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AP Biology Final Review

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Justin Dumrongkulraksa

on 19 December 2012

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Transcript of AP Biology Final Review

AP Biology Final Exam Review By Justin Dumrongkulraksa, Senna Hubbs, and Sarath Santhosh Big Idea 1:The process of evolution drives the diversity and unity of life. • Competition for limited resources results in differential survival.
• Organisms make use of available resources and evolve over time to make better use of particular resources. Different organisms evolve to make better use of different resources and thus they differentiate.

• Also, because resources are limited, only those that can best claim and make use of resources survive.

•Individuals with more favorable phenotypes are more likely to survive and produce more offspring, thus passing traits to subsequent generations.
•Evolutionary fitness is measured by reproductive success. In other words, the more evolutionarily fit you are, the more babies you are likely to be able to beget and have survive. Natural Selection • Genetic variation and mutation play roles in natural selection. A diverse gene pool is important for the survival of a species in a changing environment.
• If a population only has a small amount of gene variation, any bad genes will be carried by a greater proportion of individuals and there are fewer traits for natural selection to choose from.

• Environments can be more or less stable or fluctuating, and this affects evolutionary rate and direction; different genetic variations can be selected in each generation.

• An adaptation is a genetic variation that is favored by selection and is manifested as a trait that provides an advantage to an organism in a particular environment.

• In addition to natural selection, chance and random events can influence the evolutionary process, especially for small populations.

• Conditions for a population or an allele to be in Hardy-Weinberg equilibrium are:
• (1) a large population size, (2) absence of migration, (3) no net mutations, (4) random mating and (5) absence of selection. These conditions are seldom met because it is equivalent to no evolution.

• Phenotypic variations are not directed by the environment but occur through random changes in the DNA and through new gene combinations. Some phenotypic variations significantly increase or decrease fitness of the organism and the population. Variation and its Effects •Humans impact variation in other species through antibiotic resistance and artificial selection
•Humans are inadvertently selecting for harder to kill bacteria by killing weaker ones with antibiotics and leaving the resistant ones to proliferate.
•Genetic drift is a nonselective (RANDOM) process occurring in small populations such as a natural disaster.
•The alleles carried by the second generation are a random portion of those carried by the parent generation . Thus with genetic drift, some alleles may disappear or some alleles that are relatively uncommon in the first generation may become common in the second generation. In this way the gene pool of the local population "drifts" away from that of the global population of the organism. This may ultimately lead to speciation.
•Reduction of genetic variation within a given population can increase the differences between populations of the same species.
•If, through a process such as genetic drift or natural or artificial selection, a population loses a number of alleles, then that population no longer has all the same traits as other populations. For instance, if a kind of flower has two incompletely dominant alleles for flower color, red and white, which produces homozygous red, homozygous white, and heterozygous pink flowers; a population of that flower that lost the red allele would produce only one colour of flower, white, instead of the usual three. Evolutionary Evidence and Common Ancestry •Scientific evidence of biological evolution uses information from geographical, geological, physical, chemical and mathematical applications.
•Molecular, morphological and genetic information of existing and extinct organisms add to our understanding of evolution.
•Fossils can be dated by a variety of methods that provide evidence for evolution. These include the age of the rocks where a fossil is found, the rate of decay of isotopes including carbon-14, the relationships within phylogenetic trees, and the mathematical calculations that take into account information from chemical properties and/or geographical data.
•Morphological homologies represent features shared by common ancestry.
•Ex. the human hand, cat paw, bat wing, and dolphin flipper all have essentially the same bone structure indicating a common ancestry.
•Vestigial structures are remnants of functional structures, which can be compared to fossils and provide evidence for evolution.
•The Human tailbone and appendix are all examples of vestigial structures, as are the remnants of hind limbs found in some recent ancestors of modern wales.
•Biochemical and genetic similarities, in particular DNA nucleotide and protein sequences, provide evidence for evolution and ancestry.
•The more DNA nucleotide sequences two organisms have in common, the more closely related they are.
•Structural and functional evidence supports the relatedness of all domains.
•DNA and RNA are carriers of genetic information through transcription, translation and replication. All organisms conduct these processes to maintain life.
•Continuity of homeostatic mechanisms reflects common ancestry, while changes may occur in response to different environmental conditions.
•Major features of the genetic code are shared by all modern living systems Phylogeny •Phylogenetic trees and cladograms can represent traits that are either derived or lost due to evolution.
•Phylogenetic trees and cladograms illustrate speciation that has occurred, in that relatedness of any two groups on the tree is shown by how recently two groups had a common ancestor.
•Phylogenetic trees and cladograms can be constructed from morphological similarities of living or fossil species, and from DNA and protein sequence similarities, by employing computer programs that have sophisticated ways of measuring and representing relatedness among organisms.
•Phylogenetic trees and cladograms are dynamic (i.e., phylogenetic trees and cladograms are constantly being revised), based on the biological data used, new mathematical and computational ideas, and current and emerging knowledge. BIOLOGY Speciation •Speciation rates can vary depending on the environmental conditions.
•When adaptive radiation occurs, the avaliability of new habitats can give rise to new species.
•Species extinction rates are rapid at times of ecological stress (i.e. droughts, ice age...)

