Exam 4 Flashcards
Where does the citric acid cycle take place in the cell?
Mitochondria
In the presence of oxygen, pyruvate is converted to this
acetyl-CoA
a large, multi-subunit enzyme complex that links glycolysis and the citric acid cycle under aerobic conditions
PDH (pyruvate dehydrogenase)
provides a flexible linker between active sites within the pyruvate dehydrogenase complex
lipoamide
causes the disease Beriberi
deficiency in vitamin thiamine
the activated form of acyl groups and the fuel for the citric acid cycle
acetyl CoA
What are the steps involved in the conversion of pyruvate to acetyl CoA
- Decarboxylation
- Oxidation
- Transfer to CoA
Which of the following functions as a “flexible swinging arm” when it transfers the reaction intermediate from one active site to the next?
lipoamide
PDH phosphatase deficiency results in this
chronic elevated plasma lactate
Which PDH cofactor is affected by mercury and arsenide compounds?
Lipoamide
What are the three enzyme subunits in the PDH complex and the reactions they catalyse
E1: the PDH component and catalyzes the oxidative decarboxylation of pyruvate.
E2: is called dyhydrolipoyl transacetylase and catalyzes the transfer of an acetyl group to coenzyme A.
E3: The third enzyme subunit is dyhydrolipoyl dehydrogenase and catalyzes the regeneration of the oxidized form of lipoamide
What are the five essential cofactors for PDH?
TPP, Lipoic Acid, FAD, NAD+, CoA
How are the three active sites of PDH linked?
the long, flexible arm of the E2 subunit acts like a long robotic arm and carries the substrate from active site to active site
What are the two advantages that are derived from the coordinated actions of the three enzymes in the PDH complex?
The proximity of one enzyme to another enzyme increases the overall reaction rate and minimizes side reactions
What is the key means of regulation of PDH
The inactive form of PDH is the phosphorylated form of the E1 component. PDH phosphatase activates PDH by removing the phosphoryl group and PDH kinase phosphorylates and inactivates it again when the energy charge is high.
The formation of acetyl CoA limits the cell’s use of it to which two fates?
The oxidative decarboxylation of pyruvate to form acetyl CoA is an irreversible step in animals, so pyruvate cannot be reformed. It can either be completely oxidized to CO2 in the citric acid cycle or it can be incorporated into lipids.
the product found by the condensation of oxaloacetate and acetyl CoA
citrate
the citric acid cycle intermediate is at both the beginning and the end of the citric acid cycle
oxaloacetate
the product of the complete oxidation of carbon in the citric acid cycle
carbon dioxide
carbons from carbs enter the citric acid cycle in the form of
acetyl CoA
When is the citric acid cycle inhibited
high energy conditions
the first citric acid cycle intermediate to be oxidized
isocitrate
organisms that can convert fat into sugar use the ____ cycle
glyxolyate
a mutation in the active site of succinyl CoA synthetase where His is converted into a Lysine would result in
the loss of a sucking phosphate intermediate
isomerization of citrate is catalyzed by
aconitase
In which reaction is ATP directly formed in the citric acid cycle
conversion of succinylcholine CoA to succinate
In which step of the citric acid cycle is FADH2 formed
the conversion of succinate to fumarate
Are the acetyl carbons that enter the citric acid cycle the exact same carbons that leave as CO2? Briefly explain
No, the carbons are different. The carbons that leave as CO2 come from oxaloacetate that condensed with acetyl CoA. However, since succinate is symmetrical, and the carbons randomize, eventually all carbons are turned over.
How does the mechanism of citrate synthase prevent unwanted reactions?
The mandatory sequential binding of the two substrates prevent unwanted side reactions. Oxaloacetate must bind first to create the binding site for acetyl-CoA. This ensures that the oxaloacetate is present in the active site when acetyl-CoA so they can be condensed together. This prevents acetyl-CoA from being alone in the active site where it could be cleaved in a worthless reaction without oxaloacetate.
Explain how the citric acid cycle is regulated by the energy change and electron carrier molecules
The citric acid cycle is regulated at the two oxidative decarboxylation steps: isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase complex. Both of these reactions yield and NADH. Ultimately the CAC will yield ATP. When NADH (immediate product) and ATP (downstream product) levels are high, these enzymes are inhibited. When the energy charge is low, ADP will activate these enzymes.
