Ch.15 Tracing Evolutionary History

WHAT ARE THE DIFFERENCES BETWEEN NATURAL SELECTION AND EVOLUTION?
Evolution is a gradual process in which something changes into a different and usually more complex or better form whereas natural selection is the process in nature by which, according to Darwin's theory of evolution, only the organisms best adapted to their environment tend to survive and transmit their genetic characteristics in increasing numbers to succeeding generations while those less adapted tend to be eliminated.

HOW DOES EVOLUTION OCCUR?
Evolution is the change in frequency of the alleles in a gene pool over time. Evolution occurs with mutations and natural selections. WHat happens is that in a population of species, not all of them are the same. For example, there is a whole colony of fish. Some of the fish are faster than the others. They reproduce and pass on their genes which make their offspring fast as well. The other fish that aren't as fast, die out because they are not fast enough. The fast fish soon become more common, making the species as a whole faster. This occurs in several stages, where the slowest fish are removed each time, and the faster ones reproduce more often. The second aspect is that these fish will often have differences in their genetic codes, called mutations. While bad mutations will normally result in fatality and not get passed on, some are useful and result in increased survival. When these mutations build up, the species we previously had may then become completely different from what is here now. The two groups cannot cross breed, and have become different species.

WHAT TYPE OF EVOLUTIONARY EVENT HAS OCCURRED?
Natural selection and a genetic bottleneck. The DDT resistance is a classic example of natural selection, only the most resistant organisms surviving the treatment and establishing a new, resistant population. The near disappearance of the mosquito population for several years with the new population showing reduced fertility is characteristic of a genetic bottleneck. Only a very small number survived and the genetic diversity in the population is greatly reduced. The survivors are forced to undergo massive inbreeding and reduced fertility is quite common.


SUMMARY:
A recipe for life is raw materials, suitable environment, and energy sources. The conditions on early Earth made the origin of life possible. The chemical and physical conditions made abiotic synthesis of monomers (1st stage), formation of polymers (2nd stage), packaging of polymers into protobionts (3rd stage), and self-replication (4th stage.) In 1953, Stanley Miller tested the Oparin-Haldane hypothesis. He set up an airtight apparatus with gases circulating past an electrical discharge, to stimulate conditions on the early Earth. An alternative hypothesis states that submerged volcanoes and deep-sea hydrothermal vents may have provided the chemical resources for the first life. Cells and protobionts share four characteristics: structural organization, simple reproduction, simple metabolism, and simple homeostasis. The eukaryotic cell probably originated as a community of prokaryotes, when small prokaryotes capable of aerobic respiration or photosynthesis began living in larger cells. Oldest fossils of eukaryotes are about 2 billion years old. Sliding plates are earthquake zones. Also colliding plates form mountains. Those are geologic processes occur at plate boundaries. The supercontinent pangaea altered habitats and triggered the greatest mass extinction in Earth's history. Extinction is the fate of all species and most lineages. The history of life reflects a steady background extinction rate with episodes of mass extinction. Types of extinctions are classified by how shallow/deep water the species lived in. For example, permian extinction, cretaceous extinction.
Human development is paedomorphic, retaining juvenile traits into adulthood. In the evolution of an eye or any other complex structure, behavior, or biochemical pathway, each step must bring a selective advantage to the organism possessing it and must increase the organism's fitness. Other novel structures result from exaptation, the gradual adaptation of existing structures to new functions Natural selection doesn't anticipate the novel use: each intermediate stage must be adaptive and functional. Evolutionary trends do not mean that evolution is goal directed. Natural selection results from the interactions between organisms and their environment. If the environment changes, apparent evolutionary trends may cease or reverse. Systematics classifies organisms and determines their evolutionary relationship. Taxonomists assign each species a binomial consisting of a genus and species name. A phylogenetic tree is a hypothesis of evolutionary relationships within a group. Cladistics uses shared derived characters to group organisms into clades, including an ancestral species and all its descendents. Shared ancestral characters were present in ancestral groups. Molecular systematics compares nucleic acids or other molecules to infer related ness of taxa.


KEY TERMS:
- Macroevolution: major changes over evolutionary time
- Radiometric dating: measurement of the decay of radioactive isotopes
- Geologic record: defined by major transitions in life on Earth
- Continental drift: the slow, continuous movement of Earth's crustal plates on the hot mantle
- Adaptive radiation: a group of organisms forms new species, whose adaptations allow them to fill new habitats or roles in the communities
- Evo-devo: a field that combines evolutionary and developmental biology
- Homeotic genes: master control genes that determine basic features, such as where pairs of wings or legs develop on a fruit fly
- Species selection: the unequal speciation or unequal survival of species on a branching evolutionary tree
- Phylogeny: the evolutionary history of a species or group of species
- Convergent evolution: where analogous similarities result from in similar environments

This is a famous picture of evolution. It started out with the ape on the left, and ends with human being now on the right. It didn't happen just at once, but it took couple steps in between to become a human being from an ape. Also it took extremely long time. Like I said in the beginning, some apes who have different and better genes than others keep being alive, and other apes died out because of some reasons. And whoever that is still alive keep raising their children which are more likely to have "better" genes. This is how evolution occurs. This shows a microevlution.

