Bioinformatics

From Colettapedia
Jump to: navigation, search

Course Websites

Basic Definitions

  • Bioinformatics - the manipulation, searching, and data mining of biological data, and this includes DNA sequence data.
  • DNA - Deoxyribonucleic Acid
  • RNA - Synthesis of RNA is usually catalyzed by an enzyme—RNA polymerase—using DNA as a template, a process known as transcription.
  • mRNA - Messenger RNA (mRNA) is the RNA that carries information from DNA to the ribosome, the sites of protein synthesis (translation) in the cell.
    • miRNA - a short ribonucleic acid (RNA) molecule found in eukaryotic cells. A microRNA molecule has very few nucleotides (an average of 22) compared with other RNAs. They are post-transcriptional regulators that bind to complementary sequences on target messenger RNA transcripts (mRNAs), usually resulting in translational repression or target degradation and gene silencing.
      • RNA interference (RNAi) is a process within living cells that moderates the activity of their genes.
    • rRNA - RNA component of the ribosome, provides a mechanism for decoding mRNA into amino acids and interacts with tRNAs during translation
    • tRNA - bring the necessary amino acids corresponding to the appropriate mRNA codon to the ribosome... "bridge the four-letter genetic code (ATCG) in messenger RNA (mRNA) with the twenty-letter code of amino acids in proteins."
  • nucleotide - single unit of DNA, includes backbone and nucleobases (bases)
  • nucleobases:
    • The Purines - Adenine (bonds to Thymine in DNA and Uracil in RNA) and Guanine (bonds to Cytosine)
    • The Pyrimidines - Thymine ("5-methyluracil") and Cytosine
  • chromatin - the protein and DNA that make up the contents of the nucleus of the cell
  • chromatin proteins - e.g., histones and scaffolding over which DNA is folded and organized
  • James D. Watson and Francis Crick - discovered the double helix of DNA
  • DNA structure is anti-parallel, with upstream end called "5'" and downstream end "3'"
  • "central dogma" - the idea that genetic information flow in cells is essentially one-way, from DNA to RNA to protein.
    • except reverse transcription from retroviruses
  • codon - sequence of three nucleotides - the words in the genetic language.
    • stop codon - a nucleotide triplet within messenger RNA that signals a termination of translation.
      • UGA: "U Go Away"
      • UAA: "U Are Away"
      • UAG: "U Are Gone"
      • TAG: "They Are Gone"
      • TAA: "They Are Away"
      • TGA: "They're Going Away"
    • start codon - generally defined as the point, sequence, at which a ribosome begins to translate a sequence of RNA into amino acids.
  • ribosome - organelle. protein factory, assembles proteins according to input mRNA
  • reading frame - point of reference how you group nucleotides into codons
  • transcription - copying DNA into RNA
  • telomere - simple repeated DNA sequences composing chromosome ends. The telomere-shortening mechanism normally limits cells to a fixed number of divisions, and animal studies suggest that this is responsible for aging on the cellular level and sets a limit on lifespans. Telomeres protect a cell's chromosomes from fusing with each other or rearranging—abnormalities that can lead to cancer—and so cells are destroyed when their telomeres are consumed. Most cancers are the result of "immortal" cells that have ways of evading this programmed destruction.
  • transcription factor - a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA. Transcription factors perform this function alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of RNA polymerase (the enzyme that performs the transcription of genetic information from DNA to RNA) to specific genes.
  • intron - long stretches of DNA which are transcribed but never translated into protein (they are spliced out before translation)
    • regions often found in eukaryote genes that are removed in the splicing process (after the DNA is transcribed into RNA):
  • exon - Only the exons encode the protein.

sequence of events??

  1. DNA unzips
  2. transcription factor
  3. RNA polymerase creates mRNA
  4. mRNA goes to ribosome
  5. rRNA and tRNA build the protein
  6. miRNA regulates

Genetics

  • gene - a discrete molecular unit of heredity of a living organism
    • A union of genomic sequences encoding a coherent set of potentially overlapping functional products. This new definition categorizes genes by functional products, whether they be proteins or RNA, rather than specific DNA loci; all regulatory elements of DNA are therefore classified as gene-associated regions.
  • genes vs. alleles: colloquial usage is incorrect. genes is the basic instruction, but the allele is a variant of the gene. One has "good alleles" and not "good genes"
  • ~20,000 total genes in human (comparable to mouse, fly) by function:
    • unclassified 4061
    • transcription factors 2067
    • transferases 1512
    • nucleic acid binding 1466
    • transporters 1098
    • receptors 1076
    • signaling molecules 961
    • enzyme modulators 857
    • proteases 476
    • hydrolases 454
    • cytoskeletal proteins 441
    • membrane traffic proteins 321
    • structural proteins 280
    • ligases 260
    • transfer/carrier proteins 248
    • phophatases 230
    • chaperones 130
    • defense/immunity proteins 107
    • lyases 104
    • isomerases 94
    • cell adhesion molecules 93
    • transmembrane receptor regulatory/adapter proteins 84
    • extracellular matrix proteins 72
    • cell junction proteins 67
    • calcium-binding proteins 63
    • storage proteins 15
    • surfactants 15
    • viral proteins 7

Orgo Definititions TBD

  • methylation

Meetings

Training

NCBI Genome Browsers