Microbiology Test 2 (spring)

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Chapter 7:
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Autotroph-an organism that uses CO2, an inorganic has as its carbon source -not nutritionally dependent on other living thingsGrowth Factors: essential organic nutrients-organic compounds that cannot be synthesized by an organism b/c they lack the genetic and metabolic mechanisms to synthesize themGrowth factors-must be provided as a nutrient -essential amino acids, vitaminsCarbon source-heterotroph/autotrophChemotroph-gain energy from chemical compoundsPhototrophs-gain energy through photosynthesisMajority are chemoheterotrophs-aerobic respirationSaprobes-free-living microorganisms that feed on organic detritus from dead organisms -opportunistic pathogens -facultative parasiteParasites-derive nutrients from host -pathogens -some are obligate parasitesPassive Transport-does not require energy; substances exist in a gradient and move from areas of higher concentration toward areas of lower concentration -diffusionOsmosis-diffusion of water (passive transport)Facilitated Diffusion-requires a carrierGroup translocation-transported molecule chemically alteredBulk transport-endocytosis, exocytosis, pinocytosisDiffusion-net movement of molecules down their concentration gradient (passive transport)Endocytosis-bringing substances into the cell through a vesicle or phagosomePhagocytosis-ingests substances or cellPinocytosis-ingests liquidPassive Transport-energy expenditure by the cell is not required, substances exist in a gradient and move from areas of high concentration towards areas of lower concentration in the gradientActive Transport-energy expenditure is required molecules need not exist in a gradient, rate of transport is increased, transport may occur against a concentration gradientEnvironmental Factors affect the function of metabolic enzymes:-temperature, oxygen requirements, pH, osmotic pressure, barometric pressureMinimum temperature-lowest temp that permits a microbe's growth and metabolismMaximum temperature-highest temp that permits a microbe's growth and metabolismOptimum temperature-promotes the fastest rate of growth and metabolismPsychrophiles-optimum temperature below 15 degree C -capable of growth at 0 degree C -chlamydomonas nivalis grows on Alaskan glaciers and its photosynthesis pigments give the show a red crustMesophiles-optimum temperature 20-40 degree C -most human pathogensThermophiles-optimum temperature greater than 45 degree COxygen-is utilized it is transformed into several toxic products: -singlet oxygen (1O2), superoxide ion (O2-), peroxide (H2O), and hydroxyl radicals (OH-) -most cells have developed enzymes that neutralize these chemicals -superoxide, dismutase, catalase -if a microbe is not capable of dealing with toxic oxygen, it is forced to live in oxygen free habitatsAerobe-utilizes oxygen and can detoxify itObligate aerobe-cannot grow w/o oxygenFacultative anaerobe-utilizes oxygen but can also grow in its absenceMicroaerophilic-requires only a small amount of oxygenAnaerobe-does not utilize oxygenObligate anaerobe-lacks the enzymes to detoxify oxygen so cannot survive in an oxygen environmentAerotolerant anaerobes-do not utilize oxygen but can survive and grow in its presenceEffects of pH-majority of microorganisms grow at a pH 6 and 8 (neutrophils)Acidophiles-grow at extreme acid pHAlkalinophiles-grow at extreme alkaline pHSymbiotic-organisms live in close nutritional relationships, required by one or both membersMutualism-obligatory, dependent; both members benefitCommensalism-the commensal benefits; other member not harmedParasitism-parasite is dependent and benefits; host harmedNon-symbiotic-organisms are free-living; relationships not required for survivalSynergism-members cooperate and share nutrientsAntagonism-some members are inhibited or destroyed by others -affect the success or survival of others in the same community (competition) -antibiosisNormal microbial flora-human body is a rich habitat for symbiotic bacteria, fungi, and a few protozoa -commensal, parasitic, and synergistic relationshipsBiofilms-result when organisms attach to a substrate by some form of extracellular matrix that binds them together in complex organized layers -dominate the structure of most natural environments on earthQuorum Sensing-communicate and cooperate in the formation and function of biofilmsBiofilms formation and quorum sensing:-free-swimming cells lose their motility and settle down onto a surface or substrate -cells synthesize an adhesive matrix that holds them tightly to the substrate -when biofilm grows to a certain density (quorum), the cell release inducer molecules that can coordinate a response -enlargement of one cell to show genetic induction. inducer molecule stimulates expression of a particular gene and synthesis of a protein product, such as an