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188 Cards in this Set
- Front
- Back
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metabolism
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the sum of biochemical reactions within the cells of an organism
= anabolic (synthetic) + catabolic (degradative) |
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catabolism
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biochemical reaction that breaks down molecules and releases energy (exergonic)
when the substrate breaks into products (degradative) |
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synthetic
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a biochemical reaction that synthesizes molecules and uses energy (endergonic)
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anabolism
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a biochemical reaction that synthesizes molecule and uses energy (endergonic)
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precursor metabolites
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often produces in catabolic reactions, are used to synthesize all other organic compounds
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reduction
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reactions in which electrons are added
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oxidation
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reactions in which electrons are lost
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dehydrogenation
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reactions in which electron are lost (or reduced) -- specific to hydrogen atoms
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oxidation-reduction (redox) reactions
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oxidation and reduction always occur in pairs
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three important electron carrier molecules
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NAD+, NADP+, FAD
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phosphorylation
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the addition of phosphate to a molecule
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OIL RIG
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oxidation involves loss; reduction involves gain
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substrate-level phosphorylation
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involves the transfer of phosphate from a phosphorylated organic compound to ADP
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oxidative phosphorylation
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in which energy from redox reactions of respiration is used to attach inorganic phosphate to ADP
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photophosphorylation
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in which light energy is used to phosphorylate ADP with inorganic phosphate
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catalyst
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chemicals that increase the likelihood of a reaction but are not permanently changes in the process. reusable.
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enzymes
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organic catalysts -- they lower the activation energy. cannot make a reaction happen -- usually a protein.
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substrate
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the molecule the enzyme acts upon
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enzymes + substrate
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enzyme/substrate complex
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activation energy
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the amount of energy needed to trigger a chemical reaction
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glycolysis
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involves splitting a 6-carbon glucose molecule into two 3-carbon sugar molecules. occurs in the cytosol. happens in 3 stages -- 10 step process that results in 2 molecules of pyruvic acid and a net gain of 2 ATP and 2 NADH
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anabolic (synthetic) + catabolic (degradative)
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metabolism
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nucleotide
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it is an organic compound made up of nitrogenous base, a sugar, and a phosphate group
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substrate-level phosphorylation
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the process of moving a phosphate from metabolic products to ADP to form ATP
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What molecule is fed directly into the energy conservation stage of glycolysis?
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glyceraldehyde 3-phosphate (G3P)
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What is the fate of dihydroxyacetone phosphate (DHAP) in glycolysis?
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converted to glyceraldehyde 3-phosphate (G3P)
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What products remain after glycolysis occurs from a single molecule of glucose?
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2 ATP, 2 NADH, 2 pyruvic acid molecules
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NADH is converted to ATP in a process known as...
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oxidative phosphorylation
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1 NADH = ? ATP
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3
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1 FADH2 = ? ATP
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2
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1 molecule of pyruvic acid = ? molecules of ATP
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15
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glycolysis = ? ATP
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8
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2 pyruvic acid molecules = ? ATP
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30
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organic compounds
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molecules that contain both carbon and hydrogen atoms
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inorganic compound
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molecule lacking carbon
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metabolome
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sum total of all reactions
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ATP + H2O + CO2 = ?
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carbohydrate, i.e. Glucose -- glucose is then synthesized into starch and stored
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ethanol
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convert starch from corn into alcohol and CO2 -- C2H5OH
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cellulose
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material in plant cell wall
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cellulosic ethanol
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ethanol produced from cellulose -- alternative to deriving cellulose from corn (drives price of corn up if there is a shortage of corn)
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Brazil's approach to carbon natural fuel
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take sucrose from sugar cane to make ethanol with raising the price of sugar
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key intermediate metabolism
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pyruvic acid
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overproduction of Acetyl Coenzyme A
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if too much is made, then this is stored in the form of fatty acids or fat
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how to get rid of pyruvic acid
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oxidative phosphorylation in the presence of oxygen -- fermentation without oxygen
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cellular respiration
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metabolic process that involves the complete oxidation of substrate molecules and the production of ATP following a series of redox reactions
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electron transport chain
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a series of redox reactions that pass electrons from one membrane-bound carrier to another and to a final electron acceptor -- energy from these electrons is used to pump protons across membrane
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4 classes of carrier molecules in the electron transport chain
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flavoproteins, ubiquinones, metal-containing proteins, and cytochromes
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chemiosmosis
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ions flow down electrochemical gradient across a membrane through ATP synthase (ATPase) to synthesize ATP
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proton gradient
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an electrochemical gradient of hydrogen ions across a membrane -- has proton motive force (potential energy)
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fermentation
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partial oxidation of sugar to release energy using a cellular organic molecule rather than an electron transport chain as the final acceptor
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end-products of fermentation
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acids, alcohols and gases
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acetaldehyde
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accumulation causes hangover -- body has to convert acetaldehyde into CO2
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Pasteur's definition for fermentation
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life without air
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Actual definition for fermentation
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the pathway in which the terminal hydrogen receptor is an organic molecule -- i.e. acetaldehyde
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lactic acid makes: ??
