Midterm #1 Flashcards
The term Metabolism is used to refer to..?
Enzyme catalyze reactions collectively. This includes all reactions needed to synthesize biomolecules, and all reactions needed to break down food to provide our energy
Metabolism is ____ ____ and provides purposeful ___ _____ in which many multi enzyme systems cooperate
Highly coordinated, cell activity
Metabolism is the sum of ____ and ____
Catabolism, anabolism
What is the most critical function of metabolism?
To obtain ATP
A metabolic pathway is a term used to describe..?
A series of linked reactions that begins with a particular biomolecule and convert that starting molecule into a final product biomolecule through a series of enzyme driven steps
Pathways are ____ ____
Coordinately regulated
A key concept is that metabolic pathways can be interconnected in that they may share an ______
intermediate
The first committed step, which is often the ____ reaction in the pathway, is usually a ____ __ _____
First, point of regulation
Reactions that are regulated are often the ___-______ ___
Rate-limiting steps
Usually, the first reaction of a metabolic pathway is _____
Irreversible
Energy is required to power: ?
- Muscle contraction
- Cell movement
- Biosynthesis
Phototrophs obtain energy by capturing ____
Sunlight
Chemotrophs obtain energy through _______ __ _____ ____
Oxidation or carbon fuels
A simple way to measure the concentration of reactants and products when the reaction has reached _____, and thus ΔG is ___
Equilibrium, zero
How do cells get around the positive ΔG barrier by ?
Physically coupling two or more reactions together
The high energy bonds in ATP, of which there are 2, are called ___ ______ bonds since they are bonds between two acid groups that lose a water molecule upon formation
Acid anhydride
Why is ATP the energy carrier of the cell?
It has high phosphoryl-transfer potential, meaning that it readily transfers its phosphate group water
What are the 4 reasons that the hydrolysis of ATP is such a high energy bond?
- Electrostatic repulsion: ATP carriers four negative charges which repel one another when they are in close proximity
- Resonance stabilization: Pi, one of the products of ATP hydrolysis, has a greater resonance stabilization than any of the phosphates in ATP
- Increase in entropy: results in two molecules instead of 1, increasing the entropy
- Stabilization by hydration: water binds to ADP and Pi, which stabilizes these molecules and makes the reverse reaction less favourable
Oxidation reactions involve the ___ of electrons, the ___ of electrons is becoming reduced
loss, gain
The more reduced the starting carbon ..?
The more energy released during oxidation
What are two major sources of fuel that we use as humans: ? and ?
glucose and fatty acids
? are far more reduced than ? because the degradation of ? yields far more energy than ?
Fatty acids, glucose, fatty acids, glucose
___ is a second activated carrier of electrons
FAD
In many biosynthetic reactions, the precursor molecules are more ____ than the final product, so there is a need for ____ and ___. The primary donor is _____
oxidized, electrons, ATP, NADPH
____ is a carrier of 2-carbon units termed acetyl groups as well as longer carbon units referred to as acyl groups
Coenzyme A
Coenzyme A contains a pantothenic acid moiety, which is a __ ______
B vitamin
The metabolic pathways are regulated in 3 primary ways:
- The amount or abundance of an enzyme
- The catalytic activity of the enzyme
- Controlling the availability of substrates
The catalytic activity of an enzyme can be regulated in two ways:
- Allosteric regulation: the binding of inhibitors or activators
- Covalently modified in response to hormones and other signals that can lead to a change in the activity
In eukaryotic cells, glycolysis occurs in the _____
cytosol
Glycolysis serves two major functions:
- Generating ATP
- A number of intermediates of this pathway serve as building blocks for the biosynthesis
The capturing of energy from food occurs in 3 stages:
- Large molecules in food are broken down
- Small molecules are processed into acetyl CoA
- ATP is produced from the complete oxidation of the acetyl component of acetyl CoA
Starch and glycogen are degraded to ____, ____, and _____
glucose, maltose, oligosaccharides
In ruminants, cellulose is converted to ___ by cellulase
glucose
Lactose is converted to glucose by ____
lactase
Sucrose is converted to glucose and fructose by ____
sucrase
Maltose is converted to glucose by ______
maltase
Glucose must be ______ across cellular membranes
transported
What does Km mean?
The concentration of substrate which permits the enzyme to achieve half Vmax
Glycolysis can be divided into 2 stages:
Stage 1: net input of energy
Stage 2: net output of energy
What is the first step of Glycolysis?
Phosphorylation of glucose: when glucose enters the cell, it is rapidly phosphorylated by hexokinase to form glucose-6-phosphate
Why is the first step of glycolysis so important?
Since the phosphorylation of glucose traps it in the cell and prevents it from being transported out
What is the second step of glycolysis?
Glucose-6-P is converted to fructose-6-P by phosphoglucose isomerase. This is an isomerization reaction, which is only a rearrangement of atoms, in this case an aldose -> ketose
What is the third step of glycolysis?
Fructose-6-P is phosphorylated to form fructose-1,6-bisphosphate by phosphofructokinase, which is regulated allosterically. This is an irreversible reaction and is a regulatory step.
What is the fourth step in Glycolysis?
The cleavage by aldolase of fructose 1,6-bisphosphate to dihydroxyacetone phosphate and glyceraldehyde-3-phosphate
What is the fifth step in Glycolysis?
