Chapter twenty one: genomes and their evolution

Q1: what is genimics?

A1: with the genimes of many species fully sequenced, scientists can study whole sets of genes and their interactions.
Q2: what is bioinformatics?

A2: the applicaiton of computational methods to the storage and analysis of biological data.

Q3: how can we determin genime evolution?

A3: by comparing genome sequences provides clues to evolution and development

Five Facts:

1. new approaches have accelerated the pace of genome sequencing

2. scientists use bioinformatics to analyze genomes and their function

3. genome vary in size, number of genes, and gene density

4. multicellular eukaryotes have much noncoding DNA and many multigene families

5. duplication, rearrangmnent, and mutation of DNA contribute to genome evolution

Figure:

movement of transposons by either the cut-and-paste mechanism or the copy-and-paste mechanism incolves a double-stranded DNA intermediate that is inserted into the genome.

Summary:

One of the great achievements of modern science has been the sequencing of the human genomeProgress began with the development of techniques for making recombinant DNA, in which genes from twodifferent sources—and often different species—are combined in vitro into the same molecule.The methods for making recombinant DNA are central to genetic engineering, the direct manipulation ofgenes for practical purposes. Applications include the introduction of a desired gene into the DNA of a host that will produce thedesired protein.

DNA technology has launched a revolution in biotechnology, the manipulation of organisms or theircomponents to make useful products. Practices that go back centuries, such as the use of microbes to make wine and cheese and the selectivebreeding of livestock, are examples of biotechnology. These techniques exploit naturally occurring mutations and genetic recombination. Biotechnology based on the manipulation of DNA in vitro differs from earlier practices by enablingscientists to modify specific genes and move them between organisms as distinct as bacteria, plants, andanimals. DNA technology is now applied in areas ranging from agriculture to criminal law, but its most importantachievements are in basic research.

three-stage approach to genome seuencing.

Video:

http://www.youtube.com/watch?v=gngsL9FRpqc

Chapter twenty five: the history of life on earth

Q1: how long has teh earth exist?

A1:about 4.6 billion years ago

Q2:what is the earlest evident of life on earth?

A2:about 3.5 billion years old.

Q3: what is the first genetic material?why?

A3: RNA, because RNA molecule sequences are more stable and replicate faster and with fewer errors than other sequences.

Five Facts:

1. conditions on early earth made the origin of life possible

2. the fossil record documents the history of life

3. ket events in life's history include the origins of single-celled and multicelled organisms and the colonization of land

4. the rise and fall of dominant groups reflect continental drift, mass extinctions, and adaptive radiations

5. major changes in body form can result from changes in the sequences and regulation of developmental genes

Figure:

heterochrony is an evolutionary change in the rate or timing of developmental events. heterochrony can also alter the timing of reproductive development relative to the development of nonreproductive organs.

Summary:

Life arose consists of four main stages: small organic molecules were synthesized; small molecules joined into macromolecules, such as protein and nucleic acids; all these molecules were packaged into protobionts, membrane containing droplets, whose internal chemistry differed from that of the external environment; self-replicating molecules emerged that made inheritance possible. The fossil record is the sequence in which fossile appear in the layers of sedimentary rock that consistitue earth's surface. relative dating uses the order of rock strata to determine the relative age of fossils. Radiometric dating uses the decay of radioactive isotopes to determine the age of the rocks or fossiles. It is based on the rate of decay, or halflife of the isotope. the earliest livig organisms were prokaryotes. About 2.7 billion years ago, oxygen began to accumulate in earth's atmosphere as a result of photosynthesis. eukaryotes appeared about 2.1 billlion years ago. the endosymbiotic hypothesis proposes that mitochondria and plastids were formerly small prokaryotes that began living within larger cells. Multicellular eukaryotes evolved about 1.2 billion years ago. The colonization of land occurred about 500 million years ago, when plants, fungi, and a animals began to appear on earth.

Continental drift is the movement of earth's continents on great plates that float on the hot, underlying mantle. Mass extinxtions, loss of large numbers of species in a short period, have resulted from global environment. Adaptative radiations are periods of evolutionary change in which groups of organisms form many new species whose adaptations allow them to fill different ecological noches. Structures that evolve in one context but become co-opted for another function are sometimes called exaptations. Homeotic genes are master regulatory genes that determine tha location and organization of body parts. Hox genes are one class of homeotic genes.

