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### lecture_19_notes

Course: BIS bis2a, Spring 2009
School: UC Davis
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Word Count: 856

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Lecture 19 Linkage Finish Linkage: The frequency of recombination is used as a measure of distance between A and B. This is the called the &amp;quot;genetic distance&amp;quot;. The unity of distance are centiMorgans (~100 x # recombinants/ (recombinants + parentals) Locus: a position on a chromosome, typically meant in the context of the a gene. For example, the wrinkled locus of pea. Pl. loci....

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Lecture 19 Linkage Finish Linkage: The frequency of recombination is used as a measure of distance between A and B. This is the called the &quot;genetic distance&quot;. The unity of distance are centiMorgans (~100 x # recombinants/ (recombinants + parentals) Locus: a position on a chromosome, typically meant in the context of the a gene. For example, the wrinkled locus of pea. Pl. loci. Recombination frequencies between loci can be measured and used to assemble a map example: W-T = 20, W-Y = 10, Y-T = 30 makes a map: Y_10_W___20___T Alleles and gene function Alleles are different forms of a gene The wild-type allele is defined as the one found most frequently in a natural population Natural population: individuals of the same species in a natural environment. Example: Poppies in a meadow, grasses of a species in a prairie, Red-winged blackbirds around Davis, a human tribe in New Guinea Typically, the wild-type allele has good function. Different alleles arise continuously by mutation. Mutants, individuals in which a gene has changed in structure, arise at a frequency of 1/million - 1/100 millions per gene per generation. Given that most species have 20,000 to 40,000 different genes, the probability of carrying a recently formed mutation is very high for any individuals Mutations arise from multiple types of errors, typically in replication of DNA, and can involve any of the following: deletion: part of or the whole gene sequence is lost. Depending on the size of the deletion function loss can be partial or complete insertion: another DNA is spliced into the gene disrupting its structure. Usually loss of function is complete duplication: the whole gene is duplicated either in tandem or by transposition (copying and splicing into) to a new locus. This increases the expression level of the gene (more protein is made) and that can have no, minor, or <a href="/keyword/deleterious-effects/" >deleterious effects</a> point mutation: the sequence of DNA is changed at one base. The effect of base changes can be multiple and will be covered in a future lecture. In the mean time, however, here is a simple summary: the effects go from complete loss of function to none. In some cases, DNA base changes result in changes in protein sequence (a different amino acid is present at a given position). Summary of mutations: the effects of mutations on the function of a gene go from none (most common) to decreasing or increasing its function and even changing its function. Allele types and polymorphism. There are typically many alleles of a gene in a population. -1- The wild-type allele is most frequent. Some time, two alleles are predominant. Individuals that display different traits of a character are said to be polymorphic (multipleshapes) Polymorphisms can be phenotypic or molecular. For example, individuals that carry different alleles are polymorphic even if the alleles cause no change in function. For example, many mutations are said to be neutral, because they do not affect the phenotype of the affected individual The next common type of mutation is the deleterious one. It causes loss of function, or some type of deleterious change (more function, or function in the wrong organ or tissue). Deleterious mutations impair the affected individual. If the reproductive potential of the affected individual is decreased, there will be fewer of the mutant types in the next generation. The rarest type of mutation is the one that improves a character. This could result, for example, from a better enzyme, or from an enzyme that carries out a different, useful function. The ABO blood type. the I gene encodes a glycosyltransferase, an enzyme that attaches a sugar molecule to the lipid head of the red blood cell membrane Three alleles are common: Ia: attaches the 'A' sugar Ib: attaches the 'B' sugar Io: it does not encode an active enzyme Consider the genotype and the resulting membrane sugar group: genotype enzyme activity sugar IaIa IbIb IoIo IaIb IaIo a b none a+b a A B none AB A IbIo b B Note that