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Exam 3
BCM ETC, Photo, lipid synthesis
175
Biochemistry
Undergraduate 4
03/15/2011

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Term
What is Ubiquinone?
Definition
a electron/proton receptor, one at a time, diffusible in lipid bilayer 1 electron=semiquinone
2 electrons=ubiquinol
Term
What are Cytochromes?
Definition

electron receptor, releases H uses Fe heme

only carry one electron at a time

Term
What is the difference between A B and C cytochromes?
Definition
a/b are tightly bound to proteins and membrane bound c is convently bound to 2 cysteines and is soluble
Term
What are Iron-sulfur proteins?
Definition
varying complexities Fe held in place by Sulfur
Term
What is in each complex of ETC?
Definition
complex 1-NADH DH, FMN and Fe-S prosthetic goups
complex 2-Succinate DH, FAD, Fe-S
complex 3-ubiquinone and Cyt c, Heme Fe-S
complex 4-cytochrome oxidase,heme Cua Cub
Term
What detergent breaks up complexes?
Definition
digitonin
Term
What does complex 1 do?
Definition

FMN accepts electrons from NADH in matrix, which funnels them through Fe-S proteins to N-2, which transfers to ubiquinone forming QH2 grabs two H from inner matrix

*transfers 4 H out*

Term
What blocks transfer of Electrons to ubiquinone?
Definition
Amytal (a barbiturate), rotenone (a plant product and
insecticide), and piercidin A (an antibiotic)
Term
What is vectorial in Complex 1?
Definition
transferring 4 protons one way out of inner matrix
Term
What does complex 2 do?
Definition
transfers electrons from succinate to FAD to Fe-S proteins to ubiquinone.
Term
How does NADH from glycolysis get transferred to ETC?
Definition
Malate-aspartate shuttle
of liver, kidney and heart
or Glycerol 3-phosphate
shuttle of brain and skeletal
muscle
Term
What does mito glycerol-3-phosphate DH do?
Definition
transfers electrons to QH2 losing ATP generated from complex 1 and 2
Term
How does Beta-oxidation pass complex 1,2 ?
Definition
Acyl-CoA DH transfers from FADH2 to electron transferring flavoprotein which in turn transfers to ubiquinone
Term
What does complex 3 do?
Definition
transfers electrons from Q to cyt c. and pumpes 2 H out of matrix
Term
What are the main subunits of Complex 3
Definition
cyt b, 2 hemes , Rieske protein Fe-S protein and Cyt c
Term
What is the Q cycle?
Definition
two step process to transfer electrons to cyt c. after first cycle it leaves Q-, second cycle picks up another - and 2 H to create QH2, in turn using 2 QH2 to transfer 1 electron
Term
What does complex 4 do?
Definition
uses Cu a,b. Cua transfers electron to heme a through FE-Cu center. This bids with Cub to form complex which drops electrons to Oxygen *also pumping 4 H out*
Term
How many electrons are needed to reduce oxygen?
Definition
4, but only happens one at a time, so substrate it bound tightly until forming water
Term
What makes heme a3 easy to inhibit?
Definition
only one axial ligand is bound in place, the other can be attacked by CN, CO NO
Term
What is the term for the association of the 4 complexes?
Definition
respirasome, made possibly for cardiolipin
Term
What complexes are proton pumps?
Definition
1- moves 4
3-moves 2
4-moves 4
Term
What are the two components of the proton motive force?
Definition
difference in concentration and charge
Term
WHat happens if there is a difference in electrons moving and entering electrons?
Definition
more ROS escape, in the form of superoxide radical, from partial reduced Q
Term
How is mito defended from radicals?
Definition
dimutase converts O2 to H2O2
glutathione peroxidase converts H2O2 to H20 and GSH-GSSG
Glutathione reductase converts GSSG to 2 GSH also NADH to NADPH
nicotinamide nucleotide transhydrogenase
Term
What two ways do plants produce heat?