Video:

http://www.youtube.com/watch?v=gZtGrsr8DMY

chapter twenty four:the origin of species

Q1:what are the two major reproductive barriers?

A1:prezygotic and post zygotic.

Q2: what's speciation?

A2:the process by which one species splits into two or more species.

Q3: what are the major speciation?

A3: allopatric speciation and sympatric speciation

Five Facts:

1. the biological species concept emphasizes reproductive isolation

2. speication can take place with or without geographic separation

3. hybrid zones provide opportunities to study factors that cause reproductive isolation

4. speciation can occur rapidly or slowly and can result from changes in few or many genes

5. speciation is the process by which one species splits into two or more species.

Figure:

in a punctuated pattern, new species change most as they branch from a parent species and then change little for the rest of their existence. Other species diverge from one another much more gradually over time.

Summary:

Speciation is the process by which one species splits into two or more species. As biological species concept, a species is a group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring- but do not produce viable, fertile offspring with members of other such groups. Reproductive isolation is the barriera that impede members of two species from producing viable, fertile offspring. It includes prezygotis barriers and postzygotic barriers. Prezygotic blocks fertilization from occuring, which contains habitat isolation, temporal isolation, behavioral isolation, mechanical isolation, and gametic isolation. Postzygotic contribute to reproductive isolation after the hybrid zygote is formed. It reduces hybrid viability, hybrid fertility,and hybrid breakdown. Morphologica species concept characterizes species by body shape and other structural features. Eological species concept views a species in terms of its ecological niche, the sum of how members of the species interact with the nonliving nad living parts of their environment. Phylogenetic species concept defines a species as the smallest group of individuals that share a common ancestor, forming one branch on the tree of life.

Allopatric speciation, gene flow is interrupted when a population is divided into geographically isolated subpopulations. Reproductive isolation between teo populations generally increases as the distance between hem increases. In sympatric speciation, speciation occurs in population that live in the same geographic area. An autopolyploid is an individual that has more than two chromosome sets that are all derived from a single species. Allopolyploid is the mehcanism can change a sterile hybrid into a fertile polyploid. Hybrid zone is a region in which members of different species meet and mate, producing at least some offspring of mixed ancestry. Reinforcement: hyvrids gradually cease to be formed. Fusion: the two species fuse. Stability: continued production of hybrid individuals.

Video:

http://www.youtube.com/watch?v=v9i2WYS60L4

Chapter twenty three: the evolution of population

Q1:what's the difference between microevolution and macroevolution?

A1:microevolution is the change in allele frequencies in a population over generations. macroevolution is the broad pattern od evolution over long spans.

Q2: why is this chapter focus on population?

A2:the evolutionary impact of natural selection is only apparent in the changes in a population of organisms over time.

Q3:what are the main mechaisms that can cause allele frequenct change?

A3: natural selection, genetic drift, and gene flow.

Five Facts:

1. mutation and sexual reproduction produce the genetic variation that makes evolution possible

2. the hardy-weinberg equation can be used to test whether a population is evolving

3. natural selection, genetic drift, and gene flow can alter allele frequencies in a population

4. natural selection is the only machanism that consistently causes adaptive evolution

5. the evolutionary impact of natural selection is only apparent in the changes in a population of organisms over time.

Figure:

the bottleneck effect: a sudden change in the environmrnt, such as a fire or flood, may drastically reduce the size of a population.



Summary:

The population evolved, not its individual members. Characters that vary within a population may be discrete or quantitative. Discrete characters are determined by a single gene locus with different allels that produce distinct phenotypes. Most are quantitative characters,which vary along a continoum within a population. Average heterozygosity is the average percant of loci that are heterzygous. Geographic variation is the differences in the genetic composition of separate populations. Cline is a graded change in a character along a grographic axis. A population is a group of individuals of teh same species that live in the same area and interbreed producig fertile offspring. Gene pool consists of all the alleles for all the loci in all individuals of the population. Hardy-Weinberg principlestates that frequenceies of alleles and genotypes in a population will remain constant from generation to generatrion, provided that only Mendelian segregation and recombination of alleles are at work. p is dominant allele; q is recessive allele. p+q=1; p2+2pq+q2=1. Five condidtions:1no mutation 2random mating 3no matural selection 4extremely large population size 5 no gene flow
Natural selection , genetuic drift, and gene flow can alter alllele frequenceies in a population. Indicviduals in a population exhibit variations in their hertable traits, and those with traits that are better suited to their environmnet tend to produce more offspring than those with traits that are less well suited. Also cause adaptive evolution. Genetic drift os chance events can also cause allele frequenciesto fluctuate unpredictably from one generation to the next, especially in small populationa. Founder effect is when a few individuals become isolated from a large population, this small group may establish a new population whose gene pool differs from the source populations. Gene flow is the transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes. Relative fitness is the contribution an individual makes to the gene pool of the next generation, relative to the contibutions of other individuals.

