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UGA / Microbiology / MIBO 2500 / What are the microorganisms found in the intestinal gut?

What are the microorganisms found in the intestinal gut?

What are the microorganisms found in the intestinal gut?

Description

School: University of Georgia
Department: Microbiology
Course: Micro Health Care
Term: Fall 2015
Tags:
Cost: 25
Name: MIBO 2500, Weeks 1-5 Notes
Description: These notes cover Chapter 1, 2, 3, 4, 5, 6, 7, 10 & 11 of the textbook Nester's Microbiology: A Human Perspective
Uploaded: 02/08/2017
24 Pages 164 Views 0 Unlocks
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MBIO 2500 Mini exam 1 1/9 CHAPTER 2 • Makeup of a Protein -ribosomes** -primary structure: single chain of amino acids connected by peptide bonds -secondary: arranged according to hydrogen bonds between side chains of amino  acids -tertiary: definitive 3D shape -quaternary: includes more than one unit of protein structure held by hydrogen  bonds; “functional form” -dehydration synthesis -if this protein functioned inside the cell, which areas would be hydrophobic and  which areas would be hydrophilic? (slide) -middle of protein = hydrophobic -long skinny chains = hydrophilic -giant “chaperone” proteins engulf parts of other proteins and give them the proper  env’t to fold properly -“unfolding” = denaturation; when protein shape is changed by broken bonds -effected by: high temperature, high or low pH, certain solvents -when you unfold, you unfold from the quaternary structure -when a protein denatures, what type of bonds are broken? -hydrogen bonds (weak bonds) -peptide bonds connect amino acids together • Carbohydrates -energy sources, carry high-energy bonds, food sources (lactose, sucrose) -disaccharides -component of DNA and RNA: monosaccharides – ribose, deoxiribose • Nucleic Acids -nucleotides -carry chemical energy (ATP) -part of enzymes -act as signaling molecule – cyclic AMP -don’t memorize structure, but know 3 parts of nucleotides (phosphate group,  deoxyribose, nucleobase) CHAPTER 3-magnification (enlarged image) vs. resolution (ability to distinguish between small  objects close together) -resolution: resolving power of light microscope 200 nm • Light Microscopy -different ways of distributing the light through specimen ???? -bright field: requires dye or stain -phase contrast -dark-field: specimen only shown, no background -fluorescence: specimen is stained with fluorescent dye; expose specimen to UV,  violent, or blue light then emits bright blue, orange, green or red • Electron Microscopy -light is replaced by a beam of electrons from tungsten filament in electron gun -Transmission Electron Microscopy (TEM) -observe fine cell structure -sectioning/slicing, freeze fractures, cryo-electron microscopy -Scanning Electron (SEM) -observe surface details -coat sample with metal, then simply look at surface -Why would scientists want to see the shape and structure of cells and their  components? What type of clues or answers can be identified by electron  microscopy? -helps you understand function, structure = function -be able to tell difference between TEM and SEM by picture** • Atomic Force Microscopes -greater resolving power than electron -laser beam -which type of bacterial cell would an antibiotic be able to easily penetrate, gram  negative or gram positive? why? -gram positive is on the right because it has peptoglycan -gram neg has the outer membrane 1/18 CHAPTER 3 (cont) • Internal structures 1. cytoplasm -cell pool for all biosynthetic functions -mixture of sugars, amino acids, salts -70-80% water -packed with enzymes 2. Chromosome-irregular mass in nucleoid region -nucleoid region towards center of cell -compact but not defined area -single circular DNA -supercoiled -smaller pieces of circular DNA called plasmids 3. Plasmids -smaller circular DNA outside chromosome -contains “not necessary” genes -also super coiled elements, “twisted” -provide survivability -plasmids vs chromosomes -jason’s first step: look for the chromosome -find the gene for the toxin by reading chromosome (sequencing methods) -identify encoded gene sequence -sequence plasmid gene first, but if toxin is not there, -he looks through chromosome genes 4. Ribosomes -sites of protein synthesis -thousands per cell -free in cytoplasm or tethered to membrane -rRNA and protein -dif in proks and euks ribosome allows antibiotic targeting** 5. Endospores -for surviving environmental extremes (heat, drying, radiation, pH extremes) -rock environments, aquatic, mud, deserts -not all bacteria form endospores* -very low water content -can survive years -germination can occur to allow cell to begin growing again -sporulation: bacterial differentiation  -anthrax is a spore former • Bacteria in Resting State -endospore formers -commonly found in soil -anthrax scare after 9/11 -streptomyces -look like fungi -commonly found in soil -bottom picture is phase contrast -top picture is SEMCHAPTER 4 – dynamics of prokaryotic growth • Microbial Growth -defined as an increase in number -making a second copy of chromosome -achieved by binary fission -generation or doubling time -calculation* 10 cells = 0 20 = 