Term
|
Definition
competitive inhibitor of phosphodiesterase 5. guanosine anolog.
PDE5 converts cGMP -> GMP. cGMP activates PKG, which phosphorylates proteins that lead to Ca++ efflux from cell -> relaxation -> vasodilation |
|
|
Term
| 2 common factors in plant and animal metabolism? |
|
Definition
1. structure of INTERMEDIARY metab is similar.
2. comparable range + sophistication of COURSE & FINE metab control. (IP3/DAG, Ca/CaM/Ca-dependent PK)
3. both have DEFENSE and COMMUNICATION mechs |
|
|
Term
| 4 examples of plant defense? |
|
Definition
1. OLIGOSACCHARIDE ELICITORS (produced when insect chews; inhibit gut proteases, indigestion)
2. SYSTEMIN (secretedby damaged plant cells, transported via phloem to trigger systemic defense response in undamaged cells)
3. METHYL-ESTER (volatile; released by host cell plant to warn neighbouring plants)
4. VOLICITIN (in caterpillar's saliva) signals plant to release volatile TERPENOIDS that attract specific wasp species; wasp larvae eat caterpillar (symbiosis) |
|
|
Term
| what's the crawling leaf? |
|
Definition
Photosynthetic marine mollusc ("sea slug") that uses captured algal chloroplasts to live out its entire adult life (1 yr) on a diet of sunlight and CO2. The chloroplasts were captured when the slugs were babies - they ate green algae.
An example of how plastids are NOT unique to plants!! |
|
|
Term
| what's apicocomplexa? toxiplasmosis? |
|
Definition
|
|
Term
2D electrophoresis:
what are the 2 dimensions?
what are the 2 problems?
what's the solution? |
|
Definition
|
|
Term
| 2 ways to confirm function of a gene predicted from genome sequence annotation? |
|
Definition
|
|
Term
| what is M.E.? what are the 2 basic approaches? + and - of each? |
|
Definition
use of recombinant DNA to modify FLUX of metabolites thru pathway.
1. shotgun transformation
2. rational M.E.
p 44 |
|
|
Term
what's a major focus of rational M.E.?
what are the 2 basic approaches for rational M.E.? example of each? |
|
Definition
sites of control (typically allosteric enzymes that catalyze irrev rxn)
1. engineer new pathway by adding foreign genes into plant (e.g. PHB synthase - biodegradable palstic)
2. alter pacemaker step by circumventing a feedback control mech or manipulating [allosteric effectors] - (feedback insensitive mutant of anthranilate synthase - Trp acuumulation - aromatic compounds)
45-46 |
|
|
Term
| what 3 things does metabolic arrest entail |
|
Definition
inhibit...
1. fuel catabolism
2. protein synthesis (Tsc, Tsl)
3. active transport ("channel arrest") |
|
|
Term
|
Definition
| oxidative pentose-phosphate pathway. alternative route of GLU OXD'N impt in BIOSYNTHESIS. makes NADPH (needed for reductive anabolism) & R5P (needed for DNA + RNA syn) |
|
|
Term
| Why does the TCA cycle stop when there's no O2? |
|
Definition
| electron flow stops. NADH and NADF not oxidized. therefore no NAD+ and FAD+ (needed by PDC and TCA enzymes) |
|
|
Term
| what's the shikimate pathway? |
|
Definition
2ry metabolism - syn of aromatic compounds (F, Y, W, lignin, alkalods (drugs!), vitamins, antioxidants)
- e.g. vinblastine = alkaloid |
|
|
Term
| (a) main sources and (b) storage of hexose in plants vs. animals |
|
Definition
source: food; photosynthesis
storage: glycogen; sucrose & starch |
|
|
Term
| what are biocompatible solutes? purpose? |
|
Definition
can accumulate during freezing, dessication or salinity stress.
eg. glycerol, Gly, Ala, opines.