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yogurt, soy sauce, butter, cheese, milk and sour cream
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Pasteur effect
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shows that aerating yeasted broth causes yeast cell growth to increase, while conversely, fermentation rate decreases the rate of growth bc there is little ATP produced (2) and a lot of glucose is consumed
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CO2 and propionic acid makes: ??
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swiss cheese
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CO2 and ethanol makes: ??
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wine and beer
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acetone and isopropanol makes: ??
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nail polish remover and rubbing alcohol
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acetic acid
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vinegar, pyruvate -> ethanol -> acetic acid , (organism = gluconobactoer, acetobactor)
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lactic acid
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glucose molecule is split into 2 molecules of pyruvate -> reduction of pyruvate (organism = streptococcus, lactobacillus)
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fermentation end-products
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get organic molecules and 2 ATPs -- grow very slowly
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during Krebs Cycle, glucose is broken down into: ??
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H2O, CO2, and ATP
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decarboxylation
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when a CO2 molecule is shed
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phosphorylation relation
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adding phosphorous -- i.e. ADP+P = ATP
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hydrogen
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1 proton in the nucleus, 1 electron in the outer shell -- unstable, shares an electron with another hydrogen making it H2
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does Respiration need oxygen?
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yes -- however some bacterial grow via respiration without oxygen; energy producing pathway in which inorganic molecule is final hydrogen receptor
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respiration
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produced with oxygen; energy producing pathway in which an inorganic molecule is the terminal hydrogen receptor
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ammonia
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NH3
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H2S
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hydrogen sulfide --result of respiration (rotting egg smell)
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coupling
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oxidation phosphorylation
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uncoupling
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prevents oxidative phosphorylation
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autotroph
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no required pre-formed organic molecules
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heterotroph
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required pre-formed organic molecules
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bacteria growth media
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anything on which bacteria grow and from which they attain nutrition -- i.e. crude oil, bacteria consumption, plastic could be a media
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what do all growth media have in common?
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macro nutrients, micro nutrients, and energy
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micro nutrients
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zinc, magnesium, iron, nickel, maganese -- small amounts
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macro nutrients
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basic building blocks for macromolecules (nitrogen, sulfur, carbon, hydrogen, oxygen, phosphorus) -- large amounts
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energy as a nutrient (autotroph)
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obtain energy via photosynthesis (sun) or via inorganic metals (rust) -- mostly live in deep layers of earth
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energy as a nutrient (heterotroph)
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obtain energy from carbohydrates (glucose, fructose, starch, etc)
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complex growth medium
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cheap medium (heterotroph) -- glucose, amino acids, nucleotides, fatty acids -- bacterial grows faster, doesn't need to make everything
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defined or synthetic medium
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used for research -- has exactly every nutrient in needed quantities -- very expensive
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broth
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any liquid medium
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selective media
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add nutrients to have specific organisms grow -- i.e. samonella stool sample
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differential media
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allows more than one bacteria to grow but can differentiate bacteria via color
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mutualism
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2 organisms that live together -- can live independently but better together -- one uses the other's waste products as nutrients
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synergism
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organisms that share nutrients with one another -- organisms benefit or cooperate from this relationship -- can live freely
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paracitism
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totally dependent on other organism for it's environment and nutrients -- cannot live without host, usually free living (i.e. virus)
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agar
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solid medium containing agar powder
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commensalism
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organisms grow together but only one benefits
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antagonism
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some members are inhibited or even killed by others
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environmental requirements for bacterial growth
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gas, temp, pH, pressure, salt
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temp: psychrophile
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0 - 20 C
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temp: thermophile
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above 40 C
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TAQ
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thermophilic organisms that have adapted enzyme systems to survive in hot springs -- i.e. Yellow Stone, thermermus acquaticus
TAQ is enzyme used in PCR -- gene was cloned so can reproduce on its own |
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temp: mesophile
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20 - 40 C -- majority of bacterial organisms -- optimal range is 35 - 37 C
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pressure: barophile
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high pressure needed
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salt : halophile
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high salt concentration necessary (5%+ salt -- 1-2% is normal) i.e. marine organisms
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pH: acidophile
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6.5 and below; cloned and used to fight E. Coli
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pH: mesophile
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6.5 - 7.5; need to buffer growth media to keep pH in this range by absorbing hydrogen ions
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pH: alkliphile or kalophilic
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7.5 and above in the human gut -- i.e. vibrio cholera (8.5)
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gas: aerobic
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require oxygen (i.e. bacilli)
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gas: anaerobic - strict
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oxygen is toxic and cannot live in the presence of even small amounts -- i.e. clostridium; hydrogen binds to oxygen and kills itself in process
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katalyze
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enzyme that prevents the hydrogen from binding to oxygens and kills anaerobic organisms
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gas: anaerobic - facultative
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an organism that does not require oxygen, does not need oxygen for metabolism, can live in presence or absence of oxygen; i.e. E. Coli - does not need oxygen but can switch from fermentation to respiration
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gas: aerobic - facultative
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i.e. E. Coli uses oxygen as its hydrogen receptor during respiration
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stage A: lag phase
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time cells need to adapt to their internal control systems to new conditions -- can be of variable lengths of time depending on condition of environment or size of innoculation
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binary fission
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asexual mode of reproduction -- 1 splits to 2, 2 to 4, etc...
