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154 Cards in this Set

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What is bioenergetics?
How cells aquire and use energy
In biosynthesis how can one determine if energy was released?
If bond of the product is more stable
How do cells obtain most of their chemical energy?
Through oxidation of molecules: molecules gain an oxygen atom
In general, respiration is nothing but...
the cumbustion of hydrogen and carbon, and animals that respire are true combustible bodies that burn and consume themselves.
An oxidation reaction...
is any reaction in which electrons are wholly or partially transfered from one atom to another; loss of an electron
Thermodynamics predicts...
wether a rxn COULD occur spontaniously which is a favored situation
The first law in Thermodynamics states:
that all energy in the universe is constant but transduction my occur.
Transduction is...
if there is any change w/i a system there must be and equal and opposite change in its surroundings
The second law of Thermodynamics states that ,
In a spontanious processes the entropy of every system and its surroundings goes to one of higher entropy
In a reduction reaction...
an atom will gain an electron
What two factors need to be considered when decideing wether or not a process can occur spontaneously?
1. The enthalpy
2. The Entropy
Enthalpy is
the lowest energy state or most stable chemical bonds
Entropy is
the randomness of a system
How do biochemists look at Enthalpy? and what units is it expressed in?
delta H = delta E
+H is endothermic: needs energy input b/c bonds formed in product are less stable and heat is absorbed
-H exothermic: heat is expelled and bonds formed in product are more stable

Energy/mole
How do biochemists look at entropy?
T^S is the change in randomness of a system. Units are energy/mol.

+S means there is an increase in randomness.
A cell can decrease in entropy (randomness) only if..
the entropy of its surroundings increases.
The Gibbs free energy eqation relates entropy and enthalpy into one equation that is...
^G = T^S + ^H which can determine which direction a reacion will go and also the work/energy available
If
^G <0
^G >0
^G =0
#G < 0 "forward" rxn favored: exergonic
#G > 0 "reverse" rxn favored: endergonic
#G = 0 rxn at equilibrium
Aqueous solutions: [H2O] = 55M
pH = 7.0 (neutral)
what is the molar concentration of water?
55M
What is the notation for standard conditions of free energy?
a superscripted 0 on the delta G
delta G is simply
how far a rxn is from equilibrium or how much energy is available in the system
and another way to express the equilibrium constant K
What is the equilibrium constant equation? which is another way to express delta G.
K'eq =[C][D]/[A][B]

#Go' = -6 log K'eq
(will always be given this on exams)
To calculate delta G
#G' = #G°' + 6 log actual concentrations of products vs reactants
Kinetics prdicts?
how fast a reaction rate will occur
Enzymes change reaction rate not
equilibrium constant
ATP is
the universal energy carrier
condenstaion is
the making of a peptide bond; making of ATP
Hydrolysis
the breaking of a peptide bond by release of hydrogen; making ADP (adenosine triphosphate)
What is the basis for the large energy change -G in ATP hydrolysis?
1. Electrostatic repulsion O-
2. Resonance stabalization
3. Ionization stabalization and solvation
:gives off energy
What phospho compounds have a high evergy of hydrolysis?
Phospho-enol pyruvate (PEP)
1,3-biphosphoglyceric acid (1,3-diPGA)
Much of metabolisim involves...
the synthesis of high evnergy Phosphate compounds
ATP is important in metabolism because it can both..
donate and recieve Phosphate groups
Unfavoable reactions can be drivin by...
coupling to favorable reactions through common intermediates

Coupling a reaction to ATP breakdown

ATP + Glucose
"Gº%
kJ/mol
+13.8
–30.5
= –16.7
#Go' of multiple reactions are additive. and huge improvement!
What is the meaning of Glycolosis?
Sugar breakdown
What is the best understood pathway in metabolism?
Glycolsis
Glycogen breakdown occurs in...
the liver and muscles
Describe the hexokinase reaction
Glucose _Hexokinase__> Glucose 6-Phospate

