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MCB4150 Exam 1Study Guide With
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Microbiome - ANSWER multi-genus/species community of microorganisms that exist within a defined environment Human Microbiome - ANSWER the beneficial/neutral/adversarial community of bacteria that live on/in a human host Parts of the human that are densely populated with microbes: - ANSWER -Gastrointestinal Tract -Oral Cavity -Vagina -Skin What is microbial diversity involved in? - ANSWER -Biogeochemical cycling -Infectious disease -Microbial Degradation -Aquatic microbiology -Oxidation/Reduction reactions -Biotechnology How long have microbes evolved for? - ANSWER ~3.9 billion years Haeckel's 3 Kingdom Phylogeny - ANSWER Was the 1st attempt to categorize life 1.) Plants 2.) Animals 3.) Monera/ microorganisms Whittaker's 5 Kingdom Classification Scheme - ANSWER 1.) Plants 2.) Animals 3.) Fungi 4.) Protista 5.) Monera/ microorganisms
Woese's 3 Domains - ANSWER Groundbreaking because it showed the prokaryotes can be divided into 2 domains of Bacteria and Archaea And showed that majority of Eukaryotes are also made up of microorganisms 1.) Bacteria 2.) Archaea 3.) Eukarya Leeuwenhoek: - ANSWER -built a microscope with a single lens that had a magnification of 200x -1st to discover and describe bacteria, but called them "wee animalcules" Spallanzani - ANSWER -tried to disprove SG -put broth into a sealed container and sterilized it with heat, and showed no microbial life grew -was not accepted by people because the container was sealed, so they argued "life force" inside was killed off Pasteur - ANSWER -father of microbiology and immunology -found that pathogens/bacteria cause disease -discovered chirality and stereochemisty -found microbial origin of fermentation -treatment and prevention of rabies, cholera, and anthrax -disproved SG/Vitalism by using his Swan-necked Flask experiments, where he essentially did the same thing as Spallanzani, but because his container was open, people could not argue the "life force" could not get inside Koch - ANSWER -developed Postulates/methods to culture and isolate bacteria -methods to obtain pure cultures/ "Pure Culture Paradigm" -saw that colonies grew on a potato slice when incubated in air, and each colony must have come from a single bacteria -colonies had characteristic morphologies of shape, size, and color, which he believed could be used to classify species much like in animals -discovered specific bacteria that causes tuberculosis (Mycobacterium tuberculosis) and cholera Koch's Postulates - ANSWER -a specific microorganism must be present in all disease
-no universally accepted definition of one yet Ecological Theory of Species - ANSWER -each species has a specific job/"niche" -important to understand how microbial communities function Biological Species Concept - ANSWER -Mayr -species is a sexually interbreeding or potentially interbreeding group of individuals normally separated from other species by absence of genetic exchange -CANNOT be applied to microbes because they don't do sexual reproduction like animals Bacterial Species - ANSWER strains are of the same species if they share more than 97% 16S/18S rRNA sequence identity and more than 70% genomic hybridization 16S/ 18S rRNA - ANSWER -codes for transcription, translation, and replication -conserved in ALL cells because they have an important job and have a strong selection towards them -more than 80% of the total RNA -no lateral gene transfer -coded for in all genomes -good molecular chronometer Oligoribonucleotide cataloging of the small subunit rRNA (done by Woese) - ANSWER 1.) Grow cells with P32 label 2.) Isolate rRNA 3.) T1 ribonucleasue digestions cuts at every G (only 25% of info available) 4.) 2-D gel electrophoresis 5.) Comparison of gel to library of oligoribonucleotides (>6 nucleotides) Sanger Sequencing - ANSWER -procedure where chemical termination of daughter strands help in determining the DNA sequence -incorporation of modified dNTP (ddNTP) that had no OH stopped more nucleotides from pairing -resulted in different lengths of DNA that could be read upwards on a gel to determine a sequence
DNA-DNA Hybridization - ANSWER comparing the genomic DNA of 2 organisms -1 set of DNA is radioactively labeled -both are then sheared and heat denatures DNA -the similar sequences will hybridize, and will do a comparison of those hybridized and those not
Polymerase Chain Reaction (PCR) - ANSWER amplifies specific DNA sequences -requires dNTPs, buffer solution, polymerase capable of withstanding specific temperatures (Taq), forward and reverse primer, and a template DNA strand
How old is the common ancestor of life though to be? - ANSWER ~3.5 billion years old
Banded Iron Formations - ANSWER oxygen reacted with dissolved iron in the ocean and formed massive rock and iron deposits -proof of the "Great Oxidation Event"
Stromatolites - ANSWER Communities of blue-green algae and bacteria that build mound-like structures in marine environments -were fossilized and are proof of early life on Earth
Methods for phylogenetic comparison of sequences: - ANSWER Evolutionary Distance: count the the number of differences in DNA sequence between two organisms
Character State Method: looking for the minimal amount of evolution to diverge from a common ancestor
Phylogenetic Tree and Constituents - ANSWER -Root: common ancestor of all taxa on a tree; tree may be unrooted, but can give hypotheses of direction of evolution
-Node: an existing taxonomic unit (species, etc.)