http://www.youtube.com/watch?v=fVPadCMKJ_8


5 FACTS:
1) Homologous genes have been found in organisms separated by huge evolutionary distances
2) Molecular clocks help track evolutionary time. It can be calibrated in real time by graphing the number of nucleotide differences against the dates of evolutionary branch points known from the fossil record.
3) Life is divided into three domains: the prokaryotic domains Bacteria and Archaea and the eukaryote domain Eukarya.
4) There have been two major episodes of horizontal gene transfer, with transfer of genes between genomes by plasmid exchange, viral infection, and fusion of organisms: gene transfer between a mitochondrial ancestor and the ancestor of eukaryotes, and gene transfer between a chloroplast ancestor and the ancestor of green plants.
5) Shared characters are used to construct phylogenetic trees.

Ch.14 The Origin of Species

WHY CAN'T MULES MATE?
The basic reason why mules cannot reproduce is that a mule does not have a even number of chromosomes. They have 63 chromosomes because a horse and a donkey have different numbers of chromosomes. During mitotic cell division, each of the chromosomes copies itself and then distributes these two copies to the two daughter cells. In contrast, when the mule is producing sperm or egg cells during meiosis, each pair of chromosomes need to pair up with each other. Since the mule doesn't have an even number of homologous pairs, meiosis is disrupted and viable sperm and egg are not formed.

WHAT ARE PREZYGOTIC REPRODUCTIVE BARRIERS?
There are two general categories of reproductive isolating mechanisms: prezygotic, or those that take effect before fertilization, and postzygotic, hybrids between members of different populations through ecological, temporal, ethological, mechanical, and gametic isolation.

WHAT IS THE PHYLOGENETIC SPECIES CONCEPT?
The phylogenetic species concept defines a species as a set of organisms representing a specific evolutionary lineage. The concept of a species as an irreducible group whose members are descended from a common ancestor and who all possess a combination of certain traits. It is less restrictive than the biological species concept. Also it permits successive species to be defined even if they have evolved in an unbroken line of descent, with continuity of sexual fertility. However because slight differences can be found among virtually any group of organisms, the concept tends to encourage extreme division of species into ever-smaller groups.


SUMMARY:
Linnaeus used physical characteristics to distinguish species. His binomial system is the basis of taxonomy, the naming and classification of life's forms. The biological species concept defines a species as a group of populations whose members can interbreed and produce fertile offspring with each other but not with members of other species. Most organisms are classified based on observable phenotypic traits; the morphological species by its ecological niche. According to the phylogenetic species concept, a species is the smallest group that shares a common ancestor and forms one branch on the tree of life.
There are two types of reproductive barriers. Prezygotic barriers, which includes temporal isolation, habitat isolation, behavioral isolation, mechanical isolation, and gametic isolation. Also postzygotic barriers, which includes reduced hybrid viability, reduced hybrid fertility, and hybrid breakdown.
Geographically separated from other populations, a small population may become genetically unique as its gene pool is changed by natural selection, mutation, or genetic drift in allopatric speciation. A laboratory study has documented the beginning of reproductive isolation as fruit fly populations adapted to a new food source. Researchers have identified the specific genes involved in some cases of speciation, which is the evolution of reproductive barriers. Hybrid zones are regions in which members of different species overlap and produce at least some hybrid offspring. Over time, reinforcement may strengthen prezygotic barriers to reproduction, or fusion may reverse the speciation process as reproductive barriers weaken and extensive gene flow occurs. In stable hybrid zones, a limited number of hybrid offspring continue to be produced. Adaptive radiation can occur when populations are provided with expanded opportunities following mass extinctions, the colonization of a diverse new environment, or the evolution of new structures. The punctuated equilibrium model draws on the fossil record, where many species change most as they arise from an ancestral species and then change relatively little for the rest of their existence. But some species have evolved by the gradual accumulation of changes. The time interval between speciation events varies considerable, from a few thousand years to tens of millions of years.

     +       =

A Mule is a hybrid of a horse and a donkey. However mules cannot mate. Therefore a mule is an animal that never reproduce. A mule is not considered as a specie, because species have to be able to inbreed. In order to make a mule, a horse and a donkey needs to mate.

http://www.youtube.com/watch?v=zl1a1n6XR9g

KEY TERMS:
- Species: as a group of organisms whose members can breed and produce fertile offspring, but who do not produce fertile offspring with members of other groups
- Taxonomy: the branch of biology that names and classifies species and groups them into broader categories
- biological species concept: species as a group of populations whose members have the potential to interbreed in nature and produce fertile offspring
- Morphological species concept: classification is based mainly on phenotype
- Ecological species concept: identification of species in terms of their ecological niches, focusing on unique adaptations to particular roles in a biological community
- Phylogenetic species concept: a species as the smallest group of individuals that shares a common ancestor and that forms one branch on the tree of life.
- Reproductive barrier: a biological feature of the organism itself
- Allopatric speciation: populations separated by a geographic barrier
- Polyploid: their cells have more than two complete sets of chromosomes
- Sympatric speciation: a new species arises within the same geographic area as a parent species

