Botany 123 Exam 2 Textbook

How does shunning GMO's hurting developing nations?

- Genetic engineering is used to solve or mitigate nutritional and agricultural challenges, but fears and anxieties about "GMO" stand in the way. Crops such as water efficient maize, bananas resistant to wilt, and vitamin fortified cassavas are being developed by African scientists. -Anti-GMO sentiment, often promoted by groups headquartered in the West, continues to thwart these efforts. Protests within these countries against "GMO" crops are often interlinked with the not-entirely-misplaced distrust of foreign companies who have a history of interfering with these nations' food sovereignty.

Traits that have been improved by crop breeding include:

- Yield (increasing how much is safely grown on the same amount of land) - Resistance to pests and diseases - Adaptation to environmental stresses such as heat, drought, frost, and salty soils - Nutritional value - Ease of harvest - Efficiency of breeding techniques - Taste, color, and texture - Creation of seedless varieties of fruits and vegetables

Even though "GMOs" are routinely blamed many economic, social, and political issues, these issues aren't exclusive to genetic engineering:

-Both conventionally bred (non-GMO) and genetically engineered (GE) crops can be patented. -Farmers routinely sign contracts with seed companies, for both non-GMO and GE seeds alike. -Herbicides aren't just used with "GMOs." Herbicide tolerant crop varieties can be GE or non-GMO. -Large agricultural companies dominate across agricultural systems, as some develop and sell GE, non-GMO, and seeds that can be used in organic farming. -Corporations with GE, non-GMO, and organic interests hire lobbying groups to impact agricultural and trade policy.

reproductive barriers

1. Prezygotic: temporal (mating seasons), habitat (different habitats, do not meet), behavioral (courtship rituals, lack of attraction), mechanical (structural differences), gametic isolation (male and female gametes fail to unite) 2. Postzygotic: reduced hybrid viability (fail to reach sexual maturity), reduced hybrid fertility (sterile), hybrid breakdown (feeble and sterile)

speciation

Formation of new species

Lamarck and Evolutionary Adaptations

Fossils told of other changes in the history of life, too. Naturalists compared fossil forms with living species and noted patterns of similarities and differences. In the early 1800s, French naturalist Jean-Baptiste Lamarck suggested that the best explanation for these observa-tions is that life evolves. Lamarck explained evolution as the refinement of traits that equip organisms to perform successfully in their environments. He proposed that by using or not using its body parts, an individual may develop certain traits that it passes on to its offspring. For example, some birds have powerful beaks that enable them to crack tough seeds. Lamarck suggested that these strong beaks are the cumulative result of ancestors exercising their beaks during feeding and passing that acquired beak power on to offspring. However, simple observations provide evidence against the inheritance of acquired traits: An athlete who builds up strength through weight training will not pass enhanced biceps on to his or her children. Although Lamarck's idea of how species evolve was mistaken, his proposal that species evolve as a result of interactions between organisms and their environments helped set the stage for Darwin.

Three General Outcomes of Natural Selection

Imagine a population of mice with individuals ranging in fur color from very light to very dark gray. If we graph the number of mice in each color category, we get a bell-shaped curve. If natural selection favors certain fur-color phenotypes over others, then the population of mice will change over the generations. These three modes of natural selection are called directional selection, disruptive selection, and stabilizing selection. Such selection typically occurs in relatively stable environments, where conditions tend to reduce physical variation. This evolutionary conservatism works by selecting against the more extreme phenotypes. For example, stabilizing selection keeps the majority of human birth weights between 3 and 4 kg (approximately 6.5 to 9 pounds). For babies much lighter or heavier than this, infant mortality is greater. Evolutionary spurts occur when a population is stressed by a change in the environment, such as happened with Darwin's finches on Daphne, or by migration to a new place. When challenged with a new set of environmental problems, a popula-tion either adapts through natural selection or dies off in that locale. The fossil record tells us that the popula-tion's extinction is the most common result. Those populations that do survive crises may change enough to become new species.

Translation: The Process

In initiation, a ribosome assembles with the mRNA and the initiator tRNA bearing the first amino acid. Beginning at the start codon, the codons of the mRNA are recognized one by one by tRNAs bearing succeeding amino acids. The ribosome bonds the amino acids together. With each addition, the mRNA moves by one codon through the ribosome. When a stop codon is reached, the completed polypeptide is released. Translation is divided into the same three phases as transcription: initiation, elongation, and termination.

Natural Selection: A Closer Look

In natural selection, only the events that produce genetic variation (mutation and sexual reproduction) are random. The process of natural selection, in which individuals better adapted to the environment are more likely to survive and reproduce, is not random. Consequently, only natu-ral selection consistently leads to adaptive evolution—evolution that results in organisms better suited to their environment.

Mutations

Mutations are changes in the DNA base sequence, caused by errors in DNA replication, recombination, or mutagens. Substituting, deleting, or inserting nucleotides in a gene has varying effects on the polypeptide and organism. Any change to the genetic information of a cell or virus is called a mutation. Mutations can involve large regions of a chromosome or just a single nucleotide pair, as in sickle-cell disease. Usually, mutations are harmful. Think of a mutation as a typo in a recipe; occasionally, such a typo might lead to an improved recipe, but much more often it will be neutral, mildly bad, or disastrous.

Elongation: translation

Once initiation is complete, amino acids are added one by one to the first amino acid. Each addition occurs in the three-step elongation process. The anticodon of an incoming tRNA molecule, carrying its amino acid, pairs with the mRNA codon in the A site of the ribosome. The polypeptide leaves the tRNA in the P site and attaches to the amino acid on the tRNA in the A site. The ribosome creates a new peptide bond. Now the chain has one more amino acid. The P site tRNA now leaves the ribosome, and the ribosome moves the remaining tRNA, carrying the growing polypeptide, to the P site. The mRNA and tRNA move as a unit. This movement brings into the A site the next mRNA codon to be translated, and the process can start again with step

geologic time scale

Precambrian, Paleozoic, Mesozoic, and Cenozoic eras. Each of these divisions represents a distinct age in the history of Earth and its life. The boundaries between eras are marked by mass extinc-tions, when many forms of life disappeared from the fossil record and were replaced by species that diversified from the survivors.

Population Genetics and Health Science

Public health scientists use the Hardy-Weinberg equation to calculate the percentage of a human population that carries the allele for certain inherited diseases. Consider phenylke-tonuria (PKU), which is an inherited inability to break down the amino acid phenylala-nine. If untreated, the disorder has serious effects on brain development. PKU is caused by a recessive allele (that is, one that must be present in two copies to produce the phenotype) Thus, we can represent the frequency of individuals in the U.S. population born with PKU with the q2 term in the Hardy-Weinberg formula. Estimat-ing the frequency of a harmful allele is essential for any pub-lic health program dealing with genetic diseases.

Excessive Fungicide use (four separate articles?)