Dihydroxyacetone phosphate is readily converted to glyceraldehyde-3-P by triose phosphate isomerase in a reversible reaction since glyceraldehyde-3-P is the molecule that proceeds in the pathway
What is the sixth step in Glycolysis?
1,3-bisphosphate is generated by the oxidation of glyceraldehyde-3-P by glyceraldehyde-3-P dehydrogenase.
What is the seventh step in Glycolysis?
Phosphoryl transfer from 1,3-bisphosphoglycerate to ADP to form ATP catalyzed by phosphoglycerate kinase resulting in 3-phosphoglycerate. This is the first energy producing step in glycolysis
What is the eight step in Glycolysis?
3-phosphoglycerate is converted to 2-phosphoglycerate by phosphoglycerate mutase
What is the ninth step in Glycolysis?
2-phosphoglycerate is converted to phosphoenolpyruvate by enolase. PEP has high phosphoryl-transfer
What is the tenth step in Glycolysis?
Phosphoenolpyruvate donates its phosphate group to ADP by pyruvate kinase which produces ATP and pyruvate. This is an irreversible reaction
What is the net glycolysis reaction?
Glucose + 2Pi + 2ADP + 2NAD+ -> 2 pyruvate + 2ATP + 2NADH + 2H+ + 2H2O
The overall free energy change of glycolysis is about ?
-22 kcal/mol
Why is it referred to anaerobic glycolysis?
There is no requirement for oxygen up to this point
The metabolism of pyruvate achieves what?
Regenerating NAD+
How the metabolism of pyruvate occurs is depending on ? and ?
The organism, whether oxygen is available
What are the 3 possible fates of pyruvate?
- Acetaldehyde which turns into ethanol
- Lactate
- Acetyl CoA which is further oxidized
What is the most important aspect of the conversion of pyruvate to ethanol?
NAD+ is regenerated in the second step
What is the first step in the conversion of pyruvate to ethanol?
Pyruvate to acetaldehyde by pyruvate decarboxylase, which is a decarboxylation reaction (loss of CO2)
What is the second step in the conversion of pyruvate to ethanol?
Acetaldehyde is reduced to ethanol from electrons donated by NADH by alcohol dehydrogenase. This is a redox reaction
What is the reaction that converts pyruvate to lactate?
NADH is used to reduce pyruvate to lactate by lactate dehydrogenase, resulting in a regeneration of NAD+, this is a redox neutral reaction.
Is the reaction from pyruvate to lactate aerobic or anaerobic?
Anaerobic
Where does the reaction from pyruvate to lactate occur?
In muscle where oxygen supply is limiting
Describe the effects of lactate buildup in muscle
Lactate lowers pH, inhibits phosphofructokinase, slows the ability of muscle to metabolize glucose
Acetyl CoA is the entry point into the ? and the ? which oxidized glucose all the way to CO2 and H2O in an aerobic manner
citric acid cycle, electron transport chain
What is the reaction from pyruvate to acetyl CoA
Pyruvate consumes NAD+ and is converted to acetyl-CoA by pyruvate dehydrogenase complex and produces CO2 and NADH
Both of these sugars are metabolized by glycolysis, although the enter the pathway at different points?
Fructose and galactose
Galactose is converted to glucose 6-P by a series of 4 reactions, what is the 1st?
The phosphorylation of galactose
Galactose is converted to glucose 6-P by a series of 4 reactions, what is the 2nd?
The transfer of galactose to an activated carrier (UDP)
Galactose is converted to glucose 6-P by a series of 4 reactions, what is the 3rd?
The rearrangement of one hydroxyl group on galactose-1-P to form glucose-1-P by an epimerase, which is an isomerase
Galactose is converted to glucose 6-P by a series of 4 reactions, what is the 4th?
The product, gluose-1-P is then converted to glucose-6-P by an isomerase called phosphoglucomutase
Where does the majority of fructose metabolized?
The liver
Fructose is converted to glyceraldehyde-3-P by a series of 3 reactions, what is the 1st?
Fructose is phosphorylated to fructose-1-P by fructokinase
Fructose is converted to glyceraldehyde-3-P by a series of 3 reactions, what is the 2nd?
Fructose-1-P is then split into dihydroxyacetone phosphate and glyceraldehyde by fructose-1-phosphate aldolase
Fructose is converted to glyceraldehyde-3-P by a series of 3 reactions, what is the 3rd?
Dihydroxyacetone phosphate is an intermediate and can directly enter the pathway; but glyceraldehyde has to be phosphorylated to glyceraldehyde-3-P by triose kinase using ATP
Why can excessive fructose consumption lead to obesity, fatty leaver, and type 2 diabetes?
The key regulatory enzyme phosphofructokinase is bypassed and excess acetyl CoA is synthesized and converted into fats
Enzymes that catalyze irreversible reaction are potential sites of control; glycolysis has 3 such enzymes:
hexokinase, phosphofructokinase, and pyruvate kinase
Hexokinase, phosphofructokinase, and pyruvate kinase each have their ____ ____ increased or decreased by the binding of ___ ____ or through ____ ______
catalytic activity, allosteric effectors, covalent modification
In muscle, glycolysis is primarily controlled by the energy state of the cell, which is represented by the ___:____ ratio
ATP:AMP
In the ATP:AMP ratio: the __ the ratio the __ the energy state and less need for glycolysis; the ___ the ratio, the ___ the energy state and the more need for glycolysis
higher, greater; lower, lower
Which enzyme is the most important control point in mammalian glycolysis?
