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147 Cards in this Set

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Glycolysis:

What occurs in Reaction 9?
2-phosphoglycerate to phosphoenolpyruvate
-Dehydration (elimination) reaction
*Reversible in vivo

Enzyme: enolase
Glycolysis:

What occurs in Reaction 10?
Phosphoenolpyruvate + ADP to pyruvate + ATP
*Irreversible control point*

Enzyme: pyruvate kinase
-Kinase in reverse
-Second substrate-level ATP generating step
What is hemolytic anemia?
Occurs when blood cells lyse because they don't have a constant supply of energy to maintain structural integrity
What is the only source of energy for blood cells?
*Glycolysis* is their only source of energy b/c they lack mitochandria necessary for oxidative-phosphorylation
What defect causes hemolytic anemia?

How does this defect cause hemolytic anemia?
A partial defect in pyruvate kinase causes hemolytic anemia

This defect results in blood cells not generating enough energy to keep from exploding
Glycolysis:

What three reactions ensure that the pathway is irreversible in glycolysis?
1. Reaction 1 w/ hexokinase
2. Reaction 3 w/ phosphofructokinase-1
3. Reaction 10 w/ pyruvate kinase
What are feeder pathways?
Various cellular reactions that change other sugars into glucose so that they can be used for glycolysis
How are polysaccharides converted to glucuse?
Through Hydrolysis reactions

Each reaction has specific enzymes
How is galactose different from glucose?
The hydroxy (-OH) groups points up on C4 in Galactose

The hydroxy group points down on C4 in Glucose
How is galactose converted to glucose?

How many enzymes are needed for this conversion?
Through an Isomerization reaction

4 enzymes are necessary
What causes the metabolic deficiency galactosemia to occur?

What is a possible result of having galactosemia?
A loss of any enzyme involved in converting galactose to glucose leads to galactosemia

-Galactosemia may lead to death
What causes someone to be lactose intolerance?
A person is not able to hydrolyze lactose into glucose and galactose

Because they don't have the enzyme lactase
What is gluconeogensis?
Making glucose

*It is not the reversal of glycolysis
!Be able to draw diagram!
Why is gluconeogensis not simply the reversal of glycolysis?
There are 3 irreversible steps in glycolysis that have a large -ΔG

*Gluconeogensis requires 4 new enzymes to bypass the 3 irreversible reactions in glycolysis
What are the 4 new enzymes in gluconeogensis and what enzymes do they replace from glycolysis?
1. Glucose 6-phosphatase: replaces
hexokinase
2. Fructose 1,6-biphosphatase:
replaces PFK-1
3. Pyruvate Carboxylase: replaces
pyruvate kinase
4. PEP Carboxykinase: replaces
pyruvate kinase
What transformation does pyruvate carboxylase catalyze?

What energy molecule is also necessary?
It converts bicarbonate + pyruvate to oxaloacetate

*ATP is needed for the mechanical purpose of make the OH on bicarbonate into a good leaving group (PO4)
What is a carboxylase?
A carboxylase adds carbon dioxide, and usually requires the coenzyme biotin
What transformation does PEP carboxylase catalyze?

What high energy molecule is needed?
Converts oxaloacetate to phosphoenolypyruvate (PEP)

GTP is used in decarboxylating oxaloacetate
Where are glycolysis, PEP carboxykinase, and pyruvate carboxylase present?

What problem occurs due to their locations?
Glycolysis and PEP carboxykinase occur in the cytoplasm

Pyruvate carboxylase occurs only in the mitochandria

*A transport problem arises due to the different locations
What are the four transport problems that gluconeogenesis encounters?
1. Pyruvate needs to be transported into the mitochondria (not big problem, can be done)
2. Oxaloacetate needs to be transported out the mitochandria (PROBLEM)
3. There is no mitochondrial transport system for oxaloacetate
4. Essentially can get to mitochondria but not out
What is one solution to the transport problem gluconeogensis faces? (4 steps)
1. Convert the oxaloacetate into malate
2. Transport malate out of mitochandria (mitochandrial transport system for malate)
3. Resynthesize oxaloacetate by reducing malate
4. Continue with gluconeogensis
What is an advantage to using transport solution 1 in gluconeogensis?
The process effectively transports 1 NADH out of the mitochandria
What is another solution to the transport problem gluconeogensis faces? (2 steps)
1. Make a mitochandrial form of PEP carboxykinase

