BIOL-L211Final Exam Study GuideFINAL STUDY GUIDEThis guide contains information from the lectures that she specified will be covered on the final exam.Note: The lectures are listed according to the Professor's lecture number titles; not necessarily GradeBuddy's (which correspond to the specific day of the lecture as opposed to her numbers)Lecture 4Bacteria & Bacteriophage as Model SystemsThe Transforming Principle ExperimentsProperties of DNAWhat are the primary characteristics of bacteria?Bacteria are Prokaryotes. They lack membrane-bound organelles. They have no nucleus. Transcription and translation occur in the cytoplasm. The cell wall is made of peptidoglycan.List three features that make bacteria easy to research in the lab.1. Single Chromosome (nucleoid)2. Grow fast3. Easy to manipulateList four functions of bacteria.1. Cycle Carbon2. Produce Oxygen3. Nitrogen Fixation4. Waste DecompositionWhat is the transformation principle?The transformation principle is the process by which bacteria are able to take up foreign geneticmaterial from their environment.What are the characteristics of bacteriophages?Bacteriophages have a unique genome, a capsid (head), and occasionally tailsWhat are the two types of bacteriophage?Lytic and Lysogenic/TemperateHow does the lytic cycle proceed?1. The phage infects a bacterium and injects its genome.2. DNA is replicated.3. Phage particles are produced.4. Bacterium bursts.5. Phage is released.How does the lysogenic cycle proceed and how does it relate to the lytic cycle?1. The phage infects a bacterium and injects its genome (like the lytic cycle).2. Phage DNA integrates into bacterium DNA yielding a "Prophage" (different)3. Prophage is replicated with its new genome.4. The lysogenic cycle may switch to the lytic cycle.What is the source of genetic material for phages?Nucleic acidDescribe the structure of DNA.DNA consists of two polynucleotide chains in a double helix structure with both a major and a minor groove. DNA uses the sugar deoxyribose as the backbone (lacking an OH group), which allows it to compact and form the tight double helix structure. Each nucleotide is composed of adeoxyribose, a purine//pyrimidine base, and a phosphate group (that links the nucleotides together).What interaction occurs at the major groove?DNA binding proteins interact.Where do histone proteins interact?The minor grooveWhich nucleotides are purines and which are pyrimidines???Pyrimidines: Cytosine and Thymine (both have a y; both pyrimidines)Purines: Adenine and Guanine (note the distinct lack of a "y.")What do Chargaff's Rules consist of?Chargaff's rules state that a purine binds with a pyrimidine; specifically that Adenine binds with Thymine and Guanine binds with Cytosine. When Adenine binds with Thymine, there are twohydrogen bonds. When Guanine binds with Cytosine there are three hydrogen bonds. DNA strands run complementary and antiparallel to each other.Lecture 8Replication IWhat are the three different replication hypotheses, and which one is correct?1. Dispersive Model: parental DNA strands fragment and then serve as templates2. Semiconservative Model: DNA "unzips" and yields two identical template strands, which serve as templates for the new DNA. <- This model is correct as proved by Meselson-Stahl3. Conservative Model: Parental strands of DNA remain together throughout replication.How many origins of replication (ori) does a standard cell have?It depends. If the cell is a prokaryote, it has one. If a cell is eukaryotic, it can have hundreds to thousands.How many times are origins of replication activated per cell cycle?It depends. In prokaryotes, an ori can be activated multiple times per cell cycle. In eukaryotes, although there are multiple oris, they will only be activated once per cell cycle.In which direction is DNA synthesized?5' to 3'How do you differentiate between the leading and the lagging strand?The leading strand is synthesized toward the replication fork in one continuous piece. The lagging strand is synthesized in the direction opposite the replication fork (away from), and is synthesized piece by piece (Okazaki fragments).What makes helicases important?Helicases unwind DNA using ATP hydrolysis in order to allow it to be replicated.What are primases? What do they do? Why are they important? What happens as a result of their action?Primases are enzymes that add primers to single stranded DNA. Primers are the starting point for DNA synthesis. DNA synthesis cannot proceed without a primer. When the primer is added to the template strand, it forms the primer:template junction. The primer:template junction is important for the recruitment of DNA polymerase.What is DNA polymerase and how would you describe its structure?DNA polymerase is the enzyme that synthesizes DNA. It is like a hand. It has a "palm" area that catalyzes DNA synthesis and monitors base pairing. It has "fingers" that bend the template strand and set up the next base to be paired. It has a "thumb" that ensures that the DNA polymerase does not dissociate from DNA.What is topoisomerase? How does it work? And how does it relate to positive and negative supercoils? Topoisomerase is an enzyme that relieves structural tension. Positive supercoils are knots of DNA that build up in front of the replication fork. Topoisomerase resolves the positive supercoilsand transforms them into negative supercoils, which are a natural conformation of DNA in which replication can proceed.What would happen in the absence of DNA binding proteins (SSBs)?Newly separated DNA strands would not remain separated. They would continue interacting and prevent transcription.What are the four important deoxynucleoside triphosphates? How are phosphodiester bonds formed? How is a specific base pair connected to a triphosphate group?The four important deoxynucleosides are dATP, dGTP, dCTP, and dTTP. Each base pair is connected to the triphosphate group via a deoxyribose group. Phosphate groups are labeled alpha, beta, and gamma with respect to their proximity to the nucleoside. To form a phosphodiester bond, the beta and gamma phosphates are removed (after the alpha phosphateis attacked by the 3' OH of the primer).Lecture 9Replication IIWhat does processivity pertain to?Processivity refers to the ability of a DNA polymerase to add many dNTPs before leaving the template strand. DNA can synthesize quickly: ~1000 dNTPs/secondWhat is the function of an exonuclease? What are the limitations of exonucleases? How