Cambell Biology Chapter 21: Genomes and their Evolution

Therefore we must study when and where are proteins are produced in an organism as well as

how they interact in networks , if we are to understantd the functioning of cells and organisms

CNVs and SNPs are useful for studying

human evolution

Where is polyploidy most common?

plants; Some botanists estimate that as many as 80% of the plant species alive today, have some polyploidy occuring in their ancestral species

transposons and retrotransposons

two types of eukaryotic transposable elements comprise about a lot of human genome

Genomics

study of whole genomes, including genes and their functions

transposons

(jumping genes) short strands of DNA capable of moving from one location to another within a cell's genetic material; They move via a double-stranded DNA intermediate

Junk DNA

genomic DNA that does not encode proteins, and whose function, if it has one, is not well understood.

The Human Globin Genes

-multi-gene family -evolved by successive gene duplications

Humans have as much as

10,000 times as much as noncoding DNA as Bacteria

Other repetitive DNA

14% of the human genome consists of repetitive DNA due to resulting errors of replication. 1/3 of DNA consists of duplicated DNA from one location to another.

There are about 4,300 completely sequenced genomes with

4000 genomes of Bacteria, 186 Archea, and 183 vertebrates

Gene regulatory sequences and introns account respectively for about

5% and 20% of the human genome

The genomes of humans, rats, and mice contain alomost

500 regions of noncoding DNA that are identical in sequence for all three species

The gene FoxP2 has been evolving rapidly in humans, but not in primates. The wild type protein product of FoxP2 in mice is involved in _______. A. Vocalization B. Complex speech C. Damaging brain structure

A

Viruses like HIV most likely evolved from ______ because _________. A. retrotransposons; they encode reverse transcriptase B. transposons; they are mobile genetic elements C. retrotransposons; they always leave a copy at the original site during transposition D. transposons; they encode transposase E. transposons; they move via a "copy and paste" mechanism

A

What is the purpose of functional maps in systems biology? A. To organize genes and proteins by function. B. To learn more about Saccharomyces cerevisiae. C. To organize organs by function into body systems. D. To better understand each body system individually.

A

Which is a difference between the globin superfamily and lysozyme/alpha-lactalbumin? A. Lysozyme and alpha-lactalbumin have vastly different functions. B. Only the globin superfamily arose from gene duplication. C. The globin family came from one ancestral gene. D. Lysozyme and alpha-lactalbumin are not similar in their sequence or structure. Question 15

A

Homeobox

A 180-nucleotide sequence within homeotic genes and some other developmental genes that is widely conserved in animals. Related sequences occur in plants and yeasts. Codes for a 60-amino acid homeodomain in encoded proteins

Simple Sequence DNA

A DNA sequence that contains many copies of tandemly repeated short sequences. Accounts for about 3% of human genomes ~ included in the other repetitive DNA category

multigene families

A collection of genes with similar or identical sequences, presumably of common origin.

Homeodomain

A conserved sequence of 60 amino acids used in the binding to DNA. Usually found in transcription factors, it is used to express genes that are related, more specifically in development to make tissues associated with one another.

GenBank

A database of previously sequenced and identified genes available through the NCBI

ENCODE (Encyclopedia of DNA Elements)

A goal of the ENCODE Project is to link variations in the expression of certain genes to the development of disease. The ENCODE Project has given researchers insight into how the human genome functions

whole-genome shotgun sequencing

A method for determining the DNA sequence of an entire genome. After a genome is cut into small fragments, each fragment is sequenced and then placed in the proper order. It is widely used today

sequencing by synthesis (SBS)

A next-generation form of DNA sequencing in which the synthesis of DNA is directly monitored to deduce the base sequence. * Has resulted in massive increases in speed and decreases cost of sequencing a genome

Gene Annotation

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

The Cancer Genome Atlas (TCGA)

A project to sequence the genomes of many different cancers to identify the types of mutations that develop, , by comparing gene sequences and patterns of gene expression in cancer cells with those in normal cells

expressed sequence tag (EST)

A short sequenced fragment of a cDNA sequence that can be used to identify an actively expressed gene. These tags are found by a software and are cataloged in computer databases. This type of analysis identifies sequences that may turn out to be previously unknown protein-coding genes.

