1. Genomes and Their Evolution
Chapter 21

2. Genomics is the study of whole sets of genes and their interactions.
Bioinformatics is the application of computational methods to the storage and analysis of biological data, especially that obtained from sequencing genes.

3. Human Genome Project
The Human Genome Project began in 1990 and was an international research project
designed to discover the sequence
of the 3 billion base pairs of human DNA.
It was completed in 2003. 

4. Before the project began, scientists were aware of the banding pattern seen on the chromosomes when they were dyed.
This allowed them to create a cytogenic map.

6. The project had 3 stages:
1. Constructing a linkage map of the 23 human chromosomes
based on recombination frequencies when crossing over occurs during meiosis.
Scientists identified the locations of about 5,000 genetic markers such as RFLPs, STRs and other polymorphisms (about 200 per chromosome).

8. 2. Physical mapping –
in which the distances between the markers is determined and measured by the number of base pairs between them.
The DNA was cut by restriction enzymes into many fragments which were able to overlap.
Using probes or automated nucleotide sequencing machines, scientists were able to determine the correct order of the pieces.

10. Sequencing overlapping pieces:

11. 3. DNA sequencing – Using the dideoxy chain termination method, automated machines determined the base pair order of small pieces of DNA.

13. When all of these pieces of information are joined,
one can know all the base pairs of a DNA strand in their proper order. 
Over the course of time, methods for sequencing DNA improved vastly,
from 1000 base pairs per day in the 1980s to 1000 per second by the year 2000.

14. Venter’s approach
J. Craig Venter invented a new approach to gene sequencing
in which he skipped the linkage and physical maps
and went directly to cutting up the entire genome and sequencing random DNA fragments using a powerful computer program
to assemble the sequence of the many fragments based on their overlaps.

15. This is called the whole-genome shotgun approach.
His independent group competed with the Human Genome Project to complete the sequencing first.
They tied.

19. Recently it was found that his method can miss duplicated sequences and miss some genes that way.
A hybrid approach seems to be the best way.

20. Using bioinformatics to analyze genomes and their functions
Websites on the Internet provide for centralized access to the genome sequence databases that have been created,
as well as software for analysis.
One site, called Genbank, is constantly updated.

21. Programs are available to compare a particular DNA sequence with every sequence in Genbank.
Other programs allows comparisons of expected amino acid sequences based on a particular DNA sequence.

22. Another creates evolutionary trees based on DNA sequence relationships.
There is also a site with all the 3-D protein structures that have been determined
and their amino acid sequences.

24. Ways to identify protein-coding genes with DNA sequences
How do you know where a protein code actually is within the list of DNA base-pairs?
1. Software scans the sequence for transcription start and stop codons.

25. 2. Compare the sequence with those of already identified gene or protein sequences from other organisms. 
3. Experiment with disabling genes, such as using RNAi,
and seeing what function has been disturbed in the organism with those genes.

26. Proteomics
Proteomics is the study of the proteins that are encoded for by the genes of an organism.

27. Scientists now have a complete list of all of the genes and proteins used in a particular organism.
(Like a parts list for a car.)
Now they are working to define gene circuits
and protein interaction networks.
(How those parts actually fit and work together.)

28. Ex. Drosophila has about 10,000 predicted RNA transcripts.
Molecular techniques were used to determine which of them coded for proteins that could interact with each other.
There were 4,700 proteins that could interact in different reactions.

30. The Cancer Genome Atlas is a project that is using these techniques
to compare the gene sequences
and patterns of gene expression in normal and cancer cells.
2,000 cancer genes will be sequenced at various stages of the disease to monitor changes.

31. A human gene microarray chip has been developed which holds most of the human genes within its pits.
They are being used to analyze gene expression in patients with various diseases such as cancer.

33. Eventually we may each have our DNA sequence as a part of our medical records,
with areas highlighted that indicate a predisposition for various diseases.

34. Comparing genomes
By the summer of 2007, the genomes of 600 organisms were sequenced.
Most were bacteria and archaea.
65 were eukaryotic animals, plants, protists and fungi.

35. A. In terms of numbers of base pairs in the genome,
eukaryotic genomes tend to be larger than prokaryotic genomes.
There are 1-6 million base pairs (Mb) in prokaryotes, more than 100 Mb in eukaryotes.

36. There is no relationship between the number of base pairs and the phenotype of the organism.
Ex. A particular lily plant has 40 times more base pairs than a human. (120,000 Mb vs Mb)
An amoeba has 670,000 Mb!

37. B. In terms of numbers of genes,
eukaryotes have more than prokaryotes.
Again, the number of genes does not seem to be related to the complexity of the organism.
Ex. The roundworm C. elegans has a genome of 100 Mb with 20,000 genes. Humans have 3200 Mb but only 20,500 genes.

39. Scientists first expected humans to have about 100,000 genes based on the numbers of known human proteins.
One way that we get more proteins than genes is by alternative RNA splicing.
By cutting out the introns in several ways,
we get several proteins from the same gene sequence.

