General Biology 2 - Quarter Two Handout PDF

Define the Terms: Genetics- the study of how genes and how traits are passed down from one generation to the next. Heredity- the passing on of physical or mental characteristics genetically from one generation to another Chromosomes- threadlike structures made of protein and a...

Define the Terms: Genetics- the study of how genes and how traits are passed down from one generation to the next. Heredity- the passing on of physical or mental characteristics genetically from one generation to another Chromosomes- threadlike structures made of protein and a single molecule of DNA that serve to carry the genomic information from cell to cell. DNA- Deoxyribonucleic acid. It is the hereditary material in humans and almost all other organisms. It has a double-helix structure. Gene- the basic functional unit of heredity that carries information for certain trait. Codes for proteins and regulate genes. Allele- The alternative form or version of certain gene/genes. BASE PAIRING RULE DNA is long polymer of nucleotides. Nucleotides are monomers of DNA and they made up of the following: 1. Nitrogen-containing base (adenine, guanine, thymine, and cytosine in DNA, and adenine, guanine, uracil, and cytosine in RNA), 2. A phosphate group, and 3. A sugar molecule (deoxyribose in DNA, and ribose in RNA). The unique structure of DNA allows it to be the hereditary molecule and allows it to store instructions for directing cell activities. Nitrogenous bases that have double-ringed structure are called purines. Adenine and Guanine are purines. Nitrogenous bases that have single-ringed structure are called pyrimidines. Cytosine, Thymine and Uracil (in RNA) are pyrimidines. How DNA works Central Dogma of Molecular Biology Your DNA, or deoxyribonucleic acid, contains the genes that determine who you are. Question 1: How can this organic molecule control your characteristics? Answer: DNA contains instructions for all the proteins your body makes. Proteins, in turn, determine the structure and function of all your cells. Question 2: What determines a protein’s structure? Answer: It begins with the sequence of amino acids that make up the protein. Instructions for making proteins with the correct sequence of amino acids are encoded in DNA. DNA is found in chromosomes. In eukaryotic cells, chromosomes always remain in the nucleus, but proteins are made at ribosomes in the cytoplasm. Question 3: How do the instructions in DNA get to the site of protein synthesis outside the nucleus? Answer: Another type of nucleic acid is responsible. This nucleic acid is RNA, or ribonucleic acid. RNA is a small molecule that can squeeze through pores in the nuclear membrane. It carries the information from DNA in the nucleus to a ribosome in the cytoplasm and then helps assemble the protein. In short: DNA → RNA → Protein Base pairing Rule: In DNA, Adenine (A) always pair with Thymine (T). Cytosine (C) always pair with Guanine (G). Subsequently, these pairing makes up the double helix. In RNA, Thymine is replaced with Uracil (U) DNA template: A G T C G C T C C AAT Complementary base pair: T CAG C GAG G T TA mRNA: A G U C G C U C C AA U Using the Codon Chart, Amino Acid: Ser - Arg -Ser - Asn Note: Base pairing and coding for proteins will be part of the examination. Punnett Square is a square that is used to predict the genotypes of a particular cross or breeding experiment. It is named after Reginald C. Punnett, who devised the approach in 1905. Gene (e.g., Eye color, skin color, and other traits) is defined as a section of DNA that encodes for a certain trait. An allele (e.g., for eye color, alleles are blue, brown, hazel, etc.) is defined as an alternative form of a gene. It determines an organism's genotype. It determines an organism's phenotype. DOMINANT- an allele for a gene that masks other alleles; Symbolized by a capital letter. RECESSIVE- an allele that is masked by a dominant allele; Symbolized by a lower-case letter. Homozygous/Purebred- An organism with two of the same alleles for a gene Heterozygous/Hybrid- An organism with two different alleles for a gene Phenotype- What a trait appears like for an organism. Genotype- the alleles an organism has for a gene written out in symbols. Monohybrid Cross Problem Set A 1. In fruit flies, red eyes are dominant (E). White eyes are recessive (e). If the female fly has white eyes and the male fly has homozygous dominant red eyes, what are the possible phenotypes and genotypes of their offspring? e e Genotype of the offspring: E Ee Ee Ee Phenotype of the offspring: E Ee Ee Red-eyed Probability: There is 100 % chance that the breeding will result in red-eyed offspring. Non-Mendelian Pattern of Inheritance Codominance- a phenomenon in which two alleles (different versions of the same gene) are expressed to an equal degree within an organism. As a result, traits associated with each allele are displayed simultaneously. In humans, blood type is controlled by codominance. Monohybrid Cross Problem Set B 2. Two parents think their baby was switched at the hospital. Its 1968, so DNA fingerprinting technology does not exist