Phosphofructokinase (PFK)
PFK is controlled _____
allosterically
Why is PFK the most important control point?
- ATP binds to a site and inhibits is catalytic activity by decreasing the enzyme’s affinity for fructose-6-P
- AMP competes with ATP, but does not inhibit the enzyme
- A drop in pH also inhibits PFK during lactic acid buildup
Why isn’t hexokinase the control point in the pathway?
The phosphorylation of glucose to glucose-6-P is not the first committed step because glucose-6-P can enter other pathways like the PPP and glycogen synthesis
___ ___ which catalyzes the irreversible last step in glycolysis is the third enzyme that is regulated in muscle glycolysis. It is ______ ____ by ATP and activated by ____-__,__-______
Pyruvate kinase, allosterically inhibited, fructose-1,6-bisP
Why is pyruvate kinase activated by fructose-1,6-bisP?
Because it is an intermediate of glycolysis, and the product of phosphofructokinase. A rise in fructose-1,6-bisP is a clear indication of an increased flux through the pathway, so pyruvate kinase activity would be increased to handle the increased flux
The liver does not need energy for contraction, as it obtains most of its energy from the ?
breakdown of fatty acids
One of the main functions of the liver is to ?
maintain glucose levels in the blood
The glucose that the liver takes up is either ?, ?, or ?
- stored as glycogen
- used to generate reducing power in the form of NADPH
- converted via glycolysis
___ and __, the major regulators of PFK in muscle play ___ of a role in the liver
ATP, pH, less
___ is a major inhibitor of PFK in the liver
Citrate
Why is citrate a major inhibitor of PFK in the liver?
Since citrate is formed from acetyl CoA which is a product of pyruvate metabolism. Thus a high level or citrate is an indicator that biosynthetic precursors are at sufficient levels, and glycolysis can be slowed
Glycolysis in the liver is able to respond to high blood sugar in a unique way, what are the 3 steps?
- Glucose rises in the blood, which results in a flux through glycolysis and leads to buildup of fructose-6-P
- Fructose-6-P is converted to fructose-2,6-bisP, which is an allosteric activator of PFK
- PFK becomes activated
How does fructose-2,6-bisP function as an allosteric activator of PFK?
Increases PFK’s affinity for one of its substrates by blunting the inhibitory effect of ATP. So glycolysis is accelerated when glucose is abundant, this is called feedforward stimulation
Liver has a unique isoform of hexokinase called ___, that phosphorylates glucose once it gets transported into the cell
glucokinase
Glucokinase is a unique from muscle hexokinase in 2 key ways, what is the 1st?
Glucokinase has a 50-fold higher Km for glucose than hexokinase, so glucose-6-P is formed only when glucose is abundant, and allows the liver to take up what isn’t needed and store it as glycogen or metabolize it to other compound
Glucokinase is a unique from muscle hexokinase in 2 key ways, what is the 2nd?
Glucose in not inhibited by its product glucose-6-P, to it allows the liver to use the excess glucose that it takes up from the blood to avoid wasting it
What is gluconeogenesis?
Glucose can be synthesized from non-carbohydrate precursors
What are the three precursors of gluconeogenesis?
Lactate, amino acids, glycerol
How many reactions of glycolysis are irreversible, and must be bypassed for gluconeogenesis?
3
There are 3 reactions of gluconeogenesis that will be considered in detail, what is the 1st?
The synthesis of phosphoenolpyruvate from pyruvate by a two step reaction with oxaloacetate as an intermediate
There are 3 reactions of gluconeogenesis that will be considered in detail, what is the 2nd?
The synthesis of fructose-6-P from fructose-1,6-bisP
There are 3 reactions of gluconeogenesis that will be considered in detail, what is the 3rd?
The production of the final product, glucose, from glucose-6-P
In animals, the primary function of gluconeogenesis is to assist in ?
maintaining adequate glucose levels in the blood
What is the biggest consumer of glucose?
The brain
Gluconeogenesis is particularly important during periods of ___ or _____
fasting, starvation
In animals, gluconeogenesis occurs only in the __ and ___, with the ___ being the largest contributor
liver, kidney, liver
In plants, most of the glucose produce is used to synthesize ___, ___ and ___
starch, cellulose, sucrose
In glycolysis, most of the lactate formed by a _____ reaction in our bodies and is released into the blood and taken up by the ?
reversible, liver
Triacylglycerol can be broken down into ___ ___ and _____
fatty acids, glycerol
Glycerol is released from the ____ ____ into the blood, and taken up be the ____
adipose tissue, liver
In the liver, glycerol is converted to _________ ____
dihydroxyacetone phosphate
In glycolysis, the conversion of phosphoenolpyruvate to pyruvate is a strongly _____ reaction, and thus _____
exergonic, irreversible
For gluconeogenesis to proceed, the process starts in the _____ and involves the formation of ?, which drives the reaction forward
mitochondria, oxaloacetate by hydrolysis of ATP
What is the first step of gluconeogenesis?
Pyruvate to oxaloacetate via pyruvate carboxylase. This enzyme requires that acetyl CoA is bound to the enzyme, hence is referred to as an obligate allosteric activator
Oxaloacetate that is formed must now be ?
transported out of the mitochondria and into the cytosol
What is the second step of gluconeogenesis?
Oxaloacetate is converted to malate, and then back to oxaloacetate by the same enzyme: malate dehydrogenase
What is the third step of gluconeogenesis?