Definition
external NADH DH , alternative NADH DH and alternative oxidase which all by pass proton pumping and release heat
Term
What is the chemiosmotic model?
Definition
Hydrogens only have one way back into mito inner matrix. osmotic force and chemi to create ATP
Term
WHat is the proof of chemosmotic theory?
Definition
blocking electron transfer didnt stop Oxygen consumption
blocking atp synthase stoped oxygen consumption
ionophores alway correction of H gradient, but not ATP generated
Term
What can carry protons across Mito membrane?
Definition
DNP and FCCP
Term
What takes the most energy in ATP synthesis?
Definition
release of ATP from the
enzyme, not formation of ATP, is the major energy barrier.
Term
What are the subunits of F1?
Definition
α3β3γδε
Term
What are the subunits of F0?
Definition
1 a 2 b and 10 c
Term
What are the three stages of Beta subunits?
Definition
bound to gamma unit, bound to ATP and bound to ADP
Term
What do the B units prevent?
Definition
rotation of alpha and beta units around gamma
Term
What does Adenine nucleotide translocase do?
Definition
transfer ADP into outer shell and ATP into matrix
Term
What does phosphate translocase do?
Definition
transfers H2PO4 in along with H
Term
What does ATP synthasome contain?
Definition
Adenine nucleotide translocase
phosphate translocase
and atp synthase
Term
What is Acceptor Control of ATP synthase ?
Definition
changes in ADP can increase or decrease activity
Term
What is the HIF1 regulation of ATP synthase ?
Definition
switches direction to fix Ph gradient, prevented by HIF1 which binds to F1 and prevents atpase activity
Term
What does the uncoupling protein do in mitochondria of brown fat cells?
Definition
destroys Hydrogen gradient to release heat
Term
What is needed to synthesize steroids in mito?
Definition
P-450, also found in ER to oxidize drugs
Term
How does mito trigger apoptosis ?
Definition
cytochrome c moonlights which triggers caspases. released Permeability
Transition Pore Complex (PTPC) to open mito
Term
WHat is the key to apoptosis?
Definition
Apoptosome converts inactive caspase 9 to an active form
Term
What is heteroplasmy?
Definition
defective mito passed on to infants
Term
What is the effect of no ATP on insulin release?
Definition
can not bind to K channels, hence hyperpolarizing cell and not allowing Ca to enter and open vesicles
Term
What is exciton transfer?
Definition
transfer of electron to another molecule not emitted
Term
What are the 4 parts of a photosystem?
Definition
light harvesting antenna
reaction center
electron transporting system
set of proteins to regenerate electrons
Term
What can replace the electron lost?
Definition
inorganic, an organic acid,
hydrogen sulfide or water
Term
What is the structure of chlorophylls ?
Definition
chlorin ring holding a Mg in place
Term
What is the difference between chlorophyll a and b?
Definition
a- methyl side chain
b-CHO side chain
more a then b
Term
What is corrin?
Definition
the ring structure of B12
Term
What do carotenoids absorb?
Definition
beta-carotene absorbs red-orange
Lutein( xanthophyll) absorbs yellow
Term
What pigment is present in both RC and antenna?
Definition
chlorophyll a
Term
Why does the components of light harvesting complexes change?
Definition
there is different areas which show varying wavelengths of light to absorb
Term
What are cyanobacteria and red algae light harvesting pigments ?
Definition
phycobilins, forming phycobilisome, getting the wavelengths at the bottom of the ocean
Term
What are the two types of photosystem ?
Definition
one in green sulfur bacteria(photosystem I) and the other in purple bacteria (photosystem II).
Term
What is the pathway of photosystem 1?
Definition
RC-ferredoxin-FeS- quinone-cytochrome bc1 complex then back to RC by cyclic photophosphorylation
Term
What happens in non-cyclic PSI?
Definition
electrons are used to reduce NAD instead of returning to RC, so H2S is used to regenerate electrons
Term
What is the pathway of PSII?