•Speciation results in diversity of life forms from one species. Species can be physically separated by a geographic barrier such as an ocean or a mountain range (Allopatric), or various pre-and post-zygotic mechanisms can maintain reproductive isolation and prevent gene flow (Sympatric).
•For instance, a mouse on one side of the grand canyon cannot mate with a mouse of the same species on the other side of the canyon so populations on either side of the canyon will not mix. Thus they will diverge into two different species. If the geographic isolation were to be resolved, the sexual selection and possible zygotic barriers would continue the isolation of the species.
•New species arise from reproductive isolation over time, which can involve scales of hundreds of thousands or even millions of years, or speciation can occur rapidly through mechanisms such as polyploidy (More than two pairs of each homolog) in plants.

•Scientific evidence supports the idea that evolution has occurred in all species and continues to occur.
•Chemical resistance (mutations for resistance to antibiotics, pesticides, herbicides or chemotherapy drugs occur in the absence of the chemical)
•Emergent diseases
•Observed directional phenotypic change in a population (i.e. Galapagos finches)
•A eukaryotic example that describes evolution of a structure or process such as heart chambers, limbs, the brain and the immune system (particularly acquired immunity) Extrapolating the Origins of the Earth • Primitive Earth provided inorganic precursors from which organic molecules could have been synthesized due to the presence of available free energy and the absence of a significant quantity of oxygen. In turn, these molecules served as monomers or building blocks for the formation of more complex molecules, including amino acids and nucleotides.
• Miller-Urey Experiment: This experiment simulated early earth conditions by running an electric current through a flask containing water, ammonia, methane, and hydrogen gas. The results were formations of amino acids used to make proteins and some nucleotides necessary for life functions.

• The joining of these monomers produced polymers with the ability to replicate, store and transfer information. These complex reaction sets could have occurred in solution (organic soup model) or as reactions on solid reactive surfaces.

• The RNA World hypothesis proposes that RNA could have been the earliest genetic material (Ribozymes). The RNA would have been able to carry out protein synthesis.
• The merger of RNA with a liposome (A membrane capable of carrying out metabolic processes) would have formed the first probionts.

• The Earth formed approximately 4.6 billion years ago (bya), and the environment was too hostile for life until 3.9 bya, while the earliest fossil evidence for life dates to 3.5 bya. Taken together, this evidence provides a plausible range of dates when the origin of life could have occurred.

• Chemical experiments have shown that it is possible to form complex organic molecules from inorganic molecules in the absence of life (Miller-Urey).
• Molecular and genetic evidence from extant and extinct organisms indicates that all organisms on Earth share a universal common ancestral origin of life. UCA would have been the first probiont to which all life later descended from. Big Idea 2: Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. Positive and Negative Feedback •Negative feedback mechanisms maintain dynamic homeostasis for a particular condition (variable) by regulating physiological processes and returning the changing condition back to its target set point.
•Hormone levels can be maintained at decent levels through negative feedback to obtain homeostasis. This process is similar to how a thermostat controls room temperature
•The Parathyroid Hormone for example helps circulate calcium from bones into the bloodstream; however when the levels of calcium are decreased, the Parathyroid gland will sense this deficiency and cease production of parathyroid.
•Insulin and Glucagon are also examples of when negative feedback occurs but in alternating scenarios. Insulin decreases blood sugar levels by absorbing the glucose to the cells and liver but Glucagon increases it by breaking down glycogen (The polysacharride of glucose). When blood sugar levels are too high from glucagon or too low from insulin, negative feedback causes the production to stop.

