BIO 325 1st EditionExam # 2 Study Guide Lectures: 9 - 15LECTURE 9Why are fungi model organisms? All 4 haploid products are contained in ascus and the evidence of recombination is present in the phenotype i.e. can be observed.I. Yeast tetrad analysisa. Parental diytpe (PD)- parental gametesb. Nonparental ditype (NPD)- recombinant gametesc. Tetratype (T)- mixture of parental and recombinanti. When PD=NPD, two genes are independentii. When PD >> NPD, two genes are linkedII. Tetrads can be characterized by the number of parental and recombinant spores they containa. No crossing over=PDb. A few single cross-over= Tc. Very few double cross-over can result in all… PD, T, and NPDIII. Calculating recombination frequencya. RF= [(NPD x 1/2T)/(Total Tetrads)] x 100IV. Calculating distance to centromerea. %SDS= SDS/(FDS+SDS) x 100 (SDS-Second division segregation)What is the difference between first and second division segregation patterns? In first division segregation patterns, the gametes are identical to each other, while in second division segregation patterns the gametes are not identical to each other; recombination has occurred. LECTURE 10 Describe the make-up of DNA. DNA consists of four subunits including, a 5-carbon sugar, a phosphate, and 4 nitrogenous bases (Adenine, Cytosine, Guanine, and Thymine). The single strands of DNA are polar, having a 5’ and 3’ end. The two strands of the double helix are antiparallel.I. Two key experiments to prove that DNA is an information moleculea. Transformationi. There is something that transforms one form of bacteria to the other; phenotype changes1. We ask: what changes the phenotype? That is the entity that transforms the biological subject. We discovered that this entity is DNA because we now know that the genotype changes the phenotype i.e. DNA is the information moleculeb. Transductioni. The genetic alteration of a cell resulting from the uptake, genomic incorporation, and expression of foreign genetic material1. Frederick Griffith rat experiment: Virulent S strain transformed non-virulent R strain into virulent S strain due to substance X.2. We ask: What is substance X?a. Destroyed protein, RNA, DNA, and Lipids. Transformation occurred in all cases except for when DNA was destroyed. DNA must be the substance X responsible for the transformation process. What was the significance of the Hershey and Chase Waring blender experiment? Proved that DNA was the biological information molecule because viruses only needed to inject DNA into the host cells. What did the Erwin Chargoff experiment prove? The experiment demonstrated that ratios of A:T are always 1:1 and C:G are 1:1. What are the possible copying mechanisms of DNA? Semiconservative model is the current accepted model in which each strand of DNA acts as a template. The conservative model is one in which each parental DNA is the template. The dispersive model theorized that separate fragments of the DNA strand are copied. What are the enzymes involved in DNA replication and what do they do? DNA helicase unwinds the double helix, single-stranded binding proteins keep the helix open, RNA primase creates RNA primers to initiate synthesis, DNA polymerase is found in two forms, DNA polymerase I and III, Pol III produces new strands of complementary DNA- called the leading strand, and Pol I fills in gaps between newly synthesized Okazaki fragments, and DNA ligase welds together the fragments, creating the lagging strand.LECTURE 11What is a complementation test? A tool to characterize mutations with similar phenotypes; candefine genesWhich type of mutation, forward or reverse, is more common? Forward mutations. What are the types and consequences of mutations at the DNA sequence level? Substitution in which a purine is replaced with another purine, or a pyrimidine is replaced by another pyrimidine (ex: AG or CT) called a transition, or when a purine is replaced by a pyrimidine or vice versa (ex:AT). Effects of substitutions can be silent in which there is really no effect (the base changed, but the amino acid remains the same), missense in which the base change results in an amino acid change which may or may not have an adverse effect, or a nonsense mutation in which the base change results in a stop codon which will usually have an adverse effect. Deletion/Insertiondepends on the number of base pairs inserted; best case scenario involves an insertion or deletion that does not change the reading frame of the nucleotide sequence in multiples of 3 i.ean insertion of 2bp would be more harmful than an insertion of 9bp. Inversion, and Translocation in which nonhomologous chromosomes exchange base pairs; can lead to reproductive isolation and new species. Why are bacteria studied for mutations? Their small size, rapid growth, very large numbers, a simple genome, they are haploid (does not require several generations to uncover recessive mutations), easier to relate a phenotype to its biochemical basis, they are clonal, inexpensive, can be frozen, and their testing is humane.Interpretation of Luria-Delbruck fluctuation experiment and replica platingfluctuation test - the Luria-Delbrück experiment to determine the origin of bacterial resistance. Fluctuations in the numbers of resistant colonies growing in different petri plates showed that resistance is not caused by exposure to bactericides.Mutations do not arise in particular genes as a direct response to environmental change and can occur randomly at any time. What are the different sources of mutation at the base level? Depurination (is frequent and can be repaired), in which there is a removal of a purine base. Deamination is the removal of an amine group (can be repaired). Radiation is the breakage of the DNA backbone (cannot normally be repaired), UV light which can crosslink adjacent thymines, block gene expression or DNA replication (must be excised and repaired), oxidative damage that results in base changes (can be repaired) The mutations during DNA replication are rare but include unequal crossing over, transposons (DNA molecules that can move from one place to another in the genome), Mutagens can: replace a base, alter base structure and properties, add ethyl or methyl groups, remove amine groups, insert between bases, Ames test - screens for chemicals that cause mutations in bacterial cells.LECTURE 12How do you know if two mutations are in the same gene? Complementation test: take two mutants, cross them, and examine