Select the true statements about genomes of bacteria, archaea and eukaryotes. A. Bacteria and archea have roughly the same genome size, both of which are smaller than eukaryotes. B. Eukaryotes have many more genes on average than prokaryotes. C. Animal genomes are larger than plant genomes. D. Genome size and gene density are negatively correlated. E. The number of genes positively correlates with body size.

A, B, D

Select the true statements regarding next-gen and shotgun sequencing. A. Both require the DNA to be cut up into small pieces. B. Shotgun sequencing is newer and faster. C. Both require the use of plasmids to amplify the DNA. D. Shotgun sequencing requires the use of plasmids for cloning, next-gen does not.

A, D

Which statements accurately describe the function of homeotic genes? A. To generate the individual identities of various body regions. B. To create the human body plan from an embryo. C. To generate developmental disabilities. D. To bind to DNA using the homeobox region. E. To regulate transcription of downstream genes.

A, D, E

large segment duplications

Account for about 5-6 % of the other repetitive DNA category. These are duplications of long stretches of DNA about 10,000-300,000 base pairs long. These long segments seem to have been copied from one chromosomal location to another site on the same or a different chromosome and probably include some functional genes

duplication of entire chromosome sets

An accident in meiosis can result in one or more extra sets of chromosomes, a condition known as polyploidy

systems biology

An approach to studying biology that aims to model the dynamic behavior of whole biological systems based on a study of the interactions among the system's parts.

Lysozyme

An enzyme that destroys bacterial cell walls; in mammals, found in sweat, tears, and saliva.

The Human genome project

An international collaborative effort to map and sequence the DNA of the entire human genome. Began in 1990 Completed in 2006 The ultimate goal of mapping any genome is to determine the complete nucleotide sequence of each chromosome

Medical Relevance

Analysis of the chromosomal breakage points associated with the rearrangement showed that specific sites for used over and over again. A number of these recombination hotspots correspond to locations of chromosomal rearrangements within the human genome that are associated with congenital diseases

Homeotic Genes

Any of the genes that control the overall body plan of animals by controlling the developmental fate of groups of cells.

Bioinformatics uses

Apart from analysis of genome sequence data, bioinformatics is now being used for a vast array of other important tasks, including analysis of gene variation and expression, analysis and prediction of gene and protein structure and function, prediction and detection of gene regulation networks, simulation environments

Comparing Genomes Within a Species

As a species, humans have only been around about 200,000 years and have low within-species genetic variation Variation within humans is due to single nucleotide polymorphisms (SNPs), inversions, deletions, and duplications Most surprising is the large number of copy-number variants These variations are useful for studying human evolution and human health

Where is much of the genome's simple sequence DNA located?

At telomeres and centromeres, suggesting that this DNA plays a structural role for chromosomes

What is gene annotation? A. Observing an organism's phenotype and deducing its genotype. B. Identifying the function of a gene from its sequence. C. Identifying the genotype of an individual based on pedigree analysis. D. None of the above

B

_____% of the human genome encodes protein or ncRNA. A. 0.001% B. 1.5% C. 10% D. 30% E. 50% F. 75%

B

Scientists use bioinformatics

Bioinformatics research uses computer software and algorithms to perform gene annotation, the process of identifying genes, determining their function, and recording their position. Once genes are sequenced, they can be uploaded into a data bank used to store and compare hundreds of thousands of sequences.

Widespread conversion of Developmental Genes among animals

Biologists in the field of evolutionary developmental biology, or evo-devo as it is often called, compare developmental processes the different multicellular organisms. Their aim is to understand how these processes have evolved and how changes to them can modify existing organismal features or lead to new ones

alterations of chromosome structure

Breakage of a chromosome can lead to four types of changes in chromosome structure Deletion removes a chromosomal segment Duplication repeats a segment Inversion reverses orientation of a segment within a chromosome Translocation moves a segment from one chromosome to another

Nondisjunction events in meiosis can cause polyploidy. For which group is polyploidy a common route for speciation? A. Invertebrates B. Vertebrates C. Plants D. Archaea E. Bacteria

C

Hox Genes

Class of homeotic genes. Changes in these genes can have a profound impact on morphology. Short for homeobox-containing genes, because homeotic genes were the first genes found to have this sequence *Other homeobox-containing genes were later found that do not act as homeotic genes; that is they do not directly control the identity of body parts

Comparing genome sequences provide clues to evolution and development

Comparisons of genome sequences from different species reveal a lot about the evolutionary history of life, from very ancient to more recent. Similarly, comparative studies of the genetic programs that direct embryonic development in different species is beginning to clarify the mechanisms that generated the great diversity of Life - forms present today.