5 FACTS:
1) Reproductive barriers keep species separate
2) In allopatric speciation, geographic isolation leads to speciation
3) In sympatric speciation, speciation takes place without geographic isolation
4) Reproductive barriers may evolve as populations diverge
5) Hybrid zones provide opportunities to study reproductive isolation

Ch.13 How Populations Evolve

WHAT IS THE MAIN EVOLUTION OF HUMAN?
Humans used to be pongidae (apes) long time ago. This data is found by fossil records. In 1925, A kull which was the first to be classified as Australopithecus. It looked like ape in appearance, but had human-like teeth. As the amount of finds increased, so did the number of species. Australopithecus are small-brained gracile hominids with mixed fruit/vegetable diet. Paranthropus, smalled-brained robust hominids with a grassland vegetable diet. Homo, large-brained hominids with an omnivorous diet. These are brief descriptions of the evolution. After homo, human now have started living.

WHAT IS "ORIGIN OF SPECIES"?
A work published by Charles Darwin. Darwin introduced the concept of natural selection. Suppose a member of a species were to develop a functional advantage, such as a reptile grew wings and learned to fly. Its offspring would inherit that advantage and pass it on to future offspring. Naatural selection would act to preserve the advantageous trait. Essentially, natural selection is the naturalistic equivalent to domestic breeding. Over the centuries, human breeders have produced dramatic changes within domestic animal populations simply by selecting individuals to breed. They have been able to accentuate desirable traits and even suppress undesirable traits gradually over time. The different between domestic breeding and natural selection is: rather than human breeders making the selections, nature itself is the selector/

WHAT IS EVOLUTION, EXACTLY?
Biological evolution is change in the properties of populations of organisms or groups of such populations, over the course of generations. The development, or ontogeny, of an individual organism is not considered evolution: individual organisms do not evolve. The changes in populations that are considered evolutionary are those that are ‘heritable' via the genetic material from one generation to the next. Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportions of different forms of a gene within a population, such as the alleles that determine the different human blood types, to the alterations that led from the earliest organisms to dinosaurs, bees, snapdragons, and humans.

SUMMARY:
There are four types of adaptations: behavioral adaptations, structural adaptations, biochemical adaptations, and physiological adaptations. The primary mechanism of evolutionary change producing adaptation of organisms to their environment is natural selection. In the century prior to Darwin, the study of fossils suggested that species had changed over time. Use and disuse, and inheritance of acquired characteristics are mechanisms of evolution of life on Earth. Because of Lyell's Principles of Geology, Darwin came to realize that the organisms on Earth changes over time. He observed that organisms produce more offspring than the environment can support, and organisms vary in many traits. Darwin found convincing evidence for his ideas in the results of artificial selection, the selective breeding of domesticated plants and animals.
- Individuals do not evolve: populations evolve
- Natural selection can amplify or diminish only heritable traits; acquired characteristics cannot be passed on to offspring
- Evolution is not goal directed and does not lead to perfection; favorable traits vary as environments change
This is an example of evolution. This is how organisms keep evolving to be better depending on environment. Initial use of pesticides favors those few insects that have genes for pesticide resistance. With continued use of pesticides, resistant insects flourish and vulnerable insects die. Proportion of resistant insects increases over time.
The fossil record shows that organisms have evolved in a historical sequence. We are able to tell how old they are by layers of rock, or sand. Homologous structures and genes can be used to determine the branching sequence of an evolutionary tree. Populations may be isolated from one another, or individuals within populations may interbreed. Mutation is the ultimate source of new alleles. Occasionally, mutant alleles improve the adaptation of an individual to its environment and increase its survival and reproductive success. Sexual reproduction shuffles alleles to produce new combinations because it crosses over the chromosomes. However, sexual reproduction alone does not lead to evolutionary change in a population. Although alleles are shuffled, the frequency of alleles and genotypes in the population does not change. Hardy Weinberg principle states that allele and genotype frequencies within a sexually reproduction, diploid population will remain in equilibrium unless outside forces act to change those frequencies. If a population is in Hardy-Weinberg equilibrium, allele and genotype frequencies will not change unless something acts to change the gene pool. For a population to remain in Hardy-Weinberg equilibrium for a specific trait, it must satisfy five conditions: Very large population. No gene flow between populations. No mutations. Random mating. No natural selection.  If those five conditions are not met in a population, the population's gene pool may change. The three causes of evolutionary change: Natural selection, genetic drift, and gene flow. Stabilizing selection favors intermediate phenotypes, acting against extreme phenotypes. It is very common, especially when environments are stable. The evolution of antibiotic resistance in bacteria is a serious public health concern. Diploidy and balancing selection preserve genetic variation. Natural selection is not able to fashion perfect organisms. It can only act on existing variation, and evolution is limited by historical constraints. Adaptions are often compromises. Also chance, natural selection and the environment interact.




This is a diagram of archaeopteryx fossil. Feathers were one of the first and the most successful structures that birds evolved. It is believed the feathers first evolved from reptile scales as an adaptation to permit endothermy. As endothermic organisms, birds maintain a constant body temperature. The insulation provided by the feathers greatly reduces the amount of energy required to keep up the body heat. Without this insulation, the birds would be forced to eat impossible amounts of food, and undergo cellular respiration to produce heat.

http://www.youtube.com/watch?v=zVEjVIo-jro
This video also talks about the evolution of birds from dinosaurs.

