AP Bio Genomes and Their Evolution Notes Ch. 21

AP Bio Genomes and Their Evolution notes – Ch. 21 1

______is the study of whole sets of genes and their interactions.

______is the application of computational methods to the storage and analysis of biological data, especially that obtained from sequencing genes.

Human Genome Project The Human Genome Project began in ______and was an international research project designed to discover the ______of the ______base pairs of human DNA. It was completed in ______.

Before the project began, scientists were aware of the ______

______seen on the chromosomes when they were dyed. This allowed them to create a ______.

The project had 3 stages:

1. Constructing a ______of the 23 human chromosomes based on recombination frequencies when ______occurs during meiosis.

Scientists identified the locations of about 5,000 ______such as RFLPs, STRs and other polymorphisms (about 200 per chromosome).

2. ______- in which the distances between the markers is determined and measured by the number of ______between them. The DNA was cut by restriction enzymes into many fragments which were able to ______. Using probes or automated nucleotide sequencing machines, scientists were able to determine the correct ______of the pieces. Diagram: AP Bio Genomes and Their Evolution notes – Ch. 21 2

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

When all of these pieces of information are ______, one can know all the base pairs of a DNA strand in their proper ______.

Over the course of time, methods for sequencing DNA ______vastly, from 1000 base pairs per day in the 1980s to 1000 per ______by the year 2000.

Venter’s approach

J. Craig ______invented a new approach to gene sequencing in which he ______the linkage and physical maps and went directly to cutting up the entire genome and sequencing random DNA fragments using a powerful

______program to assemble the sequence of the many fragments based on their ______. This is called the ______

______approach. His independent group ______with the

Human Genome Project to complete the sequencing first. They tied. Recently it was found that his method can miss ______sequences and miss some genes that way. A ______approach seems to be the best way.

Using bioinformatics to analyze genomes and their functions

Websites on the Internet provide for centralized access to the ______

______databases that have been created, as well as software for analysis. One site, called ______, is constantly updated. Programs are available to compare a ______DNA sequence with every sequence in Genbank. Other programs allows comparisons of expected AP Bio Genomes and Their Evolution notes – Ch. 21 3

______sequences based on a particular DNA sequence.

Another creates ______based on DNA sequence relationships. There is also a site with all the 3-D ______structures that have been determined and their ______sequences.

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 ______start and stop codons.

2. Compare the sequence with those of ______identified gene or protein sequences from other organisms.

3. Experiment with ______genes, such as using RNAi, and seeing what ______has been disturbed in the organism with those genes.

Proteomics

Proteomics is the study of the ______that are encoded for by the genes of an organism.

Scientists now have a complete ______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 ______and protein

______networks. (How those parts actually fit and work together.)

Ex. Drosophila has about ______predicted RNA transcripts. Molecular techniques were used to determine which of them coded for proteins that could

______with each other. There were 4,700 proteins that could

______in 4.000 different reactions. AP Bio Genomes and Their Evolution notes – Ch. 21 4

The ______is a project that is using these techniques to compare the gene ______and patterns of gene ______in normal and cancer cells. 2,000 cancer genes will be sequenced at various ______of the disease to monitor changes.

A human ______has been developed which holds most of the human genes within its pits. They are being used to analyze

______in patients with various diseases such as cancer. Eventually we may each have our ______as a part of our medical records, with areas highlighted that indicate a ______for various diseases.

Comparing genomes

By the summer of 2007, the genomes of ______organisms were sequenced. Most were ______and archaea. _____ were eukaryotic animals, plants, protists and fungi.

A. In terms of ______of base pairs in the genome, eukaryotic genomes tend to be ______than prokaryotic genomes. There are 1-6 million base pairs (______) in prokaryotes, more than 100 Mb in eukaryotes. There is _____

______between the number of base pairs and the phenotype of the organism. Ex. A particular lily plant has 40 times ______base pairs than a human. (120,000 Mb vs. 3200 Mb) An amoeba has 670,000 Mb!

B. In terms of numbers of ______, eukaryotes have ______than AP Bio Genomes and Their Evolution notes – Ch. 21 5 prokaryotes. Again, the number of genes does ______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.

Scientists first expected humans to have about ______genes based on the numbers of known human proteins. One way that we get more proteins than genes is by ______. By cutting out the

______in several ways, we get several proteins from the ______gene sequence.

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

Bacteria do not have ______.

In eukaryotes, most of the DNA ______code for a protein or RNA.

We have ______times more noncoding DNA than bacteria. Some of the noncoding DNA is ______and there are more ______regulatory sequences. Eukaryotes have vast stretches of ______DNA between genes.