20 min 40 = 40 min 80 = 60 min (1 hr) • Bacterial Growth in Nature -growth in nature may differ from that in lab -biofilms: community of microbes -established by planktonic cells and a slime layer to create a strategic system  of cellular signaling and nutrient distribution  -examples of locations: teeth, sinks, rocks in streams • Biofilm problems and solutions -65% human infections involve biofilms -often resistant to antibiotic  • Obtaining a pure culture -trying to isolate things from nature -pure culture: descended from one cell slide 24 on chapter 4 – zombie cells; eating dead cell debris to survive (blue lines); surviving 1% of population Mini exam 2 1/23 continue CHAPTER 4 • At what stage(s) would cells exist in a colony on a petri plate? -as the cell starts binary fission, the nutrient is consumed -more cells continue to grow out -all nutrient is used up in the medium -outside edge of colony = log/exponential phase, because more nutrients is  available on the plate -death, stationary (in middle of plate), log (outside ring of plate) -what conditions would you maintain to grow the bacteria? • Environmental factors for growth• (1) temperature* -psychrophiles: artic regions ???? there is a “range” where they can survive, but  top of loop is where they survive best -psychrotrophs: refrigerator ???? bacteria that can grow in fridge conditions (range is much larger) -mesophiles: soil, human body ???? all pathogens -thermophiles: ideal temp is 65 ???? compost piles -hyperthermophiles: thrive best at higher temps near boiling point ???? hydrothermal vents, archaea organisms  -basically can find microorganisms everywhere in the world -methanogen: microorganism in intestinal gut -makes/emits methane gas by using CO2 -can measure on your breath -higher level of methane gas production in those who suffer from irritable  bowel syndrome (ibs) -cause and effect? -how do antibiotics alter our gut? -affects infants more than adults • (2) oxygen requirements -superoxide dismutase and catalase -some orgs have enzymes that can deactivate these radicals, some don’t -obligate aerobes: must have O2 -microaerophiles: require small amount of O2 -facultative anaerobes: grow better if O2 is present; grow slower without oxygen -can switch -aerotolerant anaerobes: O2 doesn’t harm or help -obligate anaerobes: O2 harms, toxic • Oxygen use/Tolerance Groups -O2 levels are higher at top of medium -less and less O2 as you move down medium -red brackets show where growth is indicated 1=obligate aerobe 2=facultative anaerobe 3=aerotolerant anaerobe 4=obligate anaerobe  microaerophiles: grow a little below the surface of the medium, no higher, no lower 1/25 cont CHAPTER 4• Water Availability -water -hypertonic environment may cause plasmolysis -moderate halophiles: marine env’t; requires 3% salt -halotolerant/osmotolerant: skin surface; as much as 10% salt -extreme halophiles: dead sea; requires 9% or more • You want to identify the methanogens present in a human intestine. describe the new species using cardinal terms according to: temperature, oxygen  requirement, and water availability (halophilic?) -anaerobic or mesophilic intestinal tract -would not be halophilic -can be found in intestine: -anaerobes -facaltative anaerobes (e coli) -aerotolerant • Bacterial Nutrition: required elements -(1)carbon source: -autotrophs use CO2 to make carbon products for cell; rip carbon off two  oxygen molecules -heterotrophs break down organic carbon to make carbon products – simple  sugars such as glucose -(2)growth factors: -some bacteria make all of their own amino acids, vitamins, purines,  pyrimindines -others require them from the environment; fastidious (doesn’t synthesize  things on its own) -(3)energy source: -phototrophs capture energy from sunlight; cyanobacteria, purple & green  sulfur bacteria -chemotrophs use organic or inorganic molecules for energy; organic – glucose, inorganic – other stuff CHAPTER 6 • Chemoheterotroph -what is the carbon and energy source? -carbon from organic materials  -energy from chemicals (inorganic or organic) -what is the purpose of metabolism? creating energy to for cells to run on; energy  AND carbon-overall chemical reactions that provides the energy and basic components for the  cellular reactions and growth -when a coenzyme accepts an electron, it becomes reduced. -oxidized (lose an electron)? reduced? • Metabolic pathway components for chemoheterotroph -enzymes -ATP -electron carriers -chemical energy source -precursor metabolites: compound that hasn’t quite been made into a lipid or an  amino acid, etc. • Glycolysis -most pathogens 1/30 • Pentose Phosphate Pathway -main purpose is to take organic material and form compounds to make into  nucleotides -main purpose is to produce precursor metabolites and electron carriers (reducing  power) -if it needs more nucleotides, would use this pathway more than glycolysis -pyruvate to transition step -transition step = key step; use giant enzyme -pyruvate is converted into acetoCoA • what is the purpose of glycolysis? -get pyruvate, ATP, NADH (electron carrier) made through this pathway -produces energy • what is the purpose of pentose phosphate pathway? -no