KEY TERMS:
- Biogeography: the geographic distribution of species, suggested to Darwin that organisms evolve from common ancestors
- Comparative Anatomy: the comparison of body structures in different species
- Homology: the similarity in characteristics that result from common ancestry
- Comparative Embryology: the comparison of early stages of development among different organisms
- Molecular Biology: comparisons of DNA and amino acid sequences between different organisms reveal evolutionary relationships
- Evolution: the change in heritable traits in a population over generations
- Gene Pool: the total collection of genes in a population at any one time
- Microevolution: a change in the relative frequencies of alleles in a gene pool over time
- Population Genetics: the study of how populations change genetically over time
- Modern Synthesis: connection between Darwin's theory and population genetics

5 FACTS:
1) Darwin was the first to represent the history of life as a tree.
2) Fossil record tells how old it is, and it can lead how the organism evolved.
3) There are about 8 million combinations possible in a human sperm or egg due to independent assortment during meiosis.
4) p2 + 2pq + q2 = 1 (homozygous dominant + heterozygous + homozygous recessive = 100%)
5) The Hardy-Weinberg equation can be used to test whether a population is evolving.

Ch. 12 DNA Technology and Genomics

HOW IS CLONING RELATED TO THE MOVIE "THE ISLAND"?
The movie "island" was about cloning genes. Clones were all told that they would eventually able to go to the place called the island. They believed that the island must have been like heaven. However, Lincoln, the main character, found out that it was a lie. They are clones and originals pay the company so they can be donated. For example, one lady who cannot get pregnant cloned herself and donated her husband's sperm to get her clone pregnant. As soon as the clone gave a birth, she got killed. This is what the company was having as its business. Although DNA cloning has many advantages, I think cloning a human should keep be forbidden. Because once a cloned human is made, it will be one complete person even though it is a copy of somebody. It does not matter if it should get killed after the business or not, I don't think it is a good idea to clone a human.

HOW DOES DNA FORENSICS WORK?
Any type of organism can be identified by examination of DNA sequences unique to that species. Identifying individuals within a species is less precise at this time, although when DNA sequencing technologies progress farther, direct comparison of very large DNA segments, and possibly even whole genomes, will become feasible and practical and will allow precise individual identification.

To identify individuals, forensic scientists scan 13 DNA regions, or loci, that vary from person to person and use the data to create a DNA profile of that individual (sometimes called a DNA fingerprint). There is an extremely small chance that another person has the same DNA profile for a particular set of 13 regions.

WHAT ARE THE ADVANTAGES AND DISADVANTAGES OF DNA TECHNOLOGY?
Advantages: DNA technology is mostly accurate, and it is easy to analyze. Some are not too expensive. Also the process can get done rapidly. Higher precision and accuracy.
Disadvantages: You might have to suffer some issues. Sometimes it is very expensive. If it makes a little tiny mistake, it can lead to a huge problem. It can still be developed so it is not completely done yet.



SUMMARY:
DNA technology was first used to solve a double murder in England. Today, it has been developed and used a lot more often mainly for solving crimes. Gene cloning leads to the production of multiple identical copies of a gene carrying piece of DNA. Recombinant DNA is formed by joining DNA sequences from two different sources. One source contains the gene that will be cloned. Another source is a gene carrier. Steps of gene cloning:1, plasmid DNA is isolated. 2, DNA containing the gene of interest is isolated. 3, Plasmid DNA is treated with restriction enzyme that cuts in one place, opening the circle. 4, DNA with the target gene is treated with the same enzyme and many fragments are produced. 5, Plasmid and target DNA are mixed and associate with each other. 6, Recombinant DNA molecules are produced. 7, The recombinant DNA is taken up by a bacterial cell. 8, The bacterial cell reproduces to form a clone of cells. Enzymes are used to cut and paste DNA. Restriction enzymes cut DNA at specific sequences and DNA ligase paste DNA fragments together. Genomic libraries can store cloned genes. It can be constructed with many different types of vectors, such as plasmid library, phage library, and BAC. Nucleic acid probes bind to cloned DNA. Screening a gene library explain; bacterial clones are transferred to filter paper. Cells are lysed and DNA is separated into single strands. A solution containing the probe is added, and binding to the DNA of interest is detected. The clone carrying the gene of interest is grown for further study.
DNA technology now can be used as pharmaceutical industry and medicine. Therapeutic hormones, and diagnosis, vaccines, and treatments of disease are the products of DNA technology. With recombinant DNA products, identity to human protein, purity, and quantity are able to be taken as advantages. Gene therapy may someday help teat a variety of diseases. It aims to treat a disease by supplying a functional allele. It may be a good treatment for cancer, especially. In order for gene therapy to work, we will need to take a challenge of safe delivery to the area of the body affected by the disease, and achieving a long lasting therapeutic effect. Advantages of PCR are; it can amplify DNA from a small sample, and results are obtained rapidly, and reaction is highly sensitive, copying only the target sequence.
DNA profiling has provided evidence in many forensic investigations. Forensics, establishing family relationships, indentification of human remains, and species identification are examples. Genomics is the study of an organism's complete set of genes and their interactions. Evolutionary relationships can be elucidated. Determination of the nucleotide sequence all DNA in the human genome, and identification of the location and sequence of every human gene are the goals of the human genome project now.


