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.