no browning rxn (unlike glu) |
|
|
Term
| to cope w changing water salinity, eurhaline aquatic animals either... |
|
Definition
|
|
Term
| what are tardigrades and resurrection plants? |
|
Definition
|
|
Term
| non classical glycolytic pathways involve wither... |
|
Definition
p55-56
1. using PPi/Pi to replace/augment some of the ATP/ADP dependent reactions
- e.g. Entamoeba histolytica (anerobic amoeba)
2. alternative/parallel pathways to incr metabolic flexibility
- additional plastid pathway in plants
- cytosol: invertase + ATP-PFK v. SuSy + PPI-PFK |
|
|
Term
| how many ATP/sucrose do the invertase/ATP-PFK vs. the SuSy/PPi-PFK make? |
|
Definition
|
|
Term
| Similarities and differences between fine control of glycolysis in animals vs. plants |
|
Definition
|
|
Term
F26P2 (animals)
F29P2 (animals)
Pi (plants)
what do they do re kinetics? |
|
Definition
graphs -57, 59
F26P2 (animals)
- increases ATP-PFK's affinity for F6P
- decr nH from >2 to 1
- reverses inhibitory effect of ATP
F26P2 (plants)
- increases PPi-PFK's affinity for F6P
- increases Vmax
Pi (allosteric activator of ATP-PFK in plants)
- relieves PEP inhibition of cytosolic ATP-PFK |
|
|
Term
| what are the 3 molecular mechanisms for metabolic rate depression in stress-tolerant animals? |
|
Definition
1.ppl-inhibit PFK and PK....deppl-inhibit GP
2. decr F26P2
3. glycolytic metabolon dissociates |
|
|
Term
| what metabolite wasn't discovered until 1980? why? |
|
Definition
| F26P2: bc the 2nd Pi is acid labile (and metabolites are usually extracted under acidic conditions...to kill the enzymes and keep the metabolites intact) |
|
|
Term
| 4 characteristics of signal metabolites |
|
Definition
1. work @ v. low []
2. not intermediate of any metab pathway
3. formed from common metabolites central to metab
4. only used to regulate metab |
|
|
Term
| what does F29P2 signal in msc vs. liver? |
|
Definition
msc: AEC is low (e.g. burst sk.msc work; heart attack)
liver: glucose is abundant |
|
|
Term
| in the liver, starvation leads to inactivation/activation of what enzymes? |
|
Definition
|
|
Term
| functional vs. environmental anoxia? |
|
Definition
p 62
FUNCTIONAL:
- seconds
- lack of O2 during burst msc. work
- COMPENSATORY: incr glycolytic flux
- high ATP/sec, low ATP/glucose (high ATP production rate, but low efficiency)
ENVIRO:
- hrs-yrs
- lack of O2 in natural enviro
- EXPLOITATIVE
- decr glycolytic flux
- low ATP/sec, high ATP/glucose (low rate of ATP prd'n but high efficiency) |
|
|
Term
| 3 basic req'ments for anerobic energy prd'n? |
|
Definition
1. fermentable fuel (glu/glycogen; sucrose/starch)
2. pathway for ATP prd'n via SLP
3. maintenance of cellular redox balance (terminal glycolytic dehdrogenases: LDH, ADH, MDH*) |
|
|
Term
what's the pasteur effect?