Southern farmer, sprays pay or increase yield "I don't think resistance is ever going to be an issue," Klueppel says. He bases his position primarily on two points: Growers must always use a full rate of fungicide; and ag chemical companies are going to churn out new products. Is a fungicide application with no Inte-grated Pest Management reason OK if a full rate always is sprayed? Does a plant health spray guarantee a yield increase? Can we apply fungicides with impunity as long as most of our neighbors don't? For many plant pathologists, the answer to all three questions is "no" — though it's a qualified "no" on the last one One of the discussions in regard to weed resistance is the use of half rates. Hershman reminds growers that resis- tance develops regardless of the rate used. "Preventative applications can pro- duce a profitable yield increase in soybean fields that have good yield potential and are subjected to conditions that favor dis-ease development." The take-home message: The grower who applies the standard risk measure- ments when deciding whether to spray is more likely to profit. hit your target with appropriate nozzle One of the most common questions asked at the grower meetings this year was, "What is the best type of spray nozzle to use for herbicide applications?" AI isn't the go-to nozzle fighting a fungus SOYBEANS are critical to the U.S. economy. But the third-largest crop in the nation has an enemy eating away at it — a fungus in the same family as the one that caused the infamous Irish potato famine. The fungus is called Phytophthora sojae, and is commonly known as soybean stem rot or root rot. As we've been going toward more no-till, it favors the fungus, Parrott is studying soybean genes to see if there is a way to engineer longer-lasting economical control of the fungus. He's looking at two methods. DUPONT Crop Protection will launch two new fungicides — one for corn and soybeans, and one for those crops plus wheat — by year-end,

Messenger RNA (mRNA)

The first important ingredient= mRNA produced by transcription. Once it is present, the machinery used to translate mRNA requires enzymes and sources of chemical energy, such as ATP. In addition, translation requires two other important components: ribosomes and a kind of RNA called transfer RNA.

The Founder Effect

When a few individuals colonize an isolated island, lake, or other new habitat, the genetic makeup of the colony is only a sample of the gene pool in the larger population. The smaller the colony, the less likely it is to be representative of all the genetic diversity present in the population from which the colonists emigrated. If the colony succeeds, genetic drift will continue to change the frequency of alleles randomly until the population is large enough for genetic drift to be minimal. The type of genetic drift resulting from the establishment of a small, new popu-lation whose gene pool differs from that of the parent population is called the founder effect. Numerous examples of the founder effect have been identified in geographically or socially isolated human populations. In such situations, disease-causing alleles that are rare in the larger population may become com-mon in a small colony.

RNA Processing and Breakdown

Within a eukaryotic cell, transcription occurs in the nucleus, where RNA tran-scripts are processed into mRNA before moving to the cytoplasm for translation by the ribosomes. RNA processing includes the addition of a cap and a tail, the removal of introns, and RNA splicing (the splicing together of exons).

(probably NOT important) plate tectonics/continental drift

a theory explaining the structure of the earth's crust and many associated phenomena as resulting from the interaction of rigid lithospheric plates that move slowly over the underlying mantle. This explains the patterns of biogeography, the study of the past and present distribution of organisms.

(probably NOT important) When the haploid gametes (produced by meiosis) from species A and species B combine, the (hybrid) offspring's

chromosomes are not homologous; it is sterile.

pg. 254

figure 13.11

Macroevolution

is evolutionary change above the species level, for example, the origin of amphibians through a series of speciation events. Macroevolution also includes the impact of mass extinctions on the diversity of life and the origin of key adaptations such as flight.

sympatric speciation

is the origin of a new species with-out geographic isolation. The splinter population becomes reproductively isolated even though it is in the midst of the parent population.

Gene regulation in bacteria

need to know?

Non-GMO is not actually a "luxury" because...

non-GMO foods cost 10-62% more with no added benefit. The non-GMO label does not mean that the food is healthier, better for the environment, or more sustainable. These claims persuade customers to keep buying this label.

exaptations

structures that evolve in one context but become co-opted for another function (e.g. feathers on dinosaurs used for mating displays, insulation, camouflage ---> used for flying)

Allopatric speciation

the initial block to gene flow is a geographic barrier that physically isolates the splinter population

Each massive dip in massive extinction

was followed by explosive diversification of certain survivors. Extinctions seem to have provided the surviving organisms with new environmental opportunities.

Origin of Life

(1) the synthesis of small organic molecules, such as amino acids and nucleotide monomers (2) the joining of these small molecules into macromolecules, including proteins and nucleic acids (3) the packaging of all these molecules into pre-cells, droplets with membranes that maintained an internal chemistry different from the surroundings (4) the origin of self-replicating molecules that eventually made inheritance of genetic material possible.

By shunning "GMOs," we may be forsaking sustainable and humane options

- Several genetically engineered traits can in fact decrease agricultural dependence on chemical pesticides. The addition of genes that enable resistance to pests, including fungi, insects, and viruses, has been shown to decrease the need for the application of external pesticides. - A reduction in the need to spray crops reduces farming's carbon footprint by decreasing fuel use and equipment wear-and-tear. It also keeps the farming community healthier by reducing their exposure to pesticides.

how do cavities form?

-Streptococ mutans thrives in the anaerobic environment found in the tiny crevices in tooth enamel. Using sucrose (table sugar) to make a sticky polysaccharide, the bacteria glue themselves in place and build up thick deposits of plaque (mineralizes). Within this fortress, S. mutans ferments sugars to obtain energy, releasing lactic acid as a by-product. The acid attacks tooth enamel and eventually eats through it. Other bacteria then use the entrance and infect the soft tissue in the interior of the tooth. -Early humans were hunter gatherers, living on food foraged in the wild. In a major cultural shift, this lifestyle was replaced by agriculture, which provided a diet rich in carbohydrates from grain. An even later dietary shift brought processed flour and sugar to the table. Each change in diet altered the environment inhabited by our oral microbiota. Studies of prehistoric human remains have correlated dental disease with these changes in diet.

Creationist seeks to debunk scientific fact at Dane County Fair

-The part-time nurse from West Bend seeks to convince people that the universe is only 6,000 years old and that Charles Darwin was wrong. Her booth proclaims Christianity and evolution incompatible. -took her son out of school because she didn't think the education was correct, and she shows fossils she has found as evidence -Wednesday, the first day of the fair, Weigand's booth was getting quite a bit of interest and a largely positive response (people actually believed her)

How does GMO opposition strengthen "Big Ag"

-When we demand that GE crops be held to a higher standard of regulation due to the breeding method, rather than the risk, we continue to make it difficult for small companies and startups to compete. -GE products like tear-free onions and gluten-free wheat have been shelved due to these strict regulatory hurdles. This creates a vicious circle of power, where only corporate behemoths have the resources to get a new crop through the multi-year and multi-million dollar regulatory process.

Evidence from Homologies

A second type of evidence for evolution comes from ana-lyzing similarities among different organisms. Evolution is a process of descent with modification—characteristics present in an ancestral organism are altered over time by natural selection as its descendants face different environmental conditions. As a result, related species can have characteristics that have an underlying similarity yet function differently. Similarity resulting from common ancestry is known as homology. Darwin cited the anatomical similarities among verte-brate forelimbs as evidence of common ancestry. Biologists call such anatomical similarities in different organisms homologous structures—features that often have different functions but are structurally similar because of common ancestry. If two species have homologous genes with sequences that match closely, biologists conclude that these sequences must have been inherited from a rela-tively recent common ancestor. Darwin's boldest hypothesis was that all life-forms are related. Molecular biology provides strong evidence for this claim: All forms of life use the same genetic language of DNA and RNA, and the genetic code—how RNA triplets are translated into amino acids—is essentially universal. Thus, it is likely that all species descended from common ancestors that used this code. Geneticists have also uncovered hidden molecular homologies. Organisms may retain genes that have lost their function through mutations, even though homolo-gous genes in related species are fully functional.

