Term
| What are three major similarities between animal and plant metabolism? |
|
Definition
1) Structure of many pathways of intermediary metabolism
2) Comparable range and sophistication of Fine and Coarse control
3) Capabel of aggressive, territorial and defensive behaviour |
|
|
Term
| What forms of fine and coarse metabolic control do plants share with animals? |
|
Definition
1) Control of key ENZs via allosteric effects, reversible phosphorylation
2) Extracellular signal transduction of hormones and other signals via IP3, DAG and PKc metabolism, CA/CaM dependant protein kinases, etc.. |
|
|
Term
| What are four examines of plants defenses? |
|
Definition
1) Oligosaccharide Elicitors - Produced when insects chews on the plant cell wall - triggers a damaged plant cell to produce toxic chemicals and protease inhibitor (inhibits insect gut proteases - indigestion)
2) Secrete Systemin transported through vascular system that triggers a systemic defence response in damaged cells
3) Damaged cells release a volative methyl-ester (methyl -jasmonate) to warn neighboring undamaged plants (anticipates insect attack)
4) Volicitin - Chemical in caterpillar saliva - signals plant cells to synthesize and emit volatile terpenoids that attract specific species of parasitic wasp, whose larvae eat the caterpillar and protect host plant from futher damage |
|
|
Term
| What two broad categories are plant defenses divided into? |
|
Definition
| Anatomical defenses and chemical defences |
|
|
Term
| How do aphids (insect herbivores) trigger plants defences? |
|
Definition
| They cause the host plant to release specific volatile compounds. These compounds attract predatory lady buds to the plant (not the same as Volicitin that attracts parasitic wasps) |
|
|
Term
What is the example of aphid defense show us about plant response?
Why is this so important? |
|
Definition
They are able to recognize specific herbivoric species and adjust their defense accordingly.
Becomes an important area of research for ay-biotech, as you can enhance crop defense to specific herbivoers and fungi |
|
|
Term
| What is the difference between animals and plants w.r.t to the kinome? |
|
Definition
| Plants have thousands of protein kinases, many more than animals. This helps to explain their large genome and their defesnse and stress tolerance mechanisms. |
|
|
Term
| What are the four major categories of differences between plant and animal metabolism? |
|
Definition
1) Compartmentation of metabolism (plastid is most unique feature of metabolism, supposedly)
2) Biosynthetic capabilties - They can synthesize thousands of different and highly complex aromatic compounds (alkaloids sand terpenes)
3) MEtabolic and Biochemical adaptations to environmental extremes
4) Metabolic flexibility (parallel pathways, PPi's role as autonomous energy donor) |
|
|
Term
| Why is the madagascar periwinkle important? |
|
Definition
| They are a source of anhydrovinblastine. Vinblastine, a derivative, is a potent anti-cancer durg. The periwinkle is unique because it can synthesize this vinblastine which requies trytophan and a monoterpene. |
|
|
Term
| What does vinblastine as an anti cancer drug? |
|
Definition
| It inhibits mitosis, helps stop rapidly dividing cells |
|
|
Term
| What is the shikimate pathway? where is it found? |
|
Definition
| Produces aromatic compounds like tryptophan and is inovled in creating vinblastine. IT is only found in plants, an dnot in animals |
|
|
Term
What does the dogma say about plastids?
Is this completely correct? |
|
Definition
They only occur in plant cells.
No |
|
|
Term
| Why does the crawling leaf challenge plastid dogma? |
|
Definition
| It is a photsyntehtic marine mollusc - i.e. an animal with a chloroplast |
|
|
Term
| Describe the steps that the crawling leaf (elysia chorotica) becomes photsynthetically active? |
|
Definition
1) Slugs produce eggs (but w/o chloroplasts)
2)The juvenile slugs eat green alga and then concentrates the algal chloroplast into its skin cells
3) Then, the animals digestive tract disappears - and adults begin to look like a leaf. They live and grow up to 1 year on a diet.
4) Algal chloroplast genes have been integrated into the slug's genome and continue to be expressed in its cytoplasm. |
|
|
Term
| Other than photosynthetic molluscs, where are non-green plastids found in non-plants? |
|
Definition
| In the apicomplexa phlum, which includes the human parasites of malaria and toxoplasma. |
|
|
Term
| Explain what the apicoplast is. how did it arise? |
|
Definition
| The plastids of the apicomplexa phylum, arose via endosymbiosis when ancestoral apicomplexa engulged a green alga and retained the plastid. |
|
|
Term
| What do the apicoplast look like under the TEM? |
|
Definition
|
|
Term
| Why is so important to know about the apicoplast? |
|
Definition
| Gives us, medical scientists, an ability to have selective toxicity against malaria and other parasite. If we target plastids, they die but we don't |
|
|
Term
| What two things are most important to know about Functional Genomics w.r.t to metabolic biochemisty? |
|
Definition
1) It is incredibly challenging as things not accounted for (like protein:protein) interactions may profoundly influence gene funciton in response to various developmental or enviormental cues
2)Integration of proteomics and ENZ biochemistry with Modenr mass spec can yield important discoveres concerning metabolism that would be difficult to make using another approach |
|
|
Term
| What is the transcriptome? how do you find it? |
|
Definition
| An evaluation of mRNA concentration and gene expression levels. Find it through cDNA microarrays |
|
|
Term
| What is the interactome? how do you find it? |
|
Definition
| What the protein protein interactions are - found through yeast 2 hybrid and TAP tagging |
|
|
Term
| What is the proteome? What are the issues with this? |
|
Definition
| The function of every genes in sequenced genomes, however the relationship between a primary A.A sequence and it's function is a very complex and unsolved problem |
|
|
Term
| What are the three levels of protein function? |
|
Definition
1) Phenotypic - protein's influence on entire organism
2) Cellular - proteins' location and interactino with other proteins
3) Molecular - protein's precise biochemical function and control |
|
|
Term
| What three questions does functional genomics try to answer? |
|
Definition
| What are the functional properties of every encoded protein, where and when is every gene expressed, and how do disease and other stresses influence expression and PTMs |
|
|
Term
| What % of sequenced genes encode unknown ENZs? |
|
Definition
| Up to 50%, and genomics reveals that metabolism and its control are complex and still poorly understood |
|
|
Term
| What are some main issues with genomics (2)? |
|
Definition
20% mistaken gene annotation
multiple isozymes (poorly defined properties and roles) |
|
|
Term
| What is the use of furthering our understanding of metabolism |
|
Definition
| Central issue is solving problems in human health through ME |
|
|
Term
| To fully understand metaboism and its control, we must integrate genomics with... |
|
Definition
| Metabolomics, proteomics, and a comprehensive systems biology |
|
|
Term
| What are two key proteomics tools? |
|
Definition
| 2D - page and Mass spec analysis of peptides produced by protease digestion of excise proteins pots |
|
|
Term
| what does mass spec tell us? |
|
Definition
| The protein i.d. and the type and sites of PTMs that occur in vivo |
|
|
Term
| What are the steps of 2d electrophoresis? |
|
Definition
1st separate proteins by charge (vertically), and then separate proteins by size horizontally.