Pyruvate to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase
What about steps 4-9 of gluconeogenesis?
Once phosphoenolpyruvate is formed, it is metabolized by the enzymes of glycolysis to fructose 1,6-bisP and all are reversible
What is the tenth step of gluconeogenesis?
Fructose 1,6-bisP converted to fructose 6-P by fructose 1,6-bisphosphatase, which is a hydrolase that cleaves off the phosphate group
What is the eleventh step of gluconeogenesis?
Fructose 6-P is converted to glucose 6-p by phosphoglucose isomerase, and is reversible
What is the twelve step of gluconeogenesis?
Free glucose is produced by the hydrolytic removal of the phosphate group from glucose 6-P by glucose 6-phosphatase.
Generation of glucose from glucose 6-phophate is where?
in the lumen of the ER
Glucose 6-phosphatase is only present in the ? and the ?
liver and kidney
How many high transfer-potential phosphoryl groups are spent synthesizing glucose from pyruvate
6
The synthesis of glucose from pyruvate is energetically ?
unfavorable
The overall stoichiometry of gluconeogenesis is..?
2Pyruvate + 4ATP + 2GTP + 2NADH + 2H+ + 6H2O -> glucose + 4ADP + 2GDP + 6Pi + 2NAD+
Gluconeogenesis and glycolysis are ______ regulated
reciprocally
When glucose is abundant, _____ is favored; when glucose is scarce, ___ is favored
glycolysis, gluconeogenesis
Where is the major point of regulation of gluconeogenesis?
Where fructose 1,6-bisP is converted to fructose 6-P by fructose 1,6-bisphosphatase
Where is the major point of regulation in glycolysis?
The conversion of fructose 6-P to fructose 1,6-bisP by phosphofructokinase
Both fructose 1,6-bisphophsatase and phosphofructokinase are ____ ___ in the liver by biomolecules that reflect the energy charge in the cell
allosterically regulated
AMP, which reflects a ____ energy charge, activates ______, so stimulates ____ and produces ____
low, phosphofructokinase, glycolysis, ATP
Fructose 2,6-bisP, which reflects a ____ energy charge, activates ______, so stimulates ____ and produces ____
low, phosphofructokinase, glycolysis, ATP
Citrate, which reflects a ____ energy charge, activates ______, so stimulates ____
high, fructose 1,6-bisphosphatase
The interconversion of ____ and _____ is another point of reciprocal regulation
pyruvate, phosphoenolpyruvate
______ ___ is inhibited by biomolecules that reflect a high-energy charge, such as ATP; but high levels of ADP, that occur in low-energy states, inhibit the conversion of ____ to _____, which favors glycolysis
Pyruvate kinase; pyruvate, phosphoenolpyruvate
The effect of an allosteric regulator is highly dependent on ?. Describe this effect and what does this allow?
Its concentration, linear relationship. The effect allows for very fine-tuned control of enzyme activity
Rates of glycolysis and gluconeogenesis are adjusted to maintain ?
blood sugar levels
What is the only function of phosphofructokinase-2?
The production of the allosteric regulator fructose 2,6-P
How does blood sugar levels regulate phosphofructokinase and fructose 1,6-bisphosphatase?
- Rise of glucagon
- Stimulates a cAMP signal cascade that leads to the phosphorylation of the same residue
- Activates the phosphatase activity domain while inhibiting the kinase domain activity
- Results in lowering of fructose 2,6-bisP
- Results in flux toward glucose synthesis
Normally, insulin ____ gluconeogenesis. So when people have insulin resistance, the liver ?, which is called hyperglycemia
inhibits, continuously produces glucose even when levels are sufficient
What kind of drugs are used to treat people with type 2 diabetes (aka insulin resistance)?
Inhibiting liver gluconeogenesis, and increasing insulin sensitivity
Lactate formed by muscle can be converted to glucose in the liver via the ____ ____
Cori cycle
Describe the Cori Cycle?
- When O2 is limiting, muscle produces lots of lactate from pyruvate, which gets into blood
- Much of this lactate is taken up by the liver, converted to pyruvate, then back to glucose by gluconeogenesis
- Then the liver replenishes glucose in the blood, which gets back to muscle
What is a central role of the Pentose Phosphate Pathway (PPP)?
Produce NADPH, which is the currency of reducing power
The PPP also generate ____ __-_____, which provides the sugar component for ___ and thus for ?
ribose 5-phosphate, nucleotides, DNA and RNA
The PPP shares key intermediates with glycolysis, and as such, the regulation of these pathways are ______ regulated
coordinately
The PPP has 2 phases, what is the 1st?
The oxidative phase, glucose 6-P is oxidized, NADP+ gets reduced to NADPH
The PPP has 2 phases, what is the 2nd?
Non-oxidative phase, ribulose-5-P is converted to ribose-5-P. There is also the interconversion of 3-, 4-, 5-, 6-, and 7-carbon sugars
What is the importance of the interconversions of sugars in the PPP?
A way for the excess 5-carbon sugar to be converted to intermediates of glycolysis. Important since the need for NADPH is much higher than the need for ribose-5-P, ultimately allows for greater efficiency.
The Oxidative phase of the PPP has 3 reactions, what is the 1st?
Glucose 6-P converted to 6-phosphoglucono-δ-lactone by glucose-6-P dehydrogenase, one NADPH is produced. This is a oxidation-reduction reaction
The Oxidative phase of the PPP has 3 reactions, what is the 2nd?