Human and chimpanzee genomes

Considering single nucleotide substitutions, the two genomes differ by only 1.2%. when researchers look at longer stretches of DNA, however, they were surprised to find a further 2.7% difference due to insertions or deletions of larger regions in the genome of one or the other species; many of the insertions were duplications or other repetitive DNA

Which statement might explain the disparity in gene density in prokaryotes and eukaryotes? A. Eukaryote genomes are more dense because they have much more information they have to encode. B. Eukaryote genomes are more dense because they can alternatively splice their mRNAs. C. Prokaryote genomes are more dense because they do not have regulatory sequences. D. Prokaryotes genomes are more dense because they don't have introns.

D

*

Developmental biologists have found that in addition to homeotic genes, many other genes involved in development are highly conserved from species to species. These include numerous genes encoding components of signaling pathways.

copy number variation (CNV)

Difference among individual organisms in the number of copies of any large DNA sequence (larger than 1000 bp). *Since these variants of encompass much longer stretches of DNA than the single nucleotides of SNPs, CNVs are more likely to have phenotypic consequences and to play a role and complex diseases and disorders.

Barbara McClintock

Discovered the ability of genes to change positions on the chromosome

*

Diversification of genes and their products is an important factor in the evolution of species. Thus, the accumulation of changes in the Genome of each species provides a record of its evolutionary history. To read this record, we must be able to identify genomic changes.

Which is a way that geneticists can determine the function of an unknown gene? A. Comparing the predicted amino acid sequence to those of other known genes. B. Comparing the DNA sequence with other known genes. C. Looking for cDNA that specifies known mRNAs in the DNA sequence. D. Using in situ mutagenesis or RNAi to knock out a gene, then observing what happens. E. All of the above.

E

Gene Density and Noncoding DNA

Eukaryotes generally have larger genomes but fewer genes in a given number of base pairs. Humans have hundreds or thousands of times as many base pairs in their genomes as most most bacteria, as you have already noted but only 5 to 15 times as many genes; thus gene density is lower in humans

Evo-Devo

Evolutionary developmental biology; a 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.

Globin superfamily

Evolved from mutations in the original GLOBIN ANCESTRAL GENE. Myoglobin and leghemoglobin are part of this family

Rearrangements of Parts of Genes: Exon Duplication and Exon Shuffling

Exon shuffling is the process of creating new genes by the breaking and joining of DNA molecules that results in combining some exons from one gene with some exons from another gene. The resulting "hybrid" gene may code for an entirely new protein with a new function A particular exon within a gene could be duplicated on chromosome and deleted from the other due to unequal crossing over. Quite a few protein-coding genes have multiple copies of related exons, which presumably arose by duplication and then diverged

Which is NOT a way genomes can change over time? A. Chromosomes can duplicate due to nondisjunction. B. Chromosomes can fuse together over time. C. Genes can duplicate due to errors in crossing over. D. Exons can be duplicated and shuffled around in the genome. E. Transposons can bring other genes with them during transposition. F. None of the above.

F

One transcription factor whose gene shows evidence of rapid change in the human lineage is called the

FOXP2 gene

Besides the regions encoding protein and ncRNA, the rest of the genome is "junk DNA".

False

Short repetitive sequences make sequencing more accurate than it otherwise would be because DNA fragments can be paired more easily.