Charles Darwin and The Origin of Species

Although Charles Darwin was born more than 200 years ago—on the very same day as Abraham Lincoln—his work had such an extraordinary impact that many scientists mark his birthday with a celebration of his contributions to biology. How did Darwin become a rock star of science? As a boy, Darwin was fascinated with nature. He loved collecting insects and fossils, as well as reading books about nature. His father, an eminent physician, could see no future for his son as a naturalist and sent him to medical school. But young Darwin, finding medicine boring and sur-gery before the days of anesthesia horrifying, quit medical school. His father then enrolled him at Cambridge Univer-sity with the intention that he should become a clergyman. After college, however, Darwin returned to his childhood interests rather than following the career path mapped out by his father. At the age of 22, he began a sea voyage on the HMS Beagle that helped him frame his theory of evolution.

Explaining the diversity of life

Although early naturalists and philosophers sought to describe and organize the diversity of life, they also sought to explain its origin. The explanation accepted by present-day biologists is the evolutionary theory pro-posed by Charles Darwin in his best known book, On the Origin of Species by Means of Natural Selection, published in 1859. Before we introduce Darwin's theory, however, let's take a brief look at the scientific and cultural context that made the theory of evolution such a radical idea in Darwin's time

Gene flow

Another source of evolutionary change is gene flow, which is genetic exchange with another population. A population may gain or lose alleles when fertile hypothetical wildflower population in Figure 13.17. Suppose a neighboring population consists entirely of white-flowered individuals. A windstorm may blow pollen to our wildflowers from the neighboring popula-tion, resulting in a higher frequency of the white-flower allele in the next generation—a microevolutionary change. Gene flow tends to reduce differences among popula-MECHANISMS OF EVOLUTION tions. If it is extensive enough, gene flow can eventually join neighboring populations into a single population with a common gene pool. As people began to move about the world more freely, gene flow became an important agent of microevolutionary change in human populations that were previously isolated.

Microevolution as change in a gene pool

As stated earlier, evolution can be measured as changes in the genetic composition of a population over time. It helps, as a basis of comparison, to know what to expect if a population is not evolving. A non-evolving population is in genetic equilibrium, which is also known as Hardy-Weinberg equilibrium.The population's gene pool remains constant. From generation to generation, the frequencies of alleles (p and q) and genotypes (p2, 2pq, and q2) are unchanged. Sexual shuffling of genes cannot by itself change a large gene pool. Because a generation-to-gen-eration change in allele frequencies of a population is evolution viewed on the smallest scale, it is sometimes referred to as microevolution.

Translation: The Players

As we have seen, translation is a con-version between different languages—from the nucleic acid language to the protein language—and it involves more elaborate machinery than transcription. Messenger RNA (mRNA), ribosomes, and Transfer RNA (tRNA)

The Rising Threat of Antibiotic Resistance

As you probably know, antibiotics are drugs that kill infec-tious microorganisms. A new era in human health followed the introduction of penicillin, the first widely used antibiotic, in the 1940s. However, now medi-cal experts fear that the process of evolution could end the era of antibiotics. Antibiotics select for resistant bacteria. A gene that codes for an enzyme that breaks down an antibi-otic or a mutation that alters the binding site of an antibiotic can make a bacterium and its offspring resistant to that antibiotic. Natural selection has been a problem in the efforts to eradicate malaria. Popu-lations of the parasitic microbe that causes malaria have become resistant to drugs used to treat the disease. The rapid evolution of antibiotic resistance has been fueled by their widespread use—and misuse. Subsequent mutations in such bacteria may lead to full-blown antibiotic resistance. Medical and pharmaceutical researchers are racing to develop new antibiotics and other drugs. However, experience suggests that our battle against the evolution of drug-resistant bacteria will continue into the future

DNA: Structure and Replication

Both DNA and RNA are nucleic acids=long chains (polymers) of chemical units (monomers) called nucleotides. Polynucleo-tides can be very long + may have any sequence of the four different types of nucleotides (abbreviated A, C, T, and G), so lots of varieties possible. Nucleotides are joined together by covalent bonds between the sugar of one nucleotide and the phos-phate of the next=repeating pattern of sugar-phosphate-sugar-phosphate=sugar-phosphate backbone. Each nucleotide has three components: a nitrogenous base, a sugar, and a phosphate group. The nitrogenous bases are arranged like ribs that project from this backbone. You can think of a polynucleotide as a long ladder split in half lengthwise, with rungs that come in four colors. The sugars and phosphates make up the side of the ladder, with the sugars acting as the half-rungs. (see pictures 172/173)

How are genes controlled? (need to know?)

Cancer specialists traditionally determine whether a woman should have chemotherapy by using clinical factors, such as the size of her tumor and how many lymph nodes had cancer cells in them. How can doctors tell which cases are risky enough to warrant chemotherapy? What determines how fast cancer cells spread and therefore the risk posed by a particular tumor? First, it's helpful to know how mutations lead to cancer. Many cancer-associated genes encode proteins that turn other genes on or off. When these genes are mutated, the proteins malfunction and the cell may become cancerous. Scientists can now tell which genes are mutated in a given tumor. This information allows medical professionals to pre-dict the potential growth rate of the cancer. Soon, the genes of all cancer patients may be evaluated in this way, allowing therapy to be optimized for each patient. The ability to properly control which genes are active at any given time is crucial to normal cell function.

Homeotic Genes

Cell-to-cell signaling+the control of gene expression are particularly important during early embryonic develop-ment, when a single-celled zygote develops into a multicel-lular organism. Interactions between the cells of an embryo through chemical signals coordinate the process of development. Master control genes called homeotic genes regulate groups of other genes that determine what body parts will develop in which locations. For example, one set of homeotic genes in fruit flies instructs cells in the midbody to form legs. Elsewhere, these homeo-tic genes remain turned off, while others are turned on. Mutations in homeotic genes can pro-duce bizarre effects. For example, fruit flies with mutations in homeotic genes may have extra sets of legs growing from their head Similar homeotic genes help direct early development in nearly every eukaryotic organ-ism examined so far. These similarities sug-gest that these homeotic genes arose very early in the his-tory of life and that the genes have remained remarkably unchanged over eons of animal evolution.

Did Natural Selection Shape the Beaks of Darwin's Finches?

Charles Darwin encountered many interesting organisms during his visit to the Galápagos Islands. Particularly intrigued by the 14 species of finches=Darwin's finches. These small birds are closely related and share many traits. But differ in their feeding habits and the size and shape of their beaks, which are specialized based on what they eat. Biologists hypothesize that Darwin's finches evolved from a small populations of ancestral birds that colonized one of the islands. Natural selec-tion shaped the beaks of finches to make use of diverse foods in the new environment, a process that was repeated as birds migrated to neighboring islands with distinct environ-ments. For 40 years, evolutionary ecologists Peter and Rosemary Grant and their students have studied Darwin's finches on Daphne Such long-term, observational field stud-ies are an important method for testing hypotheses about evolution.

DNA History

DNA known to be a chemical component of cells by late 1800s, but Gregor Mendel+others had no idea what role (if any) DNA played in heredity. Through lots of experiments by 1950s, knew DNA was the molecule that acts as the hereditary material. Did not understand the specific three-dimensional arrangement of atoms that gave DNA its unique properties—the capacity to store genetic infor-mation, copy it, and pass it from generation to generation. The race was on to discover the link between the struc-ture and function of this important molecule.