ATP, not needed for energy -needed for precursor metabolites, makes NADH -feed glycolysis if the cell needs it • TCA cycle (krebs) -uses acetyl coA to continue reactions in cycle -makes little ATP -makes NADH and FADH2 as electron carriers -makes lots of precursor metabolites • do all 3 make ATP? -pentose phosphate does not (bc not an energy generating pathway)-only 6 or 8 ATP made at this point (aka not energy heavy) -which make electron carriers (reducing power)? -all three -which make precursor metabolites -all three • Respiration -NAD is oxidized  -protons get pumped out of cytoplasmic membrane -youtube link -use protons to run flagella  -oxidized electron carriers go back to pick up more electrons (makes energy) • Metabolism ????catabolism -glycolysis -pp -tca -respiration (ETS and ATP synthase): goal is to just make ATP ????anabolism -uses precursor metabolites from catabolism for anabolism -lipids, amino acids, nucleotides 2/1/17 • Where do the electron carriers go? -NADH and FADH2 must drop off their electrons in order to return to glycolysis and  TCA cycle -drops off electrons to electron transport system/chain -cytoplasmic membrane (ETS) -ETS has a series of imbedded enzymes -oxidizes -where did NADH get the electron from? -electron carriers get reduced in glycolysis/TCA -pass electron along to other enzymes -reduced then oxidized -starts pushing up protons from cytoplasm to outside cytoplasmic membrane -video on ELC** -proton mode of force: gradient alone has chemical kinetic energy -proton gradient: more of one substrate on one side of membrane than on the other  side -oxygen picks up electrons at end of ETS -aerobic orgs use oxygen, facultative anaerobes, microaerophiles also-uses electrons to form water at the end -adp + phosphate = atp -ets + atp = respiration -electron carriers after they drop off electrons, they can go back to glycolysis, tca,  etc. and get another and it starts again -electron acceptor for respiration -aerobic: o2 accepts the electron at the end -oxidative phosphorylation makes more ATP  • Aerobic chemoheterotrophs???? -obligate aerobe: must run electron transport chain with O2 accepting electrons -facultative anaerobe: runs ets with O2 or can use another compound like nitrate (i.e. e coli) -also doesn’t have to run ETS at all (some organisms like e coli doesn’t even  have to run respiration to survive) • Anaerobic respiration???? -use other terminal electron acceptors -methanogens (co2 as electron acceptor): in your gut • Fermentation (cell chooses whether or not to use electron transport chain): -to maintain ATP synthesis from glycolysis -not all bacteria can ferment -another place for reducing power to drop off electrons -some don’t need ets • what happens if respiration cannot occur? -electron carriers cannot drop off electrons and return to catabolic reactions -its going to take the electrons to pyruvate (fermentation reaction) -pyruvate????lactate????lactic acid -we can force cells to ferment by removing o2—how we get waste products for  cheese, yogurt, alcohol -waste product=ethanol -without oxygen, happens slower for exam: CH 4 temperature o2 think of a scenario for ?phibrio (no oxygen available, so anaerobe): what do you  think the temperature? psychotrophicsoil=misophilic catalase & dismutase  nitrogen & phosphorus (cell has to have) this org uses co2 as carbon source, and uses chemical agents as energy, what would  it be? chemoautotroph ** scenario  chemoheterotroph = surviving from eating dead cells CH 6 metabolism—precursor metabolites are connecting part between catabolism and  anabolism group activity for b d. not covered in class – enzyme regulation, what enzymes do, how they can be  slowed down or sped up, competitive and noncompetitive inhibition j is group activity k precursor metabolites 2/3 Chapter 7 replication: process that is independent than the other two parts transcription: can start without replication (independent function from replication) translation: cannot translate until transcription happens • Replication -when cell grows and divide in log and stationary, copy of chromosome to give to  two daughter cells -origin: “starting block” of replication -dna polymerase adds floating nucleotides from cytoplasm -attaches to double stranded dna -5’ to 3’ direction -primer (made of rna) helps polymerase begin new dna strand -dna polyermase cant pull apart double stranded dna on its own -uses helicase (pulls open double stranded dna) and dna gyrase (scissors; releasing stress of dna/untwist/glues it back together ahead of helicase;  helps prevent breakage) -dna polymerase continuously adding nucleotides to one end -always adding 5’ to 3’ 2/6 -DNA polymerase -okazaki fragment -leading and lagging strand -helicase• Transcription: making mrna  -RNA: synthesized from minus strand (on bottom); almost identical to plus strand -initiation???? promoter recognized by RNA polymerase and sigma factor -elongation???? synthesis in the 5 to 3 direction -termination???? terminator and hairpin loop • Translation: making proteins -initiation -elongation -termination -prokaryotes can do transcription and translation simultaneously  -why? eukaryotes have a nucleus