enzyme -cells secrete their enzymes in unison to digest food particlesMicrobial growth occurs at 2 levels:1) growth at a cellular level with increase in size 2) increase in populationBinary Fission-division of bacterial cells occurs mainly through transverse -parent cell enlarges, duplicates its chromosome, and forms a central transverse septum dividing the cell into 2 daughter cells -chromosome replication and cell enlargement. the parent cell duplicates the chromosome and synthesizes new structures that enlarge the cell in preparation for the daughter cells -chromosome division and separation, the chromosomes affix to the cytoskeleton and are separated into the forming cells. the cell lays down a septum that begins to wall off the new cells. other components (ribosomes) are equally distributed to the developing cells -completion of cell compartments, the septum is synthesized completely through the center, and the cell membrane patches itself so that there are 2 separate cell chambers -end of cell division cycle, daughter cells are now independent units, some species will separate completely as shown here, while others will remain attached, forming chains or pairs, for example.Generation/doubling time-time required for a complete fission cycleExponential cycle-each new fission cycle increases the population by a factor of 2 -generation times vary from mins to daysGrowth curve-typically display a predictable pattern over timeLag phase-"flat" period of adjustment, enlargement; little growthExponential Growth Phase-a period of maximum growth will continue as long as cells have adequate nutrients and a favorable environmentStationary Phase-rate of cell growth equals rate of cell death caused by depleted nutrients and O2, excretion of organic acids and pollutantsDeath Phase-as limiting factors intensify, cells die exponentiallyTurbidometry-most simple -degree of cloudiness, turbidity, reflects the relative population sizeDirect cell count-count all cells present; automated or manualChapter 8:...Metabolism-all chemical and physical working of a cellCatabolism-degradative; breaks the bonds of larger macromolecules; releases energyAnabolism-biosynthesis; process that forms larger macromolecules from smaller molecules; requires energy imputEnergy of Activation-enzymes are biological catalysts that increase the rate of a chemical reaction by lowering the energy of activationEnzyme-not permanently altered in the reaciton -promotes a reaction by serving as a physical site for specific substrate molecules to positionSimple Enzyme-consist of protein aloneHoloenzymes-contain protein aloneApoenzyme-protein portion -exhibits primary, secondary, tertiary, and some quaternary structure -site for substrate binding is active siteCofactors-nonprotein portion -supporting the work of enzymes -micronutrients are needed as cofactors -act as carriers to assist the enzyme in its activtyMetallic cofactors-iron, copper, magnesiumCoenzymes, organic molecules-vitaminsInduced fit-a temporary enzyme-substrate union occurs when substrate moves into active site -appropriate reaction occurs -product is formed and releasedExoenzymes-transported extracellularly, where they break down large food molecules or harmful chemicals; cellulase, amylase, penicillinaseEndoenzymes-retained intracellularly and function there -most enzymes are endoenzymesConstitutive enzyme-always present, always produced in equal amounts or at equal rates, regardless of the amount of substrateRegulated enzyme-not constantly present; production is turned on (induced) or turned off (repressed) in response to changes in the substrate concentrationSynthesis or condensation reactions-anabolic reactions to form covalent bonds b/w smaller substrate molecules, require ATP, release one molecule of water for each bond formedHydrolysis reactions-catabolic reactions that break down substrates into small molecules; requires the input of water to break bondsSensitivity of enzymes to their environment-activity of an enzyme is influenced by the cell's environment -enzymes operate under temp, pH, and osmotic pressure of organisms habitat -when enzymes are subjected to changes in organism's habitat they become unstableDenaturation-weak bonds that maintain the shape of the apoenzyme are brokenCompetitive inhibition-substance that resembles the normal substrate competes with the substrate for the active siteNoncompetitive inhibition-enzymes are regulated by the binding of molecules other than the substrate away from the active siteEnzyme repression-inhibits at the genetic level by controlling synthesis of key enzymesEnzyme induction-enzymes are made only when suitable substrates are presentEnzyme characteristics-composed mostly of protein -act as organic catalysts to speed up the rate of cellular reactions -lower the activation energy required for a chemical reaction to proceed -enable metabolic reactions to proceed at a speed, specificity, and function -provide an active site for target molecules called substrates -much larger in size than their substrates -associate closely with substrates but do not become integrated into the reaction products -are not used up or permanently changed the reaction -can be recycled and function in extremely low concentrations -are greatly affected by temp and pH -can be regulated by feedback and genetic mechanismsEnergy-the capacity to do work or to cause change -forms of energy include: thermal, radiant, electrical, atomic, and chemicalHow do cells manage energy?