KEY TERMS:
1) Gene engineering: manipulating genes for practical purposes
2) Plasmids: small, circular DNA molecules independent of the bacterial chromosome that are used as vectors
3) Restriction fragments: sticky ends that are made by restriction enzymes
4) Genomic library: a collection of all of the cloned DNA fragments from a target genome
5) Complementary DNA (cDNA): used to clone eukaryotic genes
6) Genetically modified (GM): organisms that contain one or more genes introduced by artificial means
7) Transgenic organisms: organisms that contain at least one gene from another species
8) DNA profiling: the analysis of DNA fragments to determine whether they come from a particular individual
9) Polymerase chain reaction (PCR): a method of amplifying a specific segment of a DNA molecule
10) Short tandem repeats (STRs): genetic markers used in DNA profiling

This diagram shows how DNA cloning is happening. First, cells from the original sheep are taken. Second, unfertilized egg cell is taken and its nucleus gets removed. The nucleus of cells from the original sheep are put into the unfertilized egg with no nucleus. After that, cells keep reproducing themselves until they make an identical sheep. 

http://www.youtube.com/watch?v=70lwiFIqejw&feature=related

This video explains how to clone genes.

5 FACTS:
1. Genes can be cloned in recombinant plasmids.
2. Reverse transcriptase can help make genes for cloning.
3. Nucleic acid probes identify clones carrying specific genes.
4. Recombinant cells and organisms can mass-produce gene products.
5. Gene therapy may someday help treat a variety of diseases.

Ch.11 How Genes are Controlled

HOW DOES CLONING WORK?
On July 5, 1997, Ian Wilmut and a group of scientists announced that they had successfully cloned a sheep named Dolly. Dolly is a natural sheep and you would not notice any differences between the real sheep and Dolly. The only major distinguishing factor between the two is Dolly's conception because its embryo developed without the presence of sperm. Instead, Dolly began as a cell from another sheep that was fused via electricity with a donor egg. She is reproduced just by one sheep. Today, scientists have cloned many types of animals, such as mice, sheep, pigs, cows, and dogs. However human cloning has still been talked whether if they should do or not.

WHAT IS RNA SPLICING?
RNA splicing is a process that removes introns and joins exons in a primary transcript. An intron usually contains a clear signal for splicing. In some cases, a splicing signal may be marked by a regulatory protein, resulting in alternative splicing. In rare cases, a pre-mRNA may contain several ambiguous splicing signals, resulting in a few alternatively spliced mRNAs.

WHAT IS DNA A MICROARRAY?
A DNA microarray is a multiplex technology used in molecular biology. It consists of an arrayed series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles of a specific DNA sequence. They can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample under high-stringency conditions.
Basically DNA microarray contains DNA sequences arranged on a grid and it is used for transcription.
-mRNA from a specific cell type is isolated.
-Fluorescent cDNA is produced from the mRNA
-cDNA is applied to the microarray
-Unbound cDNA is washed off
-Complementary cDNA is detected by fluorescence

SUMMARY:
Gene expression is the overall process of information flow from genes to proteins, mainly controlled at the level of transcription. Turned on gene is transcribed to produce mRNA that is translated to make its corresponding protein. Regulatory gene codes for a repressor protein. In the absence of lactose, the repressor binds to the operator and prevents RNA polymerase action. Lactose inactivates the repressor, so the operator is unblocked. There are some types of operon control: inducible operon, repressible operon for examples. For many operons, activators enhance RNA polymerase binding to the promoter. Differentiation is controlled by turning specific sets of genes on and off, which is only in eukaryotic cells. Eukaryotic chromosomes undergo multiple levels of folding and coiling, called DNA packing. DNA packing can prevent transcription.
X-chromosome inactivation is when one of the two X chromosomes is highly compacted and transcriptionally inactive. It occurs early in embryonic development and all cellular descendants have the same inactivated chromosome. Every eukaryotic gene has its own promoter and terminator/are usually switched off and require activators to be turned on/are controlled by interactions between numerous regulatory proteins and control sequences. During alternative RNA splicing, production of different mRNA from the same transcript, it results in production of more than one polypeptide from the same gene, and it can involve removal of an exon with the introns on either side. Control of gene expression also occurs with breakdown of mRNA/initiation of translation/protein activation/protein breakdown. There are many possible control points that exist. Such as chromosome changes, control of transcription, control of RNA processing, flow through nuclear envelope, breakdown of mRNA, control of translation, and control after translation. Role of gene expression in fruit fly developments are orientation from head to tail, segmentation of the body, and production of adult features.
Most differentiated cells retain a full set of genes, even though only a subset may be expressed. Nuclear transplantation can be used to clone animals. It is used by replacing the nucleus of an egg cell or zygote with a nucleus from an adult somatic cell. Cloned animals can show differences from their parent due to a variety of influences during development. Reproductive cloning is used to produce animals with desirable traits. Human reproductive cloning raises ethical concerns. Mutations in two types of genes can cause cancer, oncogenes, and tumor-suppressor genes. Usually, four or more somatic mutations are required to produce a cancer cell. One possible scenario for colorectal cancer includes, activation f an oncogene increases cell division, inactivation of tumor gene causes formation of a benign tumor, and additional mutations lead to a malignant tumor. Healthy lifestyle choices such as avoiding carcinogens, avoiding fat and including food with fiber and antioxidants, and regular medical checkups are very helpful for preventing cancer.

