BIO II Review EXAM 1

CH 11 DNA microarray

-A DNA microarray is a glass slide with many tiny wells, each containing a different fragment of single-stranded DNA that derives from a particular gene.

CH 11 Operator

-Between the promoter and the enzyme genes, a DNA segment called an operator acts as a switch that is turned on or off, depending on whether a specific protein is bound there. -The operator and protein together determine whether RNA polymerase can attach to the promoter and start transcribing the genes.

CH 11 Why Is reproductive cloning used ?

-In agriculture, animals with specific sets of desirable traits might be cloned to produce identical herds. -In research, genetically identical animals can provide perfect "control animals" for experiments. -The pharmaceutical industry is experimenting with cloning animals for potential medical use. -Reproductive cloning is used to restock populations of endangered animals.

CH 14 Postzygotic barriers

-Reduced Hybrid Viability -Reduced Hybrid Fertility -Hybrid Breakdown

CH 14 Prezygotic barriers

-Temporal Isolation -Habitat Isolation -Behavioral Isolation -Mechanical Isolation -Gametic Isolation

CH 11 Operon

-The key is the way the three lactose-digesting genes are organized: They are adjacent in the DNA and turned on and off as a single unit. -This regulation is achieved through short stretches of DNA that help turn all three genes on and off at once, coordinating their expression. -Such a cluster of related genes and sequences that control them is called an operon. The operon considered here is the lac (short for lactose) operon.

CH 11 Repressor

-Transcription is turned off because a protein called a repressor binds to the operator and physically blocks the attachment of RNA polymerase to the promoter.

CH 11 X chromosome inactivation

-X chromosome inactivation occurs in female mammals, takes place early in embryonic development, and happens when one of the two X chromosomes in each cell is inactivated at random. •After one X chromosome is inactivated in each embryonic cell, all of that cell's descendants will have the same X chromosome turned off. •If a female has different versions of a gene on each of her X chromosomes, about half of her cells will express one version, while the other half will express the alternate version.

CH 11 Gene Expression

Definition: -A gene that is turned on is being transcribed and translated into specific proteins. The overall process by which genetic information flows from genes to proteins is called gene expression.

CH 11 gene regulation

Definition: -Cells with the same genetic information can develop into different types of cells through gene regulation, mechanisms that turn on certain genes while other genes remain turned off. -Regulating gene activity allows for specialization of cells within the body. How and Why Genes are Regulated : •Every cell in your body was produced through successive rounds of mitosis starting from the zygote, the original cell that formed after fusion of sperm and egg. •Therefore, every cell in your body has the same DNA as the zygote and every somatic (body) cell contains every gene.

CH 12 Cutting and Pasting DNA

Recognition site (recognition sequence) for a restriction enzyme Step 1: A restriction enzyme cuts the DNA into fragments. (sticky ends) Step 2: A DNA fragment is added from another source. Step 3: Fragments stick together by base pairing. Step 4: DNA ligase joins the fragments into strands.

CH 12 Cutting and Pasting DNA with Restriction Enzymes

• Recombinant DNA is produced by combining two ingredients: 1. a bacterial plasmid and 2. the gene of interest. •To understand how these DNA molecules are spliced together, you need to learn how enzymes cut and paste DNA. •The cutting tools used for making recombinant DNA are bacterial enzymes called restriction enzymes. -The DNA sequence recognized by a particular restriction enzyme is called a restriction site. -After a restriction enzyme binds to its restriction site, it cuts the two strands of the DNA by breaking chemical bonds at specific points within the sequence.

CH 11 Oncogenes and Tumor-Suppressor Genes

•A gene that causes cancer is called an oncogene. -A normal gene with the potential to become an oncogene is called a proto-oncogene. -A cell can acquire an oncogene from a virus or the mutation of one of its own proto-oncogenes. •Many proto-oncogenes code for growth factors, proteins that stimulate cell division, or for other proteins that affect the cell cycle. -When they malfunction, cancer (uncontrolled cell growth) may result. -For a proto-oncogene to become an oncogene, a mutation must occur in the cell's DNA. •Changes in genes whose products inhibit cell division are also involved in cancer. -These genes are called tumor-suppressor genes because the proteins they encode normally help prevent uncontrolled cell growth. -Any mutation that keeps a growth-inhibiting protein from being made or from functioning may contribute to the development of cancer.