Darwin's theory

Darwin spent the next two decades compiling and writing about evidence for evolution. He realized that his ideas would cause an uproar, however, and he delayed publish-ing. Darwin finally published The Origin of Species, a book that supported his hypothesis with immaculate logic and hundreds of pages of evidence drawn from observations and experiments in biology, geology, and paleontology. Conse-quently, scientists regard Darwin's concept of evolution by means of natural selection as a theory—a widely accepted explanatory idea that is broader in scope than a hypothesis, generates new hypotheses, and is supported by a large body of evidence

Evolutionary Trees

Darwin was the first to visualize the history of life as a tree in which patterns of descent branch off from a common trunk—the first organism—to the tips of millions of twigs representing the species living today. Closely related species share many traits because their lineage of common descent traces to a recent fork of the tree of life. Biologists illustrate these patterns of descent with an evolutionary tree, although today they often turn the trees sideways so they can be read from left to right. Some trees are based on a convincing combination of fossil, anatomical, and molecular data. Others are more speculative because sufficient data are not yet available.

Directional selection

Directional selection shifts the overall makeup of a population by selecting in favor of one extreme phenotype—the darkest mice, for example. Directional selection is most common when the local envi-ronment changes or when organisms migrate to a new environment. An actual example of directional selection is the shift of insect populations toward a greater fre-quency of pesticide-resistant individuals. Disruptive selection can lead to a balance between two or more contrasting phenotypes in a population. A patchy environment, which favors differ-ent phenotypes in different patches, is one situation associ-ated with disruptive selection.

Disruptive selection

Disruptive selection favors variants at opposite extremes over intermediate individuals. Here, the relative frequencies of very light and very dark mice have increased. Perhaps the mice have colonized a patchy habitat where a background of light soil is studded with dark rocks.

RNA Elongation (transcription)

During the second phase of transcription, elongation, the RNA grows longer. 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.

Termination

Elongation continues until a stop codon reaches the ribo-some's A site. Stop codons—UAA, UAG, and UGA—do not code for amino acids but instead tell translation to stop. The completed polypeptide, typically several hundred amino acids long, is freed, and the ribosome splits back into its subunits

Gene regulation in Eukaryotic cells

Eukaryotes, especially multicellular ones, have more sophisticated mechanisms than bacteria for regulat-ing the expression of their genes. This is not surprising because a prokaryote, being a single cell, does not have different types of specialized cells, such as neurons and red blood cells. Therefore, it does not require the elaborate regulation of gene expression that leads to cell specialization in multicellular eukaryotic organisms.

The Regulation of DNA Packing

Eukaryotic chromosomes may be in a more or less condensed state, with the DNA and accompanying proteins more or less tightly wrapped together. DNA packing tends to prevent gene expression by preventing RNA polymerase and other transcrip-tion proteins from binding to the DNA. Cells may use DNA packing for the long-term in-activation of genes.

How and why are genes regulated?

Every cell in your body has the same DNA as the zygote. To put it another way: Every somatic (body) cell contains every gene. However, the cells in your body are specialized in structure and function. But if every cell contains identical genetic instructions, how do cells develop differently from one another? The answer is obvious: Even though each restaurant has the same cookbook, different restaurants pick and choose different recipes from this book to prepare. Similarly, cells with the same genetic information can develop into differ-ent types of cells through gene regulation, mechanisms that turn on certain genes while other genes remain turned off. What does it mean to say that genes are turned on or off? A gene that is turned on is being transcribed into mRNA, and that mes-sage is being translated into specific proteins.

Evidence of evolutions

Evolution leaves observable signs. Such clues to the past are essential to any historical science. Historians of human civilization can study written records from earlier times. But they can also piece together the evolution of societies by recognizing vestiges of the past in modern cultures. Even if we did not know from written docu-ments that Spaniards colonized the Americas, we would deduce this from the Hispanic stamp on Latin American culture. Similarly, biological evolution has left evidence in fossils, as well as in today's organism

The diversity of life

For all of human history, people have named, described, and classified the inhabitants of the natural world. As trade and exploration connected all regions of the planet, these tasks became increasingly complex. For example, a scholar who sought to describe all the types of plants known to the Greeks in 300 b.c. had about 500 species to distinguish. Today, scientists recognize roughly 400,000 plant species. The Linnaean system includes a method ofnaming species and a hierarchical classification of species into broader groups of organisms. It is the basis for taxonomy, the branch of biology concerned with identifying, naming, and classi-fying species.

Analyzing Gene Pools

Imagine a wildflower population with two varieties of blooms that are different colors. An allele for red flowers, which we will symbolize by R, is dominant to an allele for white flowers, symbolized by r. These are the only two alleles for flower color in the gene pool of this hypotheti-cal plant population. Now, let's say that 80%, or 0.8, of all flower-color loci in the gene pool have the R allele. Because there are only two alleles in this example, the r allele must be present at the other 20% (0.2) of the gene pool's flower-color loci. Calculating frequencies? Hardy-Weinberg formula

evidence from fossil fuels

Fossils—imprints or remains of organisms that lived in the past—document differences between past and pres-ent organisms and show that many species have become extinct. The soft parts of a dead organism usually decay rapidly, but the hard parts of an animal that are rich in minerals, such as the bones and teeth of vertebrates and the shells of clams and snails, may remain as fossils. A cast forms when a dead organism that was buried in sediment decomposes and leaves an empty "mold" that is later filled by minerals dissolved in water. The min-erals harden within the mold, making a replica of the organism. Thus, the fossils in a particular stratum provide a glimpse of some of the organisms that lived in the area at the time the layer formed. Because younger strata are on top of older layers, the relative ages of fossils can be determined by the layer in which they are found. As a result, the sequence in which fossils appear within layers of sedimentary rocks is a historical record of life on Earth.a Of course, as Darwin acknowledged, the fossil record is incomplete. Many of Earth's organisms did not live in areas that favor fossilization. Furthermore, not all fossils that have been preserved are accessible to paleontologists. the thousands of fossils newly discovered each year give pale-ontologists new opportunities to test hypotheses about how the diversity of life evolved.

The evolution of populations

In The Origin of Species, Darwin provided evidence that life on Earth has evolved over time, and he proposed that natural selection, in favoring some heritable traits over others, was the primary mechanism for that change. But how do the variations that are the raw material for natural selection arise in a population? And how are these varia-tions passed along from parents to offspring? Darwin did not know that Gregor Mendel had already answered these questions. Although both men lived and worked at around the same time, Mendel's work was largely ignored by the scientific community in his life. Its rediscovery in 1900 set the stage for understanding the genetic differences on which evolution is based.

The Genetic Code (how to shorten?)

In addition to codons that specify amino acids, the genetic code has one codon that is a start signal and three that are stop signals for translation. The genetic code is the set of rules that convert a nucleotide sequence in RNA to an amino acid sequence. 61 of the 64 triplets code for amino acids. The triplet AUG has a dual function: It codes for the amino acid methionine and can also provide a signal for the start of a polypeptide chain. Three codons (UAA, UAG, and UGA—red in the figure) do not designate amino acids. They are the stop codons that instruct the ribosomes to end the polypeptide. An RNA triplet always specifies a given amino acid. For example, although codons UUU and UUC both specify phenylalanine (Phe), neither of them ever represents any other amino acid. The codons in the figure are the triplets found in RNA. They have a straightfor-ward, complementary relationship to the codons in DNA. The nucleotides making up the codons occur in a linear order along the DNA and RNA, with no gaps separating the codons. The genetic code is nearly universal, shared by organisms from the simplest bacteria to the most complex plants and animals. The universal-ity of the genetic vocabulary suggests that it arose very early in evolution and was passed on over the eons to all the organ-isms living on Earth today. In fact, such universality is the key to modern DNA technologies. Because diverse organisms share a common genetic code, it is possible to program one species to produce a protein from another species by transplanting DNA. This allows scientists to mix and match genes from various species—a procedure with many useful genetic engineering applications in agriculture, medicine, and research. Besides having practi-cal purposes, a shared genetic vocabulary also reminds us of the evolutionary kinship that connects all life on Earth.

siRNAs

In addition to microRNAs, there is another class of small RNA molecules called small interfering RNAs (siRNAs). The blocking of gene expression by siRNAs is called RNA interference (RNAi). Researchers can take advantage of siRNAs to artificially control gene expres-sion.