Noncoding DNA in Eukaryotes

It was previously thought that noncoding DNA was “______” DNA and served no purpose. However, some of the ______sequences are found in many different genomes of very ______organisms. Ex. Humans, rats and mice have 500 regions of noncoding DNA that are

______. This noncoding DNA is even more carefully ______than the DNA that AP Bio Genomes and Their Evolution notes – Ch. 21 6 codes for protein, so it must be ______in its function.

Only ______of the human genome codes for proteins or is transcribed into tRNA or rRNA. 24% codes for ______and regulatory sequences.

15% codes for ______DNA –

Ex. ______which are thought to have coded for something longer ago but have mutated and are no longer expressed.

15% is ______unrelated to transposable elements

44% is repetitive DNA that includes ______and related sequences

Pie graph:

Transposable elements

A transposable element is a stretch of DNA that can ______to another location in the genome. The process of moving is called ______.

This idea was first presented by Barbara ______in the 1940’s based on her work with the changing kernel colors found in ______corn.

2 kinds of eukaryotic transposable elements:

1. ______– They can either be completely ______AP Bio Genomes and Their Evolution notes – Ch. 21 7

from the original site and moved elsewhere, or they can be copied and a ______moved to a new site. Diagram:

2. ______– First, an ______intermediate is made from

the DNA section. Then ______makes DNA

from the RNA. The new DNA is put into the ______in a new location.

The reverse transcriptase is ______for by the retrotransposon itself. Diagram:

______of the mammalian genome is made of transposable elements such as transposons and retrotransposons.

Other Repetitive DNA

A. Some of the repeating DNA in the human genome is ______sequences of

10,000-300,000 base pairs. It is thought this DNA arises from ______in DNA replication.

B. ______– 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).

It is often found near the ______and at the telomeres of the chromosome. AP Bio Genomes and Their Evolution notes – Ch. 21 8

It may be important in the ______of the chromosome.

Ex. It may help ______the chromatin during interphase, it helps prevent important DNA ______through the telomeres and it is important in proper ______of chromatids during cell division.

C. ______(STR)- Simple

sequence DNA with 2-5 base pairs. The ______of repeats can vary from

person to person, so it is useful in comparing ______to distinguish between people’s DNA.

Genes and Multigene Families

About half of the human genes are located ______within the genome, with only ______gene existing for that protein.

The other half occur in ______– collections of two or more identical or similar genes. If the members of the multigene family are ______, they code for

______or ______, which are both needed in large quantities by the cell. Ex. There may be ______of genes for the same rRNA molecule repeated tandemly on the chromosome. The mRNA that is produced is ______into 3 pieces, which code for 3 of the 4 rRNA molecules that are needed to make a

______for protein synthesis.

______genes can also occur in families.

Ex. One family of genes on human chromosome 16 codes for various forms of ______-

______and a similar family is found on chromosome 11 codes for various forms of ______-______. Both are used in production of

______. The different forms are expressed at different AP Bio Genomes and Their Evolution notes – Ch. 21 9

______over a person’s life. One form is expressed in the embryo and fetus because it has higher ______for oxygen, so the embryo/fetus is better able to obtain oxygen from the ______blood. A different form with a

______oxygen affinity is expressed in adulthood.

Genome evolution

It is thought that the earliest forms of life would have had a ______number of genes – just those necessary for survival and reproduction.

Over time, there must be an ______the number of genes, providing raw material for gene diversification.

Methods of increasing the genome size:

A. ______– An accident in meiosis results in offspring with one or more extra ______of chromosomes. Polyploidy generally is ______in animals (they die). However, some ______are able to survive despite polyploidy. ______could occur in one set of genes to provide new proteins and traits, while the other set provides for the ______functions of the organism.

B. Alterations of chromosome structure – Sometimes chromosomes will ______together, creating organisms with fewer chromosomes. These organisms may no longer be able to mate, since ______in meiosis would be affected. This could create new ______.

Chromosomes also ______sometimes and reattach with inversions and duplications which may result in new species.

Several chromosome rearrangements result in congenital ______and miscarriage in humans. AP Bio Genomes and Their Evolution notes – Ch. 21 10

C. ______duplication and divergence – Errors in meiosis such an

______crossing over event can also result in just one gene being

______or deleted.

D. Slippage during DNA ______can also result in duplications or deletions of small areas.

It is thought that the various forms of ______are the result of duplication and divergence by mutation. A ______of gene sequences within a multigene family can suggest the ______in which the genes arose. Diagram:

Gene duplication and mutation is thought to also be able to produce genes with

______(new) functions.

Ex. ______is an enzyme that protects animals from bacteria by hydrolyzing bacterial cell walls. It is very similar to another protein called

______– which is used in milk production in mammals. Both birds and mammals make lysozyme, but only ______make lactalbumin.