Spot analysis gives us the proteome |
|
|
Term
| However, what does the plaxton analysis of aribidoposis vai 2d electrophoresis tell us? |
|
Definition
| That there was no correlation between 6 different enzymes and thus for a complete picture, we must always integrate transcriptomics with parallel biochemical metabolic studies |
|
|
Term
| What are the 2 major limitations of electrophoresis (protemics)? |
|
Definition
1) only abundant proteins are revealed
2) There is often insufficient amount of protein 'spot' availabel for a good PTM analysis via mass spec |
|
|
Term
| How do you solve the 2 issues with 2D electrophoresis? |
|
Definition
| You enrich the specific sub proteome that interest you. Rather than running an entire cell, purify specific organelles more to achieve higher [] and greater resolution |
|
|
Term
| What is the ultiamte sub -proteome? |
|
Definition
|
|
Term
| What is the plaxton lab approach and philosophy? (7 steps) |
|
Definition
1) Native ENZ purification via FPLC
2) Mass Spec analysis to i.d gene
3) Physical, immunological and kinetic characterization
4) PTM analysis (what, where, why, when and how)
5) mRNA analysis
6) cDNA cloning
7) Examine loss of function knockout mutants |
|
|
Term
| What is the protein kinase problem? |
|
Definition
| There are often hundred of protein kinase isozymes and thus it is very hard to purify |
|
|
Term
| What has been done to predict the Pkinase interactome? |
|
Definition
| High throughout genomic approaches through yeast 2 hyrbrid and tap tagging |
|
|
Term
|
Definition
The use of recombinant DNA technology to modify flux of metabolites through metabolic pathways
goal is to produce new compounds or to increase or decrease production of existing compounds |
|
|
Term
| What things will ME help with? |
|
Definition
| more food fibre and medicine, more efficient and sustainable agriculture with stress resistant crops and preserve biodiversity |
|
|
Term
| Why is biodiversity important to mankind? |
|
Definition
| Purifies air and water, keeps soilds fertile, regulate climate, controls pests and habitat provision |
|
|
Term
| WHy do we need stress resistant crops? |
|
Definition
| To conserve our precious fresh water, 70% of makind's freshwater is currently used for crop irrigation |
|
|
Term
| Earth's mass extinction? What about canadians? |
|
Definition
| Because of humans, increased the extinction rateby 1000 fold. The red list details the species that are facing high risks of extinction. Canadians are the fourth worst in using up earth, as the average canadian causes emissions of 17,000 Kg per year. Canadians use 30L of fresh water per day |
|
|
Term
| When will we see a 50% increase in populaiton? |
|
Definition
|
|
Term
|
Definition
| Helps to alleviate world hunger by engineering crops that are drought or salt tolerant |
|
|
Term
|
Definition
more food fibre and medicine
Produce stress resistant crops and trees
Conserve fresh water
Produce renewable, carbon neutral liquid fuels |
|
|
Term
| What are alternative to current forms of fuel? |
|
Definition
| Planting engineered biofuel crops on cropland, such as switchgrass, that allows for produciton of cellulosic ethanol |
|
|
Term
| What else are being engineered for biodiesel production, other than crops? |
|
Definition
| Oilseeds (jatropha), castor beans |
|
|
Term
| With Algal biofuels, where do the reactants end us as products? |
|
Definition
| End up as jet fuels (C2H2n+2), hydrogen gas, alcohols or ammonia |
|
|
Term
|
Definition
| Plant biotech where crops are transformed with various genes |
|
|
Term
| Describe Vit A deficiency? |
|
Definition
| B carotene is a vit A precursor, a plant antioxidant and light harvesting molecule that we need in our diet. VA is needs for vision, immune sytem, and bone growth. |
|
|
Term
| Who does provitamin A (Beta carotene) come from? |
|
Definition
| Carrots, red peppers, leafy greens |
|
|
Term
| How does ME help with Vit A deficiency? |
|
Definition
| ME of a B carotene biosynthetic pathways has been able to produce transgenic tropical crops, that increase [] of Beta carotene by 30 fold |
|
|
Term
| What is phytoremediation? |
|
Definition
| The use of transgenic plants to clean up polluted silds, and decrease atmospheric Co2 levels |
|
|
Term
| What are the two basic approaches to ME? |
|
Definition
| Shot gun transformation and Rational ME |
|
|
Term
| Why was shot gun ME very popular? |
|
Definition
| All you need to know is molecular biol, but it hardly ever works and has fallen out of fashion |
|
|
Term
| Describe the process of shot fun transformation? |
|
Definition
| Begins on the assumption that altering enzyme [] will alter the metabolic flux. You take a novel gene, do transgenic activities and then lead yourself to an improved phenotype. |
|
|
Term
| What are the advantages of SG transformation? |
|
Definition
| You get a short term effort that does not require much knowledge of either physiology or biochemistry |
|
|
Term
| What are the disadvantages of SG? |
|
Definition
| The actual phenotype you want is rarely obtained, as there often is little knowledge of what exactly was manipulated |
|
|
Term
|
Definition
| The targeted and purposeful alteration of a specific metabolic pathway, but does not necessarily depend on alteraton of ENZ concentration |
|
|
Term
| Advantages of rational ME? |
|
Definition
| Chances of success are great, more challenging though a more interesting and scientific process |
|
|
Term
| Disadvantages of Rational ME? |
|
Definition
| requires mol biol, but also a strong background in protein /ENZ biochem, metabolism and control, also physiology |
|
|
Term
| Why do you need protein/ENZ biochemistry in Rational ME? |
|
Definition
Allows one to identify the site of control in a specific metabolic pathway.
You should be focusing on allosteric pacemaker enzymes |
|
|
Term
| Once you have done a protein background, why do you purify? |
|
Definition
| It helps to generate tools, like specific antibodies and partial A.A sequences that help to facilitate identification and cloning of the corresponding gene cDNA |
|
|
Term
| After purification, what occurs in rational ME? |
|
Definition
| a site directed mutagenesis - produces a mutant enzyme with altered kinetic and regulatory properties |
|
|
Term
| After gene modification, why do you do a physiological analysis? |
|
Definition
| To determine if the activity and amount of the target enz have been altered. Was the pathway flux altered and with MCA, you can calculate flux control coefficients |
|
|
Term
| When is ME truly successful? |
|
Definition
| AFter dozens of iterative cycles that lead to an improved phenotype |
|
|
Term
| What are two types of rational ME approaches? |
|
Definition
| Engineer a new pathway by putting foreign genes into plants and amplify a flux controlling step by circumventing feedback control mechanism (or through allosteric effectors) |
|
|
Term
|
Definition
| PHB is a storage product that creates polyster and degradable plastics. It is much desribale to fossil fuel derived plastics. |
|
|
Term
| Outline normal PHB synthesis |
|
Definition
| Acetyl Coa (w/3-ketothiase)--> Acetoacyl Coa (w/Acetoacetyla Coa reducatase) --> Hydroxybutryl-Coa (w/PHB synthase) --> PHB |
|
|
Term
| So, once you know the PHB pathway, how does ME help? |
|
Definition
| You have to express bacterial genes that include ACetoacetyla COA reducatase and PHB synthase to ensure that PHB is favoured. |
|
|
Term
| What is the second green revolution |
|
Definition
| The production of plant based biodegradable plastics |
|
|
Term
| The example of increasing trypophan in rice is which type of Rational ME? |
|
Definition
| Type 2- amplifying a flux controlling step by circumventing a feedback control mechanism |
|
|
Term
| Why do we want to increase trp concentration in rice? |
|
Definition
Goal for plant biotech is to increase essential a.a. especially lys, met, thr and trp in plant based foods.
Also, it is a serotonin precursor and vinblastine precursor |
|
|
Term
| How does TRP synthesis begin? |
|
Definition
| Like all aromatic compounds, it begins by diverting building block precurosors into the shikimate pathway (we must obtain essential A.A's into our diet |
|
|
Term
| Why is TRP concentration in plant cells limited? |
|
Definition
| Because of TRP feedback inhibition of anthranilate synthase (a pacemaker enz of TRP b/s pathway) |
|
|
Term
| how do we ME high trp []? |
|
Definition
| So we introduce a gene that encodes a feedback insenstive allosteric mutant of anthranilate synthase (with a single substitution). This leads to 430x increase in free trp content |
|
|
Term
| How did Dr. Kang Zhu engineer a salt tolerant plant? |
|
Definition
| Through phosphorylating the Sos1 Na/H antiport. This leads to turning it on, and allowing for more Na to be pumped out of the cell. He also turned on two other Sos iso forms that allowed salt tolerant plants to have a normal phenotype in 250 mM NacL |
|
|
Term
| What is the third type of Rational ME approach (related to animals)? |
|
Definition
| Tissue specific overexpresion of a specific enzyme of energy metabolism |
|
|
Term
| What is an example of Tissue specific overexpresion of a specific enzyme of energy metabolism? |
|
Definition
| Overexpression of PEP CK in skeletal mouse in the mouse |
|
|
Term
|
Definition
It catalyzes a freely reversible rxn that links glycolysis with the TCA cycle (PEP to oxaloacetate).
Goes both ways, so its crucial for gluconeogenics (in OAA --PEP) but can function in PEP to OAA direction as well |
|
|
Term
| What did the super mouse transgenic have? |
|
Definition
| It have the muscle isozyme of PEPCK overexpressed, though a skeletal muscle specific promoter. This lead to muscle PEPCK activity increasing by up to 100x! |
|
|
Term
| What were the results of the transgenic mouse? |
|
Definition
| It ran twice as fast, lived much longer, ate more but had little fat, had less blood lactate, more mitochondria |
|
|
Term
| Did you read the PDF on biochemical adaptation? |
|
Definition
|
|
Term
| What areas are most affected by climate change? |
|
Definition
| Artic circle, boiling hot springs, arabian desert, hypersaline lakes, alpine ecosystems and trogophiles |
|
|
Term
| What must intertidal species adapt to at low tide? |
|
Definition
| Lack of o2, extreme TEMP and osmotic stresses |
|
|
Term
| What must species in the abyss adapt to? |
|
Definition
| high pressure, darkness, lack of 02, lack of food, and coldness |
|
|
Term
| Where are hydrothermal vents found? |
|
Definition
| In spreading tectonic plates on the ocean floor. 1st discovered in 1979 |
|
|
Term
| T/F biomass of hydrothermal is much smaller than tropical rainforest |
|
Definition
|
|
Term
|
Definition
| Undersea mountains that rise at least 1000m above surrounding seafloor. Considered islands of biodiversity |
|
|
Term
| What are spreading ring systems and why are they important? |
|
Definition
There are numerous new species adapting to these extreme environment which contain shallow hydrothermal vent systems. These subduction zones include marianas arc.