Review DNA to RNA to protein

In eukaryotic cells, transcription occurs in the nucleus, and the RNA is processed before it enters the cytoplasm. Translation (RNA S protein) is rapid; a single ribosome can make an average-sized polypeptide in less than a min-ute. As it is made, a polypeptide coils and folds, assuming its final three-dimensional shape.

Sexual reproduction

In organisms that reproduce sexually, most of the genetic variation in a population results from the unique combi-nation of alleles that each individual inherits. (Of course, the origin of those allele variations is past mutations.) Fresh assortments of existing alleles arise every generation from three random components of sexual reproduction: independent orientation of homologous chromosomes at metaphase I of meiosis (see Figure 8.16), crossing over (see Figure 8.18), and random fertilization. During meiosis, pairs of homologous chromosomes, one set inherited from each parent, trade some of their genes by crossing over. These homologous chromosomes sepa-rate into gametes independently of other chromosome pairs. Thus, gametes from any individual vary extensively in their genetic makeup. Finally, each zygote made by a mating pair has a unique assortment of alleles resulting from the random union of sperm and egg.

Naming and classifying the diversity of life

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. For example, the genus of large cats is Panthera. The second part of a binomial is used to distinguish species within a genus. The two parts must be used together to name a spe-cies. In our example, the scientific name for the leopard is Panthera pardus. Notice that the first letter of the genus is capitalized and that the whole binomial is italicized. The Linnaean binomial solved the problem of the ambiguity of common names (bluebells different in different places) Linnaeus also introduced a system for grouping species into a hierarchy of categories. The resulting clas-sification of a particular organism is somewhat like a postal address identifying a person in a particular apartment, in a building with many apartments, on a street with many apartment buildings, in a city with many streets, and so on. Grouping organisms into broader categories is a way to structure our understanding of the world.

Termination of Transcription

In the third phase, termination, the RNA polymerase reaches a special sequence of bases in the DNA template called a terminator. This sequence signals the end of the gene. At this point, the polymerase molecule detaches from the RNA molecule and the gene, and the DNA strands rejoin. In addition to producing RNA that encodes amino acid sequences, transcription makes two other kinds of RNA that are involved in building polypeptides. We discuss these kinds of RNA a little later

Transcription from DNA to RNA

In transcription, RNA polymerase binds to the promoter of a gene, opens the DNA double helix there, and catalyzes the synthesis of an RNA molecule using one DNA strand as a template. As the single-stranded RNA transcript peels away from the gene, the DNA strands rejoin. If you think of your DNA as a cookbook, then transcription is the process of copying one recipe onto an index card (a molecule of RNA) for immediate use. As with DNA replication, the two DNA strands must first separate at the place where the process will start. In transcription, however, only one of the DNA strands serves as a template for the newly forming RNA molecule. Notice that the RNA nucle-otides follow the usual base-pairing rules, except that U, rather than T, pairs with A. The RNA nucleotides are linked by the transcription enzyme RNA polymerase. Special sequences of DNA nucleotides tell the RNA polymerase where to start and where to stop the transcribing process.

Natural selection in action

Look at any natural environment and you will see the products of natural selection—adaptations that suit organ-isms to their environment. But can we see natural selec-tion in action? Yes, indeed! Biologists have documented evolutionary change in thousands of scientific studies. The evolution of pesticide resistance in mosquitoes, is an unsettling example of natural selection in action. A relatively small amount of poison initially kills most of the insects in the population, but a few individuals carry an allele (alternative form of a gene) that enables them to survive the chemical attack. These genetically resistant survivors reproduce and pass the allele for pesticide resistance to their offspring. Thus, subsequent applications of the same pesticide are less and less effective as the proportion of pesticide-resistant individuals increases in each generation.

Mosquitos and evolution

Malaria, a disease caused by a microscopic parasite that is one of the worst killers in human history. In 1955, the World Health Organization (WHO) launched a campaign to eradicate malaria. DDT, a recently developed pesticide in wide use at the time, was deployed in massive spraying operations to kill the mosquitoes carrying it. Although the lethal chemical killed most of the mosquitoes immediately, survivors gave rise to new DDT-resistant populations—an example of evolution in action. Eradication of the disease is no lon-ger viewed as imminent, but by using a judicious combination of mosquito-control strategies, public health agencies have made progress in the battle against malaria. WHO also monitors the evolution of drug resistance in the parasite's populations around the world. lots of diseases have followed this pattern

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 plants and animals living in temperate regions of South America more closely resembled species living in tropical regions of that continent than species liv-ing in similarly temperate regions of Europe. And the South American fossils Darwin found, although clearlyexamples 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. The Galápagos are relatively young volcanic islands about 900 kilometers (540 miles) off the Pacific coast of South America. Most of the animals that inhabit these remote islands are found nowhere else in the world, but they resemble South American species.

Mutagens

Mutations can occur in a number of ways. Spontaneous mutations result from random errors during DNA repli-cation or recombination. Other sources of mutation are physical and chemical agents called mutagens. The most common physical mutagen is high-energy radiation, such as X-rays and ultraviolet (UV) light. Chemical mutagens are of various types. One type, for example, consists of chemicals that are similar to normal DNA bases but that base-pair incorrectly when incorporated into DNA. Because many mutagens can act as carcinogens, agents that cause cancer, you would do well to avoid them as much as possible. What can you do to avoid exposure to mutagens? -not smoking and wearing protective clothing and sunscreen to minimize direct exposure to the sun's UV rays. But such precautions are not foolproof, and it is not possible to avoid mutagens entirely. Although mutations are often harmful, they can also be beneficial, both in nature and in the laboratory. Muta-tions are one source of the rich diversity of genes in the living world, a diversity that makes evolution by natural selection possible. Mutations are also essen-tial tools for geneticists. Whether naturally occurring or created in the laboratory, mutations are responsible for the different alleles needed for genetic research.

Key points about natural selection

Natural selection affects individual organisms However, individuals do not evolve. Rather, it is the population—the group of organisms—that evolves over time as adaptive traits become more common in the group and other traits change or dis-appear. Evolution refers to generation-to-generation changes in populations. Natural selection can amplify or diminish only heritable traits. Although an organism may, during its lifetime, acquire characters that help it survive, such acquired characters cannot be passed on to offspring.

Mutation

New alleles originate by mutation, a change in the nucleo-tide sequence of DNA. Thus, mutation is the ultimate source of the genetic variation that serves as raw material for evolution. 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. An organism is a refined product of thousands of generations of past selection, and a random change in its DNA is not likely to improve its genome any more than randomly changing some words on a page is likely to improve a story. In fact, mutation that affects a pro-tein's function will probably be harmful. On rare occasions, however, a mutated allele may actually improve the adap-tation of an individual to its environment and enhance its reproductive success.

Populations and the units of evolution

One common misconception about evolution is that individual organisms evolve during their lifetimes. It is true that natural selection acts on individuals: Each individual's combination of traits affects its survival and reproductive success. But the evolutionary impact of natural selection is only apparent in the changes in a population of organisms over time. We can measure evolution as a change in the prevalence of certain heritable traits in a population over a span of generations. The increas-ing proportion of resistant insects in areas sprayed with pes-ticide is one example. Different populations of the same species may be geo-graphically isolated from each other to such an extent that an exchange of genetic material never, or only rarely, occurs. When the relative frequencies of alleles in a population change over a number of generations, evolution is taking place.