•Positive feedback mechanisms amplify responses and processes in biological organisms. The variable initiating the response is moved farther away from the initial set-point. Amplification occurs when the stimulus is further activated which, in turn, initiates an additional response that produces system change.
•When ambushed by bloodthirsty ninja bears, positive feedback occurs as the body senses the need to deliver a function quickly when needed. The body will need more oxygen so the heart pumps at a higher frequency. The fight or flight hormone Epinepherine will also be produced in large quantities to stimulate the sympathetic nervous system. Positive feedback is essential in an organism’s survival (against everyday ninja bear attacks) because it amplifies a function at faster pace than ordinary production. Immunity I: Nonspecific Immunity II: Acquired •Vertebrate immune systems have nonspecific (Innate) and nonheritable (Acquired) defense mechanisms against pathogens.
•Phagocytes provide nonspecific immune defense against any pathogen. These phagocytes produce a rapid response to pathogens such as allergens and bacteria.They also serve as antigen presenting cells to activate Helper T cells against the engulfed pathogen. Another response is natural killer (NKs) cells which eliminate diseased cells. Unlike cytotoxic T cells which require an MHC molecule to act, NKs can recognize cells under stress immediately and destory it (critical against cancer). •Mammals and other vertebrates use specific immune responses triggered by natural or artificial agents that disrupt dynamic homeostasis.
•These immune responses are slower to respond and they require recognition of traits specific to particular pathogens, using a vast array of receptors. Acquired immunity is managed by Lymphocytes (T and B cells)which create antibodies and memorize surface markers of the pathogens to guard against future attacks.
•The mammalian immune system includes two types of specific responses: cell mediated and humoral.

•Humoral responses include antibodies which are produced from plasma cells.
•In the humoral response, B cells, a type of lymphocytic white blood cell, produce antibodies against specific antigen. An activated T helper cell will activate the B cells, causing the B cells to replicate and differntiate into memory and plasma cells. The plasma cells produce and abundance of unique antibodies designed specifically for the antigen presented by the Helper T cell. The memory cells can last for up to ten years, unlike plasma cells which deteriorate within days, ensuring that should the same pathogen be encountered again, antibody production will be avaliable from the start and in greater quantity than before.
•Antibodies are quite effective by blocking a specific pathogen’s receptors thus hindering its ability to attack a host cell. IgG immunoglobulins ,for example promotes opsonization signaling phagocytic cells to engulf the pathogen. IgA immunoglobulins secretions in tears and saliva neutralizes viruses by preventing it from coming in correct contact with potential host cells. •In the cell-mediated response cytotoxic T cells target cells infected by foreign agents.
•Most of the time, a Helper T cell is required for the Cytoxic T cells to become active. Similar to the humoral response, a T helper cell must come into contact with an antigen presenting cell such as a dendritic phagocyte. The T helper cell replicates and differentiates into memory and effector cells. The effector cells will activate dormant Cytoxic T cells who will also replicate and differentiate.
•These Cytotoxic T cells attach to antigens and the cell’s MHC-II surface markers ,which are displayed when the cell is infected or attacked. The infected cell is injected with granzymes dissolving and destroying it along with the pathogen. The granzymes enter pores of the cell’s membrane deteriorates the interior.

•A second exposure to an antigen results in a more rapid and enhanced immune response. Memory T helper, Cytoxic T, and B cells ensure the pathway from antigen presenting cell to response is expedient and efficient.
• Because this efficient response requires exposure to a pathogen at least once, that is why it is called "acquired" immunity. Immunity II: Acquired Big Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes. DNA: Function and Discovery •Genetic information is stored in and passed to subsequent generations through DNA molecules and, in some cases, RNA molecules (Ribonucleic Acid)

•Noneukaryotic organisms have circular chromosomes, while eukaryotic organisms have multiple linear chromosomes, although in biology there are exceptions to this rule.•Prokaryotes, viruses and eukaryotes can contain plasmids, which are small extra-chromosomal, double-stranded circular DNA molecules.•F Plasmid: The F Factor is located on this plasmid, which codes for the formation of the sex pilus necessary for conjugation
•R Plasmid: Confers antibiotic resistance
•The proof that DNA is the carrier of genetic information involved a number of important historical experiments.•Griffith’s Experiment: A strain of bacteria easily killed by a mouse’s immune system was introduced to a deadly strain. The easily killed strain became deadly and killed its hosts. This was the first experiment which made scientist ponder about DNA and bacteria ability to transfer it. •Avery-MacLeod-McCarty: A continuation of the Griffith experiment, the Avery-MacLeod-McCarty experiment combined heat killed pathogens with DNA, DNA, and proteins. Only DNA caused a transformation in the dead pathogens, providing strong evidence that DNA was responsible for Griffith’s findings.•Hershey-Chase Experiment: The scientific community was not convinced until this experiment. When viral protein was dyed and the phage infected a host, all progeny did not carry the dye. However, when the genetic material was dyed, all progeny carried the same dye, providing the evidence for the acceptance of DNA as a carrier of information.
•Contributions of Watson, Crick, Wilkins, and Franklin on the structure of DNA (The former two receive the bulk of the credit because they stole data from the latter's lab)