-cells manage energy in the form of chemical reactions that make or break bonds and transfer electronsEndergonic reactions-consume energy -Energy + A + B -(energy)-> CExergonic reactions-release energy -X + Y -(energy)-> Z + energyWhere is energy released stored?-energy released is temporarily stored in high energy phosphate molecules. the energy of these molecules is used in endergonic cell reactionRedox reaction-always occur in pairs acceptor which constitutes a redox pair -process salvages electrons and their energy -released energy can be captured to phosphorylate ADP or another compoundElectron and Proton Carriers-repeatedly accept and release electrons and hydrogen to facilitate the transfer of redox energy -most carriers are coenzymes -NAD, FAD, NADP, coenzyme A, and compounds of the respiratory chainAdenosine Triphosphate (ATP)-metabolic "currency" -3 part molecule consisting of: >adenine-a nitrogenous base >ribose-a5- carbon sugar >3 phosphate groups -removal of the terminal phosphate releases energy -ATP utilization and replenishment is a constant cycle in active cellsSubstrate-level phosphorylation-transfer of phosphate group from a phosphorylated compound (substrate) directly to ADPOxidative phosphorylation-series of redox reactions occurring during respiratory pathwayPhoto-phosphorylation-ATP is formed utilizing the energy of sunlightBioenergetics-study of the mechanisms of cellular energy release -includes catabolic and anabolic reactions -primary catabolism of fuels (glucose) proceeds through a series of 3 coupled pathways 1. gylcolysis 2. kreb's cycle 3. respiratory chain, electron transport chainHow does nutrient processing work?-it is varied, yet in many cases is based on 3 catabolic pathways that convert glucose to CO2 and gives off energyAerobic respiration-glycolysis, the kreb's cycle, respiratory chain -series or enzyme-catalyzed reactions in which electrons are transferred from fuel molecules (glucose) to oxygen as a final electron acceptorAnaerobic respiration-glycolysis, the kreb's cycle respiratory chain, molecular oxygen is not the final electron acceptorFermentation-glycolysis, organic compounds are the final electron acceptors -incomplete oxidation of glucose or other carbohydrates in the absence of oxygen -uses organic compounds as terminal electron acceptors -yields a small amount of ATP -production of ethyl alcohol by yeasts acting on glucose -formation of acid, gas, and other products by the action of various bacteria on pyruvic acidGlycolysis-glucose (6C) is oxidized and split into 2 molecules of pyruvic acid (3C), NADH is generatedTCA-processes pyruvic acid and generates 3 CO2 molecules, NADH and FADH2 are generatedElectron transport chain-accepts electrons from NADH and FADH, generates energy through sequential redox reactions called oxidative phosphorylationElectron transport and oxidative phosphorylation-final processign of electrons and hydrogen and the major generation of ATP -chain of redox carriers that receive electrons from reduced carriers (NADH and FADH2) -ETS shuttles electrons down the chain, energy is released and subsequently captured and used by ATP synthase complexes to produce ATP-oxidative phosphorylationChemiosmosis-as the electron transport carriers shuttle electrons, they actively pump hydrogen ions (proton) across the membrane setting up a gradietn of hydrogen ions-proton motive forceHow do hydrogen ions diffuse?-back through the ATP synthase complex causing it to rotate, causing a 3-D change resulting the production of ATPThe terminal step-oxygen accepts 2 electrons from the ETS and then picks up 2 hydrogen ions from the solution to form a molecule of water oxygen is the final electron acceptor -2H+ + 2e- + 1/2O2 --> H2OWhat part of aerobic respiration releases O2?