CH 14 Evolution: Mechanisms of Speciation

•A key event in the origin of a species occurs when a population is somehow cut off from other populations of the parent species. •Species can form by -allopatric speciation, in which the initial block to gene flow is a geographic barrier that physically isolates the splinter population, or -sympatric speciation, without geographic isolation

CH 12 Gene Editing

•A new DNA technology, called the CRISPR-Cas9 system, allows the nucleotide sequence of specific genes to be edited in living cells. -Such editing can reveal the function of the gene or possibly even correct a genetic mutation. -CRISPR-Cas9 is rapidly becoming one of the most important tools available for genetic engineering. -Cas9 protein will cut any DNA sequence that is complementary to an associated molecule of guide RNA complementary to a target DNA sequence, such as a gene.

CH 13 Microevolution as Change in a Gene Pool

•A non-evolving population is in genetic equilibrium, also known as Hardy-Weinberg equilibrium. -The gene pool remains constant from generation to generation. •Because a generation-to-generation change in allele frequencies of a population is evolution viewed on the smallest scale, it is sometimes referred to as microevolution.

CH 14 Reproductive Barriers between Species

•A reproductive barrier is anything that prevents individuals of closely related species from interbreeding. -Prezygotic barriers prevent mating or fertilization between species. -Postzygotic barriers operate if •interspecies mating occurs and •hybrid zygotes form.

CH 14 Allopatric Speciation

•A variety of geologic processes can isolate populations. •Speciation occurs with the evolution of reproductive barriers between the isolated population and its parent population. •Even if the two populations should come back into contact at some later time, the reproductive barriers will keep them as separate species.

CH 14 Plate Tectonics and Biogeography

•According to the theory of plate tectonics, the continents and seafloors form a thin outer layer of solid rock, called the crust, divided into giant, irregularly shaped plates that float atop the mantle, a mass of hot, viscous material. •In a process called continental drift, movements in the mantle cause the plates to move. -The boundaries of some plates are hotspots of geologic activity. -Earthquakes signal that two plates are scraping past or colliding with each other. •Continental drift has had a tremendous impact on the evolution of life's diversity by -reshaping the physical features of the planet and -altering the environments in which organisms live.

CH 12 Recombinant DNA Techniques

•Bacteria are the workhorses of modern biotechnology. Biologists often manipulate genes in the laboratory using bacterial plasmids, which -are small, circular DNA molecules that duplicate separately from the larger bacterial chromosome, -can carry virtually any gene and are passed from one generation of bacteria to the next, and -are key tools for gene cloning, the production of multiple identical copies of a gene-carrying piece of DNA. DNA cloning methods are central to most genetic engineering tasks.

CH 11 Homeotic Genes

•Cell-to-cell signaling and the control of gene expression are particularly important during early embryonic development, when a single-celled zygote develops into a multicellular organism. -Master control genes called homeotic genes regulate groups of other genes that determine what body parts will develop in which locations. Similar homeotic genes direct early development in nearly every eukaryotic organism examined. Mutations in homeotic genes can produce bizarre effects.

CH 13 Charles Darwin and The Origin of Species •The explanation of the origin of the diversity of life accepted by present-day biologists is the evolutionary theory, proposed by Charles Darwin in his best-known book, On the Origin of Species by Means of Natural Selection, published in 1859.

•Charles Darwin −was born more than 200 years ago, on the same day as Abraham Lincoln, −was fascinated with nature as a boy, −quit medical school because he found medicine boring and surgery, in the days before anesthesia, horrifying, −studied to be a clergyman at Cambridge University, and −began a sea voyage at the age of 22 on the HMS Beagle that helped frame his theory of evolution.

