Shared Flashcard Set

Details

BIOL 334
Comparative Biochemistry
334
Biology
Undergraduate 3
12/02/2012

Additional Biology Flashcards

 


 

Cards

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
Look like green dots
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
The native Enz by itself
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
What is ME? Goal of ME
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
By 2050
Term
Why is Ag-Biotech?
Definition
Helps to alleviate world hunger by engineering crops that are drought or salt tolerant
Term
Four major goals of ME?
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
How does ME happen?
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
Define Rational ME?
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
Describe PHB ME?
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
What does PEPCK do?
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
No, but i should
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
no, F, much bigger
Term
What are seamounts?
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
True~
Term
Why does the TCA cycle stop when no 02 is available?
Definition
Inability to regenerate electron carriers NADH
Term
Where does PEP occurs?
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
No, but you should
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
What is estivation
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
What is anhydrobiosis?
Definition
Life without water, example of tardigrades
Term
Why tardigrades?
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
HK PFK and PK
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
Citrate (inhibitory)
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
What does F26P2 do?
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
What does glucagon do
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
What is a kinase?
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
only 3%
Term
What is SAPK?
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
What MicroRNA?
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
What is thermogenin?
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
When did 02 levels jump?
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
What is the 02 paradox?
Definition
We can't live without it but it causes ROS and our eventual death
Term
What % of 02 is lost to ROS?
Definition
4%
Term
Why do you get ROS?
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
Why does ALS happen?
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
Why do we age?
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
What's Werner Syndrome?
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
Why do we have ROS?
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
What is PDC?
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
What is the glyoxysome?
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
PEPCK
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?
Definition
When Q becomes overly reduced and cant shuttle electrons, it begins to leak ROS
Term
What is the alternative pathway of the ETC called?
Definition
The non-energy conserving pathway
Term
In the non energy conserving pathway, what do e carriers have the option to do?
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
Term
How do non-conserving pathways of ETC work?
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
Term
Why is it called CN resistant respiration?
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
Term
Why do plants use an alternative TCA cycle?
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
Term
What is the proof that plants need AOX for stress
Definition
Transgenic plants lacking functional AOX have increased ROS level originating from their mitts
Term
Is AOX plant specific?
Definition
Probably not, originated as an ancient prokaryote, loss of AOX occured during vertebrate evolution
Term
What are two examples of fine controls of flux through the ETC?
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
Term
Why is it important to study Pi nutrition?
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
Term
What are 3 issues with Pi limitation today?
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.
Term
Why must we stop overuse of Pi fertilizers?
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
Term
3 contributing factors to the phosphate crisis?
Definition
They are inefficient (only 20% of pi is actually incorporated)
They cause dead zones and eutrophication and toxic cyanobacteria
Aquatic pollution
Term
Describe one morphological adaptation to Pi starved plants
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
Term
Why is modern agriculture unsustainable to Pi starved plants?
Definition
Because plowing and fertilizers kill mycorrhizae fungi, the symbiotic species. This makes it even harder to incorporate phosphate
Term
What are two biochemical adaptations to Pi starved plants (like SA's Erica)
Definition
Increased Pi mobilization, scavenging and recycling
Metabolic acclimation to large decreases in Pi and Adenylate levels
Term
What two ways to plants increase mobilization, acquisition and recyling of Pi?
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
Term
Describe the actions of Purple acid phosphotases?
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
Term
What was found from ME and Puple acid phosphotaese?
Definition
PAP26 is essential for efficient acclimation of arabidopsis plants to nutritional phosphate deprivation
Term
Other than PAPs, how do plants scavenge Pi?
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
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.
Term
What are three probable roles for PEPC during Pi stress?
Definition
Root organic acid (malate) excretion
Bypass to ADP limited pyruvate kinase
Intracellular Pi recycling
Term
What is so interesting about the Harsh Hakea Plants?
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
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
Term
What two methods do starved pi plants use for metabolic acclimation?
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?
Definition
It helps them to conserve the limited ATP they have while recyling Pi from PPI
Term
What rxns in Pi starved plants actually form PI?
Definition
PPI PFK and PEPC
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
Term
What did transgenic plants lacking AOX in Pi deprived environments show?
Definition
They had impaired growth and increased incidence of ROS
Term
Why is metabolic flexibility of plants so useful?
Definition
IT represents a promising area for ME of stress tolerant crops
Term
What three things include lipids?
Definition
TGs, Phospholipids and Fatty acids
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
Describe FA structure?
Definition
Usually have an even number of C-atoms and can be saturated (no dbl bonds) or unsaturated
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
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
Term
What are Trans fat?
Definition
They are fats that occur when you convert a healthy oil into a very bad oil (requires heat)
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)
Term
What is homeoviscous adaptation?
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)
Term
Where do vertebrates store excess FA?
Definition
As triglycerides in target tissues (muscle) and storage organs (liver, adipose tissue)
Term
What is the purpose of TG stores?
Definition
Usually they are reversible, so they can be respired.
Term
CAn TG stores always be reversed?
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)
Term
How do plants store FAs?
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
Term
What are the differences between using CHO or Lipids as fuels?
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.
Term
How do you mobilize TGs that are stored in adipose tissue?
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
Term
What do you do if 02 is limiting in choosing between CHO and FA?
Definition
You probably should store and use more glucose (As glycogen) because though you generate less ATP, you don't water 02 for respiration.
Term
However, what do you choose between CHO and FA if body weight is an issue?
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
Term
What is the main reason that intracellular freezing kills non adapted cell?
Definition
Because of the physical damage done to subcellular stuctures by the ice crystals
Term
CAn exracellular ice crystals be bad?
Definition
Yes, becuase they can be sharp, puncturing membranes and also destroy the cell's structural integrity
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
Term
What is the issue with a rapid reintroduction of O2 during thawing process?
Definition
Formation of ROS that can react and damage macromolecules like DNA, proteins and metabolism
Term
What are the five ways the Tree frog tolerates freezing?
Definition
Controls ice formation, regulates cell volume, metabolic arrest and anoxia tolerance, reactivation of metabolism and preventing ROS damage
Term
How does the tree frog control bad ice formation?
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.
Term
Why does the tree frog form ice crystals at high T? (2)
Definition
To slow the rate of ice formation (the longer the time to make metabolic adjustments) and to minimize osmotic shock
Term
How does the wood frog avoid cellular dehydration?
Definition
Synthesizes a lot of cryoprotectants (glycerols, glucose) that balance osmolarity of intracellular fluid to preven too much dehydration and shrinkage.
Term
How does the wood frog acquire so much glucose and glycerol to protect from cellular dehydraiton?
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
Term
Why are there a huge number of glucose transporters in the wood frog?
Definition
Because it allows for it to deal with the new and and abundant glucose movement - needed to coutneract cellular dehydration
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)
Term
How does the wood frog spontaneously reactive after thawing?
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)
Term
How does the wood frog prevent ROS damage during thawing?
Definition
It has high activities of anti-ox enzymes, like SOD and catalase. these are far greater than in non freeze tolerant species.
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
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?
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.
Term
Why is hibernation not just a shut down of metabolism?
Definition
Its a precise reorganization of metabolism such that energy production always equals the rate of energy usage
Term
T/F hibernation bouts are always broken by brief periods of arousal?
Definition
Yes, done in order to excrete urea (waste discharge) and to rehydrate
Term
Give examples of fine control in hibernation?
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.
Term
Give example of coarse control in hibernation
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
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
Supporting users have an ad free experience!