what is the metabolic basis (3 pts)
what are 2 problems with pasteur effect? |
|
Definition
rate of glucose consumption is inversely proportional to [O2] ** incr glycolytic flux with anoxia **
1. activate glycogen phosphorylase (AMPK)...GP converts glycogen to G1P <-> G6P -> glycolysis
2. activate PFK (AMPK)
3. form glycolytic metabolon on actin/myosin filaments
1. self-pollution (acidosis)
2. run out of fermentable fuel (glycogen)
(p 63) |
|
|
Term
| what are the long term effects of chronic hypoxia in humans? (i.e. high altitude for long periods of time?) |
|
Definition
| hypoxia inducible factor - TF that activates glycolytic enzymes and glucose PM transporters (COARSE metab control) |
|
|
Term
| 4 adaptations of facultative (good) anaerobes (+ how does each adaption help them?) |
|
Definition
p 64 1. metabolic rate depression: decr glyc flux, inhibit prtn syn, channel arrest (CONSERVE FERMENTABLE FUEL RESERVES)
2. store more fermentable fuel (EXTEND SURVIVAL TIME)
3. Use more energetically efficient fermentative pathways (make more ATP/glu) (CONSERVES FERMENTABLE FUELS) - use PPi in place of ATP...PPi-PFK & PPDK (microbes, 5), SuSy pathway (plants, 8), H+-PPiase (plants) - divert flux of PEP from pyr to succinate/proprionate (4/6)
4. minimize acidosis - incr buffering capacity (turtles) - make alt anaerobic end-prdts that are biocompatible (Ala, Succinate, opines) or excretible (ethanol)
|
|
|
Term
| why do molluscs divert PEP away from pyruvates? what do they divert it to? |
|
Definition
divert to succinate +/or proprionate.
2 reasons:
1. minimize acidosis (succ is biocompatible, prop is excretable)
2. make more ATP/glu
glu -> 2 pyr (=2 ATP/glu)
glu -> 2 succ (=4 ATP/glu)
glu -> 2 prop (=6 ATP/glu) |
|
|
Term
| control of anaerobic metab in the channelled whelk (2 'problems'): |
|
Definition
65, 66
1. control PEP branchpoint
- after a few hours... ppl-inhibit PK (moving flux of PEP away from pyruvate)...now PEP -> OAA -> malate -> succinate or proprionate (PEP-CK, MDH)
- make more ATP/glu (4, 6) AND succ is biocompatible / prop is excretable.
2. decr glycolytic flux (MRD)
(a) covalent mod: deppl-inactivate GP; ppl-inactivate PFK 1,2
(b) decr Fru 2,6P2 (due to ppl of PFK2)
(c) disable glycolytic metabolon (on actin/myosin) |
|
|
Term
| explain how the PEP branchpoint is controlled in channeled whelk red muscle during exposure to environmental anoxia stress |
|
Definition
p.66
EARLY ANOXIA (1st hr: glycolytic flux high
-coupled fermentation of GLYCOGEN & ASP
-PK active (PEP -> PK -> Ala)
-Asp -> OAA -> Malate -> Succinate
-"coupled" b/c glutamate needed for pyr->Ala and a-KG needed for Asp-> OAA (enz's: Ala amino-transferase & Asp amino-transferase)
LATE ANOXIA (hr-day): glyc flux low
-ppl-inhibit PK
-PEP diverted from pyr to succ+prop
-PEP -> OAA -> malate -> succ+prop
-(Es: PEP-CK, MDH)
- this incr efficiency (4,6 ATP/glu rather than 2) |
|
|
Term
| in the channeled whelk, how is decreased glycolytic flux achieved during long term anoxia stress? |
|
Definition
p 66
1. Cov mod:
-deppl-inactivate GP
-ppl-inactivate PFK (1+2)
2.Decr F2,6P2 (via PFK-2 ppl'n which converts this bifunctional E into FBPase-2)
3. Dissociate glycolytic metabolon |
|
|
Term
delta G knot primed of...
