BIO 107 1nd EditionFinal Exam Study Guide Lectures: 30 - 39 and previous study guidesWeek 12 (Lecture 30)Gene RegulationHow are prokaryotic genes regulated?A cluster of functionally related genes and the sequences that control them, or operons, are regulated by proteins that respond to biochemical signals. It starts with the promoter, or the RNA polymerase binding site where transcription starts. The operator is near the promoter and is the sequence that the repressor binds to. If the corepessor binds to the repressor, transcription is blocked. If the inducer binds to the repressor, transcription continues. Week 13 (Lecture 31-33) Gene Regulation (cont.)How are histones used to prevent transcription in eukaryotes?DNA is wrapped around the histones and the histones are tightly packed to prevent transcription. This DNA is referred to as heterochromatin. Acetylation of the histones prevents super-coiling and the DNA is expressible. This is referred to as euchromatin.What are transcription factors?Transcription factors (TFs) are proteins that bind to DNA to block or help expression of genes. They can be general or specific to a certain tissue or response. DNA can be affected at large distances and the TFs communicate by bending the DNA to form “s” curves. What is Mediator?It is a protein that loads polymerase and recruits enzymes for chromatin modification. How are proteins regulated after transcription?Introns can be alternatively spliced to give rise to different proteins. Proteins can also be labeledfor destruction. Micro RNA (miRNA) can be produced to block translation and mark RNA for destruction.Bacteria and ArchaeaWhat are the shapes that these prokaryotes can take? Cocci – spherical Bacilli – rod Spirelli – spiral What is the difference in a gram positive or gram negative organism?Gram positive organisms have a thick peptidoglycan layer that stains purple when introduced to both iodine and crystal violet. Gram negative organisms either have a very thin layer of peptidoglycan or none at all. This includes all Archaea and some bacteria.What is the purpose of an endospore?An endospore is a copy of the genome surrounded by a membrane with little water. It allows forlong term survival in harsh conditions and will burst to be used again when conditions become favorable.How is a bacterial flagellum like ATP synthase?Both have a motor that turns by allowing protons to reach equilibrium. The flagellum motor spins the tail in a corkscrew motion to allow the cell to swim.How do prokaryotes divide?Prokaryotes replicate their circular DNA by starting at one point and moving bi-directionally. Thetwo new sets move to opposite ends and associate with the membrane. The membrane pinchesoff in the middle. This process is called binary fission.How do prokaryotes adapt so quickly?They divide every 12-24 minutes. There are some mutations that occur with every replication and these can end up being useful to survival. The high rate of recombination of mutations allows them to reach optimal conditions for the environment. How can bacteria exchange genetic information? Transduction – a virus infects a cell and ends up incorporating some of the host’s DNA into its own during replication. The virus lyses the host and infects another host. Theviral DNA is destroyed by the host’s defenses and the bacterial DNA can be incorporated into the cell’s genome. Conjugation – a sex pilus is formed between an F+ and F- cell and DNA is replicated in the “rolling circle” form and sent to the F- cell. The pilus breaks and the cells separate. Transformation – bacteria die and the cell is denatured. Another cell picks up the DNA and can incorporate it into the genome or break it down to use it for its own replication.What is the difference between F+ conjugation and Hfr conjugation?F+ conjugation occurs when the cell with the F factor that codes for conjugation is in a plasmid. The plasmid is replicated and sent to the recipient cell. The recipient then becomes F+ since the F factor was transferred. In Hfr conjugation, the F factor is in the genome of the donor cell. The genome is replicated and sent to the recipient cell. Since the cells do not stay connected long enough, only some of the genome is transferred and the recipient is never made an F+ cell.What is antibiotic resistance?Antibiotic resistance is when a bacterium is not affected by antibiotics. This can be done by reducing the drug uptake in the cell, transporting the drug out of the cell, inactivating the drug by metabolizing or modifying it, or altering or amplifying the drug target. Week 14 (Lectures 34-36) Bacteria and Archaea (cont.)Why is antibiotic resistance spreading?There is an overuse and incorrect use of antibiotic in the household, agricultural business, and clinic. Bacteria can also transfer resistance by conjugation or transformation.How can prokaryotes be categorized based on metabolism? Energy sourceo Phototrophs – energy from lighto Chemotrophs – energy from chemicals Carbon sourceo Autotrophs – don’t need carbono Heterotrophs – need an organic carbon source Oxygen metabolismo Obligate aerobes – require oxygeno Obligate anaerobes – poisoned by oxygeno Facilitative aerobe – can live in either environmentWhat is nitrogen fixation?It is the conversion of atmospheric N2 to NH3. Some plants form symbiotic relationships with thebacteria to grow in low-nitrogen soils.Why do bacteria form colonies?Colonies allow for some cells to specialize so the group benefits without having to sacrifice other needed processes. Materials can be transferred between cells. How are Archaea categorized? Halophiles – live in very high salt environment Thermophiles – live in very high temperature environments Methanogens – they produce methaneWhat roles do bacteria play?Many bacteria are decomposers. They break down dead organisms to recycle nutrients. They are also pathogens that cause half of human diseases. Bacteria are also used in research and technology. They are used in fields like molecular biology, pharmaceuticals, bioremediation, andpolymer synthesis.VirusesWhat is a virus?A virus is an obligate parasite that consists of a DNA or RNA genome and a protein coat. They cannot replicate on their own. What Is the virus life cycle?A virus infects a cell by injecting its genome and some proteins into the cell. The virus uses the host’s machinery to replicate its DNA and
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