This is a diagram of operon turned on (lactose inactivates repressor.) RNA polymerase bound to promoter in DNA, and producing mRNA. This mRNA turns into protein. Then lactose comes in and attaches to the protein. The protein becomes inactive repressor. As RNA polymerase bound to promoter to make mRNA, enzymes for lactose utilization is produced as well.

This is a diagram of operon turned off (lactose absent.) On operon, protein is made by mRNA, which is made by DNA. This protein, called active repressor attaches to operator on operon. Sense active repressor is in the way,  RNA polymerase cannot attach to promoter. So there is no lactose-utilization being produced. 

http://www.youtube.com/watch?v=aEtuaEe0C-I&playnext=1&list=PL2B6EC4244AC6EF3C

KEY TERMS:
1) Operon: a group of genes under coordinated control in bacteria
2) Promoter: sequence where RNA polymerase binds
3) Differentiation: controlled by turning specific sets of genes on or off. It involves cell specialization. in both structure and function
4) Silencers: repressors hat inhibit transcription
5) DNA microarray: contains DNA sequences arranged on a grid, and used to test for transcription
6) Signal Transduction Pathway: a series of molecular changes that converts a signal at the cell's surface to a response within the cell
7) Carcinogens: cancer-causing agents that damage DNA and promote cell division
8) Nuclear Transplantation: replacing the nucleus of an egg cell or zygote with a nucleus from an adult somatic cell
9) Homeotic Genes: master control genes that determine the anatomy of the body, specifying structures that will develop in each segment
10) Alternative RNA splicing: production of different mRNA from the same transcript

5 FACTS:
1) Proteins interacting with DNA turn prokaryotic genes on/off in response to environmental changes.
2) DNA packing in eukaryotic chromosomes helps regulate gene expression.
3) Complex assemblies of protein control eukaryotic transcription.
4) Development of an animal is lead by cascades of gene expression.
5) Cancer results from mutations in genes that control cell division.

Ch.10 Molecular Biology of the Gene

HOW DO BACTERIOPHAGES EAT BACTERIA?
A bacteriophage has a head, containing DNA and a hollow tail with six jointed fibers extending from it. Bacteriophage attaches to bacterial cell, and injects DNA. It can reprogram its host cell to produce new pages, by their proteins. When the bacteria had been infected with T2 phages containing labeled protein, the radioactivity ended up mainly in the liquid, which contained phages but not bacteria. This result suggested that the phage phage protein did not enter the cells. But when the bacteria had been infected, then most of the radioactivity was in the bacteria pellet. When these bacteria were returned to liquid growth medium, the bacterial cells were destroyed, lysing and releasing new phages that contained radioactive phosphorus in their DNA but no radioactive sulfur in their proteins.

WHAT IS NUCLEOTIDE MADE OF?
DNA nucleotide is a long molecule of nucleotides, consisting of 3 parts. These 3 parts include a pentose sugar, a phosphate group, and a nitrogenous base. The nitrogenous bases include purines (adenine and guanine) and pyrimidines (cytosine and thymine). DNA includes adenine, guanine, cytosine, and thymine. RNA includes adenine, cytosine, guanine, and uracil instead of thymine.

WHAT ARE THE DIFFERENCES BETWEEN DNA AND RNA?
DNA and RNA are slightly different. In the cell RNA is usually single stranded, while DNA is double stranded. RNA nucleotides contain ribosome while DNA contains deoxyribose, which is a type of ribose that lacks one oxygen atom. In RNA the nucleotide uracil substitutes for thymine, which is present in DNA. DNA can be found in nucleus, but RNA can be found in nucleus and cytoplasm. A job of DNA is medium of long-term storage and transmission of genetic information. THe main job of RNA is to transfer the genetic code need for the creation of proteins from the nucleus to the ribosome. This process prevents the DNA from having to leave the nucleus, so it stays safe. Without RNA protein would never be made.