So at some time ______birds and mammals had branched off from each other in the evolutionary process, the lysozyme gene was ______, then mutated to form lactalbumin. AP Bio Genomes and Their Evolution notes – Ch. 21 11

Ways to create new genes by rearrangement

A. ______– Unequal crossing over during meiosis could cause one exon to be duplicated on one chromosome and create one chromosome that

______it. Remember that an exon generally codes for a ______(a structural or functional unit of a protein). The extra exon could create a new

______.

Ex. ______has a very repetitive amino acid sequence which therefore has a very ______sequence on the chromosome.

Diagram:

B. ______– The new sequence of exons on a chromosome could be created by errors in ______to eventually create a new gene from ______different exons. Diagram:

How transposable elements contribute to genome evolution

As ______elements are moved to new locations on chromosomes, they can cause new ______to develop in several different ways: A. A ______element in the middle of a protein-coding sequence AP Bio Genomes and Their Evolution notes – Ch. 21 12 will prevent a ______version of that protein from being produced. It may also create a ______protein with a new function due to the added domain.

B. If the transposable element inserts in a ______sequence, it may cause ______or decreased production of the protein.

C. The transposable element may move a gene or group of genes to a ______chromosome and create new ______when crossing over occurs with that chromosome. All of these processes will generally produce ______effects to the organism as normal proteins are disrupted, however a few might be ______in some way.

Comparing genome sequences provides clues to evolution and development

Assuming that evolution has occurred, the more similar in ______the genomes of two species are, the more ______related they are in their evolutionary history and the more ______they probably split from each other.

A. Comparing ______related species allows us to see which genes have been ______(stayed the same) over time. This can help us trace evolutionary ______.

B. Comparing ______related species genomes can help us identify the differences between them. Ex. What makes a ______different from a human?

Comparisons between human and chimp DNA

A. There are only about ______differences between humans and chimps. AP Bio Genomes and Their Evolution notes – Ch. 21 13

B. Most differences are due to ______or deletions, some are duplications and other ______DNA.

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

______in humans than in the other organisms. Ex. Genes for ______

______and resistance to malaria and TB. Ex. Genes involved in producing

______factors also differ more in humans

Ex. The ______gene involved with the production of speech varies by only

2 amino acids.

Comparisons within a species

Scientists are also comparing the sequences of ______people. Most of our differences are ______(single nucleotide polymorphisms). They have found several ______SNPs. They have also found ______, deletions and duplications that appear to have ______effects on people.

Such ______will be useful in studying human evolution and

______through history. They also can be used to identify

______genes and other genes related to human health.

Comparing developmental processes

Evolutionary developmental biology (______) compares the develop process of organisms and tries to trace its ______. They try to discover how changes in genomes can cause changes in ______. AP Bio Genomes and Their Evolution notes – Ch. 21 14

Homeotic genes and the homeobox

Homeotic genes control the identity of ______during embryo development. Most animals have a sequence of ______in their homeotic genes called a ______. One part of the homeobox codes for a 60 amino acid long ______which is used to ______the transcription factor to the DNA strand. This is, of course, ______for transcription to occur. Which ______the homeodomain attaches to it determined by ______in the homeodomain-containing protein. Different ______of homeobox genes are active in different ______of the embryo to control its development.

The homeobox sequence is very ______even between very different organisms such as people, mice and even fruit flies! This leads scientists to believe that they evolved very ______on. The homeobox sequence is sometimes called a

______for short.

In addition to the homeobox, many different species also have ______sequences for components of ______.

Changes in the regulatory ______of an organism can greatly alter its ______.

Ex. Differences in the number of ______with legs in insects vs. crustaceans such as shrimp.

The ______Hox gene may also have ______effects in different AP Bio Genomes and Their Evolution notes – Ch. 21 15

species such as turning ______different genes or increasing the expression of particular genes.

Plant vs. animal development

Differences: In animals, embryo development includes the ______of cells to new locations as part of the process. This does ______occur in plants.

Instead, plant morphogenesis depends on different ______of cell division and selective cell enlargement. Animals use ______genes as master controls but plants use ______genes which are very different from Hox genes.

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

Evolutionists conclude from this that plants and animals diverged a very ______time ago in evolutionary history and that their common ancestor was probably a single- celled ______. AP Bio Genomes and Their Evolution notes – Ch. 21 16