6-Phosphoglucono-δ-lactone is converted to 6-phosphogluconate by lactonase
The Oxidative phase of the PPP has 3 reactions, what is the 3rd?
6-phosphogluconate is converted to ribulose 5-P by 6-phosphogluconate dehydrogenase, an NADPH is formed
For every glucose-6-P molecule that enters the PPP, ? NADPH are produced?
2
The Non-Oxidative phase of the PPP has 1 reaction, what is it?
Converting ribulose-5-P to ribose-5-P by phosphopentose isomerase
Where does the PPP occur
in the cytosol
PPP is primarily regulated by the cytosolic concentration of ?
NADP+
What is the rate-limiting step of the PPP?
The first step, which is catalyzed by glucose-6-P dehydrogenase
If NADP+ is a substrate for glucose-6-P dehydrogenase, a low concentration of NADP+ will result in ? in the PPP
a low rate through the rate-limiting step
The rate-limiting step of the PPP is further inhibited by the fact that NADPH is a ______ ______ of NADP+. So when NADPH is high, there is ?
competitive inhibitor; no need for the oxidative portion of the PPP
The fate of glucose-6-P is highly dependent on the cell’s need for ____. If the need is low, then ?; if the need is high, then ?
NADPH. more will be metabolized through glycolysis; more glucose-6-P will be metabolized through the PPP
The decision as to whether glucose-6-P will be metabolized through the PPP or glycolysis is guided by ?
The need of the cell for ribose-5-P and ATP
What is Mode 1 in determining if glucose-6-P will be metabolized through the PPP or glycolysis?
- Need for Ribose-5-P is greater than the need for NADPH.
- Metabolized through glycolysis to fructose-6-P and glyceraldehyde-3-P
- These will then be used by the 2nd phase of PPP via transketolase and transaldolase to produce ribose-5-P
What is Mode 2 in determining if glucose-6-P will be metabolized through the PPP or glycolysis?
- The need for NADPH and ribose-5-P are the same
- Glucose-6-P is metabolized through phase 1 of PPP
- Ribulose-5-P produced is converted to ribose-5-P
What is Mode 3 in determining if glucose-6-P will be metabolized through the PPP or glycolysis?
- Need for NADPH is greater than ribose-5-P
- 3 reactions occur in the liver, end result is complete oxidation of glucose-6-P to CO2 with the formation of NADPH
1. Glucose-6-P converted to ribulose-5-P by phase 1 of PPP
2. Then converted to fructose-6-P and glyceraldehyde-3-P by phase 2 of PPP
3. These are used in gluconeogenesis - 1 glucose-6-P is oxidized to 6CO2 and 12NADPH
What is Mode 4 in determining if glucose-6-P will be metabolized through the PPP or glycolysis?
- Both NADPH and ATP are required
- Glucose-6-P is oxidized through phase 1 of PPP
- Ribulose-5-P produced is converted to fructose-6-P and glyceraldehyde-3-P by phase 2 of PPP
- Both then enter glycolysis and metabolized through pyruvate that produces ATP
Glycogen is a ___ of glucose and acts as a ___ form
polymer, storage
Both glycogen synthesis and breakdown pathways connect with glycolysis, gluconeogenesis, and the PPP via ?
glucose-6-P
Where does glycogen synthesis begin?
A protein called glycogenin
The two chemical linkages present in glycogen are ? and ?, which represent the branch points?
α-1,4 glycosidic bonds, α-1,6 glycosidic bonds. α-1,6 glycosidic bonds are the branch points
Where does glycogen synthesis and breakdown occur in glycogen?
Both occur at the non-reducing ends of glycogen
Due to the ____ structure, glycogen has many sites where synthesis and degradation can occur
branched
There is an ___ of energy required to ____ glycogen; how many ATP for every incorporated glucose?
input, synthesize; 2
The energy yield from the ____ of glycogen yields far ____ ATP; how many ATP for every glucose-6-P produced when completely oxidized?
breakdown, more; 31
Glycogen is an ____ storage form of glucose
efficient
______ uses an activated form of glucose, ? . This intermediate is not a part of _______
Glycogenesis, UDP-glucose. glycogenolysis
For glycogenesis, ____ itself is not the substrate, ? is used as the activated precursor
glucose, UDP-glucose
What are mutases?
Isomerases that change the position of a phosphate group
What enzyme is needed to convert glucose-1-P to UDP-glucose?
UDP-glucose pyrophosphorylase
What enzyme uses UDP-glucose to transfer the glucose portion to an existing glycogen molecule?
Glycogen synthase
Glycogen synthase ? to carbon 4 on a glycogen molecule, forming ?
adds a glucose, α-1,4 glycosidic bond
Glycogen synthase can only ass glucose units onto an oligosaccharide that consists of at least __ _____ units
4 glucose
Glycogen acts both as the ___ and a ____ for this reaction. The oligosaccharide formed on glycogenin serves as the ____ for _____ ___ to act on
catalyst, substrate. primer, glycogen synthase
Glycogen synthase only catalyzes α-1,4 linkages, so what specifically catalyzes the formation of α-1,6 linkages and thus a new branch point
branching enzyme
New branch points must be at least __ residues away from an existing one, and averages between __-__ residues apart
4, 8-12
In glycogen synthesis, ____ ____ is the regulated step
glycogen synthase
Glycogen synthase is most sensitive to ?, which is a strong allosteric activator of the enzyme
glucose-6-P
The ______ form, called glycogen synthase __, is the active form; the ____ form is called glycogen sythnase __
unphosphorylated, a; inactive, b
Both ___ and ___ influence the phosphorylation state of glycogen synthase
insulin, glucagon
The principle enzyme that degrades glycogen is ?, but because of _____ ___, there are __ additional enzymes required
glycogen phosphorylase, branch points, 2
Glycogen phosphorylase cleaves off glucose units one at a time from the non-reducing end by catalyzing a ____ reaction
phosphorolysis
Why is glycogen degraded by phosphorolysis instead of hydrolysis?