SUMMARY:
Frederick G. discovered that a transforming factor could be transferred into a bacterial cell. Alfred Hershey and Martha Chase used bacteriophages to show that DNA is the genetic material. DNA and RNA is the nucleotide, which contains 1) nitrogenous base, 2) 5-carbon sugar, and 3) phosphate group. DNA is a double-stranded helix, and it is composed of two polynucleotide chains joined together by hydrogen bonding between bases, twisted into a helical shape. DNA replication follows a semiconservative model. It begins at the origins of replication. It always occurs in the 5' to 3' direction. A gene is a sequence of DNA that directs the synthesis of a specific protein. DNA is transcribed into RNA, and RNA is translated into protein. The sequence of nucleotides in DNA provides a code for constructing a protein. Protein construction requires a conversion of a nucleotide sequence to an amino acid sequence. Transcription rewrites the DNA code into RNA, using the same nucleotide language. Each word is a codon, consisting of three nucleotides. Translation involves switching from the nucleotide language to amino acid language. The basic steps of transcription is, 1) the two DNA strands separate, this stage is called initiation 2) One strand is used as a pattern to produce an RNA chain, using specific base pairing, this stage is called elongation 3) RNA polymerase catalyzes the reaction, this stage is called termination.
Translation occurs on the surface of the ribosome.  During initiation, mRNA binds to a small ribosomal subunit and the first tRNA binds to mRNA at the start codon. And a large ribosomal subunit joins the small subunit, allowing the ribosome to function. During elongation, next tRNA binds to the mRNA at the A site. And joining of the new amino acid to the chain occurs. tRNA is released from the P site and the ribosome moves tRNA from the A site into the P site. Elongation continues until the ribosome reaches at stop codon. Mutations can be spontaneous, and induced by mutagens. Viruses have two types of reproductive cycles, lytic cycle and lysogenic cycle. Both DNA viruses and RNA viruses cause disease in animals. Some animal viruses reproduce in the cell nucleus. Aids is caused by HIV, human immunodeficiency virus. HIV is a retrovirus, containing two copies of its RNA genome, and reverse transcriptase. Three mechanisms let transfer of bacterial DNA, transformation, transduction, and conjugation.

KEY TERMS:
1) Bacteriophages: bacterial viruses that eat bacteria
2) Nucleotides: chemical units that DNA and RNA are consisting of
3) Semiconservative model: When each strand separates and each has one old strand with one new strand
4) DNA polymerases: the enzymes that link DNA nucleotides to a growing daughter strand
5) Promoter: a nucleotide sequence of the "start transcribing" signal
6) RNA splicing: the cutting-and-pasting process
7) Mutation: any change in the nucleotide sequence of DNA
8) Mutagen: a source of mutation is a physical or chemical agent
9) Plasmid: a small, circular DNA molecule separate from the bacterial chromosome
10) Conjugation: the physical union of cells and the DNA transfer between them

This is a diagram of DNA transcription. The first step, initiation, the attachment of RNA polymerase to the promoter and the start of RNA synthesis. The second step, elongation, the RNA elongates. As RNA synthesis continues, the RNA strand peels away from its DNA template, allowing the two separated DNA strands to come back together in the region already transcribed. The third step, termination, finally the RNA polymerase reaches a sequence of bases in the DNA template called a terminator. At that point, the polymerase molecule detaches from the RNA molecule and the gene, sense it signals the end of the gene.

http://www.youtube.com/watch?v=ztPkv7wc3yU&feature=related



5 FACTS:
1) Central dogma shows the processes of replication/transcription/translation to make DNA to protein.
2) During DNA replication, DNA strands separate and random nucleotides come in so they can make two identical daughter molecules of DNA
3) During transcription, as DNA strands separate, RNA nucleotides come in so they can make RNA strand
4) During translation, anticodon with amino acid come in to make polypeptide and the anticodon leaves, so they can make protein
5) DNA nucleotides: A bonds with T, T bonds with A, G bonds with C, and C bonds with G.
RNA nucleotides: A bonds with T, U bonds with A, G bonds with C, and C bonds with G.

Ch.9 Patterns of Inheritance

WHAT WERE EXPERIMENTS MENDEL CONDUCT AND WHAT WERE HIS RESULTS?
Mendel conducted pea plant experiment. He crossed different plants and came out mostly with the same result, but some had different phenotypes. Je experimented with thousands of pea plants and recorded the phenotypic and genotypic traits of both using Punnet Squares. Mendel's finding showed that phenotypic traits in pea plants were inherited in discrete packages and at predictable frequencies. Mendel stated two laws, law of independent segregation, which states that a parent plant passed only one copy of a trait to the offspring. His second law was the Law of independent assortment that states that these traits met randomly in the offspring. 

WHY DO MORE MEN THAN WOMEN HAVE COLOR BLINDNESS?

Women have the sex chromosomes XX, while men have the chromosomes XY. The gene for normal color vision is found on the X-chromosome. If a woman has one X-chromosome with the gene and one without it, she will not be color blind. On the other hand, a man with an X-chromosome that is missing the gene has no backup. He will be color blind. Color blind women have both X-chromosomes missing the color vision gene. This has less probability than having just one X-chromosome missing the gene.

WHAT ARE THE MENDELIAN LAWS?
1) Law of segregation: pair of characteristics only one can be represented in a gamete. In another words,  for any pair of characteristics there is only one gene in a gamete even though there are two genes in ordinary cells.
2) Law of independent assortment: two characteristics the genes are inherited independently.
 If you had the genotype AaBb, you would make four kinds of gametes: they would contain the combinations of either AB, Ab, aB, or ab.

