Molecular Biology Chapter 21 Outline

Front 1

Genomics

Back 1

Study of whole sets of genes and their interactions within a spp, as well as genome comparisons between spp.

Front 2

Bioinformatics

Back 2

Use of computers, software, and mathematical models to process and integrate biological info from large data sets.

Front 3

Human Genome Project

Back 3

International collaborative effort to map and sequence the DNA of the entire human genome (1990-2003).

Front 4

Linkage map

Back 4

Genetic map based on frequencies of recombination between markers during crossing over of homologous chromosomes.
i. Reveals the order of markers as well the relative distance between them.
ii. Markers = genes or sequences in DNA.

Front 5

Physical map

Back 5

Genetic map in which actual physical distances between genes or other genetic markers are expressed, usually as the number of base pairs along the DNA.
i. DNA is cut into restriction fragments and the original order is determined by
detecting overlapping segments.

Front 6

DNA Sequencing

Back 6

a) Determine the complete nucleotide sequence of each chromosome.
i. 3 billion base pairs in aploid set of human chromosomes
1980’s – 1,000 bp/day
2000’s – 1,000 bp/sec

Front 7

Shotgun Approach to Genome Sequencing

Back 7

Skips the linkage mapping and physical mapping stages and starts directly with the sequencing of random DNA fragments.

Front 8

Identifying Protein-Coding Genes and Functions
1. Reverse genetic

Back 8

From DNA sequences, geneticists can study genes directly without having to infer genotype from phenotype

Front 9

Identifying Protein-Coding Genes and Functions
2. Gene annotation

Back 9

Analysis of genomic sequences to identify protein-coding genes and determine the function of their products.

Front 10

Proteomics

Back 10

Systematic study of the full protein sets (proteomes) encoded by genomes.
a) Proteins, not the genes that code them, actually carry out most of the activities
of the cell.
b) Understanding protein function will result in a better understanding of cell and organismal function.

Front 11

Proteomics: Systematic Study of the Fruit Fly

Back 11

a) Uncovered 10,000 RNA transcripts.
b) After molecular testing and statistical analysis, 4,700 proteins were found to carry out over 4,000 functions.
c) Mathematical tools, powerful computers, and newly developed software revealed the vast number of protein-to-protein interactions.

Front 12

Proteomics: Systematic Study Applications

Back 12

a) Observing how changes in biological systems may lead to cancer.
b) Searching for common mutations by comparing gene sequences and patterns
Of gene expression in cancer and normal cells.
c) Tailor treatment to patients’ unique genetic makeup and the specifics of their diseases.

Front 13

Metagenome

Back 13

All genetic material in an environ-mental sample consisting of genomes of many individual organisms.

Front 14

Genome Size

Back 14

1. Prokaryotic genomes range in size from 1 – 6 million base pairs (Mb).
2. Eukaryotic genomes range in size from 12 (yeast) – 3,000 (humans) Mb.
3. Size among eukaryote genomes seems irrelevant compared to systematic relationships and the organism’s phenotype.

Front 15

Number of Genes

Back 15

1. Prokaryotic genes range in number from 1,500 – 7,500 genes.
2. Eukaryotic genes range in number from 5,000 (yeast) – 40,000 genes (multicellulars).
3. Size among eukaryote genomes seems irrelevant compared to the number of genes.

Front 16

Gene density

Back 16

1.The number of genes in a given length of DNA.
a) Eukaryotes have hundreds to thousands of times as many base pairs as bacteria, but only 5 - 15 times as many genes.
b) Mammals have the lowest gene density.
2. In most bacterial genomes, most of the DNA consists of genes for protein, tRNA, or rRNA; no introns.
3. In most eukaryotic genomes, most of the DNA neither encodes protein nor is transcribed into RNA molecules; presents as introns within genes.

Front 17

Coding v. Non-coding DNA

Back 17

1. 1.5% of the human genome codes for proteins or is transcribed into rRNA or tRNA.
2. Of the remaining 98.5%:
a) 24% accounts for regulatory sequences and introns.
b) 15% accounts for unique, noncoding DNA.
c) 15% accounts for repetitive DNA.
d) 44% accounts for repetitive DNA with transposable elements.