Explain how the citric acid cycle is a metabolic hub within the cell
In addition to being a pathway for the generation of ATP, the metabolic intermediates of the CAC can be used as building materials for many important biological molecules. The intermediates oxaloacetate and alpha-ketoglutarate are used in the synthesis of purine and pyrimidine bases and many amino acids. Citrate can be used for sterol and fatty acid synthesis. Succinate can be used to make heme and chlorophyll groups. In some organisms, the glycoxylate cycle overlaps some steps of the CAC to create a pathway for making additional oxaloacetate (and ultimately carbs) from fatty acids (acetyl-CoA)
the enzyme that catalyzes the reduction of O2
Complex 4 or cytochrome c oxidase
this citric acid cycle enzyme is also part of an electron transport complex
succinate dehydrogenase
the prosthetic group in Complex 1 that accepts electrons from NADH
FMN
A strong oxidizing agent has a strong tendency to ____ electron(s)
accept
carries electrons from Complex 3 to 4
cytochrome c
Path(s) taken by a pair of electrons as they travel down the ETC
1) NADH to Complex 1 to CoQ to Complex 3 to Cytochrome c to Complex 4 to O2
2) FADH2 to Complex 2 to CoQ to Complex 3 to Cytochrome c to Complex 4 to O2
How does electron flow down the ETC affect proton transport
it leads to the transport of protons across the inner mitochondrial membrane from inside the matrix to the inter membrane space
Coenzyme Q is also called
ubiquinone
Which complex does not pump protons
2
Transfers electrons from a two-electron carrier to a one-electron carrier
Q cycle
Describe the path by which electrons from FADH2 enter the ETC
Succinate dehydrogenase, which forms FADH2, is part of the succinate-Q reductase complex (Complex 2). The FADH2 does not leave this complex, but transfers electrons to the iron-sulfur centers of the complex, and then to Q.
Explain why less ATP is made from the deoxidation of FADH2 compared to NADH.
NADH can transfer electrons to Complex 1, a proton pump, but electrons from FADH2 enter at Complex 2, which does not pump protons. Because fewer protons are pumped from the electrons of FADH2, less ATP is made per FADH2 molecule compared to an NADH.
In which direction do electrons flow in the ETC (in terms of reduction potential)?
The ETC proteins are arranged so that the electrons always flow from a more negative reduction potential to components with a more positive reduction potential.
Describe the mechanism for cytochrome c oxidase.
Two molecules of oxidized cytochrome c transfer electrons to the prosthetic groups of Complex 4. These reduced groups bind a molecule of oxygen to form a peroxide bridge. Two additional oxidized cytochrome c molecules donate electrons to Complex 4 and the addition of two protons cleave the peroxide bridge. The addition of two more protons causes the release of two water molecules.
How many protons are moved across the membrane when one NADH donates to Complex 1?
10 protons are officially translocated across the membrane when electrons from one NADH enter the ETC at Complex 1: 4 from Complex 1, 4 from Complex 3, and 2 from a half turnover of Complex 4
the name given to the hypothesis proposed by Peter Mitchell to explain how ATP synthesis is coupled to electron transport
Chemiosmotic hypothesis
Which ATPase submit is responsible for phosphorylation of ADP?
beta subunit
ADP transport into the mitochondria is coupled to
the export of ATP
the number of ATP molecules produced by the transfer of electrons from NADH (in the mitochondrial matrix)
2.5
ATP synthase is divided into these two parts. Where are they located
Fo: located within the membrane
F1: located on the matrix side of the inner mitochondrial membrane
Acceptor control of oxidative phosphorylation means that the rate of respiration depends upon the level of
ADP
When glucose is totally oxidized to CO2 and H2O, how many ATP molecules are made by oxidative phosphorylation out of a maximum yield of how many ATP molecules?
26/30
The F1 component of ATP synthase is composed of
3 alpha subunits
3 beta subunits
1 gamma subunit
Which ATP synthase subunit forms a ring within the membrane that rotates as protons are transferred back across the membrane?
Subunit C
Which ATP synthase subunit rotates during proton translocation and induces the necessary conformational changes in the catalytic subunit?
gamma subunit
Which ATP synthase subunit consists of two half-channels across the membrane for protons and forces the membrane component of ATP synthase to rotate in a single direction?
