BIO 15,16,17,19.pdf - Chapter Notes

CHAPTER 15: Mutation, DNA Repair, and Cancer https://www.youtube.com/watch?v=vl6Vlf2thvI https://www.youtube.com/watch?v=sX6LncNjTFU https://www.youtube.com/watch?v=QVCjdNxJreE Xeroderma pigmentosum: mutation that decrease the ability to repair DNA, which makes highly susceptible to harmful effects...

CHAPTER 15: Mutation, DNA Repair, and Cancer https://www.youtube.com/watch?v=vl6Vlf2thvI https://www.youtube.com/watch?v=sX6LncNjTFU https://www.youtube.com/watch?v=QVCjdNxJreE Xeroderma pigmentosum: mutation that decrease the ability to repair DNA, which makes highly susceptible to harmful effects of UV light. Silent mutation: mutation to DNA but doesn’t change the protein so won’t know functionally there was a mutation there because it is not changing anything. Missense mutation: change DNA and get different amnio acid. A base substitution that changes a single amino acid in a polypeptide. (miss reading something) Frameshift mutation: A mutation that involves the addition or deletion of several nucleotides that is not a multiple of three and alters the reading frame of a protein-encoding gene. (Single base that is inserted or deleted can cause frameshift mutation) (changes the entire reading frame) nonsense mutation: A mutation that changes a normal codon into a stop codon; this causes translation to be terminated earlier than expected, producing a truncated polypeptide. Germ-line mutation: Cells that give rise to gametes, such as egg and sperm cells. (permanently on genome) (rare) Somatic Mutation: The type of cell that constitutes all cells of an animal or plant body except those that give rise to gametes. (it’s not pass on) (skins cancer, UV radiation or chemicals) Sickle cell disease: A disease due to a mutation in a hemoglobin gene that results in sickle- shaped red blood cells that are less able to move smoothly through capillaries and can block blood flow, resulting in pain and cell death of the surrounding tissue. When a person inherits two copies of the mutated gene (one from each parent), they develop sickle cell disease. If they inherit one normal gene and one mutated gene, they are considered carriers (sickle cell trait) but usually do not show symptoms. Spontaneous mutation: A mutation resulting from some abnormality in a biological process. Induced mutation: A mutation brought about by environmental agents that enter the cell and then alter the structure of DNA. Mutagen: An agent known to cause mutation. - Chemical: Nitrous acid, 5-Bromouracil, 2- Aminopurine, Nitrogen mustard, Ethylmethanesulffonate (EMS), Benzo) pyrene. - Physical: A physical agent, such as ultraviolet light (wavelength), X-rays, that causes mutations. Ames test: (test for how mutagenetic a chemical is) use Salmonella typhimurium that cannot synthesize histidine due to a point mutation. (how to tell how bad your chemical is Ames test for mutagenicity)  1. Explain the connection between a defect in DNA repair and the inherited human disease xeroderma pigmentosum. (what kind of mutation, what gene is it hitting) In the UV repair pathway. The Role of UV Radiation: When skin is exposed to UV radiation, it causes the formation of pyrimidine dimers, most commonly thymine-thymine dimers. These dimers distort the DNA helix, leading to errors during DNA replication and transcription if left unrepaired. Carcinogen: An agent that increases the likelihood of developing cancer, usually a mutagen. (such as UV light and certain chemicals in cigarette smoke, are mutagens that promote genetic changes in somatic cells.) Cancer starts as a single cell. This single cell and its lineage of daughter cells undergo a series of mutations and other genetic changes that cause the cells to grow abnormally. (Two things that must go wrong: break all tumor suppressor) At an early stage, the cells form a tumor, which is abnormal overgrowth of cells. benign tumor - Benign tumor: A precancerous mass of abnormal cells. Not invade adjacent tissues and do not spread throughout the body. (any growth from any tissue types that is not a threat to you) - Followed by genetic changes that cause some cells in tumor to lose their normal growth regulation and it becomes a Malignant tumor: A growth of cells that has progressed to the cancerous stage. (individual has cancer) - Cancerous tumors invade adjacent healthy tissues, and cancer cells may spread through the bloodstream or surrounding body fluids, a process called metastasis. (lung most common place