-Krebs cycleAnaerobic respiration-functions like aerobic respiration except it utilizes oxygen containing ions, rather than free oxygen, as the final electron acceptor -Nitrate (NO3-)and nitrite (NO2-) -most obligate anaerobes use the H+ generated during glycolysis and the kreb's cycle to reduce some compound other than O2Amphibolic-many pathways of metabolism are bi-directionalPhotosynthesis-the earth's lifeline -the ultimate source of all the chemical energy in cells come from the sun -6CO2 + 6H2O -light-> C6H12O6 +6O2Ch. 9...Genetics-the study of heredityThe science of genetics explores:-transmission of biological traits from parent to offspring -expression and variation of those traits -structure and function of genetic material -how this material changesGenome-sum total of genetic material of a cell (chromosomes and mitochondria/chloroplasts and/or plasmids) -genome of cells -DNA -genome of viruses - DNA or RNAChromosomes-DNA complexes w/ protein constitutes the genetic materialMicrobial genomes-bacterial chromosomes are a single circular loop -eukaryotic chromosomes are multiple and linearGenes-the fundamental unit of heredity responsible for a given trait3 basic categories of genes:1. structural gene - genes that code for proteins 2. genes that code for RNA 3. regulatory genes - genes that control gene expressionGenotype-all types of genes constitute the genetic makeupPhenotype-the expression of the genotype creates observable traitsGenomes vary in size:-smallest virus - 4-5 genes -E coli - single chromosome containing 4,288 genes; 1mm; 1000x longer than cell -human cell - 46 chromosomes containing 31,000 genes; 6 ft.; 180,000x longer than cellDNA-2 strands twisted into a double helixNucleotide-basic unit of DNA structureEach nucleotide contains:-deoxyribose - a 5 carbon sugar -phosphate group -a nitrogenous base -adenine, guanine, thymine, and cytosineNucleotide covalently bond...-to form a sugar-phosphate backbone -each sugar attaches to 2 phosphate -5' carbon and -3 carbonDNA (description)-nitrogenous bases covalently bond to the 1' carbon of each sugar and span the center of the molecule to pair with an appropriate complementary base on the other strand -adenine binds to thymine with 2 hydrogen bonds -guanine binds to cytosine with 3 hydrogen bonds -antiparallel strands 3' to 5' and 5' to 3' -each strand provides a template for the exact copying of a new strand -order of base constitutes the DNA codeSignificance of DNA structure-maintenance of code during reproduction - constancy of base pairing guarantees that the code will be retained -providing variety - order of bases responsible for unique qualities of each organismsThe overal replication process:-replication occurs on both strands simultaneously -creates complementary strands -semiconservative replication processDNA Replication-make an exact duplicate of the DNA involved 30 different enzymes -begins at an origin of replication -helicase unwinds and unzips the DNA double helix -an RNA primer is synthesized at the origin of replication by Primase -DNA polymerase III adds nucleotides in a 5' to 3' direction -tbc...Leading strand-synthesized continuously in 5' to 3' directionLagging strand-synthesized 5' to 3' in short segments; overall direction is 3' to 5'DNA polymerase I-removes the RNA primers and replaces them with DNA -when replication forks meet, ligases link the DNA fragments along the lagging strand -separation of the daughter molecules is completeGyrase-supercoilingHelicase-unzipping the DNA helixPrimase-synthesizing as RNA primerDNA polymerase III-adding bases to the new DNA chain, proofreading the chain for mistakesLigase-final binding of nicks in DNA during synthesis and repairTranscription-information stored on the DNA molecule is conveyed to RNA molecules through the processTranslation-information contained in the RNA molecule is then used to produce proteins in the processGene-protein connection-each triplet of nucleotides on the RNA specifies a particular amino acid -a protein's primary structure determines its shape and function -proteins determine phenotype, living things are what their parents make them -DNA is mainly a blueprint that tells the cell which kinds of proteins to make and how to make themRNA-single-stranded molecule made of nucleotides -5 cardon sugar = ribose -4 nitrogenous base - adenine, uracil, guanine, cytosine -phosphateMessenger RNA (mRNA)-sequence of amino acids in protein -carries the DNA master code to the ribosome -it can be translated -carries DNA message through complementary copy; message is in triplets called codonsTransfer RNA (tRNA)-a cloverleaf tRNA to carry amino acids -brings amino acids to ribosome during translation -made from DNA; secondary structure creates loops; bottom loop exposes a triplet of nucleotides called anticodon which designates specificity and complements mRNA; carries specific amino acids to ribosomesRibosomal RNA (rRNA)-several large structural rRNA molecules -forms the major part of a ribosome and participates in protein synthesis -component of ribosomes where protein synthesis occursPrimer-an RNA that can begin DNA replication -primer DNATranscription: the 1st stage of gene expression-RNA polymerase binds to promoter region upstream of the gene -RNA polymerase adds nucleotides complementary to the complementary to the template strand of a segment of DNA in the 5' to 3' direction -uracil is placed as adenine's complement -at termination, RNA