Hexos 6 Carbon sugar
Kinase" enzyme that can add a phosepate group
Describe Phosphohexose Isomerase
Involves rearranging
Isomerase is an enzyme that makes isomers, same struc, but bonds are rearranged.
What are some important things to note about Phosphofructokinase (PFK-1)
1. This is the rate limiting step in Glycolosis
2. Major control point: allosteric reaction
3. ATP is a substrate
With increasing oxydation what happens to the energy of a molecule?
The energy decreases --> alkanes have the highest energy
What is Nicotinamide?
NAD is a source of energy storage
Increasing introduction of Phosphate groups increases energy and provides a way to manufacture...
ATP (the universal energy carrier)
What is the logic of the enolase step in Glycolosis?
This step allows for the rearrangement of the phospate bond to make its energy more accessable to use. Prior to this the energy in this substrate is not great enough to produce ATP.
What are some gereral properties of metabolic pathways?
1. Pathway: sequence of enzyme catalized reactions
2. Overall irreversible and large negative free energy
3. Enzymes regulated to control flux of metabolites
In metabolism starting and ending compounds are usually interconvertable, but what must happen for this to work?
Irreversible steps must be bypassed by other reactions...metabolism cant simply work in reverse
Whats an irreversible reaction?
The cell is not capable of achieving the kind of conditions to reverse a reaction to force a product back into its reactant, w/o use of a different reaction pathway
What is the significance of compounds that have higher energy and lower energy than ATP?
Those of higher energy can donate a phosphate group to ATP to activate it, and those of lower are activated by ATP by recieving those phosphate groups.
Transfering phosphates around is a way ____ is moved around in a cell.
energy
ATP can both ____ and ____ phosphates.
Donate
Accept
By _____ unfavorable reactions to the breakdown of ATP via an ________, a reaction can be driven towards its products and made favorable.
coupling

intermediate
A large positive free energy change indicates an _______ reaction.
unfavorable; endothermic
Study done by Buekner which involved the fermentation of yeast from sugar showed what?
That once a cell was broken open there were chemical properties; we now know are enzymes (in yeast). and did away w/ the idea of vital force.
Many organisms, can store sugar in various forms of starch...we store starch as ____ in our liver.
Glycogen
What is the net reaction of Glycolosis in the cytoplasm?
Glycogen + 2Pi + 2NAD + 2ADP ----->

2ATP + Pyruvate + 2NADH
magnitude of energy change glucose to pyruvate is large and negative, but since ATP is made during this process the magnatude of the free energy is ______.
less, but captured in forms cell can utilize later
Glycolisis, an aspect of metabolism, uses multiple favorable reactions and capture some of that energy as _____.
ATP
Glucose is a ___ Carbon Sugar and can be broken down into two ___ Carbon compounds and then broken down into ____.
6, 3, Pyruvate
The first phase of Glycolosis is known as the _____ stage. This breaks down the initial 6 Carbon sugar into two 3 Carbon sugars, _____ and ______.
Preparatory; investment

Dihydroxyacetone-P
Glyceraldehyde-3-P
The first step in glycolosis is known as the _______ reaction. In this reaction ______ is converted to ______ by accepting a phosphate group from ______.
Hexokinase (enzyme takes P from ATP)

Glucose
Glucose-6-P
The second step in glycolosis is _______. During this step Glucose-6-P is converted to ________. Isomerase is an enzyme that makes _______.
Phosphohexose Isomerase

Fructose-6-P

Isomers: molecules w/ same chemical makeup, but different configuration.
The third step in Glycolosis is _______, where Fructose-6-P + ATP yeilds _______.
Phosphofructokinase (PFK-1)

Fru-1,6-bisP + ADP
The fourth step in Glycolosis is a ______ reaction that utilizes ______, an enzyme that splits fru 1,6-bisP into two 3 carbon sugars ______ and _____. This step has a large _____ free energy change under standard conditions, yet still occurs because______.
Cleavage

Aldolase

Dihydroxyacetone-P
Glyceraldehyde-3-P

Positive

cellular conditions are far from standard conditions.
The final enzyme involved in Glycolosis is _______. This interconverts the two 3 carbon products ____ and ____.
Trios phosphate Isomerase (TPI)

Dyhydroxyacetone-P
Glyceraldehyde-3-P
During glycolosis a stage known as ____ involves many enzymatic reactions to form ____.
The Pay off Stage

ATP
During the payoff stage, two molecules, _____ and _____ are made because they have a higher energy than ATP. This energy is then used to make _____.
1.3-bisphosphoglycerate

Phosphoenolpyruvate (PEP)