Using phosphorolysis, the release sugar (glucose-1-P) is already phosphorylated, so we don’t need to use an ATP to do so. There is hence an energy advantage
Glycogen phosphorylase stops working when it reaches a residue that is 4 glucose units away from a ___ ____
branch point
When glycogen phosphorylase stops working, it is at this point that the other two enzymes take over: ?
- Transferase moves the terminal 3 glucose residues as a block, and transfers them to another branch
- Then the debranching enzyme hydrolyzes the α-1,6 linkage, releasing a free glucose molecule
What happens to the glucose1-P that is released by glycogen degradation?
Converted to glucose-6-P by phosphoglucomutase. The fate of this molecule then depends on the tissue:
- Liver: molecule is acted on by glucose-6-phosphatase, that cleaves the phosphate group producing free glucose
- Muscle: metabolized through glycolysis for ATP
Glycogen phosphorylase is regulated by ____ interactions and reversible _____
allosteric, phosphorylation
Glycogen phosphorylase can be phosphorylated by ____ ____ to a ____ active “a” form; and, can be dephosphorylated by ____ _____ to a ___ active “b” form
phosphorylase kinase, more; phosphorylase phosphatase, less
Glycogen phosphorylase is allosterically regulated by ___, which ____ the enzyme
glucose, inhibits
The isoform of glycogen phosphorylase is not just subject to allosteric regulation, but also ____ ____
covalent phosphorylation
In muscle, AMP is a potent allosteric ___ of muscle phosphorylase b; while ___ and ? inhibit the enzyme
activator; ATP, glucose-6-P
Its only glycogen phosphorylase __ in muscle that is sensitive to allosteric modifiers; glycogen phosphorylase __ is fully active regardless of the levels of AMP, ATP, and glucose-6-P
b, a
What are the 2 hormones that trigger glycogen breakdown?
Epinephrine and glucagon
Epinephrine and glucagon work similarly in the muscle and liver to activate glycogen phosphorylase, by what is not as a ______ _____
regulatory cascade
When glucagon or epinephrine bind to their respective receptor, an enzyme called ? becomes activated
adenylate cyclase
Adenylate cyclase catalyzes the conversion of ATP to ?
cyclic AMP (cAMP)
cAMP bind to protein kinase __, and causes a _____ change such that the catalytic subunit is able to carry out _______ on target proteins. One of these proteins is _____ ____, which becomes activated when phosphorylated. It in turn phosphorylates phosphorylase __, which converts it to the active form. Glycogen breakdown is thus _____
A, conformational, phosphorylations, phosphorylase kinase. b, stimulated
Phosphorylase kinase is activated when ___ binds to a subunit of this enzyme, called ____
Ca2+, calmodulin
Muscle contraction is triggered by the release of ____, while muscle contraction is stimulated glycogen breakdown is as well, which provides the fuel for ___ ____
calcium, ATP generation
Glycogen synthesis and breakdown are ____ regulated
reciprocally
Protein phosphatase 1 (PP1) reverses the effects of kinases on _____ _____
glycogen metabolism
PP1 removes phosphate groups from both _____ ___ and ____ _____ __, which inactivates both and thus inhibits glycogenolysis
phosphorylase kinase, glycogen phosphorylase a
What are 2 ways that insulin stimulates glycogen sythesis?
- Increases the number of glucose transporters, which increases glucose uptake, then converted to glucose-6-P
- Inactivation of glycogen synthase kinase which reduces the phosphorylation state of glycogen synthase and thus increases its activity
Insulin rapidly _____ our glycogen stores
replenishes
The process of glycolysis is very ___ in terms of extracting energy
inefficient
What are the 3 stages of cellular respiration?
- Catabolism of pyruvate to acetyl CoA
- Citric Acid Cycle
- Oxidative phosphorylation
In the PDH complex, there are __ enzymes, each with multiple subunits that catalyze __ biochemical reactions; it requires __ cofactors, and is an _____ ____ reaction. This is considered an ______ reaction
3 (E1, E2, E3), 5; 5, oxidative decarboxylation. irreversible
Where is the PDH complex present?
In the mitochondria
What is the “overall” point of the PDH complex?
Convert pyruvate to Acetyl CoA + CO2 + NADH
What is the point of the MPC transporter?
Helps pyruvate get out of the cytoplasm and into the mitochondria
Cofactors are considered ____ molecules, are non-____, bound to an ____ (either tightly or loosely), required for _____, and do not ____ reactions
helper, proteins, enzyme, catalysis, catalyze
What are the 5 PDH cofactors?
- Thiamine Pyrophosphate (TPP)
- Lipoic Acid
- Coenzyme A
- FAD (electron carrier)
- NAD+ (electron carrier)
Which E(1/2/3) is TPP bound to in PDH?