DNA Replication •DNA replication ensures continuity of hereditary information.
•Replication is a semiconservative process; that is, one strand serves as the template for a new, complementary strand.
•Conservative Theory: Both strands serve as a template and are then reassembled, restoring parental double helix•Dispersive Theory: Each strand of the daughter helices contains a mixture of old and newly synthesized DNA
•Replication requires DNA polymerase plus many other essential cellular enzymes, occurs bidirectionally, and differs in the production of the leading and lagging strands:
•Helicase: Unzips the parent DNA
•Topoisomerase: Cuts and stretches DNA to stabilize unzipping
•Single Strand Binding Proteins: Along with Topoisomerase, help to anchor DNA during replication
•Primase: Attaches primers to DNA strands
•DNA Polymerase I: Adds nucleotides to the 3’ end ONLY. Different process for lagging and leading strands.
-Leading Strand: Once the primer is attached, DNA Pol I attaches nucleotides in the direction toward the replication fork.
-Lagging Strand: Primase attaches multiple primers. DNA Pol I adds nucleotides in the direction away from the replication fork. Must replicate in multiple short fragments called Okazaki Fragments.
-At origin of replication leading strand becomes lagging strand and vice versa
•DNA Polymerase III: Replaces RNA primers with DNA nucleotides
•Ligase: Merges the newly synthesized DNA with the rest of the DNA strand

•Each round of replication shortens the ends of the DNA called telomeres. The final lagging strand will be shorter because the RNA cannot be replaced with DNA. The RNA will be removed, but the exposed 5’ end of DNA cannot be extended because Pol I can only synthesize from a 3’ end. Telomeres are noncritical sequences at the ends of DNA which protect the genes.
•There is a set number of times a human cell can divide before its telomeres have been destroyed: 56. This is referred to as the Hayflick limit. Some cancers use telomerase to extend telomeres and promote uncontrolled cell growth.
Viruses I •Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA to DNA, made possible by reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. This DNA integrates into the host genome and becomes transcribed and translated for the assembly of new viral progeny.
•Viral genetic material and enzymes enter the cell. At this point one of two cycles can occur.
•Lytic Cycle: The virus utilizes host mRNA, ribosomes, and enzymes to replicate its DNA create new protein capsids. Secretion of enzyme hydrolyzes host DNA and degrades the cell membrane, causing the host cell to lyse.
•Lysogenic cycle: Viral DNA is incorporated into the host genome where it undergoes replication along with the host. The virus can remain dormant until certain signals cause the lytic cycle to occur.
DNA vs. RNA •DNA and RNA molecules have structural similarities and differences that define function.•Both have three components — sugar, phosphate and a nitrogenous base — which form nucleotide units that are connected by covalent bonds to form a linear molecule with 3'and 5' ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone.
•The basic structural differences include:
1. RNA has only one helix and one more oxygen atom in its sugar.
2. DNA contains deoxyribose (RNA contains ribose which has one more oxygen than deoxyribose).
3. RNA contains uracil in lieu of thymine in DNA.
4. DNA is usually double stranded, RNA is usually single stranded.•Single strand DNA is called complementary DNA (cDNA)
•The two DNA strands in double-stranded DNA are antiparallel in directionality.
•Both DNA and RNA exhibit specific nucleotide base pairing that is conserved through evolution: adenine pairs with thymine or uracil (A-T or A-U) and cytosine pairs with guanine(C-G).
•Purines (G and A) have a double ring structure. Pyrimidines (C, T and U) have a single ring structure.
•This structural difference governs the pairing of nitrogen bases•Two purines occupy two much space and two pyrimidines occupy too little space to be consistent with the DNA model
Types of RNA •The sequence of the RNA bases, together with the structure of the RNA molecule, determines RNA function.
1. mRNA carries information from the DNA to the ribosome (Protein Synthesis).
2. tRNA molecules bind specific amino acids and allow information in the mRNA to be translated to a linear peptide sequence.
3. rRNA molecules are functional building blocks of ribosomes.