The debate isn't really about GMO's...

One consequence of capitalist-driven crop improvement is public doubt. Given a rich history of corporate corruption in a system that benefits the wealthy and powerful, it makes sense that customers would be asking themselves: Is this technology good for me? For my family? For the environment?

Visualizing Gene Expression

Researchers can study the expression of groups of genes. For example, they can investigate which genes are active in different tissues (such as cancerous versus normal) or at different stages of development. Rather than studying just one gene, research-ers can study many or even all genes at once using DNmicroarrays. A DNA microarray (also called a DNA chip or gene chip) is a glass slide with many tiny wells, each containing a different fragment of single-stranded DNA that derives from a particular gene.

Ribosomes

Ribosomes are the organelles in the cytoplasm that coor-dinate the functioning of mRNA and tRNA and actually make polypeptides. a ribosome consists of two subunits. Each subunit is made up of proteins and a considerable amount of yet another kind of RNA, ribosomal RNA (rRNA). A fully assembled ribosome has a binding site for mRNA on its small subunit and binding sites for tRNA on its large subunit. Two tRNA molecules get together with an mRNA molecule on a ribosome. One of the tRNA bind-ing sites, the P site, holds the tRNA carrying the growing polypeptide chain, while another, the A site, holds a tRNA carrying the next amino acid to be added to the chain. The anticodon on each tRNA base-pairs with a codon on the mRNA. The subunits of the ribosome act like a vise, hold-ing the tRNA and mRNA molecules close together. The ribosome can then connect the amino acid from the tRNA in the A site to the growing polypeptide.

Sexual selection

Sexual selection is a form of natural selection in which individuals with certain traits are more likely than other individuals to obtain mates. Because sexual selection has a direct impact on relative fitness, it is an especially pow-erful form of natural selection. This distinction in appearance, called sexual dimorphism, is often mani-fested in a size difference. Among male vertebrates, sexual dimorphism may also be evident in adornment, such as manes on lions, antlers on deer, and colorful plumage on peacocks and other birds. What is the advantage to females of being choosy? One hypothesis is that females prefer male traits that are correlated with "good" alleles. In several bird species, research has shown that traits preferred by females, such as bright beaks or long tails, are related to overall male health.

cell signaling

So far, we have considered gene regulation only within a single cell. Within a multicellular organism, infor-mation must be communicated between cells. For example, a cell can produce and secrete chemicals, such as hormones, that affect gene regulation in another cell. This allows the organism as a whole to alter its activities in response to signals from the environment. Cells use protein "lookouts" to convey information into the cell, resulting in changes to cellular functions. Trans-lation of the mRNA produces a protein that can then perform the function originally called for by the signal.

Stabilizing selection

Stabilizing selection removes extreme variants from the population, in this case eliminating individuals that are unusually light or dark. The trend is toward reduced phenotypic variation and increased frequency of an intermediate phenotype.

Initiation of Transcription

The "start transcribing" signal is a nucleotide sequence called a promoter, which is located in the DNA at the beginning of the gene. A promoter is a specific place where RNA polymerase attaches. The first phase of tran-scription, called initiation, is the attachment of RNA poly-merase to the promoter and the start of RNA synthesis. For any gene, the promoter dictates which of the two DNA strands is to be transcribed (the particular strand varies from gene to gene).

Darwin's Journey

The Beagle was a survey ship. Although it stopped at many locations around the world, its main task was charting poorly known stretches of the South American coast. Darwin, a skilled naturalist, spent most of his time on shore doing what he enjoyed most—exploring the natural world. He collected thousands of specimens of fossils and living plants and animals. He also kept detailed journals of his observations. For a naturalist from a small, temperate country, seeing the glorious diversity of unfa-miliar life-forms on other continents was a revelation. He carefully noted the characteristics of plants and animals that made them well suited to such diverse environments as the jungles of Brazil, the grasslands of Argentina, the towering peaks of the Andes, and the desolate and frigid lands at the southern tip of South America

From Nucleotides to Amino Acids (repetitive?) (how to shorten?)

The DNA of a gene is transcribed into RNA using the usual base-pairing rules, except that an A in DNA pairs with U in RNA. In the translation of a genetic message, each triplet of nucleotide bases in the RNA, called a codon, specifies one amino acid in the polypeptide. Genetic information in DNA is transcribed into RNA and then translated into polypeptides, which then fold into proteins. Transcrip-tion and translation are linguistic terms, and it is useful to think of nucleic acids and proteins as having languages. To understand how genetic information passes from genotype to phenotype, we need to see how the chemical language of DNA is translated into the different chemical language of proteins. What exactly is the language of nucleic acids? Both DNA and RNA are polymers made of nucleotide mono-mers strung together in specific sequences that convey information, much as specific sequences of letters convey information in English. In DNA, the monomers are the four types of nucleotides, which differ in their nitrog-enous bases (A, T, C, and G). The same is true for RNA, although it has the base U instead of T. The language of DNA is written as a linear sequence of nucleotide bases. Every gene is made up of a specific sequence of bases, with special sequences marking the beginning and the end. A typical gene is a few thousand nucleotides in length. The process is called transcription because the nucleic acid language of DNA has simply been rewritten (transcribed) as a sequence of bases of RNA; the language is still that of nucleic acids. The nucleotide bases of the RNA molecule are complemen-tary to those on the DNA strand. This is because the RNA was synthesized using the DNA as a template. Translation is the conversion of the nucleic acid lan-guage to the polypeptide language. Like nucleic acids, polypeptides are straight polymers, but the monomers that make them up—the letters of the polypeptide alphabet—are the 20 amino acids common to all organ-isms. The sequence of nucleotides of the RNA molecule dictates the sequence of amino acids of the polypeptide. But remember, RNA is only a messenger; the genetic infor-mation that dictates the amino acid sequence originates in DNA. What are the rules for translating the RNA mes-sage into a polypeptide? In other words, what is the correspondence between the nucleotides of an RNA molecule and the amino acids of a polypeptide? Keep in mind that there are only four different kinds of nucleo-tides in DNA (A, G, C, T) and RNA (A, G, C, U). During translation, these four must somehow specify 20 amino acids. If each nucleotide base coded for one amino acid, only 4 of the 20 amino acids could be accounted for. In fact, triplets of bases are the smallest "words" of uniform length that can specify all the amino acids. There can be 64 (that is, 43) possible code words of this type—more than enough to specify the 20 amino acids. Indeed, there are enough triplets to allow more than one coding for each amino acid. For example, the base triplets AAA and AAG both code for the same amino acid. Experiments have verified that the flow of information from gene to protein is based on a triplet code. The genetic instructions for the amino acid sequence of a polypeptide chain are written in DNA and RNA as a series of three-base words called codons. Three-base codons in the DNA are transcribed into complemen-tary three-base codons in the RNA, and then the RNA codons are translated into amino acids that form a polypeptide.