Replication Transcription Start site -origin of replication -promoter site Direction of synthesis

Enzymes involved

Resulting strand


-when a protein denatures, what type of bonds are broken?



We also discuss several other topics like phys1056

2/8 Chapter 7 continued -promoter: start of transcription -accessory protein called sigma factor -sigma factor drops off and promoter starts -then elongation can begin -gets to termination site -the mrna creates a loop structure to bump polymerase off since its done -regulation: cell regulates itself when and when not to transcribe -mrna like a pizza -promoter tells rna polymerase which way to start transcription (5 to 3) -rna polymerase picks up the (template) strand that runs 3’ to 5’ -gene regulation -cell doesn’t want to use all proteins at the same time -regulate by inhibition  answer to question: to have a more efficient, energy saving method to respond to  the env’t Genome (genetic info) ???? transcription (mrna) ???? translation (proteins) ???? enzymes  ???? (inhibit/feedback) slow down or speed up metabolism • Types of regulation -constitutive (transcription always on): glycolysis  -repressible (transcription turn off): amino acids -inducible (transcription turn on when needed): lactose -inducer is a protein or component that helps start transcription  -DNA binding proteins: prevents/allows rna polymerase transcription -inducer allows transcription; it can bind to the repressor and prevent it from  binding to the operator; then it binds to promoter to transcribe -repressor binds to operator to stop transcription; encoded by a separate gene • Increasing transcription -enhanced by an activator; sometimes requires an inducer to bind to operon -activator binding site in front of promoter -activator binds to this site ^ -activator helps speed up process -lactose can act as an inducer when glucose is present KEY TERMS -sigma factor -rna polymerase -promoter -inducer -repressor -activator -operon: segment of dna that contains the promoter and can have genes; includes  operator, promoter and several genes in a row (bacterial cells, not human genes  have this) -transcribes all genes at once (polysystronic)  -transcribing one gene at a time (monosystronic)  -operator -genesMBIO 2500 Mini exam 1 1/9 CHAPTER 2 • Makeup of a Protein -ribosomes** -primary structure: single chain of amino acids connected by peptide bonds -secondary: arranged according to hydrogen bonds between side chains of amino  acids -tertiary: definitive 3D shape -quaternary: includes more than one unit of protein structure held by hydrogen  bonds; “functional form” -dehydration synthesis -if this protein functioned inside the cell, which areas would be hydrophobic and  which areas would be hydrophilic? (slide) -middle of protein = hydrophobic -long skinny chains = hydrophilic -giant “chaperone” proteins engulf parts of other proteins and give them the proper  env’t to fold properly -“unfolding” = denaturation; when protein shape is changed by broken bonds -effected by: high temperature, high or low pH, certain solvents -when you unfold, you unfold from the quaternary structure -when a protein denatures, what type of bonds are broken? -hydrogen bonds (weak bonds) -peptide bonds connect amino acids together • Carbohydrates -energy sources, carry high-energy bonds, food sources (lactose, sucrose) -disaccharides -component of DNA and RNA: monosaccharides – ribose, deoxiribose • Nucleic Acids -nucleotides -carry chemical energy (ATP) -part of enzymes -act as signaling molecule – cyclic AMP -don’t memorize structure, but know 3 parts of nucleotides (phosphate group,  deoxyribose, nucleobase) CHAPTER 3-magnification (enlarged image) vs. resolution (ability to distinguish between small  objects close together) -resolution: resolving power of light microscope 200 nm • Light Microscopy -different ways of distributing the light through specimen ???? -bright field: requires dye or stain -phase contrast -dark-field: specimen only shown, no background -fluorescence: specimen is stained with fluorescent dye; expose specimen to UV,  violent, or blue light then emits bright blue, orange, green or red • Electron Microscopy -light is replaced by a beam of electrons from tungsten filament in electron gun -Transmission Electron