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generation time
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time it takes a population to double; characteristic of a specific organism -- i.e. TB 18 hrs, E. Coli 20 min
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stage B: logarithmic or exponential
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period of max growth when all things are perfectly aligned for growth -- generation time is determined; growth happens very quickly
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stage C: stationary
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growth tapers off and population size remains stable; # new cells = # dead cells -- cells signal releasing chemicals to slow growth; mutations occur
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stage D: death
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essential nutrients are gone or toxins build up -- population crashes and cells die at exponential rate
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batch culture
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the growth curve is characteristic of a batch culture -- never add anything past the initial innoculation; inefficient
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continuous flow process
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much more efficient than batch culture -- use chemostat
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cell counting
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hose many bacterial per mL of growth bacteria
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direct count
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total count of live and dead cells -- fast, not useful. using grid counting method
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viable or plate count
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idea that if cell is alive it is going to reproduce itself via binary fission
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serial dilution
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pro: count of live cells, cons: lots of time, more error
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plaque count
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used to count virus per mL -- follow dilution method, cover petri dish in bacteria, observe plaques/holes where virus has eaten up bacteria
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disinfection
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the use of chemicals to eliminate any infectious agent on an inanimate object
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antisepsis
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the use of chemicals on living tissue
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sterilization
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freeing an object or substance of all microbial life
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cidal
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killing
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static
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stay the same; prevents organisms from reproducing by reducing numbers
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sepsis
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toxic or diseased state resulting from the growth of harmful microbes
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asepsis
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absence of infectious microbes in living tissue
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semmelweis
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studied perpetual fever in 1840's in Vienna in women -- stressed that cleanliness during childbirth was important
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lister
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principles of aseptic surgery after pasteur proposed germ theory -- used phenol (carbolic acid)
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reasons to kill microbes
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1. prevent infections of man, plans, animals, 2. prevent spoilage or food, 3. prevent interference by microbes in industrial processes, 4. prevent contamination of pure cultures
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physical control of microbes: filter
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screen filter (millipore) -- used to filter water and bacteria
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physical control of microbes: heat
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boil for 3-4 min -- will kill bacterial cells but not spores; steam in confined chamber -- contains more calories of heat; spores die at around 120 C; dry heat -- 250 C for 4 hours will kill bacteria
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autoclave
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pressure cooker -- boyles and charles law in a confined container, heat and pressure increases
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pasteurization
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not full sterilization, used against heat resistant organisms; was used initially for wine -- i.e. fever
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physical control of microbes: radiation
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known as "cold sterilization" expose to gamma rays, kills everything -- damage DNA, proteins, sometimes changes chemistry of product itself
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ultra violet light
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used on flat surface with nothing in the way, low wave length -- causes chemical bonds to form between thymine residues and DNA
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antibiotics
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substance that is the product of the metabolism of some microorganism (bacteria, mold, fungus) -- product excretes into environment and product is able to either slow down or kill other microbes; only works on bacterial infections -- only aim cell wall
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fluorine
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halogen, mild -- 1950 fluorinating water supplies
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chlorine
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halogen, bleach -- most common sporicidal (slowly), used sometimes in water supplies, can react with organic materials can create carcinogenic materials
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iodine
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halogen, sporicidal (slowly), problem is getting it into solution -- highly caustic cannot take internally
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4 important halogens
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bromine, fluorine, iodine, chlorine
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tincture
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alcoholic extract, i.e. iodine + alcohol
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phenols
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carbolic acid, very caustic -- dangerous, eat into skin, kills bacteria, viruses, fungi (not spores), agent which all other disinfectant are measured
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phenol coefficient
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if agent is less than 1, not as good as phenol; if agent is more than 1, it is better than phenol
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hexachlorophene
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version of phenol that is less toxic, not used anymore because it is a neurotoxic -- 2 phenols bonded together with 6 chlorines (chlorinated biphenol)
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alcohol
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kills most bacteria, viruses, fungi -- bigger the alcohol molecule the better the disinfectant
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alcohol structure
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C - OH (hydroxyl molecule)
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ethyl alcohol
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alcohol in drinking form
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methol alcohol cannot be consumed because...