False

*

FoxP2 experiments used mice as a model for humans because it would be unethical to carry out such experiments in humans. Mice and humans, which diverged 65 million years ago share about 85% of their genes. This genetic similarity can be exploited in studying human genetic disorders. If researchers know the organ or tissue that is affected by a particular genetic disorder, they could look for genes that are expressed in these locations in mice

Duplication and Divergence of Gene-Sized Regions of DNA

Gene duplication can occur several times over, leading to an organism having multiple copies of a given gene. With time, extra copies of a gene can undergo mutation, causing them to be slightly different from the original gene. * Usually caused by errors in meiosis and some regions may be the size f genes

Centralized Resources for analyzing Genome sequences

Government funded agencies carried out their mandate to establish databases and provide software with which scientists could analyze the sequence data EX: NCBI Not to important concept PAGE 438

Comparing Distantly Related Species

Highly conserved genes have changed very little over time These help clarify relationships among species that diverged from each other long ago Bacteria, archaea, and eukaryotes diverged from each other between 2 and 4 billion years ago Highly conserved genes can be studied in one model organism, and the results applied to other organisms Very ancient genes can still be suprisingly similar is disparate species. Can help clarify evolutionary relationships among species that diverged from each other long ago

Neanderthals

Homo sapiens neanderthalensis, a European variant of Homo sapiens that died out about 25,000 years ago. May have coexisted with other Humans

The extraordinary similarity among some developmental genes in different animal species raises the question:

How can the same genes be involved in the development of animals whose forms are so very different from each other?

Invertebrates and vertebrates of many different species are patterned by homeotic genes, abbreviated "____" genes in animals.

Hox

Evolution of Genes with related functions

In certain multigene families, the genes of the family arose due to duplication and mutation of a single gene.

unequal crossing over

Misalignment of the two DNA molecules during crossing over, resulting in one DNA molecule with an insertion and the other with a deletion

sequences related to transposable elements

Multiple copies of transposable elements and sequences related to them are scattered throughout the eukaryotic genome. A single unit is usually hundreds of thousands of base pairs long, and then dispersed "copies" are similar but usually not identical to each other. Some of these are transposable elements that can move; the enzymes required for the movement may be encoded by any transposable element, including the one that is moving. Others are sequences that have lost ability to move all together. Transposable elements and related sequences make up 25 to 50% of most mammalian genomes.

*

In embryos of drosophila and other animal species, different combinations of homeobox genes are active in different parts of the embryo. The selective expression of regulatory genes, varying over time and space, is central to pattern formation

*

In general, most bacterial genomes have somewhere around 1 to 6 million base pairs. For example, E. coli, a bacterium, has 4.6 million base pairs (which we can abbreviate as 4.6 Mb). The genome sizes for archaea are pretty similar to those of bacteria, but compared to both of these domains many eukaryotic genomes are larger Most plants and animals, which are multicellular, have genomes at least 100Mb. 165 on fruit fly, 3,000 on humans, about 500-1000 times the bacteria

Alu Elements

In humans and other planets, a large portion of Transposable element - related DNA consists of a family of similar sequences called Alu elements. These sequences alone account for approximately 10% of the human genome. Alu elements are about 300 nucleotides long, much shorter than most functional transposable elements, and they do not code for proteins. However many Alu elements are transcribed into RNA, and at least some of these RNAs are thought to help regulate gene expression

Suggested answers:

In some cases, small changes and Regulatory sequences of particular genes cause changes in gene expression patterns that lead to major changes in body form. EX:The different patterns of expression of the Hox genes along the body axis and insects and Crustaceans can explain these segmented animals. In other cases, similar genes directed different developmental processes in various organisms, resulting in diverse body shapes. Several Hox genes, for instance, are expressed in the embryonic and larval stages of the sea urchin, a non-segmented animal has a body plan quite different from those of insects and mice. PAGE 458 HAS A GOOD PICTURE

Evolution of Genes with Novel Functions

In the evolution of the globin Gene families, Gene duplication, and subsequent Divergence produced family members whose protein products performed similarly to each other. However, an alternative scenario is that one copy of a duplicated Gene can undergo alteration that lead to a completely new function for the protein product. The genes for lysozyme and a-lactalbumin are good examples of this type of situation

Metagenomics

In which DNA from an entire group of species is collected from an environmental sample and sequenced. This approach was facilitated by technological advances

WD40 Domain

Interacts with specific proteins to be degraded

What is a striking finding by the ENCODE project?

Is that about 75% of the genome is transcribed at some point in at least one of the cell type studies, even though less than 2% codes for proteins. Furthermore, biochemical functions have been assigned to the DNA elements making up at least 80% of the genome. To learn more about the different types of functional elements, parallel projects are analyzing in a similar way the genomes up to model organisms, a fruit fly and a soil nematode

Chromosomal rearrangements may be important in evolution because __________.