•The role of RNAi includes regulation of gene expression at the level of mRNA transcription.
•Ex. Preventing an mRNA from being translated
•Helps to defend against parasitic nucleotide sequences (such as from the Lysogenic cycle) Transcription and Translation •The enzyme RNA-polymerase reads the DNA molecule in the 3' to 5' direction and synthesizes complementary mRNA molecules that determine the order of amino acids in the polypeptide.•The enzymes bind near a region of DNA called the TATA box (5'-TATAAA-3')•Transcription does NOT begin at this point (around 20-25 nucleotides down the line)
•In eukaryotic cells the mRNA transcript undergoes a series of enzyme-regulated modifications. (addition of a poly-A tail, addition of a 5’ or GTP cap, excision of introns)•The introns are removed by spliceosomes (small nucleic RNA and protein factors)•Introns are useful for evolution by the increasing the capacity of an organisms gene pool and thus allowing greater chances for diversity in offspring of sexual species•The poly-A tail and 5’ cap help protect the mRNA in transit
•Translation of the mRNA occurs in the cytoplasm on the ribosome.
•In prokaryotic organisms, transcription is coupled to translation of the message.
•Both the DNA and ribosomes are freely floating in the cytoplasm
•Translation involves energy and many steps, including initiation, elongation and termination.
•The mRNA interacts with the rRNA of the ribosome to initiate translation at the (start) codon.
•The sequence of nucleotides on the mRNA is read in triplets called codons
•The start codon AUG (Methionine) signals the merger of the large and small ribosomal subunits
•Each codon encodes a specific amino acid, which can be deduced by using a genetic code chart.
•Many amino acids have more than one codon (Higher likelihood a mutation will be silent)
•tRNA brings the correct amino acid to the correct place on the mRNA.
•Amino acids are fastened to the tRNA through the enzyme Aminoacyl tRNA Synthetase
•An anticodon located on the tip of the tRNA binds only to its complementary codon on the mRNA being translated
•There are three sites which the tRNA travels to on the ribosome: E, P, and A
•The amino acid is transferred to the growing peptide chain (Held by peptide bonds)
•The process continues along the mRNA until a stop codon is reached (UGA, UAG, or UAA)
•The process terminates by release of the newly synthesized peptide/protein.
•Phenotypes are determined through protein activities
•Protein activity or lack thereof determines which genes are being expressed or suppressed
•This connection is the basis behind the DNA microarray which analyses mRNA in sample cells.
•Genetic engineering techniques can manipulate the heritable information of DNA and, in special cases, RNA.
Cell Cycle •The cell cycle is a complex set of stages that is highly regulated with checkpoints, which determine the ultimate fate of the cell.
•Interphase consists of three phases: growth (G1), synthesis of DNA (S), preparation for mitosis (G2)
•The cell cycle is directed by internal controls or checkpoints. Internal and external signals provide stop-and-go signs at the checkpoints.
•There are three checkpoints which regulate progression along the cell cycle
•There is a checkpoint near the end of G1, one immediately before M in G2, and one at the end of M
•Cyclins and cyclin-dependent kinases control the cell cycle.
•The combination of these forms a Maturation Development Factor (MDF)
•MDFs allow the cell to pass the G1 checkpoint and begin DNA replication
•Once M phase is completed the cyclin that formed the MDF degrades preventing indefinite uncontrolled cell growth. Cyclin production can be raised or lowered to control cell replication.
•Mitosis alternates with interphase in the cell cycle.
•When a cell specializes, it often enters into a stage where it no longer divides (G0), but it can reenter the cell cycle when given appropriate cues. Nondividing cells may exit the cell cycle; or hold at a particular stage in the cell cycle.
•Permanent non-division is referred to as senescence. The inability of cells to divide and replicate when approaching the Hayflick limit is responsible for aging.