Video:
http://www.youtube.com/watch?v=RtIQvkQWTZY

Chapter twenty two: Descent with Modification: A Darwinian View of Life

Q1: what's evolution defined?
A1: descent with modification
Q2: what are the two different ways of evolution?
A2: the pattern of evolutionary change is revealed by data from a range of scientific disciplines.
the process of evolution consists mechanisms that produce the observed pattern of change.
Q3: what are the three key obervations about life?
A3: the stricking ways in which organisms are suited for life in their environment; the many shared characteristics of life; and the rich diversity of life.


Five Facts:
1. the Darwinian revolution challanged traditional view of a young Earth inhabited by unchanging species
2. descent with modification by ntural selection explains the adaptations of organisms and the unity and diversity of life.
3. Evolution is supported by an overwhelming amount of scientific evidence
4. individuals that are well suited to their enironment tend to leave more offspring than other individuals.
5. favorable traits accumulate in the population


Figure:
Summary:
Aristotle viewed species as fixed, scala naturae. Carolus Linnaeus adopted classification system. Fossils are the remains or traces of organisms from the past. New layers of sediment cover older ones and compress them into superimposed layers of rock called strata. Palenotolgy is the study of fossils developed by Georges Cuvier. Catastrophism is the principle that events in the past occurred suddenly and were caused by mechanisms different from those operating in the present. Charles Lyell 's uniformitarianism stated that mechnisms of change are constent over time.Lamarck hypothesized that species evolve, but the mechanisms he proposed are not supported by evidence.
Darwin's voyage gave him lots of experience and evidences. Adaptations are characteristics of organism that enhance their survival and reproduction in specific environment. In his book The Origin of Species: that descent with modification explains life's unity and diversity and that natural selection brings about the match between organisms and their environment. Artifical selection is the process that humans have modified other species over many generations by selecting and breeding individuals that possed desired traits. Individuals do not evolve; traits are passed from organismms to their offspring; environmental factors vary form place to place and over time.
Predators are a potent force in shaping the adaptations of their food source. HIV is an example of drug-resistant pathogens. Natural selection is a process of editign rather than a creative mechanism. Natural selection depends on time and place. Similarity resulting from common ancestry is known as homology. Homologous structures that represent variations on a structureal theme that was present in their common ancestor. Vestigial structures are remmnants of features that served important functions in the organims's ancestors. Evolutionary tree is a diagram that reflects evolutionary relationship among groups of organims. Convergent evolution is the independent evolution of similar features in different lineages. Analogous is species share features because of convergent evoluion. Biogeography is the geographic distribution of species, including continetal drift. The origial single large contnent is Pangaea.

Video:evolution
http://www.youtube.com/watch?v=19PfUIovUaU&feature=related

Chapter twenty: Biotechnology

Q1: what's biotechnology?

A1: the manipulation of organisms or their components to make useful products.

Q2: what's recombinant DNA?

A2: DNA molecules formed when segments of DNA from two different sources-often different species-are combined in vitro.

Q3: what's genetic engineering?

A3: the direct manipulation of genes for practical pruposes.

Five Facts:

1. DNA cloning yields multiple copies of a gene or other DNA segment

2. DNA technology allows us to study the sequence, expression, and function of a gene

3. cloning organisms may lead to productino of stem cells for research and other applications

4. the practical applications of DNA technology affect our lives in many ways

5. biotechnology is the manipulation of organisms or their components to make useful products.

