Campbell Biology Chapt 21 Shortened Version

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Genomics

Back 1

Study of whole sets of genes and their interactions

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Bioinformatics

Back 2

Application of computational methods to the storage and analysis of biological data

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Human genome project

Back 3

Started in 1990 and completed in 2003

Used whole genome shotgun approach and dideoxy chain termination method

Technology for faster sequencing

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Whole genome shotgun approach

Back 4

O

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Metagenomics

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DNA from a group of species in an environmental sample is sequenced

Making sense of massive amounts of data from many genome sequences has started new approaches

ie: get sample of gut bacteria and find out what’s there

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Gene annotation

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The identification of protein-coding genes within DNA sequences in a database

Largely an automated process

Comparing sequences of previously unknown genes with those of known genes may help provide clues about their function

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Proteome

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Entire set of proteins expressed by a cell or group of cells

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Proteomics

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Approach to studying large sets of proteins and their properties

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Systems biology

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Genes and proteins and their function integration in bio systems

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Application of systems biology to medicine

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Cancer genome atlas: comparing gene sequences and expression in cancer vs normal cells (ten types of cancers)

Gene chip is used to understand gene expression patterns in cancer patients

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Genome size

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There is no systematic relationship btw genome size and phenotype

Eukaryotic genomes tend to be larger

Genomes of most bacteria and archaea range from 1-6 million

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Number of genes

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Not correlated to genome size

Drosophila has 165 Mb and 14,000 genes

Humans have fewer than 21,000 (same as a worm) which is far off from what was predicted: 50,000-100,000

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Transposons

Back 13

Require enzyme, trabsposase to move by mean of DNA intermediate

Cut/paste or copy/paste like

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Gene density and noncoding DNA

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Number of genes per given DNA= density

Humans have lowest gene density in length of DNA or mega base (mb)

Eukaryotes Have many introns within genes and a large amount of noncoding DNA btw genes

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Noncoding DNA-a lot of it

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98.5% of human genome does not code for proteins

Gene regulatory sequences and introns account for 5% and 20% respectively

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L1 sequences

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Retrotransposons

Low rate of transposition and may effect gene expression

May play role in diversity of neuronal cell types

Do not see these until higher order animals like primates

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Pseudogenes

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Former genes

Accumulated mutations and no longer function

A part of unique noncoding dna-15%

ie: like old abandon house

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Multigene families

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Collection of two or more identical or very similar genes

1. Identical DNA sequences usually clustered tandemly (code for rRNA)

2. Nonidentical genes

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What underlies much of genome evolution?

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Mutations

Earliest forms of life likely had only those genes needed for survival and reproduction

Size of genomes has increased over time providing gene diversification

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Polploidy

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Extra set of chromosomes

Accidents in meiosis can lead to this

Can lead to divergence of sets by accumulating mutations

Genes with novel functions can survive

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Alterations of chromosomes structure

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Humans have 23 chromosomes, while chimps have 24 bit pir chromosomes are similar so at some point separated from same ancestor

Duplications and inversions result from mistakes during meiotic recombination

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Transposons

Back 22

Require enzyme, trabsposase to move by mean of DNA intermediate

Cut/paste or copy/paste like

Front 23

Retrotransposons

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Move by means of RNA intermediate

Uses a reverse transcriptase enzyme (takes RNA and reads it back to make DNA)

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Alu elements

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Transcribed into RNA molecules

May play a role in gene regulation

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L1 sequences

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Retrotransposons

Low rate of transposition and may effect gene expression

May play role in diversity of neuronal cell types

Do not see these until higher order animals like primates

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Other repetitive DNA

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About 5-6% of human genome consist of duplication long sequences of DNA from one location to another

In contrast, simple sequence DNA contains many copies of tandemly repeated short sequences

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Multigene families

Back 27

Collection of two or more identical or very similar genes

1. Identical DNA sequences usually clustered tandemly (code for rRNA)

2. Nonidentical genes

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Junk DNA

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The DNA that does not code for proteins

Play important role due to having high level of sequence suggesting that they would have not survived evolution if they didn’t have a role

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Transposable elements

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Stretched of DNA that can move from on location to another within the genome

Jumping genes

About 75% of human repetitive DNA is made of these

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Alterations of chromosomes structure

Back 30

Humans have 23 chromosomes, while chimps have 24 bit pir chromosomes are similar so at some point separated from same ancestor

Duplications and inversions result from mistakes during meiotic recombination

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Eukaryotic transposable elements 2 types

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Transposons and retrotransposons