Includes undersea rivers of molton sulphur and CO2, and vents spewing pure sulfuric acid |
|
|
Term
| Why do we care about marinas arc? |
|
Definition
| Free living and symbiotic chemotrophic archaebacteria use H2S emited by the vens as energy sources |
|
|
Term
| What are the supports for panspermia? |
|
Definition
250 mil y.o bacteria have been isolated from salt crystals
Discovery of archae living in extreme environments in earth
80-100 tons of cemetary debris enters earth's atmosphere evey day
life may have evolved on comets, then inoculated earth? |
|
|
Term
| What things must an organism do to survive in any extreme environment? |
|
Definition
| Ensure that appropriate structural states of macromolecules are maintained and that there is an adequate level of energy turnover |
|
|
Term
What three general process is P/deP used in metabolic arrest? |
|
Definition
| to turn off 1) Fuel synthesis, 2) Protein synthesis and 3) Channel arrest - active transport off |
|
|
Term
| What was special about Peter Hochaka? |
|
Definition
| Studied the metabolic adaptations of animals ot limiting o2, but he always did scientific excursions intp how animals acclimate - study the details. |
|
|
Term
| What is glycolysis defined as? |
|
Definition
| A catabolic, linear pathway of 10 ENZs that oxidizes sugars into pyruvate, a 3-C compound. It produces some ATP via subtrate level phosphorylation, and an ancient, cytosolic pathway |
|
|
Term
| T/F all metabolic pathways feed into or out of central respiratory pathways of glycolysis and TCA cycle/ |
|
Definition
|
|
Term
| Why does the TCA cycle stop when no 02 is available? |
|
Definition
| Inability to regenerate electron carriers NADH |
|
|
Term
|
Definition
| At a major metabolic junction, it can lead to the shikimate pathway, towards pyruvate or to OAA |
|
|
Term
| What is unique about PEP chemical properties? |
|
Definition
| It occupies the highest position on the thermodynamic scale (-62 G vs -30.5 for ATP) |
|
|
Term
| Did you read the functional organization and control of plant respiration doc? |
|
Definition
|
|
Term
| Why is glycolysis so important? (7) |
|
Definition
1) Central pathway of all cells
2) most studied pathway
3) example of adapability of metabolism
4) Shows how ADP/ATP system in E transduction can be partly replaced by the PPi/Pi system
5) Glycolytic control probably involved all mechanisms of fine control
6) directly involved in many biochemical adaptions to extreme environments
7) For many species, a common defence against harsh envior is to go to metabolic arrest, which relies heavily on fine control inhibitino of glycolysis |
|
|
Term
|
Definition
| Summer or dry season dormancy, accompanied by decrease in meatabolic rate |
|
|
Term
| What is special about the lung fish? |
|
Definition
| It can breath air in hypoxic water, burrows in the mud and hibernates during the day |
|
|
Term
|
Definition
| Life without water, example of tardigrades |
|
|
Term
|
Definition
| They can be repeatedly desiscated and rehydrated and can exist in cryptobiotic state where there is an 100% decrease in metabolic rate |
|
|
Term
| What happens to animals in anhydrobiosis? |
|
Definition
| The dessication tolerance only exists in larval stage, but they completely turn and have no detectable metabolism |
|
|
Term
| What is the ressurection plant? |
|
Definition
| Cratersotiqma plantqineum |
|
|
Term
| What is the immortal bacteria? |
|
Definition
| A bacteria isolated from primary salt cystal, 250 million years old. Note that viable bacteria have also been isolated from 8million year old ice in bacteria |
|
|
Term
| What is glycolysis needed for? (2) |
|
Definition
| Anaerobic ATP production and generation of anabolic precursors |
|
|
Term
| What is the food for glycolysis? |
|
Definition
animals - Hexose mainly glucose, absorbed from gut and stored as glycoen in liver and muscle
Plants - Fixed Co2 is stored as soluble sucrose, or in plastids as insoluble starch |
|
|
Term
| What is the overall reaction for classical glycolysis? |
|
Definition
2ADP and 2PI + 2NADH + Glucose --> 2 Pyruvate + 2ATP +2NADH.
however, with oxygen you get 6aTP per glucose, not just 2 |
|
|
Term
| How is glycolysis divided? |
|
Definition
| Into the prepartory stages (initial investment) and the oxidative steps (where you get ATP and NADH production). |
|
|
Term
| Where is ATP lost in glycolysis, where is it gained? |
|
Definition
| Lost to hexokinase and PFK (1 ATP each), while 2 ATP are gained at 3-PGA Kinase and Pyruvate Kinase each. NEt total of +2 |
|
|
Term
| What is the first reaction in glycolysis and why is it so imporatnt? |
|
Definition
| It is the hexokinase and it is important because it makes the hexose impermeable to the plasma membrane and more reactive |
|
|
Term
| Why do accumulate glycolytic end-products? |
|
Definition
| To survive extreme conditions. These are typically stable end-produce |
|
|
Term
| What are some examples of biocompatible solutes? |
|
Definition
| Trehalose (dessication or salinity), Lactate and ethanol (anoxia), glycerol for freezing |
|
|
Term
| Why are biocompatible solutes so useful? |
|
Definition
They don't contain a chemically reacitve C=0 group which would form a covalent bond with the Nh2 groups
The browning reaction |
|
|
Term
| Why do we need free a.a. as biocompatible solutes |
|
Definition
| To help cells osmoconform (not the same as osmoregulate where you maintain same [ion] through ATP use) |
|
|
Term
| Why is glycerol so important? |
|
Definition
| It is a water replacement, and it is a potent antifreeze. It stabilizes membranes and proteins when liquid H20 is absent. During freezing, glycerol replaces bound water to maintain protien and membrane stability |
|
|
Term
| What are the three major sites of glycolytic control in classical glycolysis? |
|
Definition
|
|
Term
| What are two key features of classical glycolysis |
|
Definition
| Low ATP yield, and that it is metabolically inflexible |
|
|
Term
| What is an example of a non classical glyoclytic pathway? |
|
Definition
PPi adapation that replaces some of ATP dependant rxns
Increases the net ATP yield |
|
|
Term
| What does the anaerobic amoeba do if it lacks inorganic PPiase, ATP PFK and PK? |
|
Definition
It uses PPi-PFK and PPDK, which uses PPi to convert AMP to ATP
It increases the Net ATP yield to 5 and uses up 3 PPi molecules |
|
|
Term
| In plants, where does glycolysis occur? |
|
Definition
| IT exist in both the cytosol and the plastid. |
|
|
Term
| Why does glycolysis occur in the plastid as well? |
|
Definition
| to offer more flexibility, and note that there are separate plastid and cytosolic pyruvate kinase isozymes. It is imporatnt to separate them because they each have differnt kinetic profiles (example of PKc and PKp) |
|
|
Term
| How is plant glycolysis different than human glycolysis? |
|
Definition
| It is a network of alternative rxns that provide metabolic flexibility (ex of PPI dependant enz to bypass and not use ATP) |
|
|
Term
| How can you describe animal glycolysis? |
|
Definition
| As typically a top down control, 1st throough ATP -PFK and then through PK |
|
|
Term
| What are the most importnat effectors of PFK (a homotetramer) |
|
Definition
Fruc (2,6)p2 - in Liver it signal glucose is abundant
AMP (signals that adenylate charge is low)
ATP and citrate and negative effectors |
|
|
Term
| What are the main effectors of PK (a homotetramer) |
|
Definition
| Fru 1,6 p2 (the other form of Fru 2,6, p2) and positively effected by ATP and alanine |
|
|
Term
| How does ATP function as both a substrate and Inhibitor of PFK? |
|
Definition
| F26P2 relieves the inhibition of PFK by ATP, allowing ATP to bind to an allosteric activator site inside of an inhibitory site. |
|
|
Term
| Why is pyruvate kinase considered a moonlighting enzyme? |
|
Definition
| When active and associated, it has no thyroid binding activyt, but when discciated into monoers it has that activity. It is deactivated by citrate and alanine |
|
|
Term
| Another example of moonlighting enzymes? |
|
Definition
Enolase (can functional as structural protein in eye lens)
Or Phosphoglucose Isomerase (which plays four additional roles when secreted) |
|
|
Term
| how are PFK and PK converted to less active form? |
|
Definition
| Through reversible phosphorylation |
|
|
Term
| Why would pyruvate kinase be deactivated? |
|
Definition
| For GNG in liver, and during starvation which promotes catabolism |
|
|
Term
| What is a metabolic supression mechanisms related to glycolysis? |
|
Definition
| Shutting down PFK and PK through making them dissociate and inactivate |
|
|
Term
| Whereas animal glycolysis is top down, plant glycolysis is.. |
|
Definition
| bottom up because the primary control is at PEP and the secondary is at PFK |
|
|
Term
| Is adenylate charge important in plant glyolysis? |
|
Definition
| No, plant respiration is often more important in producing anabolic precursors |
|
|
Term
| What are main effector of PK (both plastid and cytosolic isozymes) |
|
Definition
|
|
Term
| What are main effector of PEPC in plants? |
|
Definition
| Malate (inhibitory) and GLu-6-P (feedforward activation), also activated by protein kinase mediated phosphorylation |
|
|
Term
| What are major similarities between animal and plant glycolysis (3)? |
|
Definition
Location of key pacemakers
Allosteric activators, inhibitors, P/deP and metabolon formation
Signal metabolites (Fru 2,6P2) is a potent effector of glycolysis and inhibitor of GNG |
|
|
Term
| Major differences between animal and plant glycolysis? |
|
Definition
Top down control in animals, Adenylate charge plays no role in plant glyoclysis.