The Idea of Fixed Species

The Greek philosopher Aristotle, whose ideas had an enormous impact on Western culture, generally held the view that species are fixed, permanent forms that 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. In the 1600s, religious scholars used biblical accounts to estimate the age of Earth at 6,000 years. Thus, the idea that all liv-ing species came into being relatively recently and are unchanging in form dominated the intellectual climate of the Western world for centuries. At the same time, however, naturalists were grappling with the interpretation of fossils—imprints or remains of organisms that lived in the past. Stunning discoveries in the early 1800s, including fossilized skel-etons of a gigantic sea creature dubbed an ichthyosaur, or fish-lizard (Figure 13.2b), convinced many naturalists that extinctions had indeed occurred

The Processing of Eukaryotic RNA

The RNA transcribed from a eukaryotic gene is processed before leaving the nucleus to serve as messenger RNA (mRNA). Introns are spliced out, and a cap and tail are added. One kind of RNA processing is the addition of extra nucleotides to the ends of the RNA transcript=the cap and tail=mark the mRNA for export from the nucleus and help ribosomes recognize the RNA as mRNA. Another type of RNA processing is made necessary in eukaryotes by noncoding stretches of nucleotides that interrupt the nucleotides that actually code for amino acids. Most genes of plants and animals, it turns out, include such internal noncoding regions, which are called introns. The coding regions—the parts of a gene that are expressed—are called exons. Both exons and introns are transcribed from DNA into RNA. However, before the RNA leaves the nucleus, the introns are removed, and the exons are joined to produce an mRNA molecule with a continuous coding sequence. This cutting-and-pasting process is called RNA splicing. RNA splicing is believed to play a significant role in humans in allowing our approximately 21,000 genes to produce several times this number of polypeptides.

Evolutionary fitness

The commonly used phrase "survival of the fittest" is misleading if we take it to mean head-to-head competi-tion between individuals. Reproductive success, the key to evolutionary success, is generally more subtle and pas-sive. In a varying population of moths, for example, cer-tain individuals may produce more offspring than others because their wing colors hide them from predators better. Plants in a wildflower population may differ in reproduc-tive success because some attract more pollinators, owing to slight variations in flower color, shape, or fragrance. In a given environment, such traits can lead to greater relative fitness, the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals. The fittest individuals in the context of evolution are those that produce the largest number of viable, fertile offspring and thus pass on the most genes to the next generation.

Protein Activation and Breakdown

The final opportunities for regulating gene expression occur after translation. For example, the hormone insulin is synthesized as one long, inactive polypeptide that must be chopped into pieces before it comes active. Other proteins require chemical modification before they become active. Another control mechanism operating after transla-tion is the selective breakdown of proteins. Some proteins that trigger metabolic changes in cells are broken down within a few minutes or hours. This regulation allows a cell to adjust the kinds and amounts of its proteins in response to changes in its environment.

Transfer RNA (tRNA)

The interpreters, it can recognize the words of one language and convert them to the other. Translation of the genetic message carried in mRNA into the amino acid language of proteins To convert the three-letter words (codons) of nucleic acids to the amino acid words of proteins, a cell uses a molecular interpreter, a type of RNA called transfer RNA (tRNA) To perform this task, tRNA molecules must carry out two distinct functions: (1) pick up the appropriate amino acids and (2) recognize the appropriate codons in the mRNA. The unique structure of tRNA molecules enables them to perform both functions. At one end of the folded molecule is a special triplet of bases called an anticodon. The anticodon triplet is complementary to a codon triplet on mRNA. During translation, the anti-codon on the tRNA recognizes a particular codon on the mRNA by using base-pairing rules. At the other end of the tRNA molecule is a site where one specific kind of amino acid attaches.

The Evolution of Bacterial Resistance in Humans

The offspring of individuals with the variations that make them better sited for the local environment will more often also have the favorable adaptions=a survival and reproductive advantage. Repeated over many genera-tions, natural selection promotes evolution of the population. Within a human population, the presence of a disease can provide a new basis for measuring those people who are best suited for survival in the local environment. For example, a recent evolutionary study examined people living in Bangladesh. This population has been exposed to the disease cholera for millennia. Because Bangladeshis have lived for so long in an environment that teems with cholera bacteria, one might expect that natural selection would favor those individu-als who have some resis-tance to the bacteria. Recent studies of people from Bangladesh revealed mutations in several genes that appear to confer an increased resistance to chol-era. Because such genes offer a survival advantage within this popula-tion, they have slowly spread through the Ban-gladeshi population over the past 30,000 years. (Bangladeshi population is evolving increased resistance to cholera) Perhaps pharmaceutical companies can exploit the proteins produced by the identified mutations to create a new gen-eration of antibiotics. If so, this will represent another way that biologists have applied lessons learned from our understanding of evolution to improve human health

gene expression

The overall process by which genetic information flows from genes to proteins is called gene expression. The control of gene expression makes it possible for cells to produce specific kinds of proteins when and where they are needed, allowing cells to respond quickly and effi-ciently to information from the environment. As an illustration of this principle, Figure 11.1 shows the patterns of gene expression for four genes in three different specialized cells of an adult human. Note that the genes for "housekeeping" enzymes, such as those that provide energy through glycolysis, are "on" in all the cells. In contrast, the genes for some proteins, such as insulin and hemoglobin, are expressed only by particular kinds of cells. One protein, hemoglobin, is not expressed in any of the cell types shown in the figure.

The Initiation of Translation

The process of translation—in which an mRNA is used to make a protein—offers additional opportunities for control by regulatory molecules. Red blood cells, for instance, have a protein that prevents the translation of hemoglobin mRNA unless the cell has a supply of heme, an iron-containing chemical group essential for hemoglobin function.

DNA Replication (how to shorten?)

The structure of DNA, with its comple-mentary base pairing, allows it to function as the molecule of heredity through DNA replication. Every cell has DNA "cookbook" that provides com-plete information on how to make and maintain that cell. When cell reproduces, it duplicates this informa-tion, providing one copy to the new offspring cell while keeping one copy for itself. Each DNA strand serves=mold to guide reproduction of other strand. Two strands of parental DNA separate, each becomes a template for the assembly of a complementary strand from a supply of free nucleotides. The nucleotides are lined up one at a time along the template strand in accordance with the base-pairing rules. Enzymes link the nucleotides to form new DNA strands. New molecule=daughter DNA molecules (no gender should be inferred from this name). DNA polymerases are the enzymes that make the covalent bonds between the nucleotides of a new DNA strand As an incoming nucleotide base-pairs with its complement on the template strand, a DNA polymerase adds it to the end of the growing daughter strand. The process is both fast and amazingly accu-rate. In addition to their roles in DNA replication, DNA polymerases and some of the associated proteins can repair DNA that has been damaged by toxic chemicals or high-energy radiation DNA replication begins on a double helix at specific sites, called origins of replica-tion. Replication then proceeds in both directions, creating what are called replication "bubbles." The parental DNA strands open up as daughter strands elon-gate on both sides of each bubble. Eventually, all the bubbles merge, yielding two completed double-stranded daughter DNA molecules. DNA replication ensures that all the body cells in a multicellular organism carry the same genetic informa-tion. It is also the means by which genetic information is passed along to offspring.

From DNA to RNA to protein: how an organism's genotype determinists phenotype

The structure of DNA, with its comple-mentary base pairing, allows it to function as the molecule of heredity through DNA replication. How an organism's Genotype determines its Phenotype An organism's genotype, its genetic makeup, is the heritable information contained in the sequence of nucleotide bases in its DNA. The phenotype, the organism's physical traits, arises from the actions of a wide variety of proteins. For example, structural proteins help make up the body of an organism, and enzymes catalyze the chemical reactions that are necessary for life. DNA specifies the synthesis of proteins. DNA dis-patches instructions in the form of RNA, which in turn programs protein synthesis. The molecular "chain of command" is from DNA in the nucleus to RNA to protein synthesis in the cytoplasm. The two stages are transcription, the transfer of genetic information from DNA into an RNA molecule, and translation, the transfer of the information from RNA into a polypeptide. Therefore, the relationship between genes and proteins is one of information flow. The function of a DNA gene is to dictate the production of a polypeptide

Details of DNA Structure (need to know?)