E1
Which E(1/2/3) is Lipoic Acid bound to in PDH? Lipoic acid exists in the _____ form and the ____ form which turns into the ____ form
E2, oxidized, reduced, acetylated
NADH is a ____ electron carrier, high energy electrons; FAHD2 is a ______ _____ electron carrier
mobile; protein bound
What is the advantage of using a protein complex?
Local concentration of substrates around enzymes is kept high, the rate of reaction is not limited, and is more efficient
What is E1 in the PDH?
oxidative decarboxylation of pyruvate ad transfer of 2 carbon unit to E2
What is E2 in the PDH?
Transfer of acetyl group to CoA to synthesize Acetyl CoA
What is E3 in the PDH?
Regenerates oxidized lipoic group of E2 and transfers protons and electrons first to FAD then to NAD+ to complete the reaction cycle
What is the overall reaction in the PDH?
Glucose → 2Pyruvate → 2Acetyl CoA + 2NADH + 2CO2
In a ____ energy charge, the complex is inhibited by its immediate products: ____, ____ __, and ____
high: NADH, acetyl CoA, ATP
In a ____ energy charge, the complex is activated by: ____ and ____, which inhibit the kinase that phosphorylates PDH
low: pyruvate, ADP
Acetyl CoA, ATP, NADH activate PDH kinase → ______ PDH
inhibits
Pyruvate, ADP, activate PDH phosphatase → ______ PDH
activates
Acetyl CoA is considered the metabolic “_____ and ____ department” for all classes of biomolecules and is a major source of metabolic ____
receiving, shipping, energy
For every round of the CAC, __ ATP is formed
1
Where does the CAC occur?
In the mitochondrial matrix
Why is the CAC considered a “true” cycle?
Because the substrate used in the 1st reaction (oxaloacetate) is produced in the last reaction
There are __ NADH and __ FADH2 formed for every round of the CAC, and for each individual molecule, there are __ high energy electrons created, making a total of __
3, 1, 2, 8
CAC cycle intermediates are ____ of other molecules
precursors
What is the difference between synthetase and synthase?
Synthetase: hydrolysis of ATP is used
Synthase: condensation reaction
The TCA involves something called ____ ____ mechanism: where molecules have to bind in a very specific order
ordered sequential
The conformational change in citrate synthase upon oxaloacetate creates a binding site for acetyl CoA and prevents ?
the wasteful hydrolysis of acetyl CoA
What is the 1st step in the CAC?
Citrate synthase catalyzes the condensation of acetyl CoA and oxaloacetate to form citrate
What is the 2nd step in the CAC?
Aconitase catalyzes the formation of isocitrate from citrate
What is an isomerization reaction
flips the H and OH, and helps facilitate the next step
What is the 3rd step in the CAC?
Isocitrate is oxidized and decarboxylated to α-ketoglutarate via isocitrate dehydrogenase
What is the 4th step in the CAC?
Succinyl Coenzyme A is formed by the oxidative decarboxylation of α-ketoglutarate by the α-ketoglutarate dehydrogenase complex
What is the 5th step in the CAC?
Succinyl CoA synthetase catalyzes the cleavage of high energy thioester linkage and forms ATP and Succinate
What is the 6th step in the CAC?
The oxidation of succinate to fumarate by succinate dehydrogenase
Which enzyme of the CAC is NOT found in the matrix of the mitochondria, but the inner membrane?
Succinate dehydrogenase
What is the 7th step in the CAC?
The hydration of fumarate to malate by fumarase
What is the 8th step in the CAC?
The oxidation of malate to oxaloacetate by malate dehydrogenase
From one turn of the CAC: __ carbons enter, __ carbons leave, __ NADH, __ FADH2, __ ATP, and ____ is regenerated
2, 2, 3, 1, 1, oxaloacetate
The electrons from each NADH in the CAC will generate ___ ATP, while FADH2 generates ___ ATP
2.5, 1.5
There are areas in the complete oxidation of one glucose molecule where the total ATP output can be changed by the type of NADH shuttle used. Glycerol 3-P shuttle generates __ ATP/glucose (liver/heart); malate/aspartate shuttle generates __ ATP/glucose (muscle)
3, 5
Is there any covalent modification in the CAC?
No
There are 2 CAC enzymes that are regulated by both allosteric mechanisms: ?
Isocitrate dehydrogenase (stimulated by ADP, inhibited by NADH and ATP)
α-ketoglutarate dehydrogenase complex (catalyzes the rate limiting step, inhibited by succinyl CoA, NADH, and ATP. No activators)
In the CAC, at rest what happens to ATP and NADH?
Increase in both
In the CAC, what happens if there is a surplus of energy?
Favors lowering CAC activity, lowers isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, PDH. Storage of excess energy
In the CAC, what happens with increasing energy consumption?
Lowering ATP, increasing ADP, lowering NADH. Once we get to an insufficient energy supply, it favors increasing the CAC activity
Can humans make glucose from fats?
No
What are anaplerotic reactions?
Reactions to replenish cycle components
A prominent anaplerotic reaction is catalyzed by ____ _____
pyruvate carboxylase
What is the major difference between the CAC and the Glyoxylate Cycle?
Glyoxylate Cycle bypasses the 2 decarboxylation steps, which allows for the synthesis of carbohydrates from fats
T or F: the CAC and Glyoxylate cycle happen at different times?