Subunit A
Compare and contrast substrate-level phosphorylation and oxidative phosphorylation
Both are ways of generating ATP. In substrate-level phosphorylation, a phosphate group is transferred to ADP from another molecule with high phosphoryl transfer potential. This reaction is done by a specific enzyme using a specific substrate. In oxidative phosphorylation electron transfer is used to generate a proton gradient across the inner mitochondrial membrane. The energy from the proton gradient is used by ATP synthase to generate ATP from ADP and Pi.
Describe the catalytic mechanism of ATP synthesis by the F1 portion of ATP Synthase.
The beta subunit is the catalytic subunit for ATP synthesis. Each beta subunit must go through three different conformations (O to L to T) in order to complete the reaction (substrate binding, catalysis and product release). These conformational changes are induced by the beta subunits’ interactions with the central gamma subunit. Three beta subunits interact with the central gamma subunit, each having a distinct conformation. As the gamma subunit rotates in the center of the beta subunits, the beta subunits cycle through the necessary conformational changes to make ATP. From the 3 beta subunits, 3 ATP molecules are produced per revolution of the gamma subunit.
Describe the experiment to prove the rotation of the gamma subunit in ATP synthase
Using cloned alpha3beta3gamma subunits, with the beta subunits tagged with a histidine that attached it to a nickel-coated slide, and using another fluorescent tag linked to the subunit, the rotation could be observed using a fluorescent microscope.
Why do the NADH molecules generated in the cytoplasm of muscle cells yield fewer ATP molecules than those generated in the mitochondrial matrix?
The electrons from the NADH molecules in the cytoplasm are transferred to FADH2 and into the Q pool and QH2 by the mitochondrial glycerol 3-phosphate dehydrogenase (glycerol shuttle). In this way, they bypass the proton pump Complex 1 and miss out on those protons
How does the number of subunit c’s contribute to the efficiency of ATP synthase
The number of subunits c’s that form the rotary motor of ATP synthase define the efficiency of ATP synthesis by determining the number of protons that must be transported to perform one revolution. The fear the subunit c molecules, the fewer protons required per revolution. Since 3 ATP molecules are always produced per revolution, fewer subunit c’s mean fewer protons required to make ATP
What is the advantage of the malate-aspartate shuttle in heart and liver cells in terms of NADH transport into the mitochondria
This allows for cytoplasmic NADH to be transported into the mitochondrial matrix. Electrons from cytoplasmic NADH are transferred to oxaloacetate to form malate which can be transported across the inner mitochondrial membrane. NADH is reformed as malate is converted back into oxaloacetate in the mitochondrial matrix. NADH in the matrix can then enter the electron transfer chain at Complex I and take full advantage of all proton-pumping complexes. This means more protons pumped per NADH relative to NADH electrons transferred using the glycerol shuttle.
What two factors contribute to the ADP/ATP exchange across the inner mitochondrial membrane using the ATP/ADP Translocase?
In the ATP/ADP Translocase, both molecules are being transported down their concentration gradients. ATP is moving out of the mitochondrial matrix and into the cytoplasm. ADP is moving out of the cytoplasm and into the mitochondrial matrix. Their relative charge difference also contributes to the energetics of their exchange across the membrane. ATP is more negative than ADP because of its additional phosphate group. Because the outside of the inner mitochondrial membrane is more positive due to the generated proton gradient, ATP has an incentive to cross the membrane based on its charge.
the process by which a bond is cleaved by the addition of orthophosphate
phosphorylysis
the type of bond that is located at the branch points in glycogen
alpha1,6 glycosydic
catalyzes the phosphorylation of glycogen phosphorylase
phosphorylase kinase
two enzymes required to degrade branches in glycogen
transferase and deb ranching enzyme (alpha 1,6 glycosidase)
Phosphoglucomutase requires this intermediate for the interconversion of glucose-1-phosphate and glucose-6-phosphate
G1,6BP
In skeletal muscle, the binding of this stabilizes phosphorylase b into the active form
AMP
Phosphorylase kinase becomes fully active by being phosphorylated and binding what
calcium
the transferase enzyme shifts a block of how many glycosyl units
three
the hydrolysis catalyzed by alpha-1,6-glucosidase releases this
a glucose molecule
In the liver, glycogen synthesis and degradation are regulated to maintain levels of ___ in the blood
glucose
Synthesis of glycogen starts with the phosphate group transfer from UTP to
glucose
the key regulatory enzyme in glycogen synthesis
glycogen synthase
serves as the primer used by glycogen synthase
glycogenin
the glycogen branching enzyme moves a block of _____ glucose residues to form a branch point at least ____ residues from a preexisting branch
7;4
glycogen synthase is converted into the active form by the action os
protein phosphatase 1
calcium binds and leads to the activation of which enzyme in glycogen degradation?