because all the blood flow and the oxygen) Oncogene: a mutation causes a gene to be overactive – have an abnormally high level of expression. This overactivity contributes to the controlled cell growth that is observed in the cancer cell. - Promote cancer by keeping the cell division signaling pathway in a permanent “on” position. Two ways: can mutate the growth factor if making too much of it or mutate the receptor so enzyme is acting abnormally fast. Proto-oncogene: (anything that promote growth) normal gene that, if mutated, can become an oncogene. Four common genetic changes. Tumor- Suppressor genes: normal role to prevent cancerous growth (everything that shut down growth) Often stop the cell cycle, or the ability replicated DNA Functions: Maintain genome integrity by monitoring and/or repairing DNA damage. - Checkpoint proteins check the integrity of the genome and prevent a cell from progressing past a certain point in the cell cycle. n Proteins called cyclins and cyclin-dependent protein kinase (cdks) responsible for advancing a cell through the four phases of the cell cycle. n Formation of activated cyclin/cdk complexes can be stopped by checkpoint proteins. n P53 – about 50% of all human cancers are associated with defects in the gene. - P53^1: G1 checkpoint protein. DNA damage induces expression to prevent cell from progressing from G1 to S phase. If DNA is repaired, cell may proceed. - P53^2: If the DNA damage is too severe, the p53 protein will also activate other genes that promote programmed cell death or apoptosis. Caspases function as proteases that digest selected cellular proteins causing the cell to break down. 1. Interphase Interphase is the longest phase of the cell cycle, during which the cell grows, performs its normal functions, and prepares for cell division. It is divided into three stages: G1 phase (Gap 1): o The cell grows in size and synthesizes proteins and organelles. o The cell performs its regular functions, like metabolizing nutrients and carrying out its specialized tasks (e.g., muscle contraction, enzyme production). o The cell prepares for DNA replication in the next phase.  S phase (Synthesis): o DNA replication occurs, so each chromosome is duplicated. o The cell now contains two copies of each chromosome, but they are still in the form of chromatin (loose, uncondensed DNA). G2 phase (Gap 2): o The cell continues to grow and prepares for mitosis by synthesizing more proteins, including those needed for the mitotic spindle and other components of cell division. o It also checks the DNA for any replication errors and repairs them if necessary. G1, S, and G2 together are called interphase, which typically takes the longest time in the cell cycle. 2. Mitotic (M) Phase This is the phase where the cell actually divides into two daughter cells. It includes mitosis and cytokinesis. Mitosis is the process of nuclear division and is divided into several stages: o Prophase: § The chromatin condenses into visible chromosomes, each consisting of two sister chromatids connected by a centromere. § The nuclear membrane begins to break down, and the mitotic spindle (a structure made of microtubules) starts to form from the centrosomes. o Metaphase: § The chromosomes align at the cell's equatorial plate (the metaphase plate) due to the action of the spindle fibers. o Anaphase: § The sister chromatids are pulled apart toward opposite poles of the cell. This ensures that each daughter cell will receive an identical set of chromosomes. o Telophase: § The separated chromatids (now individual chromosomes) reach the poles of the cell. § The nuclear membrane re-forms around each set of chromosomes, and the chromatin begins to de-condense. Cytokinesis: o Cytokinesis is the final step in cell division, where the cytoplasm divides, and two daughter cells are formed. o In animal cells, a cleavage furrow forms and pinches the cell membrane, while in plant cells, a cell plate forms and develops into a new cell wall. 3. Checkpoints Throughout the cell cycle, there are checkpoints that ensure the process is occurring correctly. These checkpoints monitor the cell's progression through the cycle and can halt the cycle if necessary: G1 checkpoint: The cell checks for sufficient nutrients, proper growth signals, and any DNA damage before proceeding to the S phase. G2 checkpoint: The cell checks that DNA has been correctly replicated and that there is no damage before entering mitosis.  