SUMMARY:
Genetic materials are only transported to offsprings. In another words, no matter how hard you work out to build your arm muscles, the offsprings will not get the muscle unless you have muscle cells that build muscles faster and easier than normally. In 1859, Mendel published a paper that says that the heritable factors retain their individuality generation after generation. He choose garden pea flower to study, using method that prevented fertilization, to cross fertilize the stamenless flower the carpel developed into a pod, and he planted. The seeds grew into offspring plants. Through these methods, Mendel was always sure of the parentage of new plants. He worked until he was sure he had true-breeding varieties. Mendel's law of segregation describes the inheritance of a single character. This starts with a cross between two parents and cross them to expect how offsprings are going to look like, using punnett square. We are able to describe phenotype and genotype of offsprings. Mendel's law of segregation states that pairs of alleles segregate during gamete formation. Homologous chromosomes state that alleles of a gene reside at the same locus on homologous chromosomes. Mendel's law of independent assortment states that each pair of alleles segregates independently of other pairs of alleles during gamete formation. From crossing P generations using punnett square, we are able to distinguish the percentage of phenotype and genotype of offsprings that will be born.
Genetic traits in humans can be tracked through family pedigrees. To analyze the pedigree, the geneticist applies logic and the Mendelian laws. Dominant traits are usually easier to occur, such as having freckles, widow's peak, and free earlobe. However people do have recessive traits, opposite of dominant traits, such as no freckles, straight hairline, and attached earlobe. Many inherited disorders in humans are controlled by a single gene. For example of recessive disorders, if both parents have gene of deaf, 25% of offsprings have possibilities to be deaf. The most common fatal genetic disease in the United states is cystic fibrosis. The CF allele is carried by about one in 25 people of European ancestry. The probability increases greatly if close relatives marry and have children. People with recent common ancestors are more likely to carry the same recessive relatives, called inbreeding, which is more like to produce offspring many types of inbred animals.
New technologies are able to provide insight into someone's genetic legacy. Genetic testing, fetal testing, fetal imaging, and ethical considerations are used. There is an incomplete phenotype. For example, if you cross red flower and white flower, there are probabilities of pink flower to be born between them.
Many genes have more than two alleles in the population. Most genes can be found in populations in more than two versions, known as multiple alleles. Although any particular individual carries, at most, two different alleles for a particular gene, in cases of multiple alleles, more than two possible alleles exist in the wider population. For example, blood group phenotype. There are four blood types, A, B, O, and AB. These letters refer to two carbohydrates, designated A and B, that may be found on the surface of red blood cells. Genotypes will be ii for O, IAIA or IAiA for A, IBIB or IBiB for B, and IAIB for AB. If I is a capital, it is a codominant; both alleles are expressed in heterozygous individuals.
Chromosome behavior accounts for Mendel's laws. The chromosome theory of inheritance was emerging. It states that genes occupy specific loci on chromosomes and it is the chromosomes that undergo segregation and independent assortment during meiosis. Thus, it is the behavior of chromosomes during meiosis and fertilization that accounts for inheritance patterns. Genes located close together on the same chromosome tend to be inherited together and they are called linked genes. They do not generally follow Mendel's law of independent assortment. Crossing over is very useful. They are used to produce new combinations of alleles, see the percentage of it, and also its data can be used to map genes.
Many animals have a pair of sex chromosomes, designated X and Y that determine and individual's sex. A gene located on either sex chromosome is called a sex-linked gene. By using punnett square, whether an individual is a male or a female is also able to be determined. Disorders can affect mostly males. For example, hemophilia, red-green color blindness, and duchenne muscular dystrophy.


KEY TERMS:
-self-fertilize: sperm-carrying pollen grains released from the stamens land on the egg containing carpel of the same flower.
-cross-fertilization: fertilization of one plant by pollen from a different plant.
-hybrids: the offspring of two different varieties
-P generation: the true-breeding parental plants
-F1 generation: true-breeding parental plants' hybrid offsprings
-F2 generation: offsprings of when F1 plants self-fertilizeor fertilize each other
-testcross: a mating between an individual of unknown genotype and a homozygous recessive individual
-phenotype: offsprings' composition, geneticists distinguish between an organism's expressed, or physical, traits
-genotype: genetic makeup such as PP, Pp, pp
-rule of addition: the probability that an event can occur in two or more alternative ways is the sum of the separate probabilities of the different ways.

This punnett square shows that both parents have gametes that can be showed as  RrYy cross over. And it shows the probabilities of offspring whether if it is going to have round yellow, round green, wrinkled yellow, or wrinkled green. In this punnett square, 1/16 have RRYY, RRyy, rrYY, or rryy, 2/16 have RRYy, rrYy, Rryy, or RrYY, and 4/16 have RrYy. This is genotype of offsprings. And 9/16 have round yellow, 3/16 have round green, or wrinkled yellow, and 1/16 have wrinkled green. It is phenotype of offsprings. 
http://www.youtube.com/watch?v=-2YPAt8hOmE

5FACTS:

1) Phenotype shows the physical looking of organism, and genotype shows the alleles.

2) Mendel's laws are valid for all sexually reproducing species, but genotype often does not dictate phenotype in the simple way his laws describe.

3) Sex chromosomes determine sex in many species. If a specie has Y, it is a male, and if it has XX, it is a female.

4) Genes are located on chromosomes, whose behavior during meiosis and fertilization accounts for inheritance patters.

5) Crossing over can separate linked alleles, producing gametes with recombinant chromosomes.