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Microbiology- Test 3
Chapters 9,10,13,14
| Question | Answer |
|---|---|
| What molecule must be degraded by aromatic catabolism? | lignin |
| enzymes speed up reactions by | decreasing the activation energy |
| fermentation pathways have in common | the oxidation of NADH to NAD+ |
| most cellular enzymes are which type of biomolecule? | proteins |
| The maximal theoretical yield of ATP molecules from the complete oxidative respiration of a single glucose molecule in bacteria is approximately | 35 ATP |
| ATP in cells is complexed with which molecule? | magnesium ions |
| If a molecule is found in greater concentration inside the cell than outside, we can conclude that | energy was required to produce the concentration gradient |
| which metabolic pathway has ribulose-5-phosphate as an intermediary | pentose-phosphate shunt |
| what is NOT a pathway to convert glucose into pyruvate | tricarboxylic acid cycle |
| An example of catabolism | glucose oxidation to pyruvate |
| Some organisms obtain energy by the reaction of oxygen gas and hydrogen gas to produce water. This is an example of | hydrogenotrophy |
| Methanogenesis is performed by organisms in which domain | archaea |
| Generation of ATP in the cytoplasm via ATP synthase in the membrane requires | an electrical or chemical gradient favoring proton (or positively charged ion) entry into the cell |
| The components of an ETS have what in common? | They all can exist in different redox states |
| Hydrogenotrophy is | the use of hydrogen gas as an electron donor |
| The proton motive force is a source of energy that can directly power | the import of other ions against their concentration gradients, the production of ATP |
| For a given electron donor, the most energy will be released when oxygen serves as the final electron acceptor because | oxygen is a stronger oxidizing agent than most other electron acceptors |
| Electron transport chains pump what across membranes? | protons |
| If the thylakoid ATP syntheses are inhibited, one can expect that | the pH of the thylakoid lumen will decrease |
| photoheterotrophic organisms | can use light to make ATP but must acquire reduced carbon from the environment |
| It is possible to create a proton motive force WITHOUT | an electron transport system |
| ATP production in bacteriorhodopsin containing halophilic archaea differs from ATP production in cyanobacteria in that | only cyanobacteria oxidize water |
| Cyanobacteria contain | both photsystems 1 and 2 |
| In oxygenic photosynthesis, the electrons come from | water (electron donor) |
| In oxygenic photosynthesis, the electrons end up in | NADPH |
| transformation | breaking open the donor cells and removing DNA from them so as to obtain a cell free purified form of DNA (naked) |
| conjugation | transfer between bacteria and plants, across domains, sex pili, attachment of 2 cells by the pili |
| transduction | a phage infects a susceptible bacterium and injects its DNA into the host |
| Methyl mismatch repair | MutS and MutHL bind and cleave the unmethylated strand, exonucleases remove the damaged strands, DNA Pol1 fills the gap and ligase seals the nick |
| Nucleotide excision repair | recognition of damage, cleavage of the P backbone, DNA Pol1 fills the gap and ligase seals the nick, NEB recognizes specific types of damage (thymine dimer) |
| base excision repair | removes just the base first, then cuts the backbone, recognizes specific DNA mutation (uracil) |
| recombinational repair (recA) | RecA binds to the sister double helices and the damaged single strand region, the gap in the damaged strand is replaced with the homologous undamaged strand, DNA Pol 1 and ligase fill the gap, nucleotide excision repair can now fix the damaged base |
| SOS repair | deinococcus radiodurans, used when both strands are damaged, catalyzed by formation of RecA filaments, activated RecA filaments cleave LexA repressor leading to up regulation/transcription of SOS genes |
| How does Deinococcus survive UV exposure? | Survives by SOS, genome features, lots of copies. Has 2 chromosomes and can reconstruct both chromosomes from small fragments of DNA, keeps multiples genome copies, protein is affected first when exposed to stress. |
| Silent Mutations | no sequence change |
| Neutral Mutation | chemically similar amino acid |
| missense | change in amino acids (mistake) |
| nonsense | change to stop codon (no sense) (most harmful) |
| frameshift | changes all codons downstream (most harmful) |
| inversion | bases inverted |
| What is the Ames test? | uses bacterial strain auxotrophic for histidine, mutation in hisG gene, cannot grow unless histidine is supplied, place on medium and chemical, mutagen causes reversion to normal, stronger mutagen |
| Is DNA damage the same thing as a permanent mutation? | No, Dna damages are physical abnormalities in the DNA such as breaks and can be recognized by enzymes. Mutations are a change in the base sequence and cannot be recognized by enzymes |
| What are jumping genes? | transposable elements insert into chromosomes and can jump from one site to another and can copy itself to a new site. discovered by Barbara Mcclintock |
| What types of genes are in the flexible gene pool? | efflux pumps, antibiotic syntehsis, symbiosis genes |
| What types of genes are in the core gene pool? | polymerase, heat shock, ribosomal proteins, housekeeping genes |
| How do you tell if a gene is likely to have been horizontally transferred? | dramatically different GC base ratios compared to the entire genome, codon usage that differs from flanking regions |
| Sensor kinase protein in plasma membrane | binds to signal, activates itself via phosphorylation |
| cytoplasmic response regulator | takes phosphate from sensor, binds operator or activator (alters transcription of target genes) |
| Low cAMP | lactose not utilized |
| Catabolite repression | glucose is preferred catabolise, lac down regulated |
| high glucose | low cAMP |
| lac 1 always binds unless | lactose is present |
| In the presence of high glucose and high lactose | low cAMP and low allolactose |
| Will allolactose ever be high levels in the cell? | no, always be low |
| Co Repressor | if present, down regulates when it binds DNA |
| Activator | always up regulating when it binds DNA, positively regulates a gene, inducer binds activator protein causing up regulation |
| Repressor | always down regulates when it binds DNA, always negative, no glucose but lactose is present, binds DNA is absence of inducer |
| lac1 blocks | transcription |
| attenuation | mechanism of regulation: lessens, down regulation, 2 conformations for mRNA |
| if tcp is abundant in attenuation then ribosomal synthesis is | fast |
| if tcp concentration is low in attenuation then ribosomal synthesis is | slow |
| tryptophan is a | co-repressor, binding to aporepressor, down regulating |
| Glycolysis | glucose to pyruvate, forms ATP and NADH |
| Fermentation | does not use TCA cycle, may not produce additional ATP or NADH |
| TCA Cycle | produces additional ATP, 1 per pyruvate, NAD+ is utilized and must be regenerated via electron transport |
| EMP (glucose catabolism) | 1 glucose- 2 pyruvates, nets 2 NADH and 2ATP, substrate level phosphorylation, high energy intermediates |
| ED | allows some gut microflora to use sugar acids in mucus, 1 glucose and sugar acids- 2 pyruvates. net 1 NADH 1 NADPH and 1 ATP, generated by substrate level phosphorylation |
| PPS (pentose phosphate shunt) | produces purines for DNA and RNA, aromatic amino acids, 1 glucose and sugars acids- 2 pyruvates, net 2 NADPH and 1 ATP |
| Carbon flow is modular when grown on | pectin via the ED pathway |
| carbon flow reverses when grown on | lectin |
| Which system is used by Rhodopseudomonas Palustris? | PS2 |
| Organisms such as Thiothrix and Beggiatoa, grow using SO4-2/H2S and O2/H2O this organism can be classified as a | lithotroph |
| When tryptophan concentrations are low | the ribosome will stall at the tcp codons and the anti attenuator loop with form |
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