M checkpoint: The cell ensures that all chromosomes are properly attached to the spindle before proceeding with anaphase. When checkpoint genes are broken by mutation, the division of normal healthy cells may not be affected because p53 is not deriving growth, there to stop barren growth. Inhibitors of cell division - Necessary to properly halt cell division otherwise division becomes abnormally accelerated. - If cannot fix the damaged, just need to apoptosis the cell. Don’t want the cell to accumulate DNA again. P53 can detect the DNA damage, stop cell cycle, can recruit machinery to fix DNA damage, if not fix can apoptosis. Most cancer are from epithelial cells cancers. Mutations accumulate in basal cells and their number increase – hyperplasia As more mutations accumulate, the basal cells develop more abnormal morphologies – dysplasia Most common cancer: Carcinomas – omas: tumor, carcin: where the tumor came from. (cancer of epithelial cell) – exposure on skin, largest organ in body. 90% of cancer start as a carcinoma and then goes somewhere else. CHAPTER 16: The Eukaryotic Cell Cycle, Mitosis, and Meiosis https://www.youtube.com/watch?v=QVCjdNxJreE&list=PLwL0Myd7Dk1HwPKULqkJoNkfOn T3aTzq6 https://www.youtube.com/watch?v=Pxujitlv8wc - In Eukaryotes, cell division via mitosis and meiosis Eukaryotic Chromosomes - Cytogenetics – field of genetics involving microscopic examination of chromosomes and cell division. (look at chromosome to see if healthy) Chromosome 1 is the longest we  have. one from mom(maternal) and one from dad(paternal). Look identical. Same chromosome, same gene, same order, but not same sequence. (homologous chromosome) - When cells get ready to divide the chromosomes become compact enough to be seen with a light microscope. - Karyotype reveals number, size, and form of chromosomes in an activity dividing cell. Sets of Chromosomes - Humans have 23 pairs of chromosomes (46 total chromosomes) n Autosomes – 22 pairs in humans n Sex chromosomes – 1 pair in humans – XX or XY - Ploidy: how many sets do you have? n Diploid or 2n – humans have 23 pairs of chromosomes (di for two chromosomes) - Diploid species, members of a pair of chromosomes are called homologs. one from mom, one from dad, same gene, same order, slight single base pairs changes. n Autosomes – each homolog nearly identical in size and genetic composition. Examples: Both carry gene for eyer color but one may be brown and other blue. (chromosome 1-22) n Sex Chromosomes – X and Y very different from each other in size and composition. (last two chromosome) n Haploid or n – gametes have 1 member of each pair of chromosomes or 23 total chromosomes Stages of the Cell Cycle Cells are diploid except germ-line cell which are haploid. If haploid are not gametes, every generation would double chromosomes. Centromere: protein attach to DNA on chromosome. Sequence of DNA. The region where the two sister chromatids are tightly associated; the centromere is an attachment site for kinetochore proteins. Centrosomes: A single structure often near the nucleus of a eukaryotic cell that forms a nucleating site for the growth of microtubules; also called a microtubule-organizing center. Centrioles: A pair of structures within the centrosome of animal cells. Most plant cells and many protists lack centrioles. Kinetochores: A group of proteins that bind to a centromere and are necessary for sorting the chromosomes. G1 Phase: Cell growth occurs - Signaling molecules can cause cell to accumulate molecular changes during G1 that promote progression through the cell cycle. - If the cell passes the restriction point, or G1 checkpoint, the cell becomes committed to enter S phase and replicate DNA. S phase (synthesis) – chromosomes replicate - After replication, two copies stay joined to each other and are called sister chromatids. - Human cell in G1 has 46 chromosomes - Same cell in G2 has 46 pairs of sister chromatids or 92 chromatids total G2 Phase: Cell synthesizes proteins needed during mitosis and cytokinesis. - Mitosis: Division of one cell nucleus into two, with separation of sister chromatids. - Cytokinesis: follows mitosis to divide the cytoplasm into two daughter cells. Checkpoint Proteins: Cyclins or cyclin-dependent kinases (cdks) responsible for advancing a cell through the phases of the cell cycle. - Amount of cyclins varies through cycle (goes up and down to drive through each phases) - Cdks are kinases controlling cell cycle. Must bind to a cyclin to be active Three Checkpoints: critical regulatory points - In