polymerase recognizes signals and releases the transcript -100-1200 bases longTranslation: the 2nd stage of gene expression-all elements needed to synthesize protein are brought together on the ribosomes -the process occurs in 5 stages: initiation, elongation, termination, and protein folding and processingThe master genetic code-represented by the mRNA codons and the amino acids they specify -code is universal among organisms -code is redundantInterpreting the DNA code-transcription produces on mRNA complementary to the DNA gene -during translation, tRNAs use their anticodon to interpret the mRNA codons and bring in the amino acidsTranslation-ribosomes assemble on the 5' end of an mRNA transcript -ribosome scans the mRNA until it reaches the start codon, usually AUG -a tRNA molecule with the complementary anticodon and methionine amino acid enters the P site of the ribosome and binds to the mRNA -a second tRNA with the complementary anticodon fills the A site -a peptide bond is formed b/w the amino acids on the neighboring tRNAs -the 1st tRNA is released and the ribosome slides down the next codon -another tRNA fills the A site and a peptide bond is formed -the process continues until a stop codon is reachedTermination codons-UAA, UAG, UGA = codons for which there is no corresponding tRNA -when this codon is reached, the ribosome falls off and the last tRNA is removed from the polypeptidePolyribosomal complex-allows for the synthesis of many protein molecules simultaneously from the same mRNA moleculeEukaryotic Transcription and Translation-do no occur simultaneously - transcription occurs in the nucleus and translation occurs in the cytoplasm -Eukaryotic start codon is AUG, but does not use formyl-methionine -Eukaryotic mRNA encodes a single protein, unlike bacterial mRNA which encodes many -Eukaryotic DNA contains introns, intervening sequences of noncoding DNA, which have to be spliced out of the final mRNA transcriptSplicing of Eukaryotic pre-mRNA-removal of introns and connections of exons -does not occur in prokaryotesRegulation of protein synthesis and metabolism-genes are regulated to be active only when their products are required -in prokaryotes this regulation is coordinated by operons, a set of genes, all of which are regulated as a single unitInducible-operon is turned on by substate: catabolic operons - enzymes needed to metabolize a nutrient are produced when neededRepressible-genes in a series are turned off by the product synthesized; anabolic operon - enzymes used to synthesize an amino acid stop being produced when they are not neededRegulator-gene that codes for repressorControl Locus-composed of promoter and operatorStructural Locus-made of 3 genes each coding for an enzyme need to catabolize lactose -B-galactosidase - hydrolyse lactose -permease - brings lactose across cell membrane -B-galactosidase transacetylase - uncertain functionLac Operon-normally off - in the absence of lactose, the repressor binds with the operator locus and blocks transcription of downstream structural genes -lactose turns the operon on by acting as the inducer -binding of lactose to the repressor protein changes its shape and causes it to fall off the operator. RNA polymerase can bind to the promoter. structural genes are transcribedArginine operon: repressible-normally on and will be turned off when the product of the pathway is no longer required -when excess arginine is present, it binds to the repressor and changes it. then the repressor binds to the operator and blocks arginine synthesis -arginine is the compressorMutation-a change in phenotype due to a change in genotype (nitrogen base sequence of DNA)Wild type (wild stain)-a natural, non-mutated characteristicsMutant Stain-an organism that has a mutation -showing variance in morphology, nutritional characteristics, genetic control mechanisms, resistance to chemicals, etc.Positive and Negative effects of mutation-mutations leading to nonfunctional proteins are harmful, possibly fatal -organisms w/ mutations that are beneficial in their environment can readily adapt, survive, and reproduce - these mutations are the basis of change in populations -any changes that confers are advantage during selection pressure will be retained by the populationGenetic recombination-occurs when an organism acquires and expresses genes that originated in another organism3 means for genetic recombination in bacteria:1. conjugation 2. transformation 3. transductionConjugation-transfer of a plasmid of chromosomal fragments from a donor cell to a recipient cell via a direct connectionTransformation-chromosome fragments from a lysed cell are accepted by a recipient cell; the genetic code of the DNA fragments is acquired by the recipient -donor and recipient cells can be unrelated -useful tool in recombinant DNA technologyTransduction-bacteriophage serves as a carrier of DNA from a donor cell to a recipient cell