CH 13 The Bottleneck Effect

•Cheetahs appear to have experienced at least two genetic bottlenecks: 1. during the last ice age, about 10,000 years ago, and 2. during the 1800s, when farmers hunted the animals to near extinction. •With so little variability, cheetahs today have a reduced capacity to adapt to environmental challenges.

CH 11 Practical Applications of Reproductive Cloning

•Cloning may also create new problems. ‒Conservationists argue that cloning •may detract from efforts to preserve natural habitats, •does not increase genetic diversity, and •is therefore not as beneficial to endangered species as natural reproduction. ‒An increasing body of evidence suggests that cloned animals are less healthy than animals produced via fertilization.

CH 12 DNA Profiling and Forensic Science

•DNA profiling -is the analysis of DNA samples to determine whether they come from the same individual and -has rapidly transformed the field of forensics—the scientific analysis of evidence for crime scene investigations and other legal proceedings. •To produce a DNA profile, scientists compare sequences in the genome that vary from person to person.

CH 13 Darwin's Journey

•The Beagle was a survey ship, charting poorly known stretches of the South American coast. •Darwin spent his time on shore −exploring the natural world, −collecting thousands of specimens of fossils and living plants and animals, −keeping detailed journals of his observations, and −carefully noting the characteristics of plants and animals that made them well suited to diverse environments.

CH 12 Gel Electrophoresis

•DNA profiling by STR analysis depends upon comparing lengths of DNA fragments. This can be done by using gel electrophoresis, a method for sorting macromolecules—usually proteins or nucleic acids. Figure 12.15 shows how gel electrophoresis separates DNA fragments from different sources. •DNA profiling can provide evidence of guilt or innocence. As of 2017, lawyers at the Innocence Project have helped to exonerate more than 350 convicted criminals, including 20 on death row.

CH 13 Darwin's Proposed:

•Darwin also proposed a scientific mechanism for how life evolves, a process he called natural selection. -In natural selection, individuals with certain inherited traits are more likely to survive and reproduce than are individuals with other traits. -He hypothesized that as the descendants of a remote ancestor spread into various habitats over millions and millions of years, natural selection resulted in diverse modifications, or evolutionary adaptations, that fit them to specific ways of life in their environment.

CH 13 artificial selection

•Darwin conceived the notion that artificial selection, the selective breeding of domesticated plants and animals to promote the occurrence of desirable traits in the offspring, was the key to understanding evolutionary change.

Ch 13 Gene Flow

•Gene flow -is another source of evolutionary change, -is genetic exchange with another population, -may result in the gain or loss of alleles, and -tends to reduce genetic differences between populations.

CH 13 Genetic Drift and the Bottleneck Effect

•Genetic drift is a change in the gene pool of a small population due to chance. •The bottleneck effect is an example of genetic drift. It results from a drastic reduction in population size which -decreases the overall genetic variability in a population, because at least some alleles are lost from the gene pool, and -results in a loss of individual variation and hence adaptability.

CH 12 Medical Applications

•Genetically modified bacteria have also been used to produce -human growth hormone (HGH), -a protein that helps dissolve blood clots, -vaccines, and -erythropoietin (EPO), used to treat anemia. •Genetically modified whole animals are also used to produce drugs.

CH 12 Genomics

•Genomics is the study of complete sets of genes (genomes). •Genomes are most often sequenced using a technique called the whole-genome shotgun method.

CH 14 Identifying Homologous Characters

•Homologous structures in different species may vary in form and function but exhibit fundamental similarities because they evolved from the same structure in a common ancestor. •Homologous structures are one of the best sources of information for phylogenetic relationships. •Convergent evolution involves superficially similar structures from different evolutionary branches that result from natural selection shaping analogous adaptations. Similarity due to convergence is called analogy, not homology.

CH 11 Promotor

•How do DNA control sequences turn genes on or off? One control sequence, called a promoter, is the site where the enzyme RNA polymerase attaches and initiates transcription.

CH 12 Short Tandem Repeat Analysis

•How do you prove that two samples of DNA come from the same person? -Repetitive DNA makes up much of the DNA that lies between genes in humans and consists of nucleotide sequences that are present in multiple copies in the genome. -Short tandem repeats (STRs) are short sequences of DNA repeated many times, tandemly (one after another), in the genome. -STR analysis is a method of DNA profiling that compares the lengths of STR sequences at specific sites in the genome.