Eukaryotes n G1 checkpoint (restriction point) n G2 checkpoint  n Metaphase checkpoint Checkpoint proteins act as a sensor to determine if the cell is in proper condition to divide. Cell cycle is delayed until problems fixed (or prevented altogether) Loss of checkpoints can lead to mutations and cancer Mitotic Cell Division - Cell divides to produce two new cells genetically identical to the original - Original is mother cell, new are daughter cells - Involves mitosis plus cytokinesis - Used for asexual reproduction or for development and growth of multicellular organism (ourselves) Preparation for cell division - DNA must be replicated - So, get sister chromatids – two identical copies with associated proteins - Chromatids tightly associated at centromere - Serves as attachment site for kinetochore used in sorting chromosomes Mitotic Spindle 1: Ensure that each daughter cell will obtain the correct number and types of chromosomes. Responsible for organizing and sorting the chromosomes during mitosis. Composed of microtubules. - Centrosomes: microtubule organizing center (MTOCs). Duplicates at the beginning of M phase. Each defines a pole. - Animal cells have centrioles, other eukaryotes don’t Spindle formed from microtubules. Microtubules formed from tubulin proteins. Three types of Microtubules - Astral microtubules: position spindle in cell - Polar microtubules: separate two poles - Kinetochore microtubules: attached to kinetochore bound to centromeres. Cell Cycle - Interphase – phase of cell cycle during which chromosomes are decondensed and found in the nucleus (G1, S, G2) - Mitosis: replication DNA, identical (sister chromatid)  - Chromosome homologous: line up chromosome one from mom and one from dad, A there and T there (not identical) n Prophase: Chromosomes have already replicated and are joined as pairs of sister chromatids. Nuclear membrane dissociates into small vesicles. Chromatids condense into highly compacted structures that are readily visible by light microscopy. n Prometaphase: Nuclear envelope completely fragments. Mitotic spindle is fully formed during this phase. Centrosomes move apart and demarcate the two poles. Spindle fivers interact with sister chromatids. Two kinetochores on each pair of sister chromatids are attached to kinetochore microtubules from opposite poles. n Metaphase: Pairs of sister chromatids are aligned along a plane halfway between the poles called the metaphase plate. Organized into a single row. When this alignment is complete, the cell is in metaphase. n Anaphase: connections broken between sister chromatids. Each individual chromatid is linked to only one pole by kinetochore microtubules. Kinetochore microtubules shorten, pulling chromosomes toward the pole to which they are attached. The two poles move away from each other as overlapping polar microtubules lengthen and push against each other. n Telophase: Chromosomes have reached their respective poles and decondense. Nuclear membranes now re-form to produce two separate nuclei. - Cytokinesis – division into two daughter cells. n In most cases, mitosis is quickly followed by cytokinesis. Two nuclei are segregated into separate daughter cells. n Process is different in animals and plants - Animals – cleavage furrow constricts like a drawstring to separate the cell - Plants – cell plat forms a cell wall between the two daughter cells Meiosis is the process by which haploid cells are produced from a cell that are originally diploid. - Diploid human cell has 46 chromosomes, but after meiosis the haploid egg or sperm has 23 chromosomes. - Two rounds od division accomplish this: meiosis I and meiosis II Like mitosis, meiosis begins after a cell has progressed through the G1, S, and G2 phases of the cell cycle. - Two differences in meiosis are that homologous pairs form a bivalent or tetrad and cross over events. Homologous pairs of sister chromatids associate with each other, lying side by side to dorm a bivalent or tetrad in process called synapsis. - Synaptonemal complex: a protein structure that connects homologous chromosomes. How ever, not actually required for chromosomes paring or combination. Function still uncertain. CROSSING OVER: physical exchange between chromosome pieces of the crossing bivalent. May increase the genetic variation of a species Chiasma – arms of the chromosomes tend to separate but remain adhered at a crossover site. Number of crossovers carefully regulated. Meiosis I - Prophase I: chromosomes condense, bivalents form the nuclear membrane breaks down.  - Prometaphase I: spindle apparatus complete, chromatids attach to kinetochore microtubules. Pairs of sister chromatids attached to single pole. - Metaphase I: bivalents organized along metaphase plate as double row. Mechanism to promote genetic diversity. - Anaphase I: segregation of homologs occurs. Connections between bivalents break, but sister chromatids stay connected together. Each joined pair of chromatids migrates to one pole, while homologous pair moves to the opposite pole. - Telophase I: sister chromatids have reached their respective poles and decondense and nuclear membrane reform - Cytokinesis: end of meiosis I – two haploid cells, with no pairs of homologous chromosomes. Meiosis II: No S phase between meiosis I and meiosis II. Sorting events of meiosis II are similar to those of mitosis. Sister chromatids separated in anaphase II, unlike anaphase I. Differences from mitosis - Mitosis produces two diploid daughter cells that are genetically identical. Example: 6 chromosomes in 3 homologous pairs. - Meiosis produces four haploid daughter cells. Example: each daughter has random mix of 3 chromosomes. Sexual Reproduction requires a fertilization event in which two haploid gametes unite to create a diploid cell called a zygote. After zygote formation, rounds of mitosis create many more diploid cells to dorm a multicellular organism. Sexual life cycle: sequence of events that produces another generation of organism. For sexually reproducing organisms, involves an alternation between haploid cells or organisms and diploid cells or organism. Diploid- dominant species: Most animal species are diploid. Haploid gametes are a specialized type of cell. Haploid-dominant species: many fungi and some protists. Multicellular organism is haploid. Haploid cells unite to form diploid zygote, then proceed immediately through meiosis to make four haploid spores. Variation in chromosome structure and number - Variations in chromosome structure and number can have major effects on organisms. n Several human diseases n Important in evolution of new species Chromosome variation - On rare occasions, structure or number of chromosomes change so that individual is different from other members of same species (abnormal) - Between species, however, it is normal or structure and number of chromosomes to vary Variation in chromosome - Chromosome composition within a given species tends to remain relatively constant. (understatement) (almost zero especially for animals’ variation are not common) - Humans – 2 sets of 23 chromosomes (total of 46) Chromosome identification - Order them by Size: one being longest, short arm is p, long arm is q - Location of centromere is another way to identify chromosome - Metacentric: middle - Submetacentric – off center - Acrocentric – near end - Telocentric – at the end Banding pattern: When look under light microscope to stain them, the more condense region (light didn’t go through them) so have a banding patter. Chromosomal mutations Deletions: segment of chromosome missing Duplications: repeated segment of chromosome Inversions: segment has a change in direction along a single chromosome (can break genes at ends or separate from regulatory regions) Translocation: one segment become attached to another chromosome. May be simple or reciprocal. - If we don’t get identical sister chromatid, it triggers apoptosis. - We know that these cells are going to mitosis and given identical DNA because they are all the same shape, the same size, and same color. But if have mutation, and don’t have identical, might have a batch that is different. - Different DNA, different products - Moles, any patch of lighter skin or darker is a Stem cell that underwent mitosis and changed its DNA. Changes the gene expression. - Somatic cell is all cell in body expect sperm and eggs. - When making sperm and eggs, take 46 chromosomes cell, double the DNA, split back to 46, and split again to 23. - 46 -92 – 46 = mitosis (PMAT) - 46- 92- 46 -26 = Meiosis (PMAT 1 and PMAT 2) P1 is when crossover occur. - Advantage of sexual reproduction is diversity, that allows you to change DNA and give the best shot of adapting to environment.  - We are diploid-dominant species (most cell is diploid) - Gametes are the only haploid cell - Yeast, fungi majority cell are haploid CH 17: Simple Patterns of Inheritance https://www.youtube.com/watch?v=fcGDUcGjcyk&list=PLwL0Myd7Dk1FVxYPO_bVbk8oO D5EZ2o5W&index=1 Mendel’s Laws of Inheritance - Gregor Mendel: took true breeding plant (plant after generation looks the same) and cross them. By doing that he was able to see which trait dominant and which trait were recessive. 