The sugar has five carbon atoms, four in its ring and one extending above the ring. The ring also includes an oxygen atom. The sugar is called deoxyribose because, compared with the sugar ribose, it is missing an oxygen atom. The full name for DNA is deoxyribonucleic acid, with nucleic referring to DNA's location in the nuclei of eukaryotic cells. The four nucleotides found in DNA differ only in their nitrogenous bases The bases can be divided into two types. Thymine (T) and cytosine (C) are single-ring structures. Adenine (A) and guanine (G) are larger, double-ring structures. Instead of thymine, RNA has a similar base called uracil (U). And RNA contains a slightly differ-ent sugar than DNA (ribose instead of deoxyribose, account-ing for the names RNA versus DNA). Other than that, RNA and DNA polynucleotides have the same chemical structure.

microRNAs

The vast majority of human DNA does not code for pro-teins. This DNA has long been thought to be lacking any genetic information. In fact, many biologists used to refer to these regions as "junk DNA" because they performed nodiscernible function. However, a significant amount of the genome is transcribed into functioning but non-protein-coding RNAs. For example, small, single-stranded RNA molecules, called microRNAs (miRNAs), can bind to com-plementary sequences on mRNA molecules (Figure 11.7). Each miRNA forms a complex with one or more pro-teins that can bind to any mRNA molecule with at least seven or eight nucleotides of complementary sequence. If the mRNA molecule contains a sequence complementary to the full length of the miRNA, the complex degrades the target mRNA. If the mRNA molecule matches the sequence along just part of the miRNA, the complex blocks its translation.

Sources of genetic variation

You have no trouble recognizing friends in a crowd. Each person has a unique genome, reflected in individual phe-notypic variations such as appearance and other traits. In addition to obvious physical differences, most populations have a great deal of phenotypic variation that can be observed only at the molecular level, such as an enzyme that detoxifies a pesticide. Of course, not all variation in a population is heritable. For instance, if you have den-tal work to straighten and whiten your teeth, you will not pass your environmentally produced smile to your offspring. Only the genetic component of variation is rele-vant to natural selection.

Types of Mutations

Type of Mutation: Substitution of one DNA base for another Insertions or deletions of DNA nucleotides Effect Silent mutations result in no change to amino acids. Missense mutations swap one amino acid for another. Nonsense mutations change an amino acid codon to a stop codon. Insertions or deletions of DNA nucleotides. Frameshift mutations can alter the triplet grouping of codons and greatly change the amino acid sequence. A substitution is the replacement of one nucleotide and its base-pairing partner with another nucleotide pair. Because the genetic code is redundant, some substitution mutations have no effect at all, such a change is called a silent mutation. Other substitutions involving a single nucleotide do change one amino acid to another, such muta-tions are called missense mutations. Some missense muta-tions have little or no effect on the shape or function of the resulting protein. However, other substitutions, as we saw in the sickle-cell case, will cause changes in the protein that prevent it from performing normally. In our recipe analogy, this would be like stopping food preparation before the end of the recipe, which is almost certainly going to ruin the dish. Because mRNA is read as a series of triplets during translation, adding or subtracting nucleotides may alter the triplet grouping of the genetic message, such a muta-tion, called a frameshift mutation, occurs whenever the number of nucleotides inserted or deleted is not a multiple of three. All the nucleotides after the insertion or deletion will be regrouped into different codons (a frameshift mutation most often produces a nonfunction-ing polypeptide).

Watson and cricks discovery of the double helix

Watson and Crick worked out the three-dimensional structure of DNA:two polynucleotide strands wrapped around each other in a double helix with a uniform diameter. Hydrogen bonds between bases hold the strands together. Each base pairs with a complementary partner: A with T, and G with C Watson saw an X-ray image of DNA produced by Rosalind Franklin. The thickness of the helix suggested that it was made up of two polynucleotide strands—double helix. At first, Watson imagined that the bases paired like with like—for example, A with A, C with C. But that kind of pairing did not fit with the fact that the DNA molecule has a uniform diameter. It soon became apparent that a double-ringed base on one strand must always be paired with a single-ringed base on the opposite strand. Moreover, Watson and Crick realized that the chemical structure of each kind of base dictated the pairings even more specifically. A pairs with T, and G pairs with C. A is also said to be "complementary" to T, and G to C. Watson, Crick, and Wilkins received the Nobel Prize for their work. (Sadly, Rosalind Franklin died of multiple cancers in 1958 at the age of 38 and was thus ineligible for the prize, which is only given to living scientists. Some suspect that her work with X-ray radiation may have caused her illness.)

Initiation: translation

brings together the mRNA, the first amino acid with its attached tRNA, and the two subunits of a ribosome. An mRNA molecule, even after splicing, is longer than the genetic message it carries. Nucleotide sequences at either end of the molecule are not part of the message, but along with the cap and tail in eukaryotes, they help the mRNA bind to the ribo-some. The initiation process determines exactly where translation will begin so that the mRNA codons will be translated into the correct sequence of amino acids. An mRNA molecule binds to a small ribosomal subunit. A special initiator tRNA then binds to the start codon, where translation is to begin on the mRNA. The initia-tor tRNA carries the amino acid methionine (Met); its anticodon, UAC, binds to the start codon, AUG . A large ribosomal subunit binds to the small one, creating a func-tional ribosome. The initiator tRNA fits into the P site on the ribosome.

Natural selection as the mechanism for evolution (shorten?)

let's look at Darwin's explanation of how life evolves. Because he hypothesized that species formed gradually over long periods of time, Darwin knew that he would not be able to study the evolution of new species by direct observation. But he did have a way to gain insight into the process of incremental change-All domesticated plants and animals are the products of selective breeding from wild ancestors. Having 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, Darwin bred pigeons to gain firsthand experience. He learned that artificial selection has two essential components: variation and heritability. Variation among individuals, for example, differences in coat type in a litter of puppies, size of corn ears, or milk production by individual cows in a herd, allows the breeder to select the animals or plants with the most desirable combination of characters as breeding stock for the next generation. Heri-tability refers to the transmission of a trait from parent to offspring. if a char-acter is not heritable, it cannot be improved by selective breeding. Darwin applied Malthus's idea to populations of plants and animals, reasoning that the resources of any given environment are limited. The production of more individuals than the environment can support leads to a struggle for existence, with only some offspring surviving in each generation. The essence of natural selection is this unequal reproduction. In the process of natural selection, individuals whose traits better enable them to obtain food, escape predators, or tolerate physi-cal conditions will survive and reproduce more success-fully, passing these adaptive traits to their offspring. Darwin reasoned that if artificial selection can bring about significant change in a relatively short period of time, then natural selection could modify species consid-erably over hundreds or thousands of generations.

Speciation occurs when

populations of the same species become genetically isolated by lack of gene flow and then diverge from each other due to natural selection, genetic drift, or mutation (think Darwin and finches)

radiometric dating

the process of measuring the absolute age of geologic material by measuring the concentrations of radioactive isotopes and their decay products. For example, a living organism contains both the common isotope carbon-12 and the radioactive isotope carbon-14 in the same ratio as that present in the atmosphere. Once an organism dies, it stops accumulating carbon, and the stable carbon-12 in its tis-sues does not change. Carbon-14, however, spontaneously decays to another element.