both Ia and Ib are dominant over Io. When together, they are co-dominant: each exerts its effect. Another pattern of dominance: semidominance snapdragon: RR -&gt; red , rr -&gt; white, Rr -&gt; pink the heterozygous phenotype is determined by a dosage response: less of the R-encoded enzyme results in less of the red pigment dosage effects are common: cystic fibrosis is caused by loss of function of Cl- channel. Individuals with the recessive alleles build up mucus in the lungs because of impaired ion balance -2- individual heterozygous for this allele appear to be more tolerant to cholera, a diarrhea causing disease, perhaps because a different ion balance alters growth of the pathogen in the intestine Copy number alleles. Some allele undergo tandem duplication. This type of variation is common in all tested organisms Copy number variant alleles have been implicated in multiple diseases and phenotypes, such as mental illness, coat pattern in dogs, HIV resistance, malaria susceptibility Mutations accumulate with time. Sexuality helps a species to get rid of deleterious mutations and to keep good mutations by scrambling the genetic material The formation of mutations allows us to clock the divergence of different organisms. -3-
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UC Davis - BIS - bis2a
Lecture 18Mendelian geneticsMendel From previous lecture: finish testcross with dihybrid (two genes) Use of probability for complex problems According to Mendel's second law, Alleles of different genes assort independently: they thus follow und
UC Davis - BIS - bis2a
Lecture 17Mendelian geneticsMendel First Law: the two copies of a gene segregate Test cross: an individual with the round phenotype has an unknown genotype. How to find out? Cross it to a wrinkled individual, whose phenotype is known by default:
UC Davis - BIS - bis2a
Lecture 16Mendelian geneticsMendel brief history (if interested see: &quot;The Monk in the Garden&quot; by R. Henig; not required at all!) studies inheritance using peas pea is a selfer (and individual fertilizes itself), but can be crossed artificially
UC Davis - BIS - bis2a
Lecture 15Meiosis (continued) Anaphase objective: move homologs apart chiasmata are disentangled and homologs are moved to opposite pole each homolog consists of a two chromatids Telophase as in mitosis. It tends to blur with the next division
UC Davis - BIS - bis2a
Life cyclesMost &quot;large&quot; eukaryotes are diploid Chromosomes have unique characteristics In the plant Arabidopsis, there are five chromosome types: 1, 2, 3, 4, 5 Each chromosome is characterized by its size, position of centromere (the constricti
UC Davis - BIS - bis2a
Lecture 13Cell division (continued)The eukaryotic chromosome (chromo=color, some=body) Structure: a single, linear dsDNA molecule, complexed with many proteins (DNA + protein = chromatin). Carries genes. Depending on the organism size of chromos
UC Davis - BIS - bis2a
BIS2A. Lecture 12Eukaryotic cell division Division can have two purposes Production of gametes for sex: meiosis. [Note: in later lectures life cycles cases where meiosis does not directly, but eventually, produce gametes are given] Growth, makin
UC Davis - BIS - bis2a
Lecture 11Photosynthesishttp:/www.school.net.th/Light energy capture Light -&gt; Chlorophyll -&gt; high energy e- from H2O (-&gt; O2) chlorophyll is inside thylakoid membrane in protein complexes called photosystems high energy electron enters e- tra
UC Davis - BIS - bis2a
Lecture 10Respiration Pyruvate oxidation (not decarboxylation); lecture notes 9 were corrected on Wed 22 amFermentation See lecture 9 Alcoholic fermentation CH3COCOOH -&gt; CO2 + CH3-COH NADH + H+ + CH3-COH -&gt; NAD+ + CH3-CH2OH Lactic fermentatio
UC Davis - BIS - bis2a
Lecture 9Harvesting of energy Cells need energy to function, to stay alive, and to grow and multiply. Without energy, a cell is dead Energy is harvested from energy-rich compounds by controlled &quot;burning&quot; Sugars, fats, amino acids are energy rich
UC Davis - BIS - bis2a
Lecture 8Review of chemical reactions How do we know if a reaction will take place? Compare G of products and reagents G is for standard amounts G is for specific amounts, and thus applies to a given condition G = G + RT lnK K is the [product
UC Davis - BIS - bis2a
Lecture 7 SPECIAL NOTICE See instructions for this Friday exam on Smartsite! Note that you are assigned a specific room for the exam. If you come to the wrong room, you will not be able to take your exam there.Membranes, continued Osmosis continue
UC Davis - BIS - bis2a
Lecture 5What is life? cellular organization sensitivity growth reproduction regulationDomains of living things Common ancestor Prokaryotes Archaea Bacteria Eukaryotes EukaryaStructure of cellsProkaryotes Outside Plasma membrane (