yet. The mother has blood type “O,” the father has blood type “AB,” and the baby has blood type “B.” O O Genotypes of the offspring: A AO AO AO, BO Phenotypes of the offspring: B BO BO Type A and Type B blood Probability: There is 50% chance that the couple will have a child who has type A blood. There is 50% chance that the couple will have a child who has type B blood. Answers: A. Mother’s genotype: OO B. Father’s genotype: AB C. Baby’s genotype: AO or BO D. Punnett square showing all possible genotypes for children produced by this couple E. Was the baby switched? No. Incomplete dominance- a form of gene interaction in which both alleles of a gene at a locus are partially expressed, often resulting in an intermediate or different phenotype. Monohybrid Cross Problem Set C 3. In Andalusian fowls, black individuals (B) and white individuals (W) are homozygous. A homozygous black bird is crossed with a homozygous white bird. The offspring are all bluish-gray. Show the cross as well as the genotypes and phenotypes of the parents and offspring. Result: W W Genotype of the offspring: B BW BW BW Phenotype of the offspring: B BW BW Bluish-gray feather Probability: There is 100% chance that breeding will result to bluish gray (BW) feathered offspring. Note: In the examination, I will put an item which is similar to this example. Sex-linked Traits- are controlled by genes found exclusively on the X-chromosome and there is no corresponding allele on the Y chromosome. It is known as the crisscross inheritance. Therefore, it is an example of non-Mendelian inheritance. In humans, as well as in many other animals and some plants, the sex of the individual is determined by sex chromosomes. The sex chromosomes are one pair of non-homologous chromosomes. Until now, we have only considered inheritance patterns among non-sex chromosomes, or autosomes. In addition to 22 homologous pairs of autosomes, human females have a homologous pair of X chromosomes, whereas human males have an XY chromosome pair. Although the Y chromosome contains a small region of similarity to the X chromosome so that they can pair during meiosis, the Y chromosome is much shorter and contains many fewer genes. When a gene being examined is present on the X chromosome, but not on the Y chromosome, it is said to be X-linked. And if the gene being investigated is only on the Y chromosome, it is said to by Y-linked. Example Problem: 1. In humans, the allele for normal blood clotting, H, is dominant to the allele for hemophilia, h. This is a sex-linked trait found on the X chromosome. A woman with normal blood clotting has four children: a normal son, a hemophiliac son, and two normal daughters. The father has normal blood clotting. What is the genotype for each member of the family? In this type of problem always remember that XX is female and XY is male. Additionally, determine what chromosome this trait/disorder is embedded whether it is in X or Y chromosome. Hemophilia is an X-linked trait. A. Father’s genotype: XHY Answer: father has only one X chromosome B. Son with Hemophilia: XhY Answer: Hemophilia is recessive C. Son without Hemophilia: XHY Answer: this son and his father has the same genotype. For the mother and two daughters, you need to predict their genotypes using a Punnett Square Since there is a trace of hemophilia in their bloodline and the father has no trait of hemophilia, then we can assume that the mother is the carrier of the disorder but has a normal blood clotting. XH Xh Mother’s genotype XH XHXH XHXh Genotypes of the two daughters Y XHY Xh Y Definition of Terms: Genetic Engineering- also called recombinant DNA technology, involves the group of techniques used to cut up and join together genetic material, especially DNA from different biological species, and to introduce the resulting hybrid DNA into an organism in order to form new combinations of heritable genetic material. Recombinant DNA- which is often shortened to rDNA, is an artificially made DNA strand that is formed by the combination of two or more gene sequences. Plasmid- a small circular DNA molecule found in bacteria and some other microscopic organisms. Restriction Enzyme - a protein isolated from bacteria that cleaves DNA sequences at sequence-specific sites, producing DNA fragments with a known sequence at each end. Ligase- an enzyme that can catalyze the joining (ligation) of two molecules by forming a new chemical bond. This is typically via hydrolysis of a small pendant chemical group on one of the molecules, typically resulting in the formation of new C-O, C-S, or C-N bonds. Gene therapy- an innovative approach to medicine that uses genetic material to prevent, treat and potentially even cure disease. Cloning- as it relates to genetics and genomics, involves using scientific methods to make identical, or virtually identical, copies of an organism, cell or DNA sequence. Additional Information: Plasmids typically have a small number of genes — notably, some associated with antibiotic resistance — and can be passed from one cell to another. Scientists use recombinant DNA methods to splice genes that they want to study into a plasmid. When the plasmid copies itself, it also makes copies of the inserted gene. Plasmids are physically separate from chromosomal DNA and replicate independently. The use of restriction enzymes is critical to certain laboratory methods, including recombinant DNA technology and genetic engineering.  