Figure:

In presence of polymerase enzyme (heat resistant) separation of a double stranded DNA (parentral strands) by heat at 95 degrees.
o Annealing: Synthetic pair of oligonucleotide probes are allowed to attach to their matcing base sequences on the separated DNA helicals.
o Since DNA polymerase is not denaturated by heat, its presence will allow the small synthesized oligonucleotide probe to extend along the specific DNA fragment – sort of replication-.
o This 3 step cycle is repeated 25 to 35 times.

Summary:

Plasmids are small circular pieces of DNA in bacterial cells that are used to insert pieces of foreign DNA.The DNA is cut using restriction enzymes. The collection of thousands of clones of bacteria containing recombinant plasmids is called a genomic library. Nucleic Acid Hybridizaion is used to detect genes. The DNA of the cell is denatured to produce single stranded DNA. The radioactive probe will hybridize with complementary bases if present. Probes can be radioactive isotopes or flourescent dyes. PCR is used to amplify DNA. Gel electrophoresis is a technique to separate DNA based on the movement of DNA fragments from neg to pos. Smaller fragments travel farther. Samples are placed in gels. Organismal cloning produce genetically identical individuals from a single somatic cell of a multicellular organism. Stem cells are relatively unspecialized cells that continue to reproduce themselves and can be induced to form specialized cells. Therapeutic cloning uses stem cells to replace organs and tissues. Reproductive cloning uses stem cells to reproduce new organisms.

DNA technology identify of human genes in which mutation plays a role in gentic diseases. Single nucleotide polymorphisms(SNPs) are useful genetic markers. When a restriction enzyme is added, SNPs result in DNA fragments with different lengths, or restriction fragment length polymorphisms(RFLP). Gene therapy is the alteration of an afflicted individual's genes. Vectors are used for delivery of genes into specific types of cells.

Video:

http://www.youtube.com/watch?v=mUcE1Y_bOQE

Chapter ninteen: viruses

Q1: is viruse alive?

A1: no, because viruses have to inject to a host cell to live and work.
Q2: what's the basic structure of viruses?
A2: viruse contain geetic materials DNA and RNA, and enclosed by protein.
Q3: who was the first person come up with the idea of viruses?
A3: Wendell Stanley.


Five Facts:
1. a virus consists of a nucleic acid surrounded by a protein coat.
2. viruses reproduce only in host cells
3. viruses, viroids, and prions are formidable pathogens in animals and plants
4. lytic cycle and the lysogenic cycle are two alternative way of reproduction
5. researches discovered viruses in the late 1800s by studying a plant disease, tobacco mosaic disease


Figure:
bacteriophage T4, like other "T-even: phages, has a complex capsid consisting of an icosahedral head and a tail apparatus.


Summary:
Many viruses' genomes consist of double or single-stranded DNA or RNA, depending one the kind of virus. The protein shell enclosing the viral genome is called a capsid. Capsids are built from a large number of protein subunits called capsomeres. Some viruses have accessory structure that help them infect their hosts. Viral envelope, which are derived form the membane of the host cell, contain host cell phopholipids an membrane protein.Many of the most complex capsods are found among the viruses that infect bacteria, called bacteriophage, or phage. Each type of virus can infect cells of only a limited variety of hosts, called the host range of the virus. This host specificity results from the evolution of recognition systems by the virus. Virus identify host cells by a "lock and key" fit.

A phage reproductive cycle that culminate in death of the host cell id known as a lytic cycle. A phage that reproduces only by a lytic cycle is a virulent phage. When phage DNA successfully enters a bacterium, the DNA often identifitied as foreign and cut up by cellular enzymes called restriction enzymes. The lysogenic cycle allows replication of the phage genome without destroying the host. Phage capable of using both modes of reproduing within a bacterium are called temperate phage. The RNA animal viruses with the most complicated reproductive cycles are the retroviruses. These viruses are equipped with an enzyme called reverse transcriptase, which transcrbes an RNA template into DNA, providing an RNA-DNA information flow. The integrated viral DNA, called a provirus, never leaves the host;s genime, remaining a permanent resident of the cell.

A vaccine is a harmless variant or derinative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen. Virods are circular RNA molecules tha infect plants. Prions appear ro cause a number of degenerative brain diseases in various animal species.



Video:
http://www.youtube.com/watch?v=41aqxcxsX2w