It may lead two populations to unsuccessfully mate, a step towards the way of becoming two separate species * Although individuals with different Arrangements could still mate and produce Offspring, The offspring would have two nonequivalent sets of chromosomes, making meiosis inefficient or even impossible

Lysozyme and a-lactalblumin

It's the proteins are quite similar and their amino acid sequences and 3 - dimensional structures. Both genes are found in mammals, whereas only the lysozyme gene is present in Birds. These findings suggest that mammals and birds have separated the lysozyme gene was duplicated in the mammalian lineage but not in the avian lineage

Comparing Genomes

Learning about characteristics that are shared or divergent between groups enhances our picture of the evolution of organisms and biological processes

Do all humans share the same genome?

No

repetitive DNA

Nucleotide sequences, usually noncoding, that are present in many copies in a eukaryotic genome. The repeated units may be short and arranged tandemly (in series) or long and dispersed in the genome. Take up most of the DNA genome Surprisingly 75% of this repetitive DNA (44% of the human genome) is made of units called transposable units and sequences related to them

Genome sizes and estimated number of genes

PAGE 442 HAS A GOOD COMPARISON TABLE

The existence of several psuedogenes among the functional globin genes show that:

Random mutations in these "genes" over evolutionary time have destroyed their function

genomes vary in number of genes

Scientists estimate that the human genome, for example, has about 20,000 to 25,000 protein-coding genes. Before completion of the draft sequence of the Human Genome Project in 2001, scientists made bets as to how many genes were in the human genome. Most predictions were between about 30,000 and 100,000.

Human and Mouse Chromosome Comparison

Scientists found in a study that large blocks of genes on human chromosome 16 are found on four Mouse chromosomes, indicating that the genes and each block stayed together in both the mouse and the human lineages during their divergent evolution from a common ancestor

copy and paste mechanism

happens in transposons

Noncoding DNA

Sequences of a gene's DNA (also known as introns) that are not coded to produce specific proteins and are excised before protein synthesis.

Genomes vary in size

Smallest virus - 4-5 genes E. coli - single chromosome containing 4,288 genes; 1 mm; 1,000X longer than cell Human cell - 46 chromosomes containing 31,000 genes; 6 feet; 180,000X longer than cell

Scientists have known long enough that

The ancestors of humans and chimpanzees diverged a species, the fusion of two ancestral chromosomes in the human line let the different haploid numbers for humans (n = 23) and chimpanzees (n = 24) *Chromosomes 12 and 13 fused together end to end

Identifying Protein-Coding genes and Understanding their Functions

Using available DNA sequences, genecists can study genes directly. A more recent approach poses a new challenge: What does a gene actually do? Given a long DNA sequence from a data base such as GenBank, scientists aim to identify all protein-coding genes in the sequence and ultimately their functions, a process called gene annotation

*

We can deduce that homeobox DNA sequence evolved very early in the history of life and was sufficiently valuable to organisms have been conserved in animals and plants virtually unchanged for hundreds of millions of years

Protein function is usually deduced through a combination of biochemical and functional studies

The biochemical approach aims to determine the three-dimensional structure of the protein as well as other attributes, such as potential binding sites for other molecules. Functional studies usually involve blocking or disabling the gene of an organism to see how the phenotype is affected. RNAi is such an example.

Comparing Closely Related Species

The genomes of two closely related species are likely to be organized similarly because of their relatively recent Divergence. The recent divergence of two closely-related species also underlies some small number of gene differences that are found when their genomes are compared. The particular genetic differences can therefore be more easily correlated with phenotypic differences between the two species. Comparing the genomes of a chimpanzee, mouse, rat, and other mammals should give us clues about what it takes to make a mammal. And comparing the human genome with that of a chimpanzee will help us answer the tantalizing question: What genomic information defines a human or a chimpanzee

"more bang for the buck"

The idea that human genes will get more for their coding sequences because of alternative splicing of RNA trancscripts. A typical human gene contains about 10 exons, and an estimated 90% or more of these multi-exon genes are spliced in at least two different ways

Two approaches which complemented each other in obtaining the complete sequence

The initial approach was a methodical one built on an earlier storehouse of human genetic information However later this was changed to an alternative strategy called the whole genome shotgun approach

Duplication and Divergence

The process of creating new genes by duplication followed by change in sequence over evolutionary time.