False
Where does the Glyoxylate Cycle occur?
In the glyoxysome of plants and bacteria
What is the main product of the Glyoxylate Cycle?
Succinate, which is then converted to oxaloacetate, then to glucose
Why can mammals not synthesize glucose from acetate (acetyl CoA)?
There is an input of 2 carbons from acetyl CoA, but then a loss of 2 carbons through CO2
The Glyoxylate Cycle is highly active in ___ seed plants, since they have stored fats and provides energy before glucose can be synthesized by _____
oily, photosynthesis
What two enzymes and product are unique to the glyoxylate cycle
Isocitrate lyase, which produces glyoxylate and succinate from isocitrate; and, malate synthase that produces malate from glyoxylate
What are the 4 pathways involved and where do they occur in the conversion of fat to glucose in plants?
- Fatty acid oxidation to generate acetyl CoA (glyoxysomes)
- Glyoxylate cycle (glyoxysomes)
- CAC cycle (mitochondria)
- Gluconeogenesis (cytoplasm)
Where does oxidative phosphorylation occur?
In the mitochondria (inner membrane)
In oxidative phosphorylation, what are the electron donors?
NADH and FADH2
Oxidative phosphorylation is carried out by a series of protein complexes at the inner mitochondrial membrane called the ____ ____ ____
electron transport chain
There are __ main protein complexes involved + ______ __: ___ for electron transport and __ for ATP synthesis
5, cytochrome c: 4, 1
What is the chemiosmotic theory?
Energy is released as electrons flow through the electron transport chain, which generates potential energy protons flow back across the membrane down the gradient through ATP synthase which uses the energy to generate ATP
What is the flow through the components of the Electron Transport Chain?
1.1 NADH + H+ go through #1
1.2 FADH2 goes through #2
2. 1.1 and 1.2 feed to Ubiquinone (Q)
3. Feeds to #3
4. Feeds to Cytochrome c
5. Feeds to #4 which converts oxygen to water
The proteins complexes of the ETC consist of ___ subunit(s)
many
Electron transport requires electron ____
carriers
What is Coenzyme Q?
Lipid soluble, shuttles electrons between less mobile carriers in a membrane, accepts 2 electrons
What are cytochromes?
Proteins that function as electron carriers. Cytochrome C carries 1 electron
What is heme?
Prosthetic group of cytochromes that carry the electrons
One proteins can have _____ iron-sulfur centers
several
What is Complex I in the ETC?
NADH dehydrogenase. Contains several iron-sulfur centers, 2 electron reduction by coenzyme Q, NADH + H+ -> NAD+. 4 protons: matrix to intermembrane space
What is Complex II in the ETC?
Succinate Dehydrogenase. Oxidizes succinate to fumarate. Electrons from succinate -> FAD -> Fe-S -> CoQ -> reduce it to QH2. NO H+ ARE MOVED
What is Complex III in the ETC?
Cytochrome C oxidoreductase. Transfers electrons from GH2 -> cytochrome c. Uses heme and Fe-S transports 4 protons from matrix. Can only accept 1 electron at a time
What is Complex IV in the ETC?
Cytochrome C oxidase. Carries electrons from cyt c to O2, reduced to water. Pumps 2H+ across membrane. O2 is final electron acceptor (need 4)
ATP synthesis in _____ cells comes from the electrochemical gradient
respiring
What is the function of ATP ssynthase?
Catalyzes the formation of ATP from ADP and Pi
Where in ATP synthase does ATP synthesis occur?
In the beta subunits
___ is the pore that spans the entire membrane, whereas ___ is the spherical head on which phosphorylation of ADP occurs
F0, F1
How do ATP synthase molecules assist in forming cristae?
Form dimers. Changes the curvature of this inner mitochondrial membrane and loop out to form cristae
What is the advantage of cristae?
It puts the pumps close together and pumping to protons into a smaller space really increases the concentration of protons in the immediate area right by ATP synthase. Larger gradient means larger energy.
The ___ complex ( beta subunit) catalyzes the synthesis of ATP
F1
The F1 complex ____ between alpha and beta subunits ( __ pairs)
alternates, 3
The F1 complex can exist in three conformations: ?
- The L (loose) form
- The T (tight) form
- The O (open) form
Describe the L form
Loose, the beta subunit traps ADP and Pi. It is locked and there is no catalysis
Describe the T form
Tight, ATP synthesized from ADP and Pi. It is made but not released
Describe the O form
Open, ATP is released from the beta subunit, and new ADP and Pi bind
For every __ protons, it causes a 120 degree turn of the _____ subunit, which causes a change in the conformation of each consecutive ___ subunit, you get __ ATP
3, gamma, beta, 1
Why does NADH produce more ATP than FADH2?
Because Complex I that takes NADH contains a proton pump
We need 3 protons to turn the gamma subunit 120 degrees, but you need 1 to get the ?
inorganic phosphate in a critical substrate
For every molecule of inorganic phosphate pumped from the cytosol into the mitochondria is a _____
proton
ATP produced in Mitochondria is Moved to the Cytosol
by the ?
ATP-ADP Translocase
The direction of the eversion is due to the ?
different chemistries of ATP vs ADP
What is the difference between white adipocytes and brown adipocytes?
White: few mitochondria, store energy
Brown: many mitochondria, dissipate energy
What is a protonophore?
Allows protons to flow through it rather than ATP synthase