ATP
Once Glycolosis enters the payoff stage, Glyceraldehyde-3-P undergoes ______ in order to form ______, which has a _____ energy than ATP.
This is a _______ reaction.
Oxydation

1,3-bisphosphoglycerate

Higher

Dehydrogenase
Dehydrogenase reactions involve ____ substrates + _____, which are oxidized into _____ + _____
reduced AH2
NAD+

oxidized compound
NADH
Recall from chemistry, If something gets oxidized....something else gets_______.
reduced
NAD or _________ is an electron carrier that is reduced during a dehydrogenase reaction. This NADH now carries ____ more electrons and 1 more _____ bond, giving it more energy to carry.
Nicotinimide Adenine Dinucleotide

2
Carbon Hydrogen
Once 1,3-bisphosphoglycerate is formed, the enzyme ________ catalyzes the next step in glycolosis to form ________ a ____ phospate compound.
Phosphoglycerate Kinase

3-Phosphoglycerate (3-PGA)

single
1,3-bisphosphoglycerate is a high energy compound that can react with ____ to form ATP.
ADP; adenosine diphospate
3-Phosphoglycerate (3-PGA) undergoes a catalyzed reaction with _______, to form _______, which is simply an Isomer or rearrangement of 3-PGA where the phosphate group is moved to the middle of the compound.
Phosphoglycerate Mutase

2-Phosphoglycerate
In the final steps of glycolosis, the compound (PEP)_______ is formed via _____, from the compound ______.
PhosphoenolPyruvate

Enolase

2-Phosphoglycerate
Enolase uses a molecule of _____ to create a ______ bond.
water

c-c double bond
Phosphoenol Pyruvate (PEP) has a high energy phosphate and can react at the active site of the enzyme ________ with ADP to form ATP and ______.
Pyruvate Kinase

Pyruvate
What is the net rection of glycolosis in the cytosol?
Glucose + 2NAD+ + 2ADP + 2Pi

---->
Pyruvate + 2ATP + 2NADH + 2H2O
_______ regulation of glycolosis allows the cell to know when to undergo glycolosis and when to inhibit the process, this is accomplished by the cell sensing high levels of ATP which _____ the process and _____ the process when compounds such as ADP are highly concentrated.
Allosteric

Inhibit

Stimulate
Two definitions that will be important in our understanding of Pyruvate are anaerobic and aerobic pathways. What is the difference between the two?
Anaerobic: -O2
Aerobic: +O2 uses oxygen
Under aerobic conditions, glycolosis produces Pyruvate that is utilized in the process of _________ and forms lots of ________.
Respiration

NADH
Under anaerobic conditions Pyruvate is utilized to form a few different compounds, ______, ________ and other fermentations.
Lactate

Ethanol
Lactate accumulats in anaerobic mucsle in order to regenerate _____.
NAD+
As Lactate (salvage) builds up in the muscles, Glucose can be regenerated by a process called ________ which occurs in the ________.
Glyconeogenesis

Liver
Another fermentation reactions that occurs after glycolisis the the two step ______ fermentation. During this process CO2 is removed from pyruvate by the enzyme ______. The resulting aldehyde is then reacted with ________ to form Ethanol.
Alcohol

Pyruvate decarboxylase

Alcohol DH (dehydrogenase)
Our livers contain the enzyme ______ because intestinal microbes produce alcohol and it is needed to detoxify our system.
Alcohol dehydrogenase (DH)
What is the Pasteaur effect?
The pasteaur effect is that yeast glucose consumption is much greater under Anaerobic conditions. but produce less ATP per molecule of oxygen
During dehydrogenase reactions, a double bond to oxygen is considered to have _____ oxydized bonds. After dehydrogenase occurs, the molecule has only ____ 1 oxidized bond and therefore contains more _____ than the previous molecule.
2,1

Energy
If glucose is consumed under ______ conditions such that there is no oxygen, the amount of ATP created is much less than that of ______conditions.
anaerobic

aerobic
In our bodies, since oxygen is available in our system, pyruvate is typically converted totally into _______ which contains a lot of energy for ATP.
CO2
In organisms that are truely anaerobic, more than _____ ATP can be created from Pyruvate.
2
The site within the cell for oxidation is known as the _______. It has a double membrane system. The inner portion contains many soluble enzymes that carry out the steps on inner metabolism including, ____, ___ and ______.
Mitochondria