NADH -> NAD+
PEP -> pyr |
|
Definition
|
|
Term
|
Definition
1. aerobic ATP prd'n (complete oxd'n of metabolic fuel to CO2 is MUCH more efficient than anaerobic, where it isn't completely oxidized)
2. make anaerobic precursors
- req's anapleurotic rxns (pyr-C in animals, PEP-C in plants)
3. thermogenesis (brown fat in animals; attracting insect pollinators in skunk cabbage)
- uncoupling prtn 'thermogenin' = mammalian H+ ionphore |
|
|
Term
| how was it shown that PK is ppl'd and inhibited after hrs of anoxia in the channeled whelk? (3) |
|
Definition
1. purified PK-aerobic and PK-anaerobic from the whelk. the latter showed:
a) decr Vmax
b) decr affinity for PEP
c) decr affinity for F16P2 (activator)
d) incr affinity for Ala (inhibitor)
2. Radioactive Pi was incorporated into PK under anoxic conditions
3. Purified PK-anoxia was treated with phosphatase (deppl-activated it) -> PK activity restored
p65 |
|
|
Term
| chaneled whelk controlling PEP branchpoint in time-dependent way was 1st ever evidence that... (2) |
|
Definition
1. controlling enz's via P/deP is an impt ADAPTATION TO ANOXIA in ANY ORG
2. molluscs can P/deP to control metab
p66 |
|
|
Term
Lou Gehrics =
Werner's syndrome = |
|
Definition
ALS: mutant SOD
Werner's: mutant DNA repair enz
p 68 |
|
|
Term
| 3 stages of aerobic respiration |
|
Definition
1. OXD'N of metab fuel to make A-CoA
2. OXD'N of acetyl groups to 2 CO2
3. e's (carribed by NADH, FADH2) channeled into ETC, eventually REDUCING H2O -> O2 |
|
|
Term
|
Definition
3 NADH
1 FADH2
1 ATP
2 CO2
1 CoA
input =
1 acetyl CoA
1 ADP + Pi
3 NAD+
1 FAD+ |
|
|
Term
|
Definition
|
|
Term
| how is the TCA cycle controlled? |
|
Definition
p 74
FEEDBACK INHIBITION OF...
1. Citrate Synthase
2. Isocitrate-DH
3. a-KG-DH
1. ATP, citrate
2. ATP, NADH
3. ATP, HADP
(plats = same minus ATP)
Also 2,3 activated by Ca2+ in msc |
|
|
Term
| purpose of glyoxylate cycle? |
|
Definition
1. plants: allows GERMINATING SEEDS to convert STORED OIL (fats in seeds) to SUGAR - gives the seedling ENERGY in the form of carb until photosynthesis can take over. makes G.N.G from fats poss!!
2. bacteria: allows them to grow on ACETATE as SOLE C-SOURCE |
|
|
Term
| GLYOXYSOME contains... (2) |
|
Definition
1. beta-oxidation enzymes
2. glyoxylate cycle enzymes
- Isocitrate Lyase
- Malate Synthase |
|
|
Term
| Bacteria don't have compartmentation (i.e. no glyoxyzome)... how do they separate glyocylate cycle + TCA cycle? |
|
Definition
Tightly controlled via P/deP!
During growth on glucose: deppl-activate IC-DH
During growth on acetate: ppl-inactivate IC-DH (allows ICL to predominate)
** a bifunctional kinase-phosphtase |
|
|
Term
| How do plants keep TCA cycle & ETC going when there is no ADP, Pi? |
|
Definition
alternative pathways:
NAD(P)H -DH (internal + external) -> UQ -> AOX.
e-s passed directly from NADH to UQ to AOX to O2, BYPASSING COMPLEXES 1,3,4 + their H+ PUMPS. Therefore, ETC (+ thus TCA) can function W/O ATP SYN.
77 |
|
|
Term
| benefits of AOX pathway in plants? |
|
Definition
ETC (+ thus TCA) can function w/o ADP+Pi (without ATP synthesis) @ COX.
Therefore...