40. C. Gene density – the number of actual genes that codes for protein compared to the number of base pairs.
Prokaryotes have greater gene density than eukaryotes.
In bacteria, most of the DNA consists of genes for protein, tRNA or rRNA
and the rest is regulatory sequences such as promoters.

41. Bacteria do not have introns.
In eukaryotes, most of the DNA does not code for a protein or RNA.
We have 10,000 times more noncoding DNA than bacteria.

42. Some of the noncoding DNA is introns and
there are more complex regulatory sequences.
Eukaryotes have vast stretches of noncoding DNA between genes.

44. Noncoding DNA in Eukaryotes
It was previously thought that noncoding DNA was “junk” DNA and served no purpose.
However, some of the same sequences are found in many different genomes
of very different organisms.

45. Ex. Humans, rats and mice have 500 regions of noncoding DNA that are identical.
This noncoding DNA is even more carefully conserved than the DNA that codes for protein,
so it must be important in its function.

46. What the human genome is made of
Only 1.5% of the human genome codes for proteins or is transcribed into tRNA or rRNA.
24% codes for introns and regulatory sequences.

47. What the human genome is made of
15% codes for unique noncoding DNA –
Ex. Pseudogenes which are thought to have coded for something longer ago but have mutated and are no longer expressed.

48. What the human genome is made of
15% is repetitive DNA unrelated to transposable elements
44% is repetitive DNA that includes transposable elements and related sequences

50. Transposable elements
A transposable element is a stretch of DNA that can move to another location in the genome.
The process of moving is called transposition.

51. This idea was first presented by Barbara McClintock in the 1940’s
based on her work with the changing kernel colors found in Indian corn.

53. 2 kinds of eukaryotic transposable elements:
1. Transposons –
They can either be completely removed from the original site and moved elsewhere,
or they can be copied and a copy moved to a new site.

55. 2. Retrotransposons – First, an RNA intermediate is made from the DNA section.
Then reverse transcriptase makes DNA from the RNA.
The new DNA is put into the chromosome in a new location.
The reverse transcriptase is coded for by the retrotransposon itself.

57. 25-50% of the mammalian genome is made of transposable elements such as transposons and retrotransposons.

58. Other Repetitive DNA
A. Some of the repeating DNA in the human genome is long sequences of 10, ,000 base pairs.
It is thought this DNA arises from mistakes in DNA replication.

59. B. Simple sequence DNA – contains many copies of a shorter sequence (up to 500 base pairs long) which is repeated many times next to each other.
Ex. GTTACTG is repeated as GTTACTG GTTACTG GTTACTG GTTACTG (on 1 DNA strand).

60. It is often found near the centromere and at the telomeres of the chromosome.
It may be important in the structure of the chromosome.

61. Ex. It may help organize the chromatin during interphase,
it helps prevent important DNA loss through the telomeres and
it is important in proper separation of chromatids during cell division.

62. C. Short tandem repeats (STR)- Simple sequence DNA with 2-5 base pairs.
The number of repeats can vary from person to person,
so it is useful in comparing genetic profiles to distinguish between people’s DNA.

63. Genes and Multigene Families
About half of the human genes are located individually within the genome,
with only one gene existing for that protein.
The other half occur in multigene families – collections of two or more identical or similar genes.

64. If the members of the multigene family are identical,
they code for RNA or histones, which are both needed in large quantities by the cell.

65. Ex. There may be thousands of genes for the same rRNA molecule repeated tandemly on the chromosome.
The mRNA that is produced is cut into 3 pieces, which code for 3 of the 4 rRNA molecules that are needed to make a
ribosome for protein synthesis.

67. Nonidentical genes can also occur in families.
Ex. One family of genes on human chromosome 16 codes for various forms of alpha-globin
and a similar family is found on chromosome 11 codes for various forms of beta-globin.
Both are used in production of hemoglobin.

69. The different forms are expressed at different times over a person’s life.
One form is expressed in the embryo and fetus because it has higher affinity for oxygen, so the embryo/fetus is better able to
obtain oxygen from the mother’s blood.
A different form with a lower oxygen affinity is expressed in adulthood.

70. Genome evolution
It is thought that the earliest forms of life would have had a minimal number of genes – just those necessary for survival and reproduction.
Over time, there must be an increase the number of genes, providing raw material for gene diversification.

71. Methods of increasing the genome size:
A. Polyploidy – An accident in meiosis results in offspring with one or more extra
sets of chromosomes.
Polyploidy generally is lethal in animals (they die).
However, some plants are able to survive despite polyploidy.

72. Mutations could occur in one set of genes to provide new proteins and traits,
while the other set provides for the essential functions of the organism.

73. B. Alterations of chromosome structure – Sometimes chromosomes will fuse together, creating organisms with fewer chromosomes.
These organisms may no longer be able to mate, since synapsis in meiosis would be affected.
This could create new species.

74. Chromosomes also break apart sometimes and reattach with inversions and duplications which may result in new species.
Several chromosome rearrangements result in congenital diseases and miscarriage in humans.

75. C. Gene-sized duplication and divergence –
Errors in meiosis such an uneven crossing over event can also result in
just one gene being duplicated or deleted.