Definition
RC P870- pheophytin (Pheo)-quinone- cytochrome bc1 complex-cytochrome c2 complex back to RC
Term
What parts of photosystems are like complex III?
Definition
cytochrome bc1 complexes
Term
What connects PSII to PSI?
Definition
QA and QB transfer to cyt b6f complex, then to soluble plastocyanin, which than activates p700(RC of PSI )
Term
What is the modified path of PSI?
Definition
electron acceptor chlorophyll molecule,
A0, a phylloquinone, A1, three Fe-S
centers, Ferredoxin and then to NAD+.
Term
How is Oxygen produced ?
Definition
electrons are taken from H2O
Term
How many photons are needed to produce a single Oxygen?
Definition
8 photons, 2 H2O and 4 electrons removed
Term
What is cyclic electron flow or cyclic
photophosphorylation?
Definition
ferredoxin flow back to cyt b6f and regenerate P700 (RC PSI) NO oxygen produced!
Term
What do purple bacteria have?
Definition
PSII, variation which regenerates electrons to RC 870
Term
What PS do green bacteria have ?
Definition
PS I but uses H2S to regenerate electrons to RC. Yields a NADPH at the expense of H2S
Term
What are the two things that can excite RC of PSI??
Definition
-light photons absorbed by LHC or electrons from PSII via plastocyanin
Term
What is the difference between Qa and Qb?
Definition
A-tightly bound to protein, only goes to semiquinone
B- free moving, can be reduced to QbH2
Term
What replaces plastocyanin in some bacteria?
Definition
cytochrome c6
Term
What is the seqeunce of PSI in cyanobacteria?
Definition
a modified chlorophyll molecule,
A0, a phylloquinone, A1, three Fe-S
centers, Ferredoxin and then to NAD+.
Term
Where do the photons go besides to remove electrons from H2O?
Definition
they are used to lift electrons to an energized state.
Term
What is oxygenic photosynthesis?
Definition
creating ATP and NADPH from Oxygen, contains both PSI and PSII
Term
What molecule transfers electrons from photo system 2 to 1?
Definition
plastocyanin
Term
Where are the PS and ATP synthase located?
Definition
PSI and ATPS are located on the stromal lamellae. FOr access to NADP and ADP
PSII is in granal lamellae
Term
What controls the transition between State 1 and 2 in chloroplasts?
Definition
concentration of PQH2
Term
What happens in blue light?
Definition
PSII is activated more, so PQH2 is high, triggers a kinase, which P a Thr on LHC II , weakening the interaction with PSII
Term
What happens in less intense red light?
Definition
(STATE 2) PSI uses up PQH2, which increase PQ triggering dephosphorylation of LHCII,
Term
How do most herbicides work?
Definition
Paraquat- accept electrons from ferredoxin, reducing oxygen to superoxide
Diuron- competes for plastoquinone preventing flow of electrons
Term
What does the water splitting complex contain?
Definition
4 Mn, 1 Cl, 1 Ca
Term
What complexes do cyanobacteria have which are common to mitochondria and chloroplasts?
Definition
cyt b6f complex, the
soluble cyt c, and ATP synthase
complex.
Term
What are the three soluble electron transporters?
Definition
plastocyanin, cyt c and cyt C6
Term
What is the prosthetic group of halo bacterium?
Definition
bacteria rhodopsin (retinal)
Term
What are the three stages of carbon fixation?
Definition
1-turning 5 carbon sugar into 2 3 carabon sugars
2- reduce phosphoglycerate to glyceraldehyde-3-phosphate
3- regenerate ribulose 1,5 bisphosphate
Term
What is the turn over rate of rubisco?
Definition
3 CO2 molecules fixed per
second at 25oC.
Term
What activates rubisco?
Definition
high pH and Mg. also in dark the affinity for RBP goes up blocking rubisco. helped by rubisco activase
Term
What does rubisco activase do?
Definition
converts rubisco into active form after being bound to RBP upon ATP increase also releases CA1P
Term
What is the final activation of rubisco?
