Transcriptional units and Protein-coding genes
1. Bioinformatics tools alone not sufficient to identify all genes from seq. genome (cant identify
start site of transcription)
2. Northern Blot: Determine whether region is transcribed/expressed and transcri
1. Genome Sequencing: DNA extractionDNA fragmentationTransform bacteria, grow,
isolate DNA vectorsequence libraryassemble contiguous fragments
2. Polyacrylamide gel ideal for sequencing bc resolves single nucleotide diff.
3. Sangers Chain Termin
1. Genetic Mapping: use classical genetics to find gene positions on chromosome (crossbreeding: monohybrid and dihybrid cross, pedigree analysis-disease gene in relation to nearby
2. Physical Mapping: use modern molecular bio techniques
Chapter 7: Eukaryotic Genomes
1. Eukaryotic genomes have linear double-stranded DNA (centromeres-sites of kinetochore
assembly, satellite DNA; telomeres-terminal structures that protect chromosome ends)
-eukaryotic organelles have circular DNA
Chapter 9: Viral Genomes and Mobile Genetic Elements
1. Smallest viral genome encodes for 2 genes (encode capsid protein and replicase protein)
2. Largest virus: Pandoravirus (2,770,000 bp); viral genomes tend to be small and compact due
to virus parasiti
Chapter 15: Genome Replication
1. Double helix model allows for three modes of DNA replication: Dispersive,
2. Meselson and Stahls heavy isotope labeling experiment (1958) supported semiconservative
3. Topological prob
Chapter 13: Proteomics and Protein Translation
1. Hubs: small clusters of proteins that interact w/ many other proteins within protein network
2. Gene Ontology proj: assign consistent term or functional description to genes and their prod.
3. Protein micr
Chapter 11: Transcription Initiation
1. RNA polymerase has to be recruited for transcription by transcription factors
2. Transcription factors (motifs) recognize specific DNA sequences by interacting with DNA
3. Zinc finger DNA-binding motifs
Chapter 8: Genomes of Prokaryotes and Eukaryotic Organelles.
1. Basic features of prokaryotic genomes
Its gene numbers in relation to genome size
o Most prokaryotic genomes are less than 5Mb in size, but the overall range
among sequenced genomes is from
Chapter 7: Eukaryotic Nuclear Genomes
1. Basic features of eukaryotic genomes:
Its gene numbers in relation to genome sizes
o Chromosome number is unrelated to biological features.
o Chromosome number is not related to genome size.
o C-value paradox: the
Chapter 6 Understanding How a Genome Functions
1. Understand basic protein techniques:
Isoelectric focusing SDS-PAGE
o Similar to RNA/DNA
o Denatures protein
o Polyacrylamide gel electrophoresis is the standard me
1. Chapter 15: Genome Replication
a. The Topological Problem Introduction
a.i. Primary concern from 1953 to 1958.
a.ii. Arises from the need to unwind the double helix in order to make copies
of its two polynucleotides.
a.iii. Main stumbling block to acce
Review topics for Exam III (BI315: Introduction to Genomics)
1) Understand basic protein-DNA binding techniques: gel shift assay, ChIP (ChIP-seq,
ChIP-chip), DNA footprinting.
a. Gel shift (Gel retardation) assay
a.i. Identifies DNA fragments
1.Griffith Experiment: injected heat-killed smooth virulent (S) into mouse and mouse healthy,
injected rough nonvirulent with heat-killed smooth virulent, mouse dies and live S bacteria in
blood sample of dead mouse
-discovered phenomenon of bacterial tra