Front 18

Pseudogenes

Back 18

DNA segment very similar to a real gene, but does not yield a functional product; inactivated in a particular spp due to mutation.

Front 19

Repetitive DNA

Back 19

Nucleotide sequences, usually noncoding, that are present in many copies in a eukaryotic genome; may be short and in a series or long and dispersed throughout the genome.

Front 20

Transposable elements

Back 20

Segment of DNA that can move within the genome of a cell by means of DNA or RNA intermediates.
a) Moves from one site to a target site within the cell’s DNA by a recombination process; “jumping genes”.
c) Example: Indian corn color.

Front 21

Transposons

Back 21

Transposable elements that move within a genome by means of a DNA intermediate.
a) Cut and paste – removes the element from original site.
b) Copy and paste – leaves a copy behind.

Front 22

Retrotransposons

Back 22

Transposable elements that move within a genome by means of a RNA inter-mediate, a transcript of the retrotransposon DNA.
a) Copy and paste – leaves a copy behind.

Front 23

Simple sequence DNA

Back 23

DNA sequence that contains many copies of tandemly repeated short sequences.

Front 24

Short tandem repeat (STR)

Back 24

Simple sequence DNA containing multiple tandemly repeated units of two – five nucleotides.

Front 25

Multigene families

Back 25

Collection of genes with similar or identical sequences, presumably of common origin.
a) Identical DNA sequences - RNA’s for final products.
b) Example: code for rRNA molecules.
c) Non-identical DNA sequences – globins for final products
d) Example: α & β polypeptide
subunits of hemoglobin (found
on chromosome 16 and
chromosome 11).

Front 26

Polyploidy

Back 26

Chromosomal alteration in which an organism possesses more than two complete sets of chromosomes (accident in meiosis). Can’t bring back the parent generation.
a) One set of genes = essential functions.
b) Other sets of genes = diversification

Front 27

Alteration of Chromosome Structure

Back 27

Chromosomal rearrangements would lead to two populations that could not successfully mate with each other, leading to two separate spp.
a) Example: Humans and chimpanzees.

Front 28

Duplication/Divergence of Gene-Sized DNA

Back 28

Duplication can lead to evolution of genes with related functions.
a) Example: α & β polypeptide subunits of hemoglobin

Front 29

Rearrangement of Parts of Genes

Back 29

1. Accidents in meiosis – unequal crossing over during prophase 1 – can result in deletion and duplication in chromosomes.
a) Exons within genes could be duplicated on one chromosome and deleted from another.
b) Genes with extra chromosomes could code for a protein with a second copy of the sequence.
i. Could alter protein property.
ii. Example: Collagen.

Front 30

Transposable Elements and Genome Evolution

Back 30

1. Promote recombination between different chromosomes by providing homologous regions for crossing over.
2. Disrupt cellular genes by “jumping” into the middle of a protein-coding region.
3. Carry entire genes to new positions in the genome during transposition (hemoglobin molecule).

Front 31

Comparing Genomes

Back 31

The more similar in sequence the genes and genomes are, the more closely related those spp are in their evolutionary history .

Front 32

Comparing Distantly Related Spp

Back 32

a) Determining which genes have remained highly conserved in distantly related spp can help clarify evolutionary relationships among spp that diverged from each other a long time ago.
b) Genomes of two closely related spp are likely to be organized similarly because of their relatively recent divergence.
i. Divergence of two closely related spp also underlies the small number of gene differences.

Front 33

Evo-devo (evolutionary developmental biology)

Back 33

Field of biology that compares developmental processes of different multicellular organisms to understand how these processes have evolved and how changes can modify existing organismal features or lead to new ones.

Front 34

Homeobox (Hox)

Back 34

180 nucleotide gene sequence with-in homeotic genes and some other developmental genes that is widely conserved in animals (Hox).
a) Genes containing homeoboxes are found in ALL eukaryotic genomes and are associated with cell
differentiation and body segmentation during embryonic development.