Microscopy (TEM) -observe fine cell structure -sectioning/slicing, freeze fractures, cryo-electron microscopy -Scanning Electron (SEM) -observe surface details -coat sample with metal, then simply look at surface -Why would scientists want to see the shape and structure of cells and their  components? What type of clues or answers can be identified by electron  microscopy? -helps you understand function, structure = function -be able to tell difference between TEM and SEM by picture** • Atomic Force Microscopes -greater resolving power than electron -laser beam -which type of bacterial cell would an antibiotic be able to easily penetrate, gram  negative or gram positive? why? -gram positive is on the right because it has peptoglycan -gram neg has the outer membrane 1/18 CHAPTER 3 (cont) • Internal structures 1. cytoplasm -cell pool for all biosynthetic functions -mixture of sugars, amino acids, salts -70-80% water -packed with enzymes 2. Chromosome-irregular mass in nucleoid region -nucleoid region towards center of cell -compact but not defined area -single circular DNA -supercoiled -smaller pieces of circular DNA called plasmids 3. Plasmids -smaller circular DNA outside chromosome -contains “not necessary” genes -also super coiled elements, “twisted” -provide survivability -plasmids vs chromosomes -jason’s first step: look for the chromosome -find the gene for the toxin by reading chromosome (sequencing methods) -identify encoded gene sequence -sequence plasmid gene first, but if toxin is not there, -he looks through chromosome genes 4. Ribosomes -sites of protein synthesis -thousands per cell -free in cytoplasm or tethered to membrane -rRNA and protein -dif in proks and euks ribosome allows antibiotic targeting** 5. Endospores -for surviving environmental extremes (heat, drying, radiation, pH extremes) -rock environments, aquatic, mud, deserts -not all bacteria form endospores* -very low water content -can survive years -germination can occur to allow cell to begin growing again -sporulation: bacterial differentiation  -anthrax is a spore former • Bacteria in Resting State -endospore formers -commonly found in soil -anthrax scare after 9/11 -streptomyces -look like fungi -commonly found in soil -bottom picture is phase contrast -top picture is SEMCHAPTER 4 – dynamics of prokaryotic growth • Microbial Growth -defined as an increase in number -making a second copy of chromosome -achieved by binary fission -generation or doubling time -calculation* 10 cells = 0 20 = 20 min 40 = 40 min 80 = 60 min (1 hr) • Bacterial Growth in Nature -growth in nature may differ from that in lab -biofilms: community of microbes -established by planktonic cells and a slime layer to create a strategic system  of cellular signaling and nutrient distribution  -examples of locations: teeth, sinks, rocks in streams • Biofilm problems and solutions -65% human infections involve biofilms -often resistant to antibiotic  • Obtaining a pure culture -trying to isolate things from nature -pure culture: descended from one cell slide 24 on chapter 4 – zombie cells; eating dead cell debris to survive (blue lines); surviving 1% of population Mini exam 2 1/23 continue CHAPTER 4 • At what stage(s) would cells exist in a colony on a petri plate? -as the cell starts binary fission, the nutrient is consumed -more cells continue to grow out -all nutrient is used up in the medium -outside edge of colony = log/exponential phase, because more nutrients is  available on the plate -death, stationary (in middle of plate), log (outside ring of plate) -what conditions would you maintain to grow the bacteria? • Environmental factors for growth• (1) temperature* -psychrophiles: artic regions ???? there is a “range” where they can survive, but  top of loop is where they survive best -psychrotrophs: refrigerator ???? bacteria that can grow in fridge conditions (range is much larger) -mesophiles: soil, human body ???? all pathogens -thermophiles: ideal temp is 65 ???? compost piles -hyperthermophiles: thrive best at higher temps near boiling point ???? hydrothermal vents, archaea organisms  -basically can find microorganisms everywhere in the world -methanogen: microorganism in intestinal gut -makes/emits methane gas by using CO2 -can measure on your breath -higher level of methane