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converted into formaldehyde -- will destroy optic nerve
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drinking too much ethyl alcohol...
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converts into acetaldehyde -- over production causes hangover
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hydrogen peroxide
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kills spores, oxidized everything, breaks down proteins and enzymes, breaks down self
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quaternary ammonium compounds
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kills some bacteria, viruses, and fungi
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soap/detergents
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lipid solvents, dissolve fats, and cell walls -- kills microorganisms, low bacterialcide
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mercurials
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heavy metal -- wipes out enzymes; cons: accumulates in the environment, passed as it is eaten, toxin for kidneys and can cause brain damage
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silver nitrate
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heavy metal -- bactericidal. cure for gonorrhea, given to babies born with disease and prevented babies from going blind
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ethylene oxide gas
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part of aldehyde group -- sporicidal, used to sterilize plastic; produced by ripening fruit, i.e. apples
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formaldehyde and glutaraldehyde
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part of aldehyde group; sporicidal
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dyes
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weak bactericidal, fungicidal -- methol blue crystal violet; stops growth of yeast -- i.e. athletes feet, gums of newborns
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chlorhexidine
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kills most bacteria, some viruses and fungi -- low toxicity
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Alexander Flemming
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1930 - father of modern day antibiotics; penicillin
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problem with overusage of antibiotics
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slowly with time kills bacteria sensitive to penicillin, leaves those that are resistant -- stapho cocci infections are hard to treat now
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resistant to antibiotics is...
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genetic -- changes in the genome results in changes in the protein structure
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MRSA
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class of stapho cocci that is resistant to many antibiotics
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resistance to antibiotics that target the cell wall
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the bacteria produce an enzyme that treats the antibiotics like a food and consumes it
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antibiotics that target cell walls
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block synthesis and repair -- i.e. penicillin or vancomyosin
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antibiotics that target DNA + RNA
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prevents the cell from making DNA and RNA, inhibits transcription and replication
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antibiotics that target ribosomes/protein synthesis
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some go after 50s or the 30s -- prevents ribosome from producing proteins; cons: many bacteria produce proteins that antibiotics have no effect on
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antibiotics that target cell membrane
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affects transport across the cell membrane -- allows everything in, kills the cell; bacterial cells have adapted and pump out unwanted things
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multiple drug resistant TB
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1900's - TB was #1 killer
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antibiotics that target folic acid synthesis
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inhibits folic acid metabolism
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classification of viruses
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animal viruses, plant viruses, bacterial viruses
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virus: icosahedral
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multisided 3-D shape -- has capsid protein coat; made up of capsomeres -- polymer that has single subunits that is repeated (i.e. influenza virus)
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virus: helical
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made up of capsomeres made around nucleic core -- most in plant viruses; i.e. tobacco mosaic virus
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virus: complex
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other virus shapes; i.e. rabies virus, vaccinia virus
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virus: bacterial virus
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E. Coli
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"naked" virus
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has icosahedra shell surrounding material
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"enveloped" virus
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has capsid, nucleic acid membrane, original host cell; membrane has various surface proteins sticking out i.e. NA = neuromeradase, HA = hemegluttine
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how to characterize virus
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host, shape, type of nucleic acid, "naked" or "enveloped"
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John Enders
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Won Nobel Prize for method of growing cells in petri dish
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Hela cells
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1940 to 1950s at John Hopkins -- extracted tumor cells from Henrietta Lax and created immortal cell line
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growth of Influenza virus to make vaccine
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create hole in egg, inject influenza virus onto membrane, day 7 seal with beeswax, day 14 break open egg and embryonic membrane is cut out and cultured, purify to get virus preparation
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bacterial virus replication
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1. Adsorption, 2. Injection, 3. Eclipse (early viral protein, replicate viral DNA, late viral protein), 4. Assembly, 5. Lysis
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animal virus replication
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1. Adsorption, 2. Absorption, 3. Uncoating, 4. Eclipse, 5. Assembly, 6. Release
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capsomeres
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polymer that has single subunit that is repeated over and over again (protein coat on virus)
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potential energy
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resting energy
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kinetic energy
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energy needed to create reaction
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potential energy
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resting energy
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kinetic energy
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energy needed to create reaction
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chemostat
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a bioreactor to which fresh medium is continuously added, while culture liquid is continuously removed to keep the culture volume constant
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