bottom up control in plants (feedback inhibition) vs. feedforwrad and top down control in animals |
|
|
Term
| Compare the allosteric effectors of ATP vs. PPI PFK? |
|
Definition
ATP is mainly activated by Pi and inhibited by PEP,
While PPi PFK is activated by F26p and inhibited by Pi. |
|
|
Term
| Discuss F26P use in ATP vs PPi PFK? |
|
Definition
| It's a moderately important effector in ATP-PFK, but elicits a 10x increase in Vmax with the PPiPFK - so it's much more important for stress |
|
|
Term
|
Definition
It is a potent activator of PFK1 and inhibitor of Liver FBPase
Notes: works at micromolar levels and took a while to be discovered because of is phopshpate group, which made it incredibly acid labile.
A strong inhibitor of FBPase (GNG). So it coordinates both glycolysis and GNG |
|
|
Term
| What are the four characteristics of a signal metabolite? |
|
Definition
1) not intermediates of other pathways
2) formed from common metabolites central to metabolism
3) only regulate metabolism
4) Work at low mM range |
|
|
Term
| Describe how PFk-2 activaties are oppositely regulated? |
|
Definition
| Through F26p2 and also through AMPk (which phosphorylates during burst action) |
|
|
Term
| Describe what occurs with cAMP and the liver? |
|
Definition
| Starvation induced increases in cellular caMP levels leads to caMP dependant protein kinase phosphorylation other other key enzymes to promote GNG |
|
|
Term
| Why does starvation lead to much more GNG? |
|
Definition
| Because brain neurons can't use fatty acids as fuel, they must use gluocse and stay aerobic. Regulation of blood glucose is critical |
|
|
Term
|
Definition
| It leads to increase cAMP to activate GNG and inhibit glycolysis. cAMP acts on PKA, which leads to enzyme phosphylation - leads to glycogen synthase inactivaiton, glycogen phosphorylate activation (you want glycogen breakdown in order to make glucose) pyruvate kinase inactivation, FBPase-2 activation, PFK inactivation, and production and export of glucose |
|
|
Term
When was anaerobic life dominant?
Aerobic life? |
|
Definition
4 billion years for some anaerobic life
3.5 billion for some aerobic life |
|
|
Term
| How long can various organisms exist without oxygen? |
|
Definition
| Humans only a few minutes, but some turtles and fish can exist for months, while eukaryotes can live indefinitely |
|
|
Term
| What are the distinct types of anoxia stress? |
|
Definition
Functional Anoxia (duration is seconds - durin gburst muscle work when aerobic capacity is outstripped)
Environmental Anoxia - Duration is hrs to days to months and is due to lack of 02 in a natural habitat |
|
|
Term
| What three requirements are needed for anaerobic energy productions? |
|
Definition
Fermentable fuel (usually glucose, or a.a., but not fatty acids)
ADP phosphoryalted to ATP via substrate level phosphorylation
Maintenance of cellular Redox balance - Optimal ratio of NADH: NAD must be maintained |
|
|
Term
| Where do classical glycolysis lead to in anaerobic conditions? |
|
Definition
| Pyruvate leads to Lactate (via LDH) and this requires transferring a NADH to a NAD+. This is helpful because the NAD+ then goes back into glycolysis to help fuel more processes |
|
|
Term
| What is the strategy for adaptation to functional anoxia? |
|
Definition
| Compensatory - you increase your anaerobic metabolic rate - you try to get more ATP through inefficient means. This depends on getting an eventual return to 02 quickly |
|
|
Term
| What is the means of adaptation to environmental anoxia? |
|
Definition
| Exploitative - try to decrease the overall metabolic rate. This form of anaerobic metabolism has higher efficiency, but low ATP production and does not depend on return to 02 |
|
|
Term
| What is the Pasteur Effect |
|
Definition
| The rate of glucose consumption is inversely proportional to O2 |
|
|
Term
| What does the pasteur effect apply to? |
|
Definition
| Applies to functional anoxia, as ATP demand greatly increases during anaerobic muscle work. Even without a change in ATP demand, glycolytic flux must increase 18x in order to meet ATP demands (2 ATP vs. 36) |
|
|
Term
| What are the three metabolic bases of the pasteur effect |
|
Definition
Activation of glycogen phosphorylase
PFK activation due to decrease Energy Change w/ anoxia
Glycolytic metabolon forms on actin/myosin filament of exercising muscle |
|
|
Term
| Why does decreased adenylate energy charge lead to the pasteur effect? |
|
Definition
| Because AMP (a PFK activator) increase and ATP and ctirate decrease (both inhibitors). Also, Fru26-2 increases showing glucose starvation. FRU26p2 is a pFK-1 activator. |
|
|
Term
| Why does FRU2,6P2 increase during anoxia? |
|
Definition
| Because of phosphoactivation of Muscle PFK-2 by AMP-K |
|
|
Term
| Why is it important that during burst work a glycolytic metabolon forms on the contractile machinery (cytoskeletal) proteins? |
|
Definition
| Because dynamic association of metabolon allows to generate massive amount of ATP, which are desperately needed to power muscle contraction |
|
|
Term
| What are the two issues with the pasteur effect? |
|
Definition
That glycogen (the fermentable fuel) is quickly depleted
Acidosis - self pollution ocurs through a toxic end product - lactate.
This means that duration of functional anoxia is very short term |
|
|
Term
| What is HIF? Why does it get activated? |
|
Definition
| Hypoxia inducible factor is a transription factor that promotes increase synthesis of glycolytic enzymes and glucose transporters. This is a long term effect of chronic hypoxia in humans |
|
|
Term
| What are four key adaptions of facultative anaerobes to environmental anoxia stress? |
|
Definition
They store more fermentable fuel
The produce end products that are either excretable or biocompatible
They can increase ATP yeild/gluocse used
They use metabolic rate depression to deal with it |
|
|
Term
| How do good anaerobes minimize acidosis? (2) |
|
Definition
| They increase the tissues buffering capacties (turtles) or they produce anaerobic end products that are excretable of biocompatible --> no self pollution |
|
|
Term
| In anoxic conditions, what is pyruvate converted to in good anaerobes? What enzymes are used |
|
Definition
EThanol and CO2, not lactate.
Done via acetaldehye (enzs are pyruvae decarboxylase and alcohol dehydrogenase) |
|
|
Term
| How do good anaerobes conserve fuel reserves? (2) |
|
Definition
During anoxia they use PPi in place of ATP as P-donor, which conserves ATP or
They divert flux of PEP away from pyruvate towards succinate or propionate |
|
|
Term
| Why is it good that anaerobes direct PEP away from pyruvate and towards succinate? (2) |
|
Definition
| It is essentially teh 3 rxns of the TCA cycle but in opposite direction and it generates ATP and NAD+. Also it creates proprionate which is exretable |
|
|
Term
| What are two methods of conserving ATP during anoxia (outside of PPi use)? |
|
Definition
| Decrease rate of protein synthesis (transcription and translation decrease by 95%) and to channel arrest to maintain ion gradients which decreases ATP consumption via active transport |
|
|
Term
| What is the model animals for anaerobic metabolism and anoxia tolerance? |
|
Definition
| The channeled whelk, because it can easily survive several days of anoxia stress |
|
|
Term
| What two central methods does the channeled whelk use to control anaerobic metabolism? |
|
Definition
| Control the PEP branch point (towards OAA) and decrease glyoclytic flux during long term anoxia |
|
|
Term
| What did study of channeled whlek provide 1st evidence for? |
|
Definition
ENZ control by P/deP is imporatnt adpation to anoxia stress in all organism
And the regulatory ENZ phosphorylation in any molluscs species |
|
|
Term
| What changed between the anaerobic and aerobic red muscle pyruvate kinase of whelk w.r.t to kinetics? |
|
Definition
When Aerobic, the pyruvate kinase was dephosphorylated and it's vmax was very high (and Nh was 1.0) - PEP saturation was low.