Definition
lysine is carbamoylated, then CO2 binds to rubisco, then Mg goes to form activated complex.
Term
What is a transition state analog in the dark to rubisco?
Definition
2-carboxyarabinitol 1-
phosphate (CA1P)
Term
What binds ribulose 1,5 bisphosphate ?
Definition
magnesium, which is attached by glutamate, asparate, and lysine carbamate forming a reactive enedoilate species
Term
What are the two steps of reducing 3-phosphoglycerate ?
Definition
phosphorylate to 1,3 bis phosphoglycerate
reduce to glyceraldehyde 3 phosphate
Term
What does the reduction of 3-phosphoglyerate cost?
Definition
2 ATP/CO2
2 NADH/CO2
Term
What is stage three of CO2 fixation?
Definition
convert 5 glyceraldehyde 3 phosphate to 3 ribulose 1,5 bisphosphate
Term
What enzyme does the chloroplast lack for glycolysis?
Definition
phosphoglycerate mutase
Term
What enzymes do animals lack for regeneration of ribulose?
Definition
Rubisco, SB and
Erythrose 4-Sedoheptulose 1,7-bisphosphate RPK and assimilate
SB
(5) Sedoheptulose 1,7-bisphosphate → Sedoheptulose 7-P + Pi RPK, thus cannot CO2
Term
Where does the cost of CO2 fixation come from?
Definition
6 ATP and 6 NADPH from creating the triose sugars
3 ATP to regenerate ribulose 1,5 bisphosphate
Term
What is the purpose of P-triose antiporter?
Definition
to put P back into stroma for ATP synthesis
also effectively moves
ATP and reducing
equivalents NAD(P)H from the chloroplast to the cytosol
Term
What is the effect of fructose 1,6-bisphosphatase?
Definition
used for sucrose synthesis, activated by light, High pH and Mg concentration
Term
What product is produced when oxygen binds to rubisco?
Definition
2-phosphoglycolate
Term
What are the steps for savaging energy from 2-phosphoglycolate?
Definition
1- convert to glycolate in chloroplast
2- oxidize to glyoxylate then convert to glycine in peroxisome
3- combine two glycine to form serine in mitochondria releasing CO2
Term
How is serine used for energy in plants?
Definition
sent to peroxisome, turned into hydroxypyruvate then glycerate. Shipped to chloroplast and put back into Calvin cycle
Term
What is the cost of photo respiration?
Definition
2 oxygen, releasing a carbon dioxide and one ATP
Term
What is glycine carboxylase?
Definition
used to condense glycine to serine, similar to PDH has different substrates.
PLP
lipoamide
THF
FAD
NAD+
accounts for alot of CO2 production during bright sun light
Term
What is unique about C4 plants?
Definition
PEP carboxylase is used in mesophyll cells to convert HCO3- to CO2, leading to OAA as first intermediate. OAA is converted to malate by Malate DH then transported to bundle sheath cell to release CO2 and proceed in calvin cycle
Term
What three enzymes allow for an enriched CO2 state in C4 plants?
Definition
malate DH, Malate enzyme and PEP carboxylase
Term
Why is C4 favored when it spends 5 ATP instead of the normal 3?
Definition
C3 plants become less productive and used extra ATP in regeneration of 2-phosphoglycolate
Term
What is unique about CAM plants?
Definition
they generate malate at night and store for day time use, to conserve water.
Term
Where are starch and sucrose made?
Definition
starch-plastids
sucrose-cytosol
Term
What is the activated form of glucose used to create strach?
Definition
ADP-glucose (not UDP glucose)
Term
What is the substrates of sucrose synthesis?
Definition
UDP-glucose and fructose 6-phosphate
Term
What is the benefit of sucrose?
Definition
inert, both anomeric carbons are used to form the glycosidic bond
Term
How is Sucrose phosphate synthase regulated?
Definition
SPS kinase inhibits, SPS phosphatase activates Glc-6-p inhibits SPSK, activites SPS
Term
How is SPS directly inhibited?