Citric acid cycle
Fatty acid oxydation
Pyruvate oxidation
The enzyme that converts pyruvate to acetyl Co-A is ________, which is made up of 3 enzymes + 5 coenzymes.
Pyruvate dehyrogenase complex
During the conversion of pyruvate to acetyl Co-A, Lipoic Acid is utilized as a common carrier in a reduced or oxidized state on enzyme ____. Whereas TPP which has a stable _____ is used.
2

anion (Thiamine Pyrophospate)
In the first step of Pyruvate DH, the stable anion _____ reacts with Pyruvate to form an intermediate, which with the loss of _____ becomes ________. Next the lipoic acid groups S-S bond is oxidized on ______, which furthermore reacts w/ ______ to form acetyl Co-A
TPP Thiamine Phyrophospate
CO2
Hydroxyethyl TPP
Enzyme 2
CoA-SH
In the final steps of Pyruvate DH, the lipoic acid oxidized state, reduces back to its s-s bond and transfers its electrons to ______ which is then reduced to ______ which further tranfers its reducing power to NAD to become ______. This returns the enzyme ______ complex to its original groundstate.
FAD

FADH2

NADH

Pyruvate Dyhydrogenase Complex
The oxydation of pyruvate is coupled w/ the formation of ______ so that some energy can be conserved in these forms.
NADH and Acetyl-CoA
Coupling does one of two things....
1. it drives unfavorable reactions

2. it saves some energy to be stored in favorable reactions.
Thiamine is also known as _______.
Vitamin B
When polishing rice became popular, thiamin was being stripped from the rice and large deficiencies led to a build up of _____ in the blood, known as _____. Which is medically relevent to Pyruvate DH.
Pyruvate
Beri Beri
name some important characteristics of the Krebs Cycle.
1. Central energy yeilding path
2. Point of convergence of catabolism of fats, carbs and proteins
3. Source of precusors for biosynthesis
4. Intermediates recycled
5. In mitchondria of eukaryotes
The Krebs cycle is also called ________ and ________ cycle.
The Citric Acid Cycle

