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by: Rien Notetaker

Microbiology Chem 343

Rien Notetaker

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Exam 2
Introductory Organic Chemistry
Samuel Gellman
Class Notes
Microbiology, Vocabulary
25 ?




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This 5 page Class Notes was uploaded by Rien Notetaker on Friday August 19, 2016. The Class Notes belongs to Chem 343 at University of Wisconsin - Madison taught by Samuel Gellman in Fall 2016. Since its upload, it has received 5 views. For similar materials see Introductory Organic Chemistry in Chemistry at University of Wisconsin - Madison.


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Date Created: 08/19/16
1 Lactic acid bacteria: g+; mostly firmicutes; often aerotolerant; produce lactic acid as product of fermentation; found on many animals/plants; two pathways for lactic acid production Homolactic fermentation: e donor=sugars; pyruvate=e acceptor; products= 2 molec. lactic acid=homogenous Heterolactic fermentation: oxidative step=NADH-NAD; Redox=NAD-NADH; products= 1 lactic acid, 1 ethanol, 1 co2, 1 atp/glucose. Ethanol fermentation: converts sugars such as glucose, fructose, and sucrose into cellular energy, producing ethanol and carbon dioxide as a side-effect. Malting: seed activates own enzymes and starches turn into simple sugars, like glucose, because yeast can’t do it. Acetic acid bacteria: proteobacteria; aerobic respiration; e donor=ethanol; e acceptor=O2; product=acetic acid; used to make vinegar; g- Methanogen: a methane-producing bacterium, especially an archaeon that reduces carbon dioxide to methane. Polyphosphate: polymer of phosphate ions; energy store; stays inside cell and phosphate is removed from the environment; encouraged to happen at wastewater treatment centers. Nitrification: ammonia-nitrite-nitrate; reduced N as e donor Denitrification: nitrate as e acceptor for respiration; turns into nitrogen gas Transcription: DNA->mRNA; 3 steps= initiation, elongation, termination; sigma factors in bacteria; archaea and eukarya don’t have sigma factors and use transcription factors instead. Translation: mRNA nucleotide sequence->amino acids->protein; defining feature of living organisms Gene: functional unit of DNA; encodes for an RNA or protein Promoter: site on DNA to which the enzyme RNA polymerase can bind to initiate transcription Operon: A set of genes transcribed under the control of an operator gene. More specifically, an operon is a segment of DNA containing adjacent genes including structural genes, an operator gene, and a regulatory gene. Gene upstream region: Gene downstream region: RNA polymerase: enzyme that is responsible for making rna from a dna template. Sigma factor: searches for promoter to tell RNA polymerase where to bind. 2 Consensus sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. Coding strand: same sequence as transcribed mRNA; has promoter sequence, start codon, stop codon Template strand: template for the mRNA to be transcribed. mRNA: template for translation; contains code rRNA: part of ribosome tRNA: translation role; translates code genetic code: order of triplet codons codon: sequences of nucleotides; grouped in 3s anticodon: complementary to codon in mRNA start codon: Where transcription starts; AUG (methionine) stop codon: where transcription stops (UAG, UAA, AGU) aminoacyl tRNA synthetase: enzyme that attaches the appropriate amino acid onto its tRNA 50S ribosome subunit: large subunit 30S ribosome subunit: small subunit Initiator fMet-tRNA: Initiation factors: proteins that bind to the small subunit of the ribosome during the initiation of translation Elongation factors: facilitate translation; set of proteins that are used in protein synthesis E site: P site: A site: Reading frame: way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets In-frame: within the reading frame Shine-Dalgarno sequence: a ribosomal binding site in prokaryotic messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning the ribosome with the start codon. 