steps!
Steps 4 and 5 are where bioinformatics and computational biology play a role.
Why?
Use polymerase chain reaction (PCR) to massively replicate the DNA.
PCR doubles the amount of DNA at every iteration (amount of DNA grows exponentially)
Why?
Use various restriction enzymes to chop up the DNA at specific points.
Bioinformatics or Computational Biology are generally defined as the analysis, prediction, and modeling of biological data with the help of computers.
in silico
Allows researchers to compare query sequences (your sequence of interest) with entries in current biological databases
Great for predicting the function of unknown sequences using alignment to similar, known sequences
Emphasis is on speed: as a result, it does not search for an optimal result, but uses a heuristic to identify matches or close matches with high probability
Similar to BLAST in that it takes a query sequence of an unknown protein and returns known active sites in proteins with similar amino acid sequences
Critical component of computational genomics and proteomics.
Even further downstream, analyses of the primary structure can yield