1. Traits are dominant and recessive n Dominant variant is displayed in hybrids n Recessive variant is masked by dominant 2. Genes and alleles n They thoughts that there a particulate mechanism of inheritance n Mendel’s called it “unit factors” are genes n Every individual has two genes for a character. n A gene has two variant forms, or alleles Segregation of alleles - Two copies of a gene carried by a F1 plant segregate (separate) from each other, so that each sperm or egg carries only one allele. F2 traits follow approximately 3:1 ratio. - Mendel’s Law of Segregation: Two copies of a gene segregate from each other during the transmission from parent to offspring. Genotype: genetic composition of an individual TT: Homozygous dominant tt: Homozygous recessive Tt: heterozygous Phenotype: Physical or behavioral characteristics that are the result of gene expression. TT and Tt are tall tt is dwarf Punnett Square: A common method for predicting the outcome of simple genetic crosses. If we know genotype, we know phenotype, but it’s not the case with if we know phenotype, we don’t know genotype. Testcross: 1. A cross to determine if an individual with a dominant phenotype is a homozygote or a heterozygote. 2. A cross to determine if two different genes are linked. - A dwarf pea plant must be tt - A tall pea plant could either be TT or Tt, so genotype must be determined by a testcross. - Cross the unknown individual (TT or Tt) to a homozygous recessive individual (tt). If some offspring are dwarf, unknown individual must have been Tt, if all offspring are tall, unknow individual was TT. Two-factor cross: A cross in which an experimenter simultaneously follows the inheritance of two different characters. - Follow inheritance of two different traits - Can determine linkage - Possible patters: Two genes are linked – variants found together in parents are always inherited as a unit. (seen together generation after generation) Two genes are independent – variants are randomly distributed. n Dihybrid offspring – offspring are hybrids with respect to both traits. n Data for F2 hybrids is consistent with independent assortment Mendel’s Law of Independent Assortment: Alleles of different genes assort independently of each other during gamete formation. Chromosome Theory of Inheritance - Chromosomes contain the genetic material (DNA). Genes are found in the chromosomes. - Chromosomes are replicated and passed from parent to offspring. They are also passed from cell to cell during the development of a multicellular organism. - The nucleus of a diploid cell contains two sets of chromosomes, found in homologous pairs. Maternal and paternal sets of homologous chromosomes are functionally equivalent; each set carries a full complement of genes. - At meiosis, one member of each chromosome pair segregates into each daughter nucleus. During the formation of haploid cells, the members of different chromosome pairs segregate independently of each other.  - Gametes are haploid cells that combine to form a diploid cell during fertilization, with each gamete transmitting one set of chromosomes to the offspring. Mendel’s Law of Segregation can be explained by the pairing and segregation of homologous chromosomes during meiosis. The physical location of a gene on a chromosome is called its locus. The Law of Independent Assortment can also be explained by the behavior of chromosomes during meiosis. Random alignment of chromosome pairs during meiosis I leads to the independent assortment of genes found on different chromosomes. Pedigree Analysis of Human Traits - Inherited trait is analyzed over the course of several generations in one family. Cystic fibrosis (CF) example - Approximately 3% of Americans of European descent are heterozygous carriers of the recessive CF allele, and phenotypically normal - Individuals who are homozygous exhibit disease symptoms Many of the alleles causing human genetic disease are recessive, like Cystic Fibrosis. But some are dominant, like Huntington disease. - Huntington disease has an autosomal dominant inheritance pattern - Gene is on one of 22 pairs of autosomes Autosomes: All of the chromosomes found in the cell nucleus of eukaryotes except for the sex chromosomes. Disease genes can also be found on the sex chromosomes Sex Chromosomes are