3 Release factor: a protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence. Repressor: substance that acts on an operon to inhibit mRNA synthesis. Activator: substance that acts on an operon to cause mRNA synthesis Operator: segment of DNA to which a transcription factor binds to regulate gene expression. The transcription factor is a repressor, which can bind to the operator to prevent transcription. Genome: all of the genetic material; blueprint of self; important for continued survival; most bacteria and archaea have one. Chromosome: Plasmid: much smaller than chromosomes (but some may be bigger); usually don’t contain genes necessary for survival; contain any other genetic material; can carry useful genes; thousands of different plasmids (naturally occurring pieces of DNA); have ori for replication. Ori: origin of replication in plasmids DnaA: Binds to ori C (bacterial protein) and recruits other proteins. Primase: makes RNA primer (enzyme that DNA works off of) Helicase: opens strands Topoisomerase: unwinds DNA; travels ahead of replication fork; relieves twisting forces. DNA polymerase: makes new DNA; needs primer to start; adds nucleotides at 3’ end only (5’ to 3’); sliding clamp holds DNA polymerase in place Mutation: change in genome/genotype of organism. Mutant: Proofreading: looking for and correcting mistakes in DNA as it is synthesized. Mutagen: a physical or chemical agent that changes the genetic material, usually DNA, of an organism and thus increases the frequency of mutations above the natural background level. Genotype: nucleotide sequence of the genome. Phenotype: observable properties of an organism (how interacts with other organisms and environment) Point mutation: when a single base pair is altered Nonsense mutation: a stop codon is in for a sense codon and transcription terminates early; could be catastrophic (protein probably won’t be functional at all). 4 Missense mutation: change amino acid sequence, which changes the protein; we don’t know what impact it has until we isolate it and test it in a lab. Silent mutation: when protein sequence doesn’t change, no phenotypic change; we don’t know what the impact is Frameshift mutation: caused by a deletion or insertion in a DNA sequence that shifts the way the sequence is read Insertion: base pairs inserted; scrambles message; can be small or big; if it’s not in multiples of 3, the coding sequence is thrown way off. Deletion: base pairs removed; scrambles message; can be small or big; if it’s not in multiples of 3 the coding sequence is thrown way off. Wild-type strain: a phenotype, genotype, or gene that predominates in a natural population of organisms or strain of organisms in contrast to that of natural or laboratory mutant forms Core genome: black; common to all in a species and makes up most of the chromosome. Pan genome: colors; variable within a species; 4,000 or so genes. Horizontal (lateral) gene transfer: very common in bacteria and archaea, but not microbial eukaryotes; happens at a high frequency; is how adapt to environment Transformation: uptake of free DNA from environment Competence: naturally able to take up foreign DNA Transduction: virus-mediated transfer Conjugation: direct transfer from one cell to another Restriction enzyme: an enzyme produced chiefly by certain bacteria, having the property of cleaving DNA molecules at or near a specific sequence of bases; restricts foreign DNA Methylase enzyme: adds a methyl group to self DNA to mark as self DNA ORF: open reading frame; potential protein; go through DNA searching for 5 things (promoters, RBS, start/stop codon, etc.) Cloning vector: plasmid Expression vector: used to introduce a specific gene into a target cell, and can commandeer the cell's mechanism for protein synthesis to produce the protein encoded by the gene. Insert: DNA you want to clone; put into plasmid Sticky end (DNA): created by restriction endonucleases when they cut DNA. 5 Selectable marker: a gene introduced into a cell, especially a bacterium or to cells in culture, that confers a trait suitable for artificialselection. PCR: polymerase chain reaction; procedure to selectively amplify a piece of DNA; in vivo Primers: a strand of short nucleic acid sequences (generally about 10 base pairs) that serves as a starting point for DNAsynthesis. It is required for DNA replication because t Thermostable DNA polymerase: can survive the denaturation step in pcr Thermus aquaticus: species of bacteria that can tolerate high temperatures Pyrococcus woesi: ultra-thermophilic marine archaebacterium. It is sulfur-reducing and grows optimally between 100 and 103 °C. Agrobacterium tumefaciens: g-; Ti plasmid: circularplasmid that often, but not always, is a part of the genetic equipment that Agrobacterium tumefaciens and Agrobacterium rhizogenes use to transduce its genetic material to plants. T-DNA: transferred DNA of the tumor-inducing (Ti) plasmid of some species of bacteria Vir genes: region on the Ti/Ri plasmid is a collection ofgenes whose collective function is to excise the T-DNA region of the plasmid and promote its transfer and integration into the plant genome Bacillus thuringiensis: a Gram-positive, soil-dwelling bacterium, commonly used as a biological pesticide. Bt toxin: naturally occuring bacteria that produces a protein toxic to certain types of insects


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