When anaerobic, it was phosphorylated, vmas was low and hill coefficient was high . |
|
|
Term
| What are the three mechanisms for decreasing glyoclytic flux? |
|
Definition
Phosphorylated key control enzymes to their less active forms (glycogen phylase, PFK-1, PK)
Decrease Fru26p2
Disrupt the glycolytic metabolom |
|
|
Term
| When flux is low, what is true about F26P2 and the glycolytic metabolon? |
|
Definition
| F26p2 is also low, it can't activate PFK or PK and the glycotic metabolon doesn't form |
|
|
Term
| Did you read the oxygen limitation file on moodle? |
|
Definition
| No, but I probably should |
|
|
Term
| Did you read the oxygen limitation file on moodle? |
|
Definition
| No, but I probably should |
|
|
Term
| What are some protectants against freeze tolerance? |
|
Definition
| High glucose, glycerol, sorbitol and ice nucleates |
|
|
Term
| Why does blood glucose rise in cryo species (like the wood frog)? |
|
Definition
| Triggered by ice formation and made from liver glycogen. Most of it comes from liver, than core organs and then the periphery |
|
|
Term
| What does glycogen phosphorylase do? |
|
Definition
| Takes glycogen and and turns it into G-1_ |
|
|
Term
|
Definition
| enzyme that covalently modified a substrate through phosphorylation. 2-3% of genome, reversed by protein pho sphatases |
|
|
Term
| How many kinases does a crypto wood frog activate? |
|
Definition
|
|
Term
|
Definition
| A phosphorylase that modified genes in the nucleus. A likely target for freeze tolerance animals |
|
|
Term
| What are some of the freeze induced changes? |
|
Definition
Protein synthesis slows to 1%
Pumps become closed
PRoduction of energy slows to 5%
Utilization of energy slows to 2%
and few SAP kinases are activated - whilemany protein phosphatases are activated |
|
|
Term
| What five cellular processes are decreased during freezing? What about ATP turnover? |
|
Definition
DNA/RNA synthesis
Protein synthesis
Fuel MEtabolism
Ion Pumping
Work, ATP decreases to less than 5% of normal |
|
|
Term
| What are some of the epigenetic changes? |
|
Definition
| most genes are inactivated and mRNA levels decrease |
|
|
Term
| What is epigenetics? how is it done? |
|
Definition
| Stable changes in gene activity that don't involve changes in DNA sequence. Done typically through DNA methylation, histone modification, regulatory non coding RNAs |
|
|
Term
|
Definition
| Small RNAs 22 nucleotides, that are highlighy conserved across many species. They bind to the 3' UTR (untransribed region) of mRNAs. They have a role in blocking translation of mRNA , bindng mRNA into stress granules and targeting mRNA for degradation |
|
|
Term
| Describe the miRNA processing pathway? |
|
Definition
| pre-miRNA leave the nucleus and then undergoes dicer processing to become a mature mIRNA, this can then repress mRNA |
|
|
Term
| What is the Storey Lab approach to miRNA? |
|
Definition
Start with a miRNA array comparing various sammples from control vs. frozen/hibernating species
Then do lead identification and lastly Q-PCR validation |
|
|
Term
| Do miRNA levels change in frozen models? |
|
Definition
| Yes, certain miRNAs were up-regulated in hibernating 13-lined ground squirrels. |
|
|
Term
| What does low miRNA levels in frozen animals tell us? |
|
Definition
| There is definitive gene inactivation |
|
|
Term
| Are any genes upregulated in freeze tolerance studies? |
|
Definition
| Yes, but only 1%. Examined which mRNAs are created through a cDNA library |
|
|
Term
| What genes are upregulated during frozen life? |
|
Definition
| Transcription factors that code for shock proteins and antioxidant enzymes |
|
|
Term
| What are various transcription factors that they found? |
|
Definition
| ATF (glucose regulated proteins), HIF (o2 tolerance), and a thousand more |
|
|
Term
| Where are a few future dieections they can go? |
|
Definition
| novel proteins, novel phosphorylations, turn it all of via miRNA |
|
|
Term
| What is the association between freeze tolerance and medicine? (2) |
|
Definition
Organ cryopreservation
A diabetes model - understanding the level of resistance to damage animals experienced by high glucose |
|
|
Term
| What are the unavoidable metabolic costs to freezing? |
|
Definition
| Severe metabolic depression causing cellular damages |
|
|
Term
| What dominates Mito metabolism? |
|
Definition
| The 8 ENZ metabolic, the TCA cycle |
|
|
Term
| What does the TCA cycle allow? |
|
Definition
| Allows for the complete oxidation of metabolic fuels (mainly CHOs and fatty) for ATP production |
|
|
Term
| Other than ATP, why use the TCA? |
|
Definition
| To generate low mol. wt precursors for anabolism - especially in growing tissues |
|
|
Term
|
Definition
| The uncoupling of the E.T.C for ATP production to rathrher use the gradient to make heat |
|
|
Term
| How did mitos come to eukaryotes? |
|
Definition
| Through endosymbionts in an ancestral bacterium that phagocytosed archaic aerobic bacterium |
|
|
Term
|
Definition
| During the cambrian explosion, led to a sudden burst in species diversity. Up to 30% saturation during dinosaur ears |
|
|
Term
| What are the three stages of Aerobic respiration? |
|
Definition
Oxidatin of fuels to make acetyl-CoA
Oxidation of Acetyl Group to 2co2
And high energy e-s carried by NADH funneling into the respiratory E.T.C, reducing 02 to H20 |
|
|
Term
|
Definition
| We can't live without it but it causes ROS and our eventual death |
|
|
Term
| What % of 02 is lost to ROS? |
|
Definition
|
|
Term
|
Definition
| Abiotic stresses, UV-B radiation and as an unwanted byproduct of E.T.C |
|
|
Term
| Why do we need antioxidants? |
|
Definition
To eliminate ROS
and to repair or catabolize damaged DNA, proteins and membranes |
|
|
Term
|
Definition
Because of mutant Superoxide Dismutase
SOD helps to turn the superoxide radical into hydrogen peroxide which is then taken care of by Catalse |
|
|
Term
|
Definition
Leaky Mitos that increase ROS production which damages DNA and other things
Also, we decrease our capacity to detoxify these ROS |
|
|
Term
| What is the mito genome redundancy? |
|
Definition
| We have about 5 copies of every gene, and thus when one is mutated by a ROS, the next copy can take over |
|
|
Term
| What is the free radical theory of aging proff? |
|
Definition
| ME knocked out SOD isozyme and it resulted in their very premature death |
|
|
Term
|
Definition
Mutant DNA repair enzyme and can't repair ROS damage
-premature aging |
|
|
Term
| What might be the only way to achieve immortality? |
|
Definition
Is to not carry out mito respiration
- Cancer cells turn off mitos and only use glycolysis for ATP production |
|
|
Term
| What are HeLa cells and why are they relevant? |
|
Definition
Cancer cell cultures from 1951 that are still in use
Cancer cells turn of mitos and restrict calories that leads to their longer life.
Thes have helped many biomedical advances and there are 50tons of these cells today |
|
|
Term
Did ROS detoxifying enzymes exist before 02?
What does catalase tell us about the anaerobic envt? |
|
Definition
Possibly, because lack of ozone layer exposed earth's surface to massive ionizing radiation
- Lead to constant ROS accumulation in shallow water
We needed these detox enzymes from teh begiging.
And since catalase creates 02, therefore there probably was a limited form of aerobic respiration that may have evolved alongisde life's origins |
|
|
Term
|
Definition
1)A cellular 2nd messenger crucial for growth stimulation and inflammation
2) Crucial for combating infection and bacterial pathogen (neutrophils use ROS to kill bacteria)
- NADPH oxidase catalyzes ROS formation |
|
|
Term
| Why did O2 have a role in sexual reproduction? |
|
Definition
Female fetus produces all of her eggs at birth
These eggs contain unused and brand new mito's that don't respire until ovulation occurs as an adult.