Figure 1: Cloning procedure in cows Figure 2: Genetic engineering procedures. Definition of Terms: Geologic Time Scale- a reference and communication system for comparing rocks and fossils from throughout the world and is geology's equivalent of the periodic table of the elements. Radiometric Dating- method of dating rocks and minerals using radioactive isotopes. This method is the fundamental tool to determine age of rocks and fossils. Isotope- is a distinct nuclear species of the same element but has difference in number of neutrons. Eon- is the broadest category of geological time. Earth's history is characterized by four eons; in order from oldest to youngest, these are the Hadean, Archean, Proterozoic, and Phanerozoic. Era- Eons of geological time are subdivided into eras, which are the second-longest units of geological time. The Phanerozoic eon is divided into three eras: the Paleozoic, Mesozoic, and Cenozoic. Age- subdivisions of different Epochs. Period- eras are subdivided into units of time called periods. The most well-known of all geological periods is the Jurassic period of the Mesozoic era Epoch- subdivisions of the different period in geologic time scale Mass Extinction- is a short period of geological time in which a high percentage of biodiversity, or distinct species—bacteria, fungi, plants, mammals, birds, reptiles, amphibians, fish, invertebrates—dies out. Discussion: Humans subdivide time into useable units such as our calendar year, months, weeks, and days; geologists also subdivide time. They have created a tool for measuring geologic time, breaking it into useable, understandable segments. For the purposes of geology, the “calendar” is the geologic time scale. One way to distinguish and define each segment of time is by the occurrence of major geologic events and the appearance (and disappearance) of significant life-forms, starting with the formation of Earth’s crust followed by the appearance of ever-changing forms of life on Earth. The geologic time scale grew out of necessity: organizing the immensity of geologic time and correlating geologic events on a worldwide scale. No one person or expert committee proposed the geologic time scale used today. It grew by trial and error through the efforts of numerous geologists working independently. Today the recognition of formal subdivisions of geologic time is determined by international committees. Jo The mass extinction that known as “The Great Dying” First emerged living organisms are the cyanobacteria Longest eon of the geologic time scale Figure 3: The Geologic Time Scale and its significant events. Earths was born around 4.6 billion years ago. Definition of Terms: Evolution- the process by which modern organisms have descended from ancient ancestors. Evolution is responsible for both the remarkable similarities we see across all life and the amazing diversity of that life Speciation- is when a group of organisms within a species evolves to become genetically distinct and can no longer interbreed with the original species. Charles Darwin- (1809-1882) was an English naturalist whose scientific theory of evolution by natural selection became the foundation of modern evolutionary studies. An affable country gentleman, Darwin at first shocked religious Victorian society by suggesting that animals and humans shared a common ancestry. However, his nonreligious biology appealed to the rising class of professional scientists, and by the time of his death evolutionary imagery had spread through all of science, literature, and politics. Darwin, himself an agnostic, was accorded the ultimate British accolade of burial in Westminster Abbey, London. Darwin formulated his bold theory in private in 1837–39, after returning from a voyage around the world aboard HMS Beagle, but it was not until two decades later that he finally gave it full public expression in On the Origin of Species (1859), a book that has deeply influenced modern Western society and thought. His theory was supported and influenced greatly by the works of Alfred Wallace. MECHANISMS OF EVOLUTION: All of these mechanisms can cause changes in the frequencies of genes and other genetic elements in populations, and so all of them are mechanisms of evolutionary change. However, natural selection and genetic drift can only change the frequency of different genes and genetic, they cannot introduce fundamentally new traits to a population. Without genetic variation, some key mechanisms of evolutionary change like natural selection and genetic drift cannot operate. 