gas production in those who suffer from irritable  bowel syndrome (ibs) -cause and effect? -how do antibiotics alter our gut? -affects infants more than adults • (2) oxygen requirements -superoxide dismutase and catalase -some orgs have enzymes that can deactivate these radicals, some don’t -obligate aerobes: must have O2 -microaerophiles: require small amount of O2 -facultative anaerobes: grow better if O2 is present; grow slower without oxygen -can switch -aerotolerant anaerobes: O2 doesn’t harm or help -obligate anaerobes: O2 harms, toxic • Oxygen use/Tolerance Groups -O2 levels are higher at top of medium -less and less O2 as you move down medium -red brackets show where growth is indicated 1=obligate aerobe 2=facultative anaerobe 3=aerotolerant anaerobe 4=obligate anaerobe  microaerophiles: grow a little below the surface of the medium, no higher, no lower 1/25 cont CHAPTER 4• Water Availability -water -hypertonic environment may cause plasmolysis -moderate halophiles: marine env’t; requires 3% salt -halotolerant/osmotolerant: skin surface; as much as 10% salt -extreme halophiles: dead sea; requires 9% or more • You want to identify the methanogens present in a human intestine. describe the new species using cardinal terms according to: temperature, oxygen  requirement, and water availability (halophilic?) -anaerobic or mesophilic intestinal tract -would not be halophilic -can be found in intestine: -anaerobes -facaltative anaerobes (e coli) -aerotolerant • Bacterial Nutrition: required elements -(1)carbon source: -autotrophs use CO2 to make carbon products for cell; rip carbon off two  oxygen molecules -heterotrophs break down organic carbon to make carbon products – simple  sugars such as glucose -(2)growth factors: -some bacteria make all of their own amino acids, vitamins, purines,  pyrimindines -others require them from the environment; fastidious (doesn’t synthesize  things on its own) -(3)energy source: -phototrophs capture energy from sunlight; cyanobacteria, purple & green  sulfur bacteria -chemotrophs use organic or inorganic molecules for energy; organic – glucose, inorganic – other stuff CHAPTER 6 • Chemoheterotroph -what is the carbon and energy source? -carbon from organic materials  -energy from chemicals (inorganic or organic) -what is the purpose of metabolism? creating energy to for cells to run on; energy  AND carbon-overall chemical reactions that provides the energy and basic components for the  cellular reactions and growth -when a coenzyme accepts an electron, it becomes reduced. -oxidized (lose an electron)? reduced? • Metabolic pathway components for chemoheterotroph -enzymes -ATP -electron carriers -chemical energy source -precursor metabolites: compound that hasn’t quite been made into a lipid or an  amino acid, etc. • Glycolysis -most pathogens 1/30 • Pentose Phosphate Pathway -main purpose is to take organic material and form compounds to make into  nucleotides -main purpose is to produce precursor metabolites and electron carriers (reducing  power) -if it needs more nucleotides, would use this pathway more than glycolysis -pyruvate to transition step -transition step = key step; use giant enzyme -pyruvate is converted into acetoCoA • what is the purpose of glycolysis? -get pyruvate, ATP, NADH (electron carrier) made through this pathway -produces energy • what is the purpose of pentose phosphate pathway? -no ATP, not needed for energy -needed for precursor metabolites, makes NADH -feed glycolysis if the cell needs it • TCA cycle (krebs) -uses acetyl coA to continue reactions in cycle -makes little ATP -makes NADH and FADH2 as electron carriers -makes lots of precursor metabolites • do all 3 make ATP? -pentose phosphate does not (bc not an energy generating pathway)-only 6 or 8 ATP made at this point (aka not energy heavy) -which make electron carriers (reducing power)? -all three -which make precursor metabolites -all three • Respiration -NAD is oxidized  -protons get pumped out of cytoplasmic membrane -youtube link -use protons to run flagella  -oxidized electron carriers go back to pick up more electrons (makes energy) • Metabolism ????catabolism -glycolysis -pp -tca -respiration (ETS and ATP synthase): goal is to just make ATP ????anabolism -uses precursor metabolites from catabolism