1. helps during Pi starvation
2. resistant to cyanide (COX-inhibitor)
3. prevents over-reduction of UQ (and ROS generation) - AOX = an e-valve
4. allows for thermogenesis (flowe
rs) w/o ATP prd'n
5. allows for biosynthesis from TCA intermediates w/o ATP prd'n
77 |
|
|
Term
morphological adaptations of Pi starved plants? (3)
biochemical adaptions? (3) |
|
Definition
1. incr root growth, decr shoot growth
2. incr root hairs
3. mycorrhizae fungi (symbiosis: fungi gets sugar from plant; plant gets more Pi - a "trade")
1. High affinity PM Pi transports
2. Pi scavenging enz's
- PAPs (take Pi from P-esters)
- take Pi from membranes
3. Root org acid secretion
- induce PEPC + ppl-activate it
- PEP -> OAA -> malate -> excretion
- malate solubilizes Pi from rock-Pi
4. Bypasses + adenylate- and Pi-dependent rxns of glycolysis, ETC, vacuolar pH maintenance
- Glyc: PPi-PFK, PEP-C
- ETC: AOX + NADH-DHs
- tonoplast pumping: H+-PPiase
5. Pi recycling (2ry role of #4)
- PPi-PFK, PPDK, H+-PPiase, PEP-C |
|
|
Term
| How do cluster roots adapt to Pi starvation? |
|
Definition
INCR SA by growing root hairs
SECRETE HUGE AMOUNTS OF PEP-C
Roles of PEP-C in Pi stress:
1. Root org acid excretion:
- PEP -> OAA -> malate
- malate solubilizes Pi from rock
2. Bypass to ADP-limited PK
- PEP -> OAA -> malate -> pyr
3. intracellular Pi recycling
PEP + HCO3 -> OAA + Pi |
|
|
Term
| how was it shown that AOX helps plants during Pi starvation? |
|
Definition
transgenic tobacco plants lacking functional AOX had
a) impaired growth and
b) increased ROS
during Pi starvation |
|
|
Term
| functions of lipids in plants v. animals |
|
Definition
BOTH:
1. E store
2. phosphlipid bilayer
3. signal transduction (DAG + IP3)
ANIMALS:
1. metabolic fuel for ATP prd'n
2. insulation
3. floatation (sperm whale)
PLANTS:
1. In germinating seeds, stored oils (in seeds)used to make sugars (glyoxylate cycle)
2. Pi storage (via phospholipids) |
|
|
Term
| Where are fats synthesized and degraded in plants v. animals? |
|
Definition
ANIMALS:
synthesized in cytosol
degraded in mito matrix
PLANTS:
made in plastid
degraded in glyoxysome |
|
|
Term
| what's homeoviscous adaptation? |
|
Definition
in poikilothermic animals & many plants...
incr % unsaturated FAs during cold, high P
incr % saturated FAs during hot, low P |
|
|
Term
explain trade-off btwn energy yield and metabolic req'ments (whether to use sugar or fat as energy source)
Why do we start jogging on glucose then switch to FAs? |
|
Definition
FATS: higher ATP/g of fuel
SUGARS: higher ATP/O2
If weight is a problem: store + use more TAGs (lighter weight).
If O2 is limiting (high altitude, anoxia), store + use more glycogen
Reason 1:
Glyc: fast, O2-independent, inefficient
Os-Phos: slow, O2-dependent, efficient
Reason 2:
Glycogen mobilized faster, but there's less of it. TAGs mobilized slower, but there's more of them. |
|
|
Term
Describe freezing injury
What orgs have adaptations? |
|
Definition
1. physical damage (intra & extra-cellular)
2. Hyperosmotic stress -> cell dehydration
3. Freezing halts vital functions
4. Rapid thawing -> ROS
insects
intertidal molluscs
amphibs + reptiles |
|
|
Term
| 5 adaptations of verts to freeze tolerance |
|
Definition
1. Start freezing early (accumulate nucleating proteins).. why?
a. Time: allow adaptation (promote blunt ice formation rather than sharp crystals)
b. Minimal osmotic shock
2. Make biocompatible cryoprotectants (glycerol, glucose)
- ppl-activate GP
- incr glu transporters
3. Metabolic arrest: ppl-inactivate enz's involved in...
- energy metab
- prtn synthesis
- active transport
(and during thawing, reactivation of metab by deppl-activate the above)
5. induction of antioxidant Es and shock prtns |
|
|