found in many (but not all) species with two sexes. - X-Y system: males XY and females XX - X-O system: females XX and males X or XO - Z-W system: males ZZ and females ZW  - Not all chromosomal mechanisms involve sex chromosome’s: Bees are haplo-diploid – male is haploid and female is diploid. Other mechanisms also exist. Sex controlled by environment (temperature) in some reptiles and fish. Plant: some have a single type of plant making male and female gametophytes. Others have sexually distinct plants making male or female gametophytes only. X-linked traits: A gene found on the X chromosome but not on the Y. - In humans, X chromosome is larger and carries more genes than the Y chromosome. - Genes found on the X but not the Y are X-linked genes n Sex-linked genes are found on one sex chromosome but not the other Males are hemizygous for X-linked genes (one X chromosome) - Example: Hemophilia A is caused by recessive X-linked gene. Simple Mendelian inheritance - Alleles are dominant or recessive - Phenotype ratios follow Mendel’s laws - Recessive allele does not affect phenotype of heterozygote - Single copy of the dominant allele makes enough functional protein to provide a normal phenotype, masking recessive allele. - Sometimes heterozygote may even upregulate the lone functional allele to provide high enough expression. - More complex forms of inheritance - Incomplete dominance: The phenomenon in which a heterozygote that carries two different alleles exhibits a phenotype that is intermediate between the phenotypes of the corresponding homozygous individuals. Heterozygote shows intermediate phenotype. Neither allele is dominant. (mix red and white and get pink). Re-fertilize and get pink, white, and red again. - Codominance: The phenomenon in which a single individual expresses two alleles. Can have multiple alleles – three or more variants in a population. Phenotype depends on which two alleles are inherited. Example: ABO blood types in humans. Type AB is codominant – expresses both alleles equally. Genotype: - Cross between true-breeding purple flowers and true-breeding white produced (as expected): F1 – all purple- flowered plant. F2 – 3:1 purple to white- flowered - Cross between two varieties of white-flowered peas crossed produced surprising results: F1 – all purple-flowered plants. F2 – (:7 purple to white flowered. n C (purple) dominant to c (white) n P (purple) dominant to p(white) n If either cc or pp homozygous, flowers are white CH 19: Genetics of Viruses and Bacteria https://www.youtube.com/watch?v=8FqlTslU22s https://www.youtube.com/watch?v=agQpPPQ5IVQ https://www.youtube.com/watch?v=Gd09V2AkZv4&t=40s - Viruses and viroids are nonliving particles with nucleic acid genomes that require the assistance of all living cells to reproduce. - Tobacco Mosaic Virus (TMV) first virus discovered. Viruses: small infectious particle that consists of nucleic acid enclosed in a protein coat. - Over 4,000 different types  - Vary greatly in their characteristics, including their host range, structure, and genome composition. Viruses are not alive, and they come in different. There is single-stranded RNA that’s the whole virus. Or just double stranded DNA, which is the whole virus. Host Rang: number of species and cell types that can be infected. - All viruses have a capsid (protein coat), but it varies in shape and complexity. - Some have viral envelope derived from host cell plasma membrane. Structure: Genome: DNA versus RNA, single stranded (ss) versus double stranded (ds), linear versus circular. Viruses are not alive. They are not cells or composed of cells. They cannot carry out metabolism on their own. Viral reproductive cycle can be quite different among types of viruses. CORONAVIRUS: one of those that is enclosed, and it enter cell that’s very specific receptors. It lets its RNA out; the cell see the RNA and translated it into protein. The protein that was made by the cell is an RNA dependent and RNA polymerase (it reads RNA and make RNA). When it got ton of RNA made, those specific translated into virus itself and grab the membrane again. There could be Latency in bacteriophage. - Some viruses can integrate their genomes into a host chromosome. - Prophage or provirus is inactive or latent - Most viral genes silenced - When host cell replicates also copies prophage - Lysogenic cycle – integration, replication, and excision - Lytic cycle: synthesis, assembly, and release (faster) - Temperate phages have a lysogenic cycle, but