•Mitosis passes a complete genome from the parent cell to daughter cells.
•Mitosis occurs after DNA replication. Mitosis followed by cytokinesis produces two genetically identical diploid daughter cells.
•Mitosis plays a role in growth, repair, and asexual reproduction
•Bacteria may reproduce asexually through Binary Fission which is very similar to Mitosis
•Mitosis is a continuous process with observable structural features along the mitotic process.
•Prophase: Chromatin in the nucleus begin to condense into Chromsomes with the help of Histones
•Metaphase: The nuclear envelop dissolves and the Chromosomes align in the center of the cell along a Metaphase Plate, the invisible line which separates sister chromatids. Spindle microtubules connect the kinetochore of each chromosome to the centrosomes on each end of the cell.
•Anaphase: Sister chromatids are divided along the metaphase plate. Kinetochores disassemble the microtubules, transporting the new daughter chromosomes to each end of the cell.
•Telophase: The chromosomes reform into chromatin and two daughter nuclei begin to from. All that remains is cytokinesis.
Meiosis •Meiosis, a reduction division (One diploid parent yields four haploid daughters), followed by fertilization ensures genetic diversity in sexually reproducing organisms.•Meiosis ensures that each gamete receives one complete haploid (1n) set of chromosomes.
•During meiosis, homologous (identical) chromosomes are paired, with one homologue originating from the maternal parent and the other from the paternal parent. •Orientation of the chromosome pairs along the metaphase plate is RANDOM. This is called the Law of Independent Assortment.
•Separation of the homologous chromosomes ensures that each gamete receives a haploid (1n) set of chromosomes composed of both maternal and paternal chromosomes.•The Law of Independent Assortment ensures there is a random distribution of maternal and paternal chromosomes in each of the gametes, increasing diversity.
•During meiosis, homologous chromatids exchange genetic material via a process called “crossing over,” which increases genetic variation in the resultant gametes.•The homologous chromosomes are held in synapsis until Anaphase I of Meisois. During this time, the homologues exchange genetic material and from X-shaped linkages called chiasma. Because they are still attached when Anaphase I begins, the separation of the two causes part of each chromosome to contain information from the other.
•Fertilization involves the fusion of two gametes, increases genetic variation in populations by providing for new combinations of genetic information in the zygote, and restores the diploid number of chromosomes.
Heredity and Genetic Variation •Rules of probability can be applied to analyze passage of single gene traits from parent to offspring
•Segregation and independent assortment of chromosomes result in genetic variation.
•The Law of Segregation states that alleles separate during meiosis
•Segregation and independent assortment can be applied to genes that are on different chromosomes.
•Genes that are adjacent and close to each other (Distances are measured in centiMorgans) on the same chromosome tend to move as a unit. The probability that they will segregate as a unit is a function of the distance between them. Low frequency of non-parental phenotypes is indicative of closely linked genes.
•The pattern of inheritance (monohybrid, dihybrid, sex-linked, and genes linked on the same homologous chromosome) can often be predicted from data that gives the parent genotype/phenotype and/or the offspring (Punnett Squares).
•Phenotypes: The physical expression of a genotype
•Genotypes: The genetic makeup of an organism
•Certain human genetic disorders can be attributed to the inheritance of single gene traits or specific chromosomal changes, such as nondisjunction (Failure to separate properly during Anaphase I of II).
•Nondisjunction results in Aneuploidy which is an abnormal number of chromosomes
•The abnormality may be either a monosomy (n-1) or trisomy (n+1)
•Ex. Turner Syndrome is a monosomy of the X chromosome in humans. Down syndrome is a trisomy of Chromosome 21.
•Patterns of inheritance of many traits do not follow ratios predicted by Mendel’s laws and can be identified by quantitative analysis, where observed phenotypic ratios statistically differ from the predicted ratios (Chi-Squared).
•Some traits are determined by genes on sex chromosomes which reside on sex chromosomes (X in humans).
•In mammals and flies, the Y chromosome is very small and carries few genes.
•In mammals and flies, females are XX and males are XY; as such, X-linked recessive traits are always expressed in males. Some traits are sex limited, and expression depends on the sex of the individual, such as milk production in female mammals and pattern baldness in males.
•Signal transmission within and between cells mediates gene expression and between cells it mediates cell function.
•Alterations in a DNA sequence can lead to changes in the type or amount of the protein produced and the consequent phenotype.
•DNA mutations can be positive, negative or neutral based on the effect or the lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are conferred by the protein.
•Positive mutations that enhance survival and reproduction will be selected for while negative ones will be selected against (How much depends on the magnitude for each)
•Errors in DNA replication or DNA repair mechanisms, and external factors, including radiation and reactive chemicals, can cause random changes, e.g., mutations in the DNA
•Changes in chromosome number often result in new phenotypes, including sterility caused by triploidy and increased vigor of other polyploids.