2. Transport PEP from mitochandria to cytoplasm
What is the grand total of gluconeogensis?
Need 4 ATP and 2 GTP (6 nucleotide triphosphates)

Need 2 NADH

*Buidling glucose from pyruvate is costly
What four things regulate hexokinase?
1. Isozymes
2. Allosteric regulation
3. Inhibitor protein binding
4. Differential compartmentalization
What are Isozymes?
Different forms of the same enzyme
Why is the transport of NADH out of the mitochondria useful to the cell?
NADH is needed in the cytoplasm for one of the reversible reactions to make glucose
What are 5 ways in which an enzyme can be regulated?
1. Sequestration (compartmentalization)
2. Association w/ regulatory protein
3. Allosteric regulation
4. Covalent modification (phosphorylation)
5. Isozymes
There are 4 isozymes of hexokinase. In what organ does each type regulate?
1. Type 1: muscle; inhibited by glucose
6Pi
2. Type 2: muscle
3. Type 3: muscle
4. Type 4 (glucokinase): liver
What are four properties of the type 4 hexokinase isozyme glucokinase?
1. Weak affinity for glucose
2. Directly regulated by glucose level in blood
3. Insensitive to glucose 6-Pi
4. Inhibited by fructose 6-Pi
What are the two functions of the liver in regards to glucose?
1. Stores and releases glucose

2. Keeps level of glucose in blood constant
How does the liver keep glucose levels constant?

Two ways...
1. When glucose is abundant, liver converts excess into storage form

2. When glucose is scarce, liver converts the glycogen back to glucose and releases it into the bloodstream
Which enzyme, hexokinase I or hexokinase IV, would get saturated first with glucose?

Why does this happen?
Hexokinase I gets saturated first

This is because hexokinase I is in the muscles and quicker saturation ensures that the muscles get fed first
What enzymes does fructose 2,6-biphosphate regulate?

Two of 'em...
1. PFK-1 (used in glycolysis)

2. FBPase-1 (used in gluconeogensis)
How is phosphofructokinase 1 regulated?

Three ways...
1. Allosterically inhibited by ATP and citrate
2. Activated by ADP and AMP (cell needs energy)
3. Activated by fructose 2,6-biphosphate (lots of glucose)
How is fructose biphosphatase-1 regulated?

Two ways...
1. Inhibited by fructose 2,6-biphosphate (lots of glucose so more isn't needed)

2. Inhibited by AMP (cell needs energy)
What does fructose 2,6-biphosphate signal about glucose concentration?

What does the signal stimulate/inhibit?
Fructose 2,6-biphosphate signals high glucose concentration

Stimulates glycolysis, inhibits gluconeogenis
What are three reciprocal regulators for PFK-1 and FBP-1?
1. Fructose 2,6-biphosphate
2. ATP/ADP
3. Citrate
What are two ways to regenerate NAD+?
1. Oxidative phosphorylation (produce ATP as well)

2. Fermentation (won't produce ATP)
How does oxidative phosphorylation regenerate NAD+?
When oxygen is available, NAD+ can be generated from NADH by dumping excess electrons on oxygen
How does fermentation regenerate NAD+?
If oxygen is not available, NAD+ can be regenerated from NADH by dumping the electrons on pyruvate or another organic molecule
How does one put electrons on pyruvate?

Two conversions...
1. Conversion to lactate

2. Conversion to ethanol
What enzyme is used in the conversion of pyruvate to lactate?
Lactate dehydrogenase
What enzymes are used in the conversion of pyruvate to ethanol?

Two enzymes...
1. Pyruvate decarboxylase

2. Alcohol dehydrogenase
What cofactor does pyruvate decarboxylate use?

What does this cofactor do?
Thiamin (TPP) is the cofactor

Thiamin is used to move the 2 carbon "active acetaldhyde" unit
What chemicals are responsible for a chunky hangover?

Two things...
1. Acetaldehyde

2. Acetic Acid
How are acetaldhyde and acetic acid formed to result in a hangover?

Two steps...
1. Alcohol dehydrogenase generates acetaldehyde
2. Acetaldehyde is converted to
Acetyl-CoA via acetic acid
Alcohol dehydrogenase is able to use various substrates. What are the outcomes when it uses ethanol, methanol, and ethylene glycol?
1. Ethanol: converted to acetyaldhyde and gives you a hangover

2. Methanol: converted to formic acid and leads to blindness

3. Ethylene glycol: converted to oxalic acid which causes death by formin insoluble crystals that plug the kidney
What are some good things that result from fermentation