In the human genome and the genomes of many other plants, solitary genes make up less than half of the total gene-related DNA.

The rest occur in multigene families

Are homeobox sequences similar in invertebrates and vertebrates.

The sequences are very similar between humans and fruit flies

Genome Size

The total amount of DNA contained within one copy of a single genome

Metagenome

The total gene content of the organisms present in an environment

Bioinformatics

The use of computers, software, and mathematical models to process and integrate biological information from large data sets.

Although many transposable elements encoded proteins,

These proteins do not carry out normal cellular functions. Therefore transposable elements are usually included in the "noncoding" DNA category, along with other repetitive sequences

How Transposable Elements Contribute to Genome Evolution

Transposable elements (TEs) are DNA sequences that are capable of integrating into the genome at a new site within the cell of its origin. Sometimes, the change in their positions creates or reverses mutations, thereby altering the cell's genotype. Transposable elements can cause deletions or inversions of DNA. When transposition generates two copies of the same sequence in the same orientation, recombination can delete the DNA between them. If the two copies are in the opposite orientations, recombination will invert the DNA between them. * When they move they may carry along a gene or even a group of genes to a new position on a genome. By a similar process, an exon from one gene may be inserted in a mechanism similar to that of exon shuffling during recombination

Retrotransposons

Transposable elements that move within a genome by means of an single-stranded RNA intermediate, a transcript of the retrotransposon DNA. Uses reverse transcriptase

The more similar the genomes, the closer related the species are.

True

Gene duplication due to unequal crossing over

Unequal crossing over is a type of gene duplication or deletion event that deletes a sequence in one strand and replaces it with a duplication from its sister chromatid in mitosis or from its homologous chromosome during meiosis * Can cause species to diverge

Retrotransposition

a form of transposition in which the element is transcribed into RNA. The RNA is then used as a template via reverse transcriptase to synthesize a DNA molecule that is integrated into a new region of the genome via integrase

FOXP2

a gene that is important in language and speech production Its gene product turns on genes involved in vocalization

The development of technology for faster sequencing was

a major push for the Human Genome project

Sometimes...

a newly identified sequence will match at least partially, the sequence of a gene or protein and other species whose function is well known

a-lactalbumin

a nonenzymatic protein that plays a role in milk production in mammals

TPA (tissue plasminogen activator)

a powerful chemical that dissolves blood clots in vessels supplying the brain Is thought to be a product of exon shuffling in the wat that it may have arise by several instances of exon shuffling and duplication

Human Gene Microarray Chip

a silicon, glass chip that is placed in patients with various types of cancer/disease. the chip enables researchers to know the gene expressed within the patient to help them find treatment.

Transposition

a transposable element moves from one site in a cell's DNA to a different target site by a type of recombination process Can be transposons or retrotransposons (retrotransposition)

The total amount of DNA that is gene-related is

about 25% of the human genome including coding and noncoding strands

The genes in one or more of the extra sets can diverge by

accumulating mutations these variations may persist if the organism carrying them survives and reproduces

How was the human genome sequenced?

by looking for overlapping regions between sequenced DNA fragments Mainly using sequencing machines

The systems biology approach

can be applied to define gene circuits and protein interaction networks PAGE 441

template slippage

causes frameshift mutations Strand slips and bases pop out or hydrogen bonds slip a little which cause DNA polymerase to think it didn't add bases, so it adds in more Basically, a segment of DNA is deleted or duplicated

1.5% of the DNA sequences in the Human Genome

code for proteins or is transcribed into rRNAs or tRNAs

Describe and give an example of each of the following: multigene families of identical DNA sequences and multigene families of nonidentical genes

collections of 2+ identical or very similar genes, sequences are usually randomly clustered, ex: family of identical DNA sequences that are the genes for the three largest RNA molecules, so basically the rRNA gene family, and this is what allows millions of ribosomes to be made two related families of genes that encode globins, ex: in humans embryonic and fetal forms of hemoglobin have a higher affinity for oxygen than the adult forms One family which encodes the 'a' globin is located on chromosome 16, while the family that encodes for 'b' globin is located on chromosome 11 *The different forms of each globin are expressed at different times in development, allowing hemoglobin to function effectively in the changing environment of the developing animal.