•The horizontal acquisitions of genetic information primarily in prokaryotes via transformation (uptake of naked/environmental DNA), transduction (viral transmission of genetic information), conjugation (cell-to-cell transfer) and transposition (movement/“JUMPING” of DNA segments within and between DNA molecules) increase variation.
•Sexual reproduction in eukaryotes involving gamete formation, including crossing-over during meiosis and the random assortment of chromosomes during meiosis, and fertilization serve to increase variation.
•Reproduction processes that increase genetic variation are evolutionarily conserved and are shared by various organisms. A greater variation allows a species to respond better as a whole to changes.
Viruses II: Reproduction •Viral replication differs from other reproductive strategies and generates genetic variation via various mechanisms.
•A virus is NOT a living organism
•Viruses have highly efficient replicative capabilities that allow for rapid evolution and acquisition of new phenotypes. Viruses replicate via a component assembly model allowing one virus to produce many progeny simultaneously via the lytic cycle.
•Virus replication allows for mutations to occur through usual host pathways. RNA viruses lack replication error-checking mechanisms, and thus have higher rates of mutation.
•HIV is a well-studied system where the rapid evolution of a virus within the host contributes to the pathogenicity of viral infection.
•Retroviruses like HIV use Reverse Transcriptase which has a relatively high error rate
•“Sometimes nature favors the exceptionally stupid.”- John Chvatal 2012
•Related viruses can combine/recombine information if they infect the same host cell.
•The reproductive cycles of viruses facilitate transfer of genetic information.
•Viruses transmit DNA or RNA when they infect a host cell. Transposons “cut and paste” the viral genetic material into the host’s genome.
•Some viruses are able to integrate into the host DNA and establish a latent (lysogenic) infection. These latent viral genomes can result in new properties for the host such as increased pathogenicity in bacteria
•Sometimes, a portion of the host’s DNA is left over and repurposed into a new virus. This new phage can infect other bacterium and integrate itself conferring the previous host’s gene to the new host (Ex. Antibiotic resistance). This process is Transduction.
Cell Signaling I •Correct and appropriate signal transduction processes are generally under strong selective pressure.
•In single-celled organisms, signal transduction pathways influence how the cell responds to its environment.
•Use of chemical messengers by microbes to communicate with other nearby cells and to regulate specific pathways in response to population density (quorum sensing)
•Certain genes may become expressed or suppressed when signals are detected from other bacterium
•Use of pheromones to trigger reproduction and developmental pathways
•Yeast cells use signaling for sexual reproduction
•Response to external signals by bacteria that influences cell movement
•In multicellular organisms, signal transduction pathways coordinate the activities within individual cells that support the function of the organism as a whole. (e.g. epinephrine stimulation of glycogen breakdown in mammals during “Fight of Flight”)
•Immune cells interact by cell-cell contact, antigen-presenting cells (APCs), helper T-cells and killer T-cells.
•The interaction of Th Cell with an APC causes cellular cloning of the Th into effector and memory cells. Effector Th cells activate cytotoxic T-Cells which will now seek out all cells with that specific antigen.
•Cells communicate over short distances by using local regulators that target cells in the vicinity of the emitting cell.
•Endocrine signals are produced by endocrine cells that release signaling molecules, which are specific and can travel long distances through the blood to reach all parts of the body.
•Paracrine: Endocrine cells secrete signals intended for cells in the immediate vicinity
•Endocrine: Signals are secreted and transported via the bloodstream
•Signaling begins with the recognition of a chemical messenger, a ligand, by a receptor protein.
•Two types of receptors are the Tyrosine Kinase Receptor and G-Protein Receptor
•Different receptors recognize different chemical messengers, which can be peptides, small chemicals or proteins, in a specific one-to-one relationship.
•Insulin is specific to the Tyrosine Kinase Receptor
•Epinephrine is specific to the G-Protein Receptor
•A receptor protein recognizes signal molecules, causing the receptor protein’s shape to change, which initiates transduction of the signal.
•Signal transduction is the process by which a signal is converted to a cellular response.
•Signaling cascades relay signals from receptors to cell targets, often amplifying the incoming signals, with the result of appropriate responses by the cell.
•Because ligands and receptors are a one-to-one interaction, the signaling cascade allows numerous messengers to be sent throughout the cell, amplifying the response.
•Second messengers such as cyclic AMP, Calcium and IP3 are often essential to the function of the phosphorylation cascade.
•Many signal transduction pathways include protein. Phosphorylation cascades in a series of protein kinases adding a phosphate group to the next protein in the cascade sequence.
Cell Signaling II: Nervous System •The neuron is the basic structure of the nervous system that reflects function.
•A typical neuron has a cell body, axon and dendrites. Many axons have a myelin sheath that acts as an electrical insulator.•The speed at which a neural signal is sent is proportional to the diameter of the axons. Myelin allows for fast communication without large axons.•The Nodes of Ranvier at the junction between myelin sheathes prevents the signal from rebounding.•Schwann cells, which form the myelin sheath, are separated by gaps of unsheathed axon over which the impulse travels as the signal propagates along the neuron
•The structure of the neuron allows for the detection, generation, transmission and integration of signal information.

