Chapter 8: Genomes, Transcriptomes, and Proteomes

Objectives:

  • Define genome, homolog, ortholog, paralog, and synteny

  • Use databases to analyze genetic information

  • Describe the genomes of adenoviruses, Picornaviruses, and retroviruses

  • Define metagenomics and describe ways it would be used

  • Describe the sequence composition of the human genome

  • Describe the major genetic changes that make us human, not chimps

  • Locate yourself on a phylogenetic tree: use outgroups to analyze mutations

  • Describe aspects of the out of Africa hypothesis

Notes:

Genome:

  • A genome is the haploid genetic content of a typical cell or organism

    • Most cell sincludes one copy of wach autosome, and the x and y if present

    • Gemones = DNA, unless your a virus and you play by your own rules

  • Animals have mitochondria, while plants have chloroplasts

    • Have their own genome, so whole nother ball park

Key vocab:

  •    Homolog: Two genes with sequence similarity, regardless of function

  • Ortholog: Genes in different species with clear similarity in sequence and function

    • Ex: HBB gene in humans and mic

  • Paralog: Related genes within a species

    • Ex: Human hemoglobin alpha (HBA) and hemoglobin beta (HBB) genes

  • Synteny: Conserved sequence of genes over a large distance or whole chromosome

    • Ex: Human chromosome 9 and mouse chromosome 2

      • similar genes on both chromosomes

Virus genomes (have to memorize):

  • Adenoviruses = Double-stranded DNA

  • Picornaviruses = Single-stranded DNA & +sense RNA

  • Paramyxoviruses = -sense RNA

  • Retroviruses: RNA that converts to DNA
       

Metagenomics:'

  • Analyzes all the genomes in a given sample

  • Guy went around on a boat and sampled genomes from around the world

The human genome:

  • Transposons make up the most amount of our DNA

    • Bad becuase out of control could end up being detrimental to humans

  • With Protein-coding genes making up the least amount in our genes

Major genetic event:

  •    Duplication: a type of mutation where a segment of DNA is duplicated, resulting in two or more copies of a gene or chromosomal region within a genome

  • Transposition: DNA moves from one gene or chromosome to another gene or chromosome

  • Inversion: A segment of DNA breaks off, flips and reinserts itself into the chromosome, reversing the chromosome order

Human and monkeys:

  • We aren’t monkeys because our chromosome 2 is one long chain, while a chimpanzees chromosome 2 is broken up into 2 smaller chains

  • Differences:

    • 4% genetic difference

    • Fused chromosome 2 on the human side of things

    • neuronal gene changes- not really mutations to genes, more expression

Human origins and migration:

  •    Out of Africa theory:

    • Can look and see Africa is the most genetically diverse

    • There is also a common mitochondrial EVE and Y-Chromosome ADAM that can be found

  • Believed to have done a migration all around the world and eventually the other human groups were beaten out by humans (neanderthals)

Transcriptomes and proteomes:

  • Transcriptome: Gene expressed in a cell under a given set of circumstances

    • RNA-based

    • Evaluated using microarrays and RNA-seq

  • Proteomes: Proteins present in a cell under a given set of conditions

    • Evaluated using 2D gel analysis

    • Why ould proteome be different than transcriptome?