virulent phages do not - Environmental conditions influence integration and length of latency Latency in human viruses Two different mechanisms - Virus integrates into host genome and may remain dormant for long periods of time. Example: HIV - Other viruses can exist as episomes – genetic elements that replicate independently but occasionally integrate into host DNA. Example: Herpes simplex type I and II, varicella zoster (chicken pox) Emerging viruses are ones that have risen recently or have recently become more infectious. Examples: New strains of influenza, like H1N1, Zika virus, spread by Aedes mosquitoes, HIV/ AIDS. Human immunodeficiency virus (HIV) is the causative agent of acquired immune deficiency syndrome (AIDS). AIDS is primarily spread by sexual contact between infected and uninfected individual. Can also spread  - By transfusion of HIV-infected blood - By sharing of needles among drug users - From infected mother to unborn child AIDS destroyed a type of white blood cell called a helper T cell (play an essential role in the mammalian immune system) When T cells are destroyed by HIV, the immune system is seriously compromised. Patient becomes susceptible to opportunistic infections that would not occur in a healthy person. HIV reverse transcriptase lacks proofreading function. - Makes more errors - Tends to create mutant strains of HIV - Makes it difficult to create vaccine In U.S., the estimated annual number of AIDS- related deaths fell 14% from 1998 to 2002 due in part to the use of new antiviral drugs. Viroids composed solely of a single-stranded circular RNA molecule a few hundred nucleotides in length. It infects plant cells. Some replicate in host cell nucleus, others in chloroplast, RNA genome does not code for proteins, Disease mechanism not well understood. Prions composed entirely of protein. Disease causing conformation PrP. Normal protein expressed at low levels on surface of neurons. Prion converts normal proteins to abnormal form. Several types of neurodegenerative diseases of human and livestock. Group of diseases called transmissible spongiform encephalopathies (TSE). Compaction: typical bacterial chromosome must be compacted about 1,000-fold. DNA supercoiling - Topoisomerase twist the DNA and control degree of supercoiling Plasmids: small, circular pieces of DNA that exist independently of the bacterial chromosome. - Occur naturally in many strains of bacteria and in a few types of eukaryotic cells, such as yeast. - Own origin of replication that allows it to be replicated independently of the bacterial chromosome. - Not usually necessary for survival but can provide growth advantages. - Episome – plasmid that can integrate into bacterial chromosome. Four Types of Plasmids - Resistance plasmids (R factor): confer resistance against antibiotics and other types of toxins - Degradative plasmids: enable the bacterium to digest and utilize an unusual substance - Virulence plasmids: turn a bacterium into a pathogenic strain - Fertility plasmids (F factors): allow bacteria to mate Reproduction - Some species like E. coli can divide every 20 to 30 minutes - Single cell can form a bacterial colony in less than a day - Reproduce by binary fission – not mitosis  - Unless a mutation occurs, each daughter cell contains an identical copy of the mother cell’s genetic material. - Does not involve genetic contributions from two different parents - Plasmids may replicate independently of the bacterial chromosome. Gene Transfer Between Bacteria Genetic diversity in bacteria – from mutations or genetic transfer 1. Conjugation: direct physical interaction transfers genetic material from donor to recipient cell 2. Transformation: DNA released from a dead bacterium into the environment is taken up by another bacteria. n Does not require direct contact between bacterial cells n Living bacterial cell imports a strand of DNA that another bacterium released into the environment when it died. n Only competent cells with competence factors are capable of transformation, n Competence factors facilitate binding of DNA fragments to the bacterial cell surface, uptake of FNA into the cytoplasm, and incorporation of imported DNA into the bacterial chromosome. 3. Transduction: a virus transfers genetic information from one bacterium to another n Viruses that infect bacterial can transfer bacterial genes from one bacterium to another n Usually an error in a phage lytic cycle n Newly assembled phages incorporate pieces of host DNA instead