for anabolism -lipids, amino acids, nucleotides 2/1/17 • Where do the electron carriers go? -NADH and FADH2 must drop off their electrons in order to return to glycolysis and  TCA cycle -drops off electrons to electron transport system/chain -cytoplasmic membrane (ETS) -ETS has a series of imbedded enzymes -oxidizes -where did NADH get the electron from? -electron carriers get reduced in glycolysis/TCA -pass electron along to other enzymes -reduced then oxidized -starts pushing up protons from cytoplasm to outside cytoplasmic membrane -video on ELC** -proton mode of force: gradient alone has chemical kinetic energy -proton gradient: more of one substrate on one side of membrane than on the other  side -oxygen picks up electrons at end of ETS -aerobic orgs use oxygen, facultative anaerobes, microaerophiles also-uses electrons to form water at the end -adp + phosphate = atp -ets + atp = respiration -electron carriers after they drop off electrons, they can go back to glycolysis, tca,  etc. and get another and it starts again -electron acceptor for respiration -aerobic: o2 accepts the electron at the end -oxidative phosphorylation makes more ATP  • Aerobic chemoheterotrophs???? -obligate aerobe: must run electron transport chain with O2 accepting electrons -facultative anaerobe: runs ets with O2 or can use another compound like nitrate (i.e. e coli) -also doesn’t have to run ETS at all (some organisms like e coli doesn’t even  have to run respiration to survive) • Anaerobic respiration???? -use other terminal electron acceptors -methanogens (co2 as electron acceptor): in your gut • Fermentation (cell chooses whether or not to use electron transport chain): -to maintain ATP synthesis from glycolysis -not all bacteria can ferment -another place for reducing power to drop off electrons -some don’t need ets • what happens if respiration cannot occur? -electron carriers cannot drop off electrons and return to catabolic reactions -its going to take the electrons to pyruvate (fermentation reaction) -pyruvate????lactate????lactic acid -we can force cells to ferment by removing o2—how we get waste products for  cheese, yogurt, alcohol -waste product=ethanol -without oxygen, happens slower for exam: CH 4 temperature o2 think of a scenario for ?phibrio (no oxygen available, so anaerobe): what do you  think the temperature? psychotrophicsoil=misophilic catalase & dismutase  nitrogen & phosphorus (cell has to have) this org uses co2 as carbon source, and uses chemical agents as energy, what would  it be? chemoautotroph ** scenario  chemoheterotroph = surviving from eating dead cells CH 6 metabolism—precursor metabolites are connecting part between catabolism and  anabolism group activity for b d. not covered in class – enzyme regulation, what enzymes do, how they can be  slowed down or sped up, competitive and noncompetitive inhibition j is group activity k precursor metabolites 2/3 Chapter 7 replication: process that is independent than the other two parts transcription: can start without replication (independent function from replication) translation: cannot translate until transcription happens • Replication -when cell grows and divide in log and stationary, copy of chromosome to give to  two daughter cells -origin: “starting block” of replication -dna polymerase adds floating nucleotides from cytoplasm -attaches to double stranded dna -5’ to 3’ direction -primer (made of rna) helps polymerase begin new dna strand -dna polyermase cant pull apart double stranded dna on its own -uses helicase (pulls open double stranded dna) and dna gyrase (scissors; releasing stress of dna/untwist/glues it back together ahead of helicase;  helps prevent breakage) -dna polymerase continuously adding nucleotides to one end -always adding 5’ to 3’ 2/6 -DNA polymerase -okazaki fragment -leading and lagging strand -helicase• Transcription: making mrna  -RNA: synthesized from minus strand (on bottom); almost identical to plus strand -initiation???? promoter recognized by RNA polymerase and sigma factor -elongation???? synthesis in the 5 to 3 direction -termination???? terminator and hairpin loop • Translation: making proteins -initiation -elongation -termination -prokaryotes can do transcription and translation simultaneously  -why? eukaryotes have a nucleus