UC Davis - BIS - bis2a
Lecture 4Nucleic acids (continued)Pyrimidines: Cytosine, Thymine, Uracil. Single ring. Purines: Adenine, Guanine. Double ring. Polymer can be of two types: DNA, deoxyribonucleic acid, chemically more stable; RNA, ribonucleic acid, chemically less
UC Davis - BIS - bis2a
Lecture 3pHdefinition acid: R-H -&gt; R- + H+, CH3-COOH, HCl base: R + H+ -&gt; RH+, NaOH measuring concentration of compounds mole = to mol weight H2 mw = 2, 1 mole = 2 g CH3-CH2-OH mw = 46 (2 C x 12, 1 O x 16, 6 H x 1), 1 mole = 46 g 1Molar solu
UC Davis - BIS - bis2a
Lecture 2 (4/1/09)Proteins continued polymer concept: make a complex, large molecule from small repeating subunits structure, ionization of amino acid, R-group (= side chain) Asp, D: -c-coo, Asn, N: -c-conh2(*), Cys, C: c-sh, Phe, F: c-ring pep
UC Davis - BIS - bis2a
Lecture 1. 3/30/09 Introductions: Greg Simonds, Phillip Conklin, Divya Denduluri, Wesley Sughrue, Rebecca Wright Website: https:/smartsite.ucdavis.edu Waitlist: situation, what to do Course organization: Lectures, clickers (25 pt), Midterms (3x75), F
UC Davis - BIS - bis2a
Study questions 13Consider the drawing above, which depicts structures observed inside cells. 1. What are these structures? 2. Could M and N be taken from the same species. If not explain why. If yes explain the difference. 2. What is 'o'? What is
UC Davis - BIS - bis2a
Study questions 141. Pure blue eyes are recessive. Brown eyes are dominant. A blue eyed woman married to a brown eyed man, Joe, has a blue eyed baby. Is the husband the father? 2. The same couple are having a second baby. What is the probability tha
UC Davis - BIS - bis2a
Study questions 191. Rank the following mutations according to the damage potential toward the function of a gene a. frameshift b. first position changes c. missense d. nonsense e. third position changes 2. In an extraterrestrial creature investigat
UC Davis - BIS - bis2a
Study questions 18(Most of these questions are from past Intro Biology exams) Aphids have both a sexual and a clonal life cycle. During clonal reproduction a mother aphid forms progeny through embryogenesis of somatic cells, i.e. of non-zygotic cell
UC Davis - BIS - bis2a
BIS2A Spring 09Study questions 17 (from an old Comai exam)1 The end of each polymer indicated below is the _ end: Choose the best row. polymer F a b c d e 2 5 3 5 5 3 T 5 amino terminal amino terminal carboxy-terminal carboxy-terminal LL 5 5 3 3 5
UC Davis - BIS - bis2a
Study questions 161. Write the base-paired complementary strand underneath each of the following sequences, which are all listed 5' to 3':aaaaccctacgttc ttttgattacattt cccctactctacat ggggatcatcatgg2. Write the complementary strand, 5' to 3', for
UC Davis - BIS - bis2a
Study questions 20. Gene regulation1. The -35 and -10 regions are made of this polymer _ the numbers refer to the _ of this process _ are bound by this molecule _ Answer polymer a b c d e DNA RNA protein RNA DNA refer to the _ start end start end st
UC Davis - BIS - bis2a
Study Questions 15. Genetics.Solving genetics problems is the only way to learn genetics. This set was contributed by Dr. Bonny Brewer, Department of Genome Sciences, University of Washington, Seattle 1. The sequence of a strand of DNA reads (from 5
UC Davis - BIS - bis2a
Study questions 12In a simple pathway of bacteria two regulators are working as follows:cell enlargement -&gt;R-&gt; T-&gt; chromosomal replication 1. What is the effect on this system of losing the function of R? 2. What is the effect on this system of lo
UC Davis - BIS - bis2a
Study questions 111. Compare and contrast (if appropriate) the characteristics of each item common to the electron transport chain (ETC) of respiration vs the ETC of photosynthesis: Table of questions Item Direct donor of eUltimate e- acceptor Ultim
UC Davis - BIS - bis2a
BIS2A. Spring 2009. Comai Study questions. Lecture 2 1. Define the side chain of the following amino acid: amino acid a b c d e Cysteine Aspartic acid Phenylalanine Glycine Asparagine structure hydrophylic?2. The peptide bond plays a determining ro
UC Davis - BIS - bis2a
BIS2A. Spring 2009. Comai Study questions. Lecture 1 1. Consider each compound pair (look up the structure in wikipedia). Which one of the two has more energy on a molecule by molecule basis? pair compound 1 a b c d e propane propanol H2 methane acet
UC Davis - BIS - bis2a
BIS2A Study questions 10Two species of non-photosynthetic bacteria, L and M, have similar metabolism, but for the absence of the Krebs cycle and the electron transport chain in M. Using separate flasks, you introduce 1000 cells of each L and M in a
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