- We need to prevent o2 respiration in order to transfer mitos |
|
|
Term
| What are the three main components of a Mito? |
|
Definition
Outer membrane - contains protein porin that transports low mol wt molecules
Inner membrane - contains E.T.C and transporter proteins, these have infoldings called cristae
Matrix - highly concentrated and soluble interior. Contains the metabolic enzyme and mito-DNA |
|
|
Term
| What is the mitochondrial reticulum? |
|
Definition
| The dynamic and interconnected mito netowrk, organized through the cytoskeleton filaments of actin and myosin |
|
|
Term
| Which organisms would you expect to have highest mito %? |
|
Definition
| Those with the highest aerobic capacity (like hummingbirds, not carps) |
|
|
Term
| Describe mito protein incorporation process? |
|
Definition
| Starts as inactive precursors with a transit (signal) peptide on the free cytosolic ribosoms. IT is then incorporated via a membrane contact site, the signal is cleaved and the mature protein can become active |
|
|
Term
| What is the mito chromosome? |
|
Definition
The few mito protiens that are incorporated into a mito genome and made use mito ribosomes, rRNA and tRNA
- These are maternally derived, reproduce by binary fissions (adding membrane to existing replicated then dividing) |
|
|
Term
| What are the 2 roles of the TCA cycle? |
|
Definition
Aerobic ATP production
Generation of biosynthetic precursors |
|
|
Term
| What is the net reaction of one turn of the TCA cycle? |
|
Definition
OAA + acetyl-coa+NDP +pi +(FAD+) and 3 NAD(+)==> OAA and 2CO2 and NTP and FADH2 and 3 NADH
= 12 ATP |
|
|
Term
| Are fatty acids good aerobic fuels? |
|
Definition
| Yes, in fact you can generate 150 ATP per molecule of palmitate (common c16 acid) |
|
|
Term
| Describe bear Beta oxidation? |
|
Definition
| They keep their body temp close to 32, unlike most hibernators. They decrease their metabolic rate, but still use a lot of calories. So they use body fat as sole fuel during hibernation and the fat oxidation produces lots of water to replenish water lost during breathing |
|
|
Term
| Describe how the TCA cylce may be used for anabolism? |
|
Definition
| 50% of the carbon can be divereted away from ATP but rather to things like Fatty acids, glutamate, proteins, porphyrins, and aspirate - nucleic acids. |
|
|
Term
| In order to create biosynthetic precursors from the TCA cycleN, what must exist? |
|
Definition
| Needs an abundance of anaplerotic carboxylase in order to replenish the TCA cycle intermediates (Especially OAA) that have been diverted and drained towards biosynthesis |
|
|
Term
| Where is the role of generating bio precursors from the TCA cycle most important? |
|
Definition
| In actively growing tissues |
|
|
Term
| Why do anaerobic bacteria still do the TCA cycle? |
|
Definition
| Because they wnat a source of biosynthetic precursors, even though they lack alpha ketoglutarate dehydrogenase, and can't carry out the entire pathway. |
|
|
Term
|
Definition
| Multienzyme metabolon that controls entry of pyruvate into acetyl coa and thus controls glycolytic flux into the TCA cycle |
|
|
Term
| What two enzymes are closely associated with PDC? |
|
Definition
| THe PDC kinase and PDC phosphatase (PDC is active when de-p, so activating PDC phosphatase activates PDC) |
|
|
Term
| Why is CoA necessary for the acetyl group? |
|
Definition
| It contains a high energy thioester bond and therefore cna activate the acetate molecules |
|
|
Term
| What is the exact run PDC catalyses? |
|
Definition
| Pyruvate + NAD+ + CoA --> Acetyl-CoA and NADH + CO2 |
|
|
Term
Other than it's substrates, what does PDC need to do catalysis?
What is most important and why |
|
Definition
It has 96 subunbits and needs 5 different cofactors
most important is thiamine, needs it to function. No thiamine leads to no PDC and no aerobic respiration - leads to beriberi and loss of neural function |
|
|
Term
| How is plant PDC different than animal PDC? |
|
Definition
| Because a separate isozyme of PDC exists inside plastid |
|
|
Term
| What direct control exist on animal PDC, and animal PDC kinase phosphotase? |
|
Definition
Aniamls PDC is inhibited by high NADH, ATP And Acetyla COA. Animal PDC kinase is activated by high ATP and NADH.
- Kinase turns off PDC, so high adenylate charge turns down TCA respiration |
|
|
Term
| What direct controls exist on plant PDC and PDC kinase? |
|
Definition
Plant PDC is also inhibited by NADH, and acetyla COa (no ATP, adenylate charge doesn't matter)
- But, PDC kinase is inhibited by purvate (so lots of pyruvate keeps PDC active) |
|
|
Term
| What do we know about PDC phosphotase |
|
Definition
| not much, but that it should be inhibited whenever PDC is active. Also, that a muscle isozyme of PDC phosphotase is activated by Ca ions, which makes sense because they also trigger contractions which needs ATP. |
|
|
Term
| When is Animal and Plant PDC inactivated? |
|
Definition
| when phosphorylated by PDC kinase |
|
|
Term
| Other than PDC, what are the three most important enzymes of the TCA cycle? |
|
Definition
Citrate synthase (CS)
ISocitrate dehydrogenase (ICDH)
Alpha ketoglutarate Dehydrogenase (A-KG)
All catalyze non EM irreversible rxns |
|
|
Term
What feedbacks and inhibits CS, ICHD and a-KG in animals and plants?
What activates ACDH and a-KG ? |
|
Definition
CS is inhibited by Citrate and ATP, but ICDh and a-KG are inhibited by ATP and a high NADH:NAD+ ratio. ATP and Ca have no effect on plant ENZs, rather they care about NADH:NAD+ Ratio
However, increase in Ca leads to activating ICDH And A-KG to regenrate ATP consumed during contraction |
|
|
Term
| Why do plants do the glyoxylate cycle? |
|
Definition
They don't want fatty acids for ATP, but rather for biosynthesis. So they can't respire fatty acids in their mitos, rather do this to bypass 2 co2 releasing rxn of the TCa cycle.