CH 12 Human Gene Therapy

•Human gene therapy is intended to treat disease by introducing genes into an afflicted person. -In some cases, a mutant version of a gene may be replaced or supplemented with the normal allele, potentially correcting a genetic disorder, perhaps permanently. -In other cases, genes are inserted and expressed only long enough to treat a medical problem.

CH 13 Analyzing Gene Pools

•Imagine a wildflower population with two varieties of blooms that are of different colors. -An allele for red flowers, which we will symbolize by R, is dominant to an allele for white flowers, symbolized by r. -Now, let's say that 80%, or 0.8, of all flower-color loci in the gene pool have the R allele. The letter p will represent the relative frequency of the R allele in the population. -The Hardy-Weinberg formula can be used to calculate the frequencies of genotypes in a gene pool from the frequencies of alleles, and vice versa.

CH 14 Inferring Phylogeny from Homologous Characters

•In cladistics, organisms are grouped by common ancestry. -A clade consists of an ancestral species and all its evolutionary descendants and forms a distinct branch in the tree of life. -Thus, identifying clades makes it possible to construct classification schemes that reflect the branching pattern of evolution.

CH 14 Sympatric Speciation

•In sympatric speciation, a new species arises within the same geographic area as its parent species. •Factors that can reduce gene flow in sympatric populations include -polyploidy, in which a species may originate from an accident during cell division that results in an extra set of chromosomes, -habitat complexity, and -sexual selection. •Two distinct forms of polyploid speciation have been observed. 1. In one form, polyploidy arises from a single parent species. A failure of cell division might double the chromosome number from the original diploid number (2n) to tetraploid (4n). 2. A second form of polyploid speciation can occur when two different species interbreed and produce hybrid offspring. •Many of the plant species we grow for food are polyploids, including oats, potatoes, bananas, strawberries, peanuts, apples, sugarcane, and wheat.

CH 12 Bioinformatics: DNA Sequencing

•In the past decade, new experimental techniques have generated enormous volumes of data related to DNA sequences. -The need to make sense of an ever-increasing flood of information has produced bioinformatics, the application of computational methods to the storage and analysis of biological data. -Researchers can exploit the principle of complementary base pairing to determine the complete nucleotide sequence of a DNA molecule, known as DNA sequencing.

CH 13 The Idea of Fixed Species

•The Greek philosopher Aristotle generally held the view that species are fixed, permanent forms and do not change over time. •Judeo-Christian culture reinforced this idea with a literal interpretation of the biblical book of Genesis, which tells the story of each form of life being individually created in its present-day form.

CH 13 Darwin's Observations

•Many of Darwin's observations indicated that geographic proximity is a better predictor of relationships among organisms than similarity of environment. −For example, the organisms living in temperate regions of South America more closely resembled species living in tropical regions of that continent than species in temperate regions of Europe. −Also, the South American fossils Darwin found, though clearly examples of species different from living ones, were distinctly South American in their resemblance to the contemporary plants and animals of that continent. •Darwin was particularly intrigued by the geographic distribution of organisms on the Galápagos Islands. −Most of the animals that inhabit these remote islands were found nowhere else in the world, but they resemble South American species. −Darwin noticed that Galápagos marine iguanas had flattened tails that aid in swimming and are similar to, but distinct from, land-dwelling iguanas on the islands and on the South American mainland. −Each island had its own distinct variety of giant tortoise.

CH 13 Mutation

•Mutation is the ultimate source of the genetic variation that serves as raw material for evolution. -New alleles originate by mutation, a change in the nucleotide sequence of DNA. -In multicellular organisms, however, only mutations in cells that produce gametes can be passed to offspring and affect a population's genetic variability. -A change as small as a single nucleotide in a protein-coding gene can have a significant effect on phenotype, as in sickle-cell disease. •Mutation that affects a protein's function will probably be harmful. •On rare occasions, a mutated allele may -improve the adaptation of an individual to its environment and -enhance its reproductive success. •This kind of effect is more likely when the environment is changing in such a way that mutations that were once disadvantageous are favorable under the new conditions.