phosphorylase kinase
how is phosphorylase b converted into phosphorylase a
through the addition of a phosphate to a serine residue
phosphorylase kinase is regulated by
calcium ions and cAMP-activated PKA
two critical hormones that signal for glycogen breakdown are
glucagon and epinephrine
consists of dimer proteins, self-assembles eight glycosyl units, is the primer for glycogen synthase
glycogenin
creates a 1,6-glycosidic bond
branching enzyme
what are the three steps in glycogen degradation
1) Release of Glucose 1-phosphate from glycogen
2) remodeling of glycogen substrate
3) formation of glucose 6-phosphate
How does insulin stimulate glycogen synthesis?
Insulin triggers a pathway that activates protein kinases. These kinases phosphorylate and thus inactivate glycogen synthase kinase. Under these conditions, the PP1 removes the phosphoryl group from glycogen synthase, activating it.
How does glucagon inhibit glycogen synthesis?
Glucagon triggers a pathway that stimulates protein kinase A, which inactivates glycogen synthase through the action of glycogen synthase kinase.
Describe the mechanism by which hormones relay information about blood glucose levels to the glycogen synthesis and degradation enzymes.
The hormones interact with a membrane protein receptor, which converts GDP to GTP to activate adenylate cyclase. The production of cAMP starts a kinase activation cascade to control activity.
Compare and contrast the regulation of phosphorylase and glycogen synthase
Both are allosteric enzymes that can have a and b conformations (depending on phosphorylation) and T/R forms which give a gradient amount of activity. In the case of phosphorylase, the phosphorylated for is the a form which is more active. In the case of glycogen synthase, the phosphorylated form by is the b form, which is less active. Phosphorylase is activated by a kinase, while glycogen synthase is inactivated by a kinase. Alternatively, phosphorylase is inactivated by a phosphatase, while glycogen synthase is activated by a phosphatase.
the key source of biosynthetic reducing equivalents
NADPH
excess carbons of the pentose phosphate pathway are shunted to what other metabolic pathway?
glycolysis
ribulose 5-phosphate is the result of the ____ phase
oxidative
two molecules of this are formed in phase II of the pentose phosphate pathway
fructose 6-phosphate
the committed step of the pentose phosphate pathway
glucose 6-phosphate dehydrogenase
transfers a two-carbon fragment from a ketose to an aldose
transketolase
what tripeptide molecule is a redox buffer in the cells?
glutathione
Which sugars are converted into ribulose-5-phosphate by a single enzymatic step?
Ribose-5-Phosphate and xyulose-5-phosphate
the purpose of the pentose phosphate pathway
generating ATP & synthesizing 5-carbon sugars
What is the net reaction of the transketolase and transaldolase steps?
3C5 <=> 2C6 + C3
Glucose 6-phosphate dehydrogenase is inhibited by low levels of
NADP+
Several physiological modes are possible for the metabolic need for NADPH, ribose 5-phosphate, and ATP. In one scenario, such as found in adipose tissue, much more NADPH is required than ribose 5-phosphate. How is this maintained?
Under these conditions, NADPH is formed by the oxidative phase of the pentose phosphate pathway. Then the ribose 5-phosphate is converted via a series of reactions, including gluconeogenesis to regenerate G6P.
Explain the mode for the pentose phosphate pathway when only ribose 5-phosphate is needed.
Ribose 5-phosphate can be generated from F6P and GAP (glycolytic products) by running the nonoxidative phase reactions in reverse.
How does NADPH protect red blood cells from hemolysis?
In red blood cells, NADPH is used to reduce glutathione to its sulfhydryl form by the enzyme glutathione reductase. Under normal levels of reduced glutathione, peroxides, a reactive oxygen species, are eliminated by the enzyme glutathione peroxidase. This enzyme uses reduced glutathione as a reducing agent.
How can a deficiency of glucose 6-phosphate confer a physiological advantage?
The deficiency appears to be protective against falciparum malaria. The pentose phosphate path provides reduced glutathione and other molecules that this parasite requires for optimal growth. Thus, the deficiency of these products acts as a protection mechanism against malaria and is observed in greater frequency among populations from malaria-infested regions.