Definition
Pi binds to SPSP inactivating it, and directly effects SPS inhibitory
Term
What inhibits/activates PFK-2?
Definition
triose inhibits, while Pi activates
Term
What will favor starch synthesis?
Definition
slow triose production or defective f1,6Pase
Term
What is odd about cellulose synthesis?
Definition
created in cell, assembled outside of cell
Term
What enzymes are used by cellulose complex ?
Definition
sucrose synthase and cellulose synthase
Term
What is the transport molecule of plants?
Definition
OAA
Term
What is the precursor of both membrane lipids and triacylglycerol?
Definition
phosphatidic acid
Term
What is used to make phosphatidic acid?
Definition
fatty acyl-CoA and glycerol-3-phosphate
Term
How is Phosphatidic acid converted to TAG?
Definition
converted to diacylglycerol by Phosphatidic acid phosphatase
Then to TAG by acylation
Term
What is a secondary pathway of phosphatidic acid?
Definition
turning into glycerolphospholipid by adding a head group.
Term
What is insulins effect on TAG synthesis?
Definition
normal function stores carbs and FA.
In diabetes lack of Glut 4 channels so gluconeogenesis occurs and no FA stored.
Term
What is the triacylglycerol cycle?
Definition
constant breakdown of TAG and movement around the blood stream resynthesis in liver and shipped back to adipose tissue
Term
What enzyme converts TAG's back to FA and glycerol at adipose tissue?
Definition
lipoprotein lipase
Term
Where does the glycerol go before it enters the adipose tissue?
Definition
breaks off and stays in blood.
Term
How do the hormones glucagon and epinephrine effect FA synthesis?
Definition
They suppress glycolysis stimulating release of FA, since G-3P and DHAP are not supplied
Term
How does adipose tissue produce G-3P?
Definition
use some part of gluconeogenesis to get to G-3P, pyruvate comes from Amino acid breakdown
Term
What is the effects of glucocorticoids?
Definition
stimulates gluconeogenesis and glyceroneogenesis in liver and suppresses glyceroneogenesis in adipose tissue
Term
What enzyme does glucocorticoid regulate?
Definition
PEP carboxykinase by gene expression. causing more FFA in blood.
Term
What can glucocorticoids be used to treat?
Definition
chronic obstructive pulmonary disease
may lead to diabetes symptoms
Term
What are the mechanism of type 2 diabetes?
Definition
inhibition of glucose uptake by muscle, reduction of pancreatic insulin secretion, and inhibition of glycogen synthesis in
liver
Term
What is Thiazolidinediones used to treat?
Definition
activates PPARgamma2, increasing expression of PEP carboxykinase increasing glyceroneogenesis inturn reducing FFA in blood.
Term
Where are phospholipids created?
Definition
every cell except RBC
Term
What are the general pathways for phospholipid synthesis?
Definition
connecting CDP-phospholipid with alcohol
connecting CDP-alcohol with diacylglycerol
Term
How is phosphatidylcholine synthesized? (lecithin)
Definition
transferring activated choline (CDP-choline) to diacylglycerol
Term
What is the strategy for making phosphatidylethanolamine?
Definition
combining CDP-ethanolamine with diacylglycerol
Term
What is the livers unique mechanism for PC creation?
Definition
decarboxylation of PS and methylation of phosphatidylethanolamine
PS-PE-PC
Term
How is PS created? where?
Definition
made in ER, head group exchange of PE and PC
Term
How are cardiolipin and phosphatidylinositol synthesized?
Definition
activated CDP-diacylglycerol is transfered with alcohol
Term
What is the structure of cardiolipin?
Definition
two phosphatidyl group linked on the same glycerol
Term
What is the starting point of spingomyelin synthesis?
Definition
palmitoyl-CoA
Term
What is the precursor of cerebroside ?
Definition
adding a glucose head group to ceramide
Term
WHat is the process of cholesterol synthesis?