Replication Transcription Start site -origin of replication -promoter site Direction of synthesis

Enzymes involved

Resulting strand


What type of clues or answers can be identified by electron microscopy?




-Why would scientists want to see the shape and structure of cells and their components?



We also discuss several other topics like pragmatic resource conservation definition
We also discuss several other topics like a contra account is an account that is linked with another
We also discuss several other topics like econ 1120 cornell
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2/8 Chapter 7 continued -promoter: start of transcription -accessory protein called sigma factor -sigma factor drops off and promoter starts -then elongation can begin -gets to termination site -the mrna creates a loop structure to bump polymerase off since its done -regulation: cell regulates itself when and when not to transcribe -mrna like a pizza -promoter tells rna polymerase which way to start transcription (5 to 3) -rna polymerase picks up the (template) strand that runs 3’ to 5’ -gene regulation -cell doesn’t want to use all proteins at the same time -regulate by inhibition  answer to question: to have a more efficient, energy saving method to respond to  the env’t Genome (genetic info) ???? transcription (mrna) ???? translation (proteins) ???? enzymes  ???? (inhibit/feedback) slow down or speed up metabolism • Types of regulation -constitutive (transcription always on): glycolysis  -repressible (transcription turn off): amino acids -inducible (transcription turn on when needed): lactose -inducer is a protein or component that helps start transcription  -DNA binding proteins: prevents/allows rna polymerase transcription -inducer allows transcription; it can bind to the repressor and prevent it from  binding to the operator; then it binds to promoter to transcribe -repressor binds to operator to stop transcription; encoded by a separate gene • Increasing transcription -enhanced by an activator; sometimes requires an inducer to bind to operon -activator binding site in front of promoter -activator binds to this site ^ -activator helps speed up process -lactose can act as an inducer when glucose is present KEY TERMS -sigma factor -rna polymerase -promoter -inducer -repressor -activator -operon: segment of dna that contains the promoter and can have genes; includes  operator, promoter and several genes in a row (bacterial cells, not human genes  have this) -transcribes all genes at once (polysystronic)  -transcribing one gene at a time (monosystronic)  -operator -genes
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