•Action potentials propagate impulses along neurons.•Membranes of neurons are polarized by the establishment of electrical potentials across the membranes. The regulated amounts of K+ (Majority) and Na+ (Minority) cause this polarization.•In response to a stimulus, Na+ and K+ gated channels sequentially open and cause the membrane to become locally depolarized. The Na+ channels open first and Na+ through diffusion rushes into the cell causing the depolarization. When the voltage depolarizes to a certain point, the K+ channels begin to open, reducing the positive charge created by the influx of Na+. •Na+/K+ pumps, powered by ATP, work to maintain membrane potential at rest. It works against diffusion by drawing more of the abundant K+ and expelling the scarce Na+. The pumps reset the cells and return the voltage to its resting point (Around -70 mV)
•Transmission of information between neurons occurs across synapses.•In most animals, transmission across synapses involves chemical messengers called neurotransmitters. These neurotransmitters are released by Ca2+ and open the ion channels (Na+ and K+), allowing for the transmission to travel across neurons.•Transmission of information along neurons and synapses results in a response.•The response can be stimulatory or inhibitory and controls the autonomic nervous system (Parasympathetic, Sympathetic, and Enteric). Big Idea 4: Biological systems interact, and these systems and their interactions possess complex properties Nucleic Acids •In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate and a nitrogen base (adenine, thymine, guanine, cytosine or uracil).
•DNA and RNA differ in function and differ slightly in structure, and these structural differences account for the differing functions.
•DNA stores and preserves genetic information necessary for life while RNA carries this information to create the materials for life.
•Nucleic acids have ends, defined by the 3' and 5' carbons of the sugar in the nucleotide, that determine the direction in which complementary nucleotides are added during DNA synthesis and the direction in which transcription occurs.•Nucleic acids of DNA can only be synthesized 5’ to 3’. RNA can only be synthesized 3’ to 5’. This difference is to avoid accidental synthesization of proteins, and to avoid accidental interactions between RNA or DNA.
Proteins •In proteins, the specific order of amino acids in a polypeptide (primary structure) interacts with the environment to determine the overall shape of the protein, which also involves secondary, tertiary, and quaternary structures, and thus its function.
•The R group of an amino acid can be categorized by chemical properties (hydrophobic, hydrophilic and ionic), and the interactions of these R groups determine structure and function of that region of the protein.
• Hydrophobic R groups indicate a protein will be operating in a nonpolar solvent (i.e. NOT water). Hydrophilic and ionic R groups allow proteins to operate in polar solvents such as water. ANY reversal of solvent will cause a catastrophic inversion of the protein rendering it inoperable.
•Proteins have an amino (NH2) end and a carboxyl (COOH) end, and consist of a linear sequence of amino acids connected by the formation of peptide bonds by dehydration synthesis between the amino and carboxyl groups of adjacent monomers.
•Amino Ends are Amino and Carboxyl combinations. The Amino acts as a base, and Carboxyl creates strong covalent bonds.

•Ribosomes are small, universal structures comprised of two interacting parts: ribosomal RNA and protein. In a sequential manner, these cellular components interact to become the site of protein synthesis where the translation of the genetic instructions yields specific polypeptides.
•Change in the structure of a molecular system may result in a change of the function of the system.
•Structure of molecular systems is essential as it recognizes other systems in the body or cell. The structure of proteins, for example, determine its function. Chaperonins, for example, help keep a protein in its structure and releases it back when it’s correctly folded again by simulating an ideal environment.
•The shape of enzymes, active sites and interaction with specific molecules are essential for basic functioning of the enzyme.
•Active sites are where substrates connect to enzymes, and therefore activates interactions with the enzyme. Inhibitors decrease the Enzyme’s function by hindering itss structure. Enzymes are catalysts which means they increase reaction rate without energy loss. Enzymes are used within the body to speed up procedures such as digestion.
•For an enzyme-mediated chemical reaction to occur, the substrate must be complementary to the surface properties (shape and charge) of the active site. In other words, the substrate must fit into the enzyme’s active site.
•Enzymes only react to its corresponding substrate; therefore each enzyme has its own specific function. When enzymes become denatured they cannot configure with its substrate.
Genetics •Multiple copies of alleles or genes (gene duplication) may provide new phenotypes.•Gene duplication is well known to cause speciation (i.e. polyploidy) , and leads to evolution of a species. •Gene duplication is caused by errors in homologous recombinations , replication of DNA , or even duplication of an entire chromosome. When this occurs it causes two identical genes, called paralogs, to be produced within the DNA. This change may be selected for or against depending on its effects.

•A heterozygote may be a more advantageous genotype than a homozygote under particular conditions, since with two different alleles, the organism has two forms of proteins that may provide functional resilience in response to environmental stresses.•Sickled cell trait (Heterozygote of Sickle Cell Anemia) is beneficial to occupants of malaria infected areas. Heterozygote produce enough hemoglobin to carry out normal lives, but the recessive sickle cell allele makes it difficult for malaria to survive in the body. Sick homozygous genotypes are affected fully by the disease and their blood oxygen transportation is severely compromised. While this still confers protection from malaria, sickle cell trait is the preferred genotype.
•Gene duplication creates a situation in which one copy of the gene maintains its original function, while the duplicate may evolve a new function.
•Paralogous genes are found in more than one copy in the same genome. After a species obtains Paralogous genes it obtains the same function but it changes when more genetic information mutates between them, creating a new function. The Olfactory receptor gene family in humans has diverged from ancestors through paralogous and orthologous genes.

The End How are you? Having Fun? Give a chuckle if this amuses you.
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