Definition
1.) condense 3 acteyl-CoA to form mevalonate
2.)convert to isoprene
3.) polymerize 6 isoprene to for 30 carbon chain squalene
4.) cyclization and changes
Term
What enzyme does statin inhibit?
Definition
HMG-reductase
Term
What is the committed step of cholesterol synthesis?
Definition
HMG-reductase
converting HMG-CoA to mevalonate
Term
What is the common precursor of cerebroside and sphingomyelin ?
Definition
ceramide
Term
When glucose is added to N-acylsphinganine it creates what?
Definition
cerebroside
Term
When adding the head group of PC to ceramide it creates ?
Definition
sphingomyelin
Term
What is atherosclerosis?
Definition
thinning of arteries
Term
What is isoprenylation?
Definition
the attachment of isopreniods to proteins on membranes. usaully attached to farnesyl
group (15-C) or geranylgeranyl group (20-C)
Term
How does concentration of cholesterol effect synthesis?
Definition
High concentrations stop expression of LDL receptors and inhibit HMG-redutase by activation protealysis, promotes esterifcation and storage of cholesterol
Term
How does glucagon regulate cholesterol synthesis?
Definition
phosphorylates and inactivates HMG redutase, insulin is opposite
Term
How does insulin promote expression of HMG reductase?
Definition
it goes through SREBP
Term
What is familial hypercholesterolemia
Definition
LDL receptor gene is defective, leadingto high blood levels of LDL
Term
What does failure to remove cholesterol do?
Definition
lower levels of HDL which leads to heart problems
Term
How do statins work?
Definition
similar to mevalonate so it competes for synthesis
Term
What makes up the core of lipoproteins?
Definition
cholesterol esters and Tags
Term
What is on the outside of lipoproteins?
Definition
phospholipids, cholesterol, AA and apolipoproteins
Term
What makes up chylomicrons?
Definition
TAGs apoB-48, apoC-II and apo-E
Made in ER of small intestine
Term
What does apoC-II do?
Definition
binds and activates lipoprotein lipase in capillary beds of aidpose, heart, muscle releasing FA for energy.
Term
A failure of apoB-48 production causes what?
Definition
build up on TAGs in intestine, since chylomicrons can not be created.
Term
What happens to the remnants of chylomicrons?
Definition
the apo-E receptor in liver causes endocytosis releasing cholesterol and degrading apolipoproteins
Term
Why is the difference in Km of adipose and heart lipoprotein lipase different?
Definition
so heart can always access fat in blood, fat can only when FA are high.
Term
What is type 1 hyperlipoproteinemia?
Definition
lack of apoC-II or lipoprotein lipase, leading to high chylomicrons in blood
Term
How are de novo TAG's packed?
Definition
VLDL to ship to other tissues from liver
Term
What do VLDL contain?
Definition
apoB-100, apoC-II apo-E rest is similar to chylomicrons
Term
What makes up LDL
Definition
cholesterol, cholesterol esters,apoB-100,
Term
How are LDL taken up?
Definition
apoB-100 mediated endocytosis at extrahepatic cells in order to supple cholesterol
Term
Lack of apoB-100 causes what?
Definition
failure to up take LDL (in liver) and leads to hypercholesterolemia
Term
What does HDL contain?
Definition
apoA-1, some phospholipid starting in the liver and intestinal epithelium
Term
What do HDL contain that combine cholesterol and FA?
Definition
LCAT lecithin-cholesterol acyl transferase, creating cholesterol esters
uses phosphatidylcholine and the starting point.
Term
What happens after LCAT acts?
Definition
cholesterol esters stay in HDL, lysophosphatidylcholine binds to serum albumin
Term
Once HDL are high is cholesterol esters what happens?
Definition
liver and steriodogenic tissue uptake. Liver engulfs whole thing, adernal cortex only takes cholesterol.
Term
What is the difference between nascent and mature HDL?
Definition
nascent have little cholesterol, and activate LCAT.
Term
What do Prednisolone and prednisone do?
Definition
anti inflammatory, synthetic cortisol
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