Tricarboxylic
What is true about a cycle is that there is no net _____ of end products at the end. and any step in a cycle can be considered the ______ step.
gain
first
When acetyl Co-A enters the Krebs cycle, it has ______ reduced bonds which can be ________ to produce energy. due to this, ______ and ______ are found as reduced compounds within the cycle.
4
Oxidized
NAD+ and FAD (NADH & FADH2)
I "first" step in the Krebs cycle, Acetyl Co-A reacts with _______ to for a 6 carbon compound called ____.
Oxaloacetate (OAA)
Citric Acid (citrate)
Once citrate is formed in the cell, the enzyme _______ facilitates a rearrangement of the molecule by removal and addition of a _____ molecule to form _______ which will be the reactant for the next reaction.
Aconitase
Water
Isocitrate
During Isocitrate dehydrogenase of the Krebs cycle, Isocitrate loses CO2 in a reaction called ________. to go from 6C--> __. _____ is reduced.
Oxidative Decarboxylate
5C a-ketoglutarate (a-KG)
NAD
a-ketoglutarate dehydrogenase complex is similar to ______ dehydrogenase. In this step another C-C bond is oxidized in the form _____ and _____ is formed. Some energy is conserved in the ______.
Pyruvate
CO2
Succinyl Co-A
Thiolester C-S-CoA
Once succinyl Co-A is formed, the enzyme _____ facilitates a reaction that attempts to harvest energy from the Thiolester bond and the formation of ______.
Succinyl Co-A Synthetase
Succinate
During Succinate Dehydrogenase two _____ are lost and two double bonds form the new molecule _____. _____ is reduced.
H
Fumarate
FAD
Once citrate is formed in the cell, the enzyme _______ facilitates a rearrangement of the molecule by removal and addition of a _____ molecule to form _______ which will be the reactant for the next reaction.
Aconitase
Water
Isocitrate
During Isocitrate dehydrogenase of the Krebs cycle, Isocitrate loses CO2 in a reaction called ________. to go from 6C--> __. _____ is reduced.
Oxidative Decarboxylate
5C a-ketoglutarate (a-KG)
NAD
a-ketoglutarate dehydrogenase complex is similar to ______ dehydrogenase. In this step another C-C bond is oxidized in the form _____ and _____ is formed. Some energy is conserved in the ______.
Pyruvate
CO2
Succinyl Co-A
Thiolester C-S-CoA
Once succinyl Co-A is formed, the enzyme _____ facilitates a reaction that attempts to harvest energy from the Thiolester bond and the formation of ______.
Succinyl Co-A Synthetase
Succinate
During Succinate Dehydrogenase two _____ are lost and two double bonds form the new molecule _____. _____ is reduced.
H
Fumarate
FAD
Fumerate undergoes a process known as _______ where a molecule of water converts it to ______ by the enzyme _____.
Hydration
L-Malate
Fumerase (Fumarate Hydratase)
L-Malate is converted to _____ by malate dyhydrogenase. in which L-Malate is oxidized and _____ is reduced.
oxaloacetate
NAD
Succinate Dehydrogenase is a membrane bound enzyme attached to electron carriers of the _______.
Mitochondrial membrane
The conversion of L-Malate to Oxyloacetate has a large positive free energy, but is overall negative in the cell b/c concentration of oxyloacetate is kept _____ and following rxn is favorable and has large free energy so oxyloacetate is converted rapidly, and drives L-malate conversion.
Low
The energy yeild of Glucose oxidation is about ____ ATP.
32
One point to note about the citric acid cycle is to note that many things are coming in and out of the cycle's intermediates such as amino acids for other metabolic pathways. Therefore there needs to be ways to keep intermediate levels high enough to keep the citric acid cycle going, which is called ______ . The citric acid cycle is therefore considered a _______.
Anaplerotic Reactions (replenish)
Metabolic Hub
One notable anaplerotic reaction is the direct conversion of Pyruvate to Oxyloacetate. During this reaction some ATP is required for OAA's formation. If OAA is to low this is a way of keeping the ______ cycle going. This is metabolically possible, b/c there is no more _____ in oxylacetate than in Pyruvate.
Citric Acid
Energy
The ______ vitamins are intrically important in production of important metabolic cofactors such as _____.
B
NADH
In many organisms other than animals, there is a reaction known as the _____ cycle that converts fats to ______ that occurs in the ______ which resides in a ____ body found in a seed.
Glyoxylate
Glucose
Glyoxysome
Lipid
What is the function of lipids?
Structural
Vitamins, hormones
ENERGY CARRIERS
The greater energy potential of lipids, is mostly in part to that it has more ______ bonds than carbohydrates or Proteins.
C-C and C-H
The important lipid that we will be focusing on is ______.
Triacylglycerol
Digestion is facilitated by _____, which are derived from _____. These act as _______ breaking up the ______ and allowing enzymes to have better access to free fatty acids. These enzymes are called ______. These cleave fatty acids so that they can cross cellular membranes and be built back up again and stored as _______ in various locations. Triacylglycerols are then incorporated w/ cholesterol to form ______ which move through the lymphatic system and blood stream to tissues.
Bile Salts

Cholesterol

detergents

Triacylglycerols

Lipases

Triacylglycerols

Chylomicrons
Free fatty acids are very effective _____ and if stored in a cell this would disrupt it.
Detergents
fatty acids are directly utilized by cells as _____.
energy
Once inside the cell fatty acids are activated by ____ on the outer membrane of the ____ the powerhouse of the cell.
Acyl CoA synthetases

mitochondria
Co enzyme A is a very versital coenzyme that can ____.
carry intermediates
To get a fatty acid into the mitochondria, a sort of ____is utilized. Coenzyme A gives up its fatty acid to another carrier called ____. This can then carry the fatty acid to then inner part of the membrane. THere is a specific transporter that can bring this carnatine carrier into the cell mitochondrial ____. The fatty acid is then transfered back to Coenzyme A realeasing Carnatine to be able to do process all over again.
shuttle system

Carnatine

matrix
_______ was the first example of how to trace a compound through metabolism. Syn fatty acids joined to a benzene ring, even vs odd number of carbons. Fed them to dogs to see what was left after metabolized. What he found was regardless of length of fatty acid if even the product was 2C plus benzene. if odd carboxyilc attached to benzene. Must be stepwise breakdown of 2C units. Must be occuring at b-carbon relative to carboxylic group.
The Knoop experiment
step one of B-oxidation is a ___ reaction where the B-H and a-H are removed and a C=C is formed. this step is a membrane bound situation. Step 2 is a _____ reation and step 3 is a ____ reaction. Step 4 is ______ facilitated by the enzyme _____. The key concept to this is after every B-oxidation an nAcetyl CoA can be formed from each acetyl group (CH2-CH2) being clipped off and freed or ___ B-oxidations.
dehydrogenation