78. D. Slippage during DNA replication can also result in duplications or deletions of small areas.

79. It is thought that the various forms of globin are the result of duplication and divergence by mutation.
A comparison of gene sequences within a multigene family
can suggest the order in which the genes arose.

81. Gene duplication and mutation is thought to also be able to produce genes with novel (new) functions.
Ex. Lysozyme is an enzyme that protects animals from bacteria by hydrolyzing bacterial cell walls.
It is very similar to another protein called lactalbumin – which is used in milk production in mammals.

82. Both birds and mammals make lysozyme,
but only mammals make lactalbumin.
So at some time after birds and mammals had branched off from each other in the evolutionary process,
the lysozyme gene was duplicated, then mutated to form lactalbumin.

83. Ways to create new genes by rearrangement
A. Exon duplication – Unequal crossing over during meiosis could cause one exon to be duplicated on one chromosome
and create one chromosome that lacks it.
Remember that an exon generally codes for a domain (a structural or functional unit of a protein).

84. The extra exon could create a new protein.
Ex. Collagen has a very repetitive amino acid sequence
which therefore has a very repetitive exon sequence on the chromosome.

85. Diagram

86. B. Exon shuffling – The new sequence of exons on a chromosome
could be created by errors in crossing over to eventually create a new gene from
several different exons.

88. How transposable elements contribute to genome evolution
As transposable elements are moved to new locations on chromosomes,
they can cause new genes to develop in several different ways:

89. A. A transposable element in the middle of a protein-coding sequence
will prevent a normal version of that protein from being produced.
It may also create a different protein with a new function due to the added domain.

90. B. If the transposable element inserts in a regulatory sequence,
it may cause increased or decreased production of the protein.

91. C. The transposable element may move a gene or group of genes to a new chromosome
and create new possibilities when crossing over occurs with that chromosome.

92. All of these processes will generally produce harmful effects to the organism as normal proteins are disrupted,
however a few might be beneficial in some way.

93. Comparing genome sequences provides clues to evolution and development
Assuming that evolution has occurred, the more similar in sequence the genomes of two species are,
the more closely related they are in their evolutionary history
and the more recently they probably split from each other.

95. A. Comparing distantly related species
allows us to see which genes have been highly conserved (stayed the same) over time.
This can help us trace evolutionary history.

96. B. Comparing closely related species genomes can help us identify the differences between them.
Ex. What makes a chimp different from a human?

97. Comparisons between human and chimp DNA
A. There are only about 4% differences between humans and chimps.
B. Most differences are due to insertions or deletions,
some are duplications and other repetitive DNA.

98. C. When the genes that vary between chimps and humans are compared with those of other mammals such as mice,
it appears that some genes are evolving faster in humans than in the other organisms.

99. Ex. Genes for brain size and resistance to malaria and TB.
Ex. Genes involved in producing transcription factors also differ more in humans
Ex. The FOXP2 gene involved with the production of speech varies by only 2 amino acids.

102. Comparisons within a species
Scientists are also comparing the sequences of different people.
Most of our differences are SNPs (single nucleotide polymorphisms).
They have found several million SNPs.

103. They have also found inversions,
deletions and duplications that appear to have no ill effects on people.
Such polymorphisms will be useful in studying human evolution and migration through history.
They also be used to identify disease genes and other genes related to human health.

104. Comparing developmental processes
Evolutionary developmental biology (Evo-devo) compares the develop process of organisms
and tries to trace its evolution.
They try to discover how changes in genomes can cause changes in body form.

105. Homeotic genes and the homeobox
Homeotic genes control the identity of body parts during embryo development.
Most animals have a sequence of 180 nucleotides in their homeotic genes
called a homeobox.

107. One part of the homeobox codes for a 60 amino acid long homeodomain
which is used to attach the transcription factor to the DNA strand.
This is, of course, essential for transcription to occur.

108. Which actual gene the homeodomain attaches to it determined by
other domains in the homeodomain-containing protein.
Different combinations of homeobox genes are active in
different parts of the embryo to control its development.

109. The homeobox sequence is very similar even between very different organisms such as people, mice and even fruit flies!
This leads scientists to believe that they evolved very early on.
The homeobox sequence is sometimes called a Hox gene for short.

110. In addition to the homeobox, many different species also have similar sequences for
components of signaling pathways.  

111. Changes in the regulatory sequence of an organism can
greatly alter its shape.
Ex. Differences in the number of segments with legs in insects vs. crustaceans such as shrimp.

113. The same Hox gene
may also have different effects in different species such as
turning on different genes
or increasing the expression of particular genes.

114. Plant vs. animal development
Differences: In animals, embryo development includes the movements of cells to new locations as part of the process.
This does not occur in plants.

115. Instead, plant morphogenesis depends on different planes of cell division and selective cell enlargement.
Animals use Hox genes as master controls
but plants use Mads-box genes which are very different from Hox genes.

116. Similarities: Both use a cascade of transcriptional regulators,
systematically turning genes on and off in sequence.

117. Evolutionists conclude from this that plants and animals diverged a very long time ago in evolutionary history
and that their common ancestor was probably a single celled eukaryote.