Allows them to convert stored oil into sugars and for bacteria to grow on acetate as sole C-source |
|
|
Term
| Why do plants want to conver F.A to sucrose? |
|
Definition
| Becuase lipids are insoluble and sucrose is soluble, it will give the seedling energy in a soluble form |
|
|
Term
|
Definition
| A specialized organelle that contains B oxidation and glyoxylate cycle enzymes |
|
|
Term
| What are the two specific glyoxylate cycle enzymes? |
|
Definition
ISocitrate lyase - converts isocitrate into glyoxylate and succinate
Malate synthase - glyoxylate can become malate |
|
|
Term
| why do you need the two specialty enzymes of the glyoxylate cycle? |
|
Definition
| Because you want to create succinate to reincorporate into the TCA cycle to make sure it still can produce ATP in other ways and for precursors, but you dont want to waste carbons in order to get more ATP. These enzymes allow you to have the precursors for the TCA and use malate to create sucrose |
|
|
Term
| What is the net reaction of one turn of the glyoxylate cycle? |
|
Definition
| 2 acetyl-coa--> malate and 2Coa |
|
|
Term
| What converts OAA to PEP? |
|
Definition
|
|
Term
| Why is compartmentation crucial for glyoxylate cycle? |
|
Definition
| The acetyl-coa from fatty acids is not supposed to be sent to the mitochondria to be respired. Therefore plants put it to the glyoxysome in order to rather create malate and succinate, bypassing the ATP generating steps and making soluble sucrose. IF there was no compartmentation, ACetyl-coa would be unnecessarily used in the TCA cyle for respiration |
|
|
Term
| Describe the glyoxylate cycle in bacteria that lack compartmentation? |
|
Definition
| It allows bacteria to live on acetate as their sole C source. However, in order to ensure you create glucose and not ATP, the branchpoint at isocitrate must be tightly regulated |
|
|
Term
| How do bacteria regulate the conversion of acetyl coa to glucose? |
|
Definition
Through reversible phosphorylation of ICDH
- Through a bifuctional protein kinase - phosphatase. When it is growing on acetate, ICDH needs to be turned off so that the TCA doesn't happen, and thus is phosphorylated and acetyl coa shunts to the glyoxlyate cylce to make glucose. However, when it is grown on normal media, it can dephosphoryalted ICHD to activate it and allow the path to go to the TCA cycle - and respire glucose |
|
|
Term
| What does oxidative phosphorylation always depend on? |
|
Definition
| Upon 02 being present as the final electron acceptor, because otherwise their will be no way to pump protons and generate a PMF |
|
|
Term
| Why do we couple the e- flow to H+ pumping? |
|
Definition
| Because NADH to NAD+ is highly exergonic, and thus it can help push the endergonic proton pumping. |
|
|
Term
| What does H+ Pumping create? |
|
Definition
| A chemical and electrical gradient, known as the PMF |
|
|
Term
| What is the PMF used for? What else could it be used for? |
|
Definition
PRimariy to convert ADP and Pi --> ATP
Also could be used energy transport of metabolite and proteins into mito matrix and thermogenesis |
|
|
Term
| When can PMF generate heat(2)? |
|
Definition
Through proton pumping and ATPsynthase uncoupling with thermogenin
Also through non-energy and proton pumping thermogenesis through AOX pathway |
|
|
Term
| How many complexes are in E.T.C? |
|
Definition
| 4 respiratory complex (I to IV) and two mobile electron carriers (Q and Cytochrome C) |
|
|
Term
| In classical respiration, what happens with no pi or ADP? |
|
Definition
| There is no O2 consumption, because the E.T.C actually requires the phosphorylation of ADP (unless it's uncoupled) |
|
|
Term
| Other than hibernation, why do thermogenesis? |
|
Definition
| To help keep babies and hibernating bears warm |
|
|
Term
| what produces more ATP - NADH or FADH2? |
|
Definition
| NADH because it enters the ETC earlier, thus pumping more H+ and generating a bigger gradient (3 vs 2) |
|
|
Term
| What is the major cause of ROS production? |
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Definition
| When Q becomes overly reduced and cant shuttle electrons, it begins to leak ROS |
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Term
| What is the alternative pathway of the ETC called? |
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Definition
| The non-energy conserving pathway |
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Term
| In the non energy conserving pathway, what do e carriers have the option to do? |
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Definition
| They can transfer electrons directly to Q, instead of respirating complexes, and withhold from creating a H+ gradient. Thus, ADP and PI are no longer needed, as they are only crucial in relieving a PMF |
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Term
| How do non-conserving pathways of ETC work? |
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Definition
| NADH is internally dehydrogenated, passes electrons directly to Q, who then is oxidized and reduced Alternative oxidase (AOX). none of this requires proton pumping |
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Term
| Why is it called CN resistant respiration? |
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Definition
| CN can bind to and block Compound IV, blocking up the ETC and preventing all energy formation, also leading to many ROS. However, in plants, you can use the AOX pathway to prevent respiration from reaching compound iv and thus bleed off Q without causes damage via ROS |
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Term
| Why do plants use an alternative TCA cycle? |
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Definition
1) Thermogenic flowers
2) Biosynthetic role - you can make sure the TCA cycle still happens and precursors are made by NADH is oxidized - TCA cycle would stop if no NAD+ was available
3) Most importantly you do it to allow for plant acclimation to extreme environments when Pi or ADP aren't available. Normally, this would limit e flux and cause ROS, but AOX pathways allow for draining of e and limits the deleterious effects of environmental stress |
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Term
| What is the proof that plants need AOX for stress |
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Definition
| Transgenic plants lacking functional AOX have increased ROS level originating from their mitts |
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Term
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Definition
| Probably not, originated as an ancient prokaryote, loss of AOX occured during vertebrate evolution |
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Term
| What are two examples of fine controls of flux through the ETC? |
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Definition
Mammalian Complex I - Active when phosphorylated by cAMP protein kinase, and less active when de-p by protein phosphatase
Plant AOX - active when in reduced dithiol form via mitochondrial thioredoxin, Less active in oxidized disulphide form |
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Term
| Why is it important to study Pi nutrition? |
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Definition
Pi plays a crucial role in growth and metabolism
needed for DNA/RNA synthesis, P-lipid membrane synthesis, energy transduction (ATP) and metabolic control |
|
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Term
| What are 3 issues with Pi limitation today? |
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Definition
over 70% of soils are soluble Pi limited
Most crops require large inputs of Pi fertilizers for optimal yield
And 80% of Africa's farmland has become infertile due to overcultivation. |
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Term
| Why must we stop overuse of Pi fertilizers? |
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Definition
Over 100 million metric tons are applied /yr
Most produced from Rock -Pi which are fossilized bones and a limited resource.
It's expensive, energy intesinve and environmentaly destructive |
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Term
| 3 contributing factors to the phosphate crisis? |
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Definition
They are inefficient (only 20% of pi is actually incorporated)
They cause dead zones and eutrophication and toxic cyanobacteria
Aquatic pollution |
|
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Term
| Describe one morphological adaptation to Pi starved plants |
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Definition
They try to increase their root's surface area to increase the absorption of limiting Pi
- They focus on increasing root size and decreasing shoot length. This leads to many fine root hairs colonized by symbiotic fungi. Thus, they trade sugar for Pi
Overall, strategies are to increase SA for absorption of limiting Pi |
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Term
| Why is modern agriculture unsustainable to Pi starved plants? |
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Definition
| Because plowing and fertilizers kill mycorrhizae fungi, the symbiotic species. This makes it even harder to incorporate phosphate |
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Term
| What are two biochemical adaptations to Pi starved plants (like SA's Erica) |
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Definition
Increased Pi mobilization, scavenging and recycling
Metabolic acclimation to large decreases in Pi and Adenylate levels |
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Term
| What two ways to plants increase mobilization, acquisition and recyling of Pi? |
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Definition
1) HAve more high affinity Pi transporters (transport Pi at mmol levels) and increases efficiency of Pi uptake
2) PAPs, nucleases to help scavange and recyle enzymes |
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Term
| Describe the actions of Purple acid phosphotases? |
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Definition
| They function at acidic pH as intra and extracellular Pi salvage systems that hydrolyze Pi from esters. this is good because organic Piesters comprise >50% of total P content of many soils |
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Term
| What was found from ME and Puple acid phosphotaese? |
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Definition
| PAP26 is essential for efficient acclimation of arabidopsis plants to nutritional phosphate deprivation |
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Term
| Other than PAPs, how do plants scavenge Pi? |
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Definition
Through mobilizing membrane phospolipids and replace them with galacto and sulfonyl lipids instead
PRoven by showing that mutants defective in sulfolipid synthase show impaired growth in Pi deprivation |
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Term
| How does root organic acid excretion occur and what is it useful for? |
|
Definition
Helps to mobilize Pi for Pi starved plants.