1. Mutation- At the most basic level, a mutation is a change in an organism’s DNA sequence. These changes can occur during DNA replication before cell division, but they can also be caused by environmental factors such as exposure to radiation or certain chemicals. Mutations that occur in germ line cells can be passed on to offspring, and mutations that occur only in an organism’s somatic cells aren’t passed on. Hence the germline mutations are the one that matter in evolution. Mutation has a bad connotation to people; however, mutations happen in the DNA of living things all the time, and not all of them are bad. In fact, mutations can even help organisms survive. 2. Gene Flow- any movement of an individual and/or trait from one population to another. Gene flow is an important event resulting to genetic variations. Science Fact: The genetic variation in modern human populations has been critically shaped by gene flow. For example, by sequencing ancient DNA, researchers have reconstructed the entire Neanderthal genome – and they’ve found that many snippets of these archaic sequences live on in modern humans. It’s clear that ancient humans and Neanderthals interbred, and that this gene flow introduced new genetic variation to the human population. Furthermore, this ancient gene flow seems to affect who we are today. Neanderthal gene versions have been linked to immune functions, metabolic functions (e.g., affecting one’s risk of developing diabetes), and even skin color. 3. Genetic Drift- Random evolution. In each generation, some individuals may, just by chance, leave behind a few more descendants and genes than other individuals. The genes and other genetic elements of the next generation will be those of the “lucky” individuals, not necessarily the healthier or “better” individuals. That, in a nutshell, is genetic drift. It happens to ALL populations — there’s no avoiding the vagaries of chance. Types: A. Bottleneck effect- The term “bottleneck” refers to a point of congestion in a system, drawing an analogy to the constricted neck of a bottle that reduces the flow of a liquid. Population bottlenecks are evolutionary events attributed to the loss of genetic variability over a short period of time. These can occur due to environmental damage, hunting, limited resources, and drastic climatic changes that cause random fluctuations in the levels of populations. The sudden reduction of population size results in a new gene pool that is not reflective of the diversity and variability of the original gene pool. Figure 4: Illustration that shows how bottleneck effect happens. B. Founder effect- An example of genetic drift when a population separates from the rest of the members of their species, the frequency of different genes and traits will shift based on the genetic makeup of the founder population. For example, if a species of birds is made up of 50% white and 50% brown individuals, and then a group of this species which consists of 25% white birds and 75% brown birds, is separated from the main group, this new group will most likely end up with a different frequency and percentage of color traits as time progresses than the original population.  Figure 5: Illustration that shows how founder effect happens 4. Natural Selection: The knowledge that organisms that are more adapted to their environment are more likely to survive and pass on the genes that aided their success. 5. Artificial Selection: Long before Darwin and Wallace, people were using selection to change the features of plants and animals. Farmers and breeders allowed only the plants and animals with desirable characteristics to reproduce, causing the evolution of farm stock. This process is called artificial selection because people (instead of nature) select which organisms get to reproduce. Definition of terms: Taxonomy- the scientific study of describing, identifying, naming, and classifying organisms. Carl von Linnae; latinized name: Carolus Linnaeus. Father of Taxonomy. SYSTEMATICS AND CLASSIFICATION The famous paleontologist George Gaylord Simpson defined systematics as the "scientific study of the kinds and diversity of organisms and of any and all relationships among them. In more general terms, systematics can be thought of as the study of biodiversity. This field of systematics has two major components: taxonomy and phylogenetics. A. Taxonomy is the field of biology and paleontology that concerns the naming of living (extant) and ancient (extinct) plants, animals, and other organisms. This process is governed by a universal system of rules and conventions derived from the approach pioneered by Carl Linnaeus in the 18th century.  Figure 6: At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same species because they can breed and produce viable offspring, but they are different enough to be classified as different subspecies. B. Phylogenetics is the study of the evolutionary relationships among organisms. These relationships are typically depicted by tree-like diagrams. Carl von Linnae; latinized name: Carolus Linnaeus. Father of Taxonomy. ▪ The first to frame principles for defining natural genera and species of organisms and to create a uniform system for naming them. ▪ Linnaeus devised two systems to in classifying organisms: Binomial Nomenclature (scientific naming) and Taxonomic Figure 7: Carolus Linnaeus Classification System (from Domain to Species Taxon)