Additional polypeptide diversity

could also result from post-transitional modifications such as cleavage or addition of carbohydrate groups

One important use of systems biology is to

define gene and protein interaction networks. To map the protein interaction network in yeast for instance researchers use sophisticated techniques to knock out pairs of genes, one pair at a time, creating doubly mutant cells. They then compared the fitness of each double mutant to that predicted from the fitness of each of the two single reasons. The researchers reasoned that if the observed fitness matched the prediction, then the products of the two genes didn't interact with each other, but if the observed fitness match the prediction, then the products of the two genes interacted in the cell. They then graph this using a computer software and build a graphic model

Evidence that unequal crossing-over and template slippage during DNA replication lead to

duplication of genes is found in the existence of multi-gene families such as the globin family

How is fetal hemoglobin different from adult hemoglobin? What is the selective advantage of these different B-globin genes?

fetal hemoglobin have a higher affinity for oxygenhelps ensure efficient transfer of oxygen from mother to fetus

Psuedogenes and gene fragments

former genes that have accumulated mutations and are nonfunctional account for about 15% of the DNA

National Center for Biotechnology Information

funded by US tax dollars and is one of the world's best collections of databases for biomedical information

high throughput

methods that can analyze biological materials very rapidly and produce enormous volumes of data.

In all bacterial genomes

most of the DNA consists of genes for proteins, tRNA, or rRNA; the small amount remaining consists mainly of non transcribed regulatory sequences, such as promoters

Systems Biology is a very efficient way to

study emergent properties at the molecular level

The DNA at telomeres is essential for

preventing genes from being lost as DNA shortens with each round of replication. Telomeric DNA also binds proteins that protect the ends of a chromosome from the degradation and from joining two other chromosomes. Short repetitive sequences like those described here provide a challenge for the whole-genome shotgun sequencing, because the presence of many short repeats hinder accurate reassembly of fragment sequences by computers.

Besides duplication and divergence of whole genes

rearrangement of existing DNA sequences within genes has also contibuted to genome evolution. The presence of introns may have promoted the evolution of new proteins by facilitating the duplication of shuffling of exons.

Transposable elements

stretches of DNA that can move from one location to another within the genome Genetic element that has the ability to move (transpose) from one site on a chromosome to another. Do transposition

How Systems are studied

systems biology approach model the dynamic behavior of whole biological systems, gene circuits and protein interation networks, microarrays, cancer project iin different stages to look at the entire organism as one body

Due to redundancy of the genetic code

the DNA sequence itself may vary more among species than protein sequences. The scientists are interested in protein and often compare the predicted amino acid sequences of a protein to that of other proteins

Proteome

the entire set of proteins expressed by a given cell or group of cells

Transposase

the enzyme which recognizes host DNA and cuts and glues transposons in and out of the genome generally coded by transposons, and can use both mechanisms of transposons: cut-and-past, and copy-and-paste which uses a double-stranded DNA intermediate

There are more Alu elements in

the human genome than in the chimpanzee genome, and the latter contains many copies of a retroviral provirus not present in humans

The DNA at centromeres is essential for

the separation of chromatids and cell division. Centromeric DNA, along with simple sequence DNA located elsewhere, may also help organize the chromatin within the interphase.

Proteonomics

the study of an organism's complement of proteins and functions mediated by the proteins

Function of Homeobox encoded homeodomain is to

to bind to the DNA when the protein functions as a transcription factor. Elsewhere in the protein, domains that are more variable interact with other transcription factors, allowing the homeodomain-containing protein to recognize specific enhancers and regulate the associated genes. Proteins with homeodomains probably regulate development by coordinating the transcription of batteries of developmental genes, switching them on or off PAGE 457 HAS A GOOD PICTURE

LINE-1 (L1)

~ type of retrotransposons ~ accounts for approx. 17% of the human genome ~ 6,500 base pairs long ~ low rate of transposition ~ L1 blocks progress of RNA Polymerase which is needed for transposition ~seem to be more active in the brain and developing neurons