Hydrolysis

Dehydrogenation

Thiolytic cleavage

Thiolase

n-1
Plant mitochondria do not contain enzymes of B-oxidations and therefore all utilization of fatty acids in plants occurs in _____.
Peroxisomes and Glyoxyzomes
Essentially the only thing that is differnt in B-Oxidation is in first oxidation. In the Mitochondria the first electrons can feed right into respiratory chain, but glyoxysomes and peroxisomes cant do that and reduction power builds up. The solution to this is to ____
take e- and instead of using them simply give them to oxygen to form peroxide wihch is broken down by catalase into water and oxygen.
What happens when metabolism goes array? when fatty acids are used in animals at a very high rate. The citric acid cycle intermediates can become depleated causing build of of acytl CoA and Ketone bodies can be formed. This build up of Ketone bodies can lower pH of blood and cause individual to go into a coma and die. This is known as ____. Usually happens when individual is starving.
Ketosis
The process to incorporate Ammonia into organic molecules involves two steps. The first enzyme that is involved is ___when combined which glutamate and ATP ammonia is added to the molecule and produces glutamine. The second step involves ___which makes glutamate by transfering fixed ___ groups to form two glutamate amino acids from a citric acid cycle intermediate a-ketoglutarate and Glutamine.
glutamine synthetase

glutamate synthase

NH2
The NET reaction of incorporation of ammonia to organic molecules is...
a-KG + NH4 --> Glutamate
Transamination ivolve a a-KG and thus glutamate with a corresponding ___such as alanine --> Pyruvate.
amino acid
Aminotransferases are not available to balance out ___ amino acids.
essential
Ammonia is formed from the Glutamate dehydrogenase reaction, an oxidation in which Glutamate is oxidized to ___ and reducing power reduces NAD -NADH.
a-ketoglutamate + NH4
Ammonia can be formed from a process called transdeamination which involves an ___ + _____which via aminotransferase goes to Glutamate + a-keto acid. Glutamate is then transformed back into an a-ketogluterate + NH4 via ___.
a-amino acid
a-ketogluterate
glutamate dehydrogenase
Glutamate + NH4 are converted to ___ in humans to transport excess N in blood in other tissues to the liver.
Glutamine or alanine
Ammonia is excreated by humans in the form of ___ through the urine. This is formed by taking 2 NH4 and combining them with ___.
Urea
CO2
lecture 6 Urea cycle
go over it
The process to incorporate Ammonia into organic molecules involves two steps. The first enzyme that is involved is ___when combined which glutamate and ATP ammonia is added to the molecule and produces glutamine. The second step involves ___which makes glutamate by transfering fixed ___ groups to form two glutamate amino acids from a citric acid cycle intermediate a-ketoglutarate and Glutamine.
glutamine synthetase

glutamate synthase

NH2
The NET reaction of incorporation of ammonia to organic molecules is...
a-KG + NH4 --> Glutamate
Transamination ivolve a a-KG and thus glutamate with a corresponding ___such as alanine --> Pyruvate.
amino acid
Aminotransferases are not available to balance out ___ amino acids.
essential
Ammonia is formed from the Glutamate dehydrogenase reaction, an oxidation in which Glutamate is oxidized to ___ and reducing power reduces NAD -NADH.
a-ketoglutamate + NH4
ATP Synthase is the process within the mitochondria of a cell by which a ____ engine uses the potential difference across the ____to power a chemical transformation of ADP into ATP
rotary
bilipid layer
ATP can be formed without energy at the active site of the enzyme, but it cannot be released without energy. Therefore the ____helps to release ATP.
Proton gradient force
In the complete process of ATP synthesis the electrochemical energy of the proton gradient is converted into ___ and, via structural/mechanical changes in the ___, ultimately into the chemical energy of ATP.
mechanical energy
catalytic sites
The proton gradient is also used to transport __ out of the mitochondria and ___ in without any additional energy input.
ATP
ADP