Done largely by PEPC induction, which helps to make OAA and eventually malate. Malate helps to solubilize Pi from insoluble Rock Pi (which is coordinated to Ca). Malate then becomes Ca-Malate and Pi is freed. |
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|
Term
| What are three probable roles for PEPC during Pi stress? |
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Definition
Root organic acid (malate) excretion
Bypass to ADP limited pyruvate kinase
Intracellular Pi recycling |
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Term
| What is so interesting about the Harsh Hakea Plants? |
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Definition
| They have amazing adaptability to low Pi levels and are killed when Pi fertilizers are applied. EVen though they live in a harsh climate, there is amazing biodiversity in SW Australia |
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Term
| Why are Harsh Hakea so good at living in low Pi? |
|
Definition
Because they have cluster roots that excrete huge amounts of PEPC derived malate and citrate
Malate solubilized Pi from the other insoluble Rock Pi found in the soil. PEPC isozyme is activated by Protein kinase mediated phosphorylation |
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|
Term
| What two methods do starved pi plants use for metabolic acclimation? |
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Definition
Bypass adenylate and Pi dependant rxns through upregulating Pi and ATP independent enzymes in glycolysis, ETC and others rxns
Also, through using PPIase to conserve pH in vacuole, instead of ATP |
|
|
Term
| Why do plants upregulate H+ PPIase? |
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Definition
| It helps them to conserve the limited ATP they have while recyling Pi from PPI |
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|
Term
| What rxns in Pi starved plants actually form PI? |
|
Definition
|
|
Term
| What effect would large decreases in Pi and ADP have on E flow in ETC? |
|
Definition
| Should lead to severe decrease in flow through classical pathway. However plants use AOX and the non energy conserving pathway to allow TCA stuff to still happen and it also prevents excessive ROS production |
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|
Term
| What did transgenic plants lacking AOX in Pi deprived environments show? |
|
Definition
| They had impaired growth and increased incidence of ROS |
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Term
| Why is metabolic flexibility of plants so useful? |
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Definition
| IT represents a promising area for ME of stress tolerant crops |
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|
Term
| What three things include lipids? |
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Definition
| TGs, Phospholipids and Fatty acids |
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Term
| What are the roles of lipids? |
|
Definition
A store that provides aerobic fuels (via Fa in animal motos)
They provide a physiological effect, allowing animals to float
They are needed for signal transduction (DAG and IP3)
Membrane structure (p-lipids) |
|
|
Term
|
Definition
| Usually have an even number of C-atoms and can be saturated (no dbl bonds) or unsaturated |
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|
Term
| How are FA metabolized? Animals, Plants? |
|
Definition
They are made from/degraded to Acetyl-Coa
Animals - Synthesized in cytosol, and catabolized in Mito
Plants - Synthesized in plastid, and catabolized in glyoxysome |
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Term
| What do plants and animals use Acetyl Coa for? |
|
Definition
Plants use it for the gloxylate cycle to convert FA into Sucrose
Animals use it for TCA respiration and ATP production |
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|
Term
|
Definition
| They are fats that occur when you convert a healthy oil into a very bad oil (requires heat) |
|
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Term
| What does the fluidity of membranes depend on? |
|
Definition
Degree of FA saturation
When packed tighter with more satruated fatty acids, it leads to increases melting temp (harder to metl, more interactions)
When packed with unsaturated acids, it packs less tightly and thus it decreases the melting temp. (easier to melt, fewer interations) |
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Term
| What is homeoviscous adaptation? |
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Definition
| Where Poikilothermic animals and plants maintain an optimal level of membrane fluidy by increasing the number of unsaturated FAs as temp decreases (or pressure increases) |
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|
Term
| Where do vertebrates store excess FA? |
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Definition
| As triglycerides in target tissues (muscle) and storage organs (liver, adipose tissue) |
|
|
Term
| What is the purpose of TG stores? |
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Definition
| Usually they are reversible, so they can be respired. |
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|
Term
| CAn TG stores always be reversed? |
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Definition
| No, in some non-metabolic cases they can't, like with insulation or blubber of marine animals |
|
|
Term
| Give an example of a non-metabolic TG store? |
|
Definition
| In the sperm whale, the spermaceti oil organ (comprised of TG stores) helps the whale to match the density of surrounding water. In shallow, low density water, converts the TG stores to liquids. However, in deep water (they are more solid and dense) |
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|
Term
|
Definition
| Also as TG but usually in seeds. These are used as an energy source following germination, but only after conversion to soluble sucrose via glyoxylate cycle and GNG |
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Term
| What are the differences between using CHO or Lipids as fuels? |
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Definition
| Glycolysis is very fast and doesn't require O2, but is inefficient. OXidative phosphorylation is slow and oxygen dependant, but create much more ATP and thus is more efficient. |
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Term
| How do you mobilize TGs that are stored in adipose tissue? |
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Definition
It requires phosphorylation-activation of TG lipase
TG lipase needs to be activated by PKA (which is cAMP dependant). Converts a TG to 3 fatty acids and glycerol |
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Term
| What do you do if 02 is limiting in choosing between CHO and FA? |
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Definition
| You probably should store and use more glucose (As glycogen) because though you generate less ATP, you don't water 02 for respiration. |
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Term
| However, what do you choose between CHO and FA if body weight is an issue? |
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Definition
| You want to have the fuel that gives you the most ATP/g, i.e. the most efficient fuel. So birds and flying insects are best to store and use TGs, even though there is a greater O2 requirement and it takes longer |
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Term
| What is the main reason that intracellular freezing kills non adapted cell? |
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Definition
| Because of the physical damage done to subcellular stuctures by the ice crystals |
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Term
| CAn exracellular ice crystals be bad? |
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Definition
| Yes, becuase they can be sharp, puncturing membranes and also destroy the cell's structural integrity |
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|
Term
| What is the most devastating effect of freezing on an unprotected cell? |
|
Definition
| Osmotic shock and cell volume collapse because the extracellular solutes become very concentrated due to ice formation. Thus, water leaves the cell and cellular dehydration |
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|
Term
| What is the issue with a rapid reintroduction of O2 during thawing process? |
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Definition
| Formation of ROS that can react and damage macromolecules like DNA, proteins and metabolism |
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Term
| What are the five ways the Tree frog tolerates freezing? |
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Definition
| Controls ice formation, regulates cell volume, metabolic arrest and anoxia tolerance, reactivation of metabolism and preventing ROS damage |
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Term
| How does the tree frog control bad ice formation? |
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Definition
| It accumulates ice nucleating proteins in the fall, that induce a controlled extracellular ice formation at high (subzero) temperatures. This modulates the rate of acclimation and minimizes the physical damage it can cause as it forms blunt ice. |
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Term
| Why does the tree frog form ice crystals at high T? (2) |
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Definition
| To slow the rate of ice formation (the longer the time to make metabolic adjustments) and to minimize osmotic shock |
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Term
| How does the wood frog avoid cellular dehydration? |
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Definition
| Synthesizes a lot of cryoprotectants (glycerols, glucose) that balance osmolarity of intracellular fluid to preven too much dehydration and shrinkage. |
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Term
| How does the wood frog acquire so much glucose and glycerol to protect from cellular dehydraiton? |
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Definition
| IT catabolizes a huge glycogen reserve (through phosphorylating glycogen phosphorylase via cAMP mediated PK cascade). Partial dehydration leads to adenyl cyclase activation - activating cAMP - and activating glycogen phosphorylase. This allows blood glucose to spike from 1-5mM all the way to 400mM |
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Term
| Why are there a huge number of glucose transporters in the wood frog? |
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Definition
| Because it allows for it to deal with the new and and abundant glucose movement - needed to coutneract cellular dehydration |
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|
Term
Why does the wood frog do metabolic arrest?
How? (2) |
|
Definition
Allows the cell to be maintained over the long term.
Done through fine control regulation of pacemaker ENZs, mostly phosphorylation and shutting off of key metabolism enzymes (like PDC).
Also done through shutting down protein synthesis through phosphoryaltion of various tran factors and channel arrest to limit ATP consumption (helps with anoxia) |
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Term
| How does the wood frog spontaneously reactive after thawing? |
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Definition
| Throuhg dephosphorylation and activation of phosphoprotein phosphates, most notably activating pacemaker metabolic enzymes. It deP trans factors to allow protein synthesis to resume and also transcribed for AqPors to alllow for bulk water movement from extracellular to intracellular compartment (as ice thaws) |
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Term
| How does the wood frog prevent ROS damage during thawing? |
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Definition
| It has high activities of anti-ox enzymes, like SOD and catalase. these are far greater than in non freeze tolerant species. |
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Term
| What does hibernation provide a great example of? |
|
Definition
| The adaptive strategies of metabolic rate depression in order to survive extended periods of extremes. Falls below 2% of normal rate. Hibernation is not limited to cold, but also during dry seasons |
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Term
| Why are hibernation studies so useful? |
|
Definition
| For organ transplant technology |
|
|
Term
How do mammals that hibernate prepare?
What do they do during hibernation? |
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Definition
They eats lots of at to build up lipid fuel reserves
During hibernation, they iniitally use glucose/glycogen, but progressively increase use of storage/lipids (triglycerides) as their major metabolic fuel. |
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|
Term
| Why is hibernation not just a shut down of metabolism? |
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Definition
| Its a precise reorganization of metabolism such that energy production always equals the rate of energy usage |
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|
Term
| T/F hibernation bouts are always broken by brief periods of arousal? |
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Definition
| Yes, done in order to excrete urea (waste discharge) and to rehydrate |
|
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Term
| Give examples of fine control in hibernation? |
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Definition
| Phosphorylation (shut down) of key control enzymes of CHO catabolism, which promotes use of lipid stores.Channel arrest to save ATP. activation of phosphorylating proteins is accomplished through cAMP 2nd messangers, especially true of PDC which is phosphorylated and inactived. |
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Term
| Give example of coarse control in hibernation |
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Definition
| Some genes are upregulated, like PDC Kinase, ENZ involved solely in fat metabolism, antioxidant Enzy in ROS metabolsm. Increases expression arises from phosphorylation (Acivation) of several key transcription factors due to stress activated protein kinase cascade that involves phosphorylation of tryosine residues on the target proteins |
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Term
| Describe how viagra leads to increased blood flow? |
|
Definition
| More calcium leads to more contraction and less dilations. With more Cyclic nucleotides, you have more PK-A and PK-G activations, which phosphorylates various proteins, causing CA efflux, leading to less contraction and blood dilation. However, calcium levels only stay low until cAMP is broken into AMP via Phosphodiesterase isozymes. What viagara drug, as a structural analgous of guanosie and blocks active site of PDE5 (a potent inhibitor). What happens is that it maintains an increased cGMP level and decreases Ca and relaxes blood vessels in the penis |
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