Metabolism - ANSWER sum of all biochemical reactions within an organism
Catabolism - ANSWER Breakdown of complex things to yield energy -conserves energy from Redox reaction and couples them to make a PMF for ATP generation
Anabolism - ANSWER Energy-requiring reactions that build the macromolecules that are broken down in Catabolism
Fermentation vs. Respiration - ANSWER Fermentation: energy-rich bonds are not broken and an organic product is produced
Respiration: compound is completely oxidized to CO2, consequently making higher yields of ATP per unit molecule
Fermentation - ANSWER -proceeds without an external e- acceptor -Redox balance achieved by donating e- generated to a compound internal to electron pathway --> regenerates NAD+ from NADH -Substrate-level Phosphorylation: ATP made when an intermediate in pathway forms energy rich phosphate bond transferred to ADP to make ATP -Glycolysis is most well-known fermentative reaction
Respiration - ANSWER -substrate is completely oxidized to CO2, which makes higher yields of ATP -e- are funneled through an ETC by NADH to make a proton gradient across a membrane -e- used to reduce an external e- acceptor (O2 to H2O) -Oxidative Phosphorylation: energy stored in proton gradient used to generate ATP -maintains balance by donating e- generated from Substrate Oxidation to terminal e- acceptor O
Citric Acid Cycle - ANSWER -when an external e- acceptor is present, fermentation is not required to maintain Redox balance -pyruvate is able to completely oxidize in this cycle making: 3 CO2, 1 GTP, and 5 reducing equivalents (NADH or FADH) -FADH and NADH are oxidized in ETC in respiring cells -makes total of 38 ATP per glucose
All respiratory and photosynthetic pathways have a common theme: - ANSWER -e- are yielded from the oxidation of an organic/inorganic compound or phototrophic process -e- traverse a membrane-associated ETC and generate a PMF -electrical energy of PMF is conserved by cell to make ATP
The Eukaryotic-Prokaryotic Dichotomoy - ANSWER 1.) Eukaryotes are a monophyletic group 2.) Bacteria and Archaea are no ore related to each other than they are to Eukaryotes 3.) Neither the Eukaryote or Prokaryote is simpler
Lipids in Archaea vs Bacteria/Eukarya - ANSWER B&E: -fatty acid bonded in ester linkage to a molecule or glycerol
A: -long chains of hydrocarbons bonded by an ether linkage to glycerol -long carbon chains from from alternating isoprene -2 different hydrocarbons allows for both monolayers (better in heat) and bilayers in Archaea
Woese's Tripartite/ 3 Domain Hypothesis is Controversial - ANSWER -Woese said Archaea were different enough to have their own domain -some felt Woese came to this through low sampling
Differences in information transfer between Prokaryotes and Eukaryotes: - ANSWER P: -organized into operons and transcribed into 1 polycistronic mRNA, encoding more than 1 product
E: -protein-encoding region is split into 2 or more exons and introns, separating coding regions -transcription and translation are spatially separated
Importance of Sigma Factors - ANSWER Sigma Factors make contact with the Core Enzyme/ RNA Polymerase which allows it to bind to different promoter regions on the DNA
3 Elements Crucial for Promoter Recognition in Archaea: - ANSWER 1.) Initiator Element 2.) TATA Box 3.) B recognition element (BRE)
-structure of archaeal promoters resembles that of eukaryotic promoters -RNA Pol similar to RNA Pol 2 in Eukaryotes -share 3 main recognition sequences
-Archaeal Protein Synthesis more strongly resembles Eukaryotes than Bacteria