CH 13 Key Points about Natural Selection

•Natural selection can amplify or diminish only heritable traits. •Although an organism may, during its lifetime, acquire characteristics that help it survive, acquired characteristics cannot be passed on to offspring. •Natural selection is not goal-directed; it does not lead to perfectly adapted organisms. A trait that is favorable in one situation may be useless—or even detrimental—in different circumstances.

CH 11 Gene Regulation in Bacteria

•Natural selection has favored bacteria that express only the genes whose products are needed by the cell. Imagine an Escherichia coli bacterium living in your intestines.

CH 13 Lamarck and Evolutionary Adaptations

•Naturalists compared fossil forms with living species and noted patterns of similarities and differences. •In the early 1800s, French naturalist Jean-Baptiste de Lamarck suggested that life evolves. −He explained evolution as the refinement of traits that equip organisms to perform successfully in their environments. −He proposed that by using or not using the body parts, an individual may develop certain traits that pass on to his offspring.

CH 11 Reproductive Cloning of Animals

•Nuclear transplantation involves replacing the nucleus of an egg cell or a zygote with a nucleus removed from an adult body cell. -If the animal to be cloned is a mammal, further development requires implanting the early embryo into the uterus of a surrogate mother. -This type of cloning is called reproductive cloning because it results in the birth of a new animal. -In 1996, researchers used reproductive cloning to produce the first mammal cloned from an adult cell, a sheep named Dolly.

CH 11 RNA Processing and Breakdown

•RNA processing includes: -the addition of a cap and a tail, -the removal of introns (the noncoding DNA segments that interrupt the genetic message), and -RNA splicing (the splicing together of exons). •Within a cell, exon splicing can occur in more than one way, generating different mRNA molecules from the same starting RNA molecule. With this sort of alternative RNA splicing, an organism can produce more than one type of polypeptide from a single gene. Exons are with the numbers Introns are the spaces in between the numbers

CH 11 The Genetic Potential of Cells

•Regeneration is the regrowth of lost body parts. -When a salamander loses a tail, certain cells in the tail stump reverse their differentiated state, divide, and then differentiate again to give rise to a new tail. -Many other animals, especially among the invertebrates, can regenerate lost parts. -Isolated pieces of a few relatively simple animals can dedifferentiate and then develop into an entirely new organism.

CH 11 silencers

•Repressor proteins, which may bind to DNA sequences called silencers, inhibit the start of transcription.

CH 12 Genetic Engineering

•Scientists construct recombinant DNA by combining pieces of DNA from two different sources—often from different species—to form a single DNA molecule. -Recombinant DNA technology is widely used in genetic engineering, the direct manipulation of genes for practical purposes.

CH 13 Evidence from Homologies

•Similarity resulting from common ancestry is known as homology. -Characteristics present in an ancestral organism are altered over time by natural selection as its descendants face different conditions. -As a result, related species can have characteristics that are similar yet function differently. -Darwin cited the anatomical similarities among vertebrate forelimbs as evidence of common ancestry.

CH 14 What Is a Species?

•Species is a Latin word meaning "kind" or "appearance." •The biological species concept defines a species as "a group of populations whose members have the potential to interbreed with one another in nature and produce fertile offspring (offspring that can reproduce)." •The biological species concept cannot be applied in all situations, including asexual organisms and fossils.

CH 13 Defintions

•Taxonomy is the branch of biology concerned with identifying, naming, and classifying species. •In the Linnaean system, each species is given a two-part Latinized name, or binomial. −The first part of a binomial is the genus (plural, genera), a group of closely related species. −The second part of a binomial is used to distinguish species within a genus.

CH 14 Classifying the Diversity of Life: Classification and Phylogeny

•Taxonomy is the naming and classification of species. •Systematics includes taxonomy and focuses on -classifying organisms and -determining their evolutionary relationships. •Biologists use phylogenetic trees to -depict hypotheses about the evolutionary history of species and -reflect the hierarchical classification of groups nested within more inclusive groups.

CH 12 The Human Genome

•The Human Genome Project was a massive scientific endeavor to determine the nucleotide sequence of all the DNA in the human genome and identify the location and sequence of every gene. -At the end of the project, more than 99% of the genome had been determined to 99.999% accuracy. -This ambitious project has provided a wealth of data that may illuminate the genetic basis of what it means to be human. -The biggest surprise from the Human Genome Project is the relatively small number of human genes—currently estimated to be about 21,000. •Like the genomes of most complex eukaryotes, only a small amount of total human DNA consists of genes that code for proteins, tRNAs, or rRNAs. •Bioinformatics can also provide insights into our evolutionary relationships with nonhuman animals.

CH 13 Populations as the Units of Evolution

•The evolutionary impact of natural selection is apparent only in the changes in a population of organisms over time. -A population is a group of individuals of the same species that live in the same area and interbreed. -Different populations of the same species may be geographically isolated from each other to such an extent that an exchange of genetic material never, or only rarely, occurs. -Such isolation is common in populations confined to different lakes. •At the population level, biologists focus on the gene pool, which consists of all copies of every type of allele, at every locus, in all members of the population. •For many loci, there are two or more alleles in the gene pool.

CH 14 Structure/Function: Adaptation of Old Structures for New Functions

•The first utility of feathers may have been for insulation. •Once flight itself became an advantage, natural selection would have gradually remodeled feathers and wings to fit their additional function. •Structures such as feathers that evolve in one context but become co-opted for another function are called exaptations.

CH 13 The Founder Effect

•The founder effect -is likely when a few individuals colonize an isolated habitat, -represents genetic drift in a new colony, and -explains the relatively high frequency of certain inherited disorders in some small human populations.

CH 12 Polymerase Chain Reaction

•The polymerase chain reaction (PCR) -is a technique by which a specific segment of DNA can be amplified (by targeting and copying it quickly and precisely) and -permits a scientist to obtain enough DNA from even minute amounts of blood or other tissue to allow a DNA profile to be constructed.

CH 11 Therapeutic Cloning and Stem Cells: Embryonic Stem Cells

•The purpose of therapeutic cloning is not to produce a living organism but rather to produce embryonic stem cells. -In mammals, embryonic stem (ES) cells are obtained by removing cells from a several day-old embryo and growing them in laboratory culture. -Embryonic stem cells can divide indefinitely and, under the right conditions, can (hypothetically) develop into a wide variety of specialized cells. -If scientists can discover the right conditions, they may be able to grow cells for the repair of injuredor diseased organs.

CH 13 Mechanisms of Evolution—Natural Selection

•What mechanisms can change a gene pool? •The three main causes of evolutionary change are 1. natural selection, 2. genetic drift, and 3. gene flow. •Natural selection is the most important, because it is the only process that promotes adaptation.

CH 13 New Insights

•While on his voyage, Darwin was strongly influenced by the newly published Principles of Geology by geologist Charles Lyell, which presented the case for an ancient Earth sculpted over millions of years by gradual geological processes that continue today. •By the time Darwin returned to Great Britain, he had begun to seriously doubt that Earth and all its living organisms had been specially created only a few thousand years earlier. •Back in England, Darwin -reflected on his observations, analyzed his specimen collections, discussed his work with colleagues, and -concluded that the evidence was better explained by the hypothesis that present-day species are the descendants of ancient ancestors, which they still resemble in some ways. -Over time, differences gradually accumulated by a process that Darwin called "descent with modification," his phrase to describe evolution.

CH 11 Gene ? (Not Sure if that's right )--->

•Within a cell, exon splicing can occur in more than one way, generating different mRNA molecules from the same starting RNA molecule. With this sort of alternative RNA splicing, an organism can produce more than one type of polypeptide from a single gene. •After an mRNA is produced in its final form, its "lifetime" can be highly variable, from hours to weeks to months. Controlling the timing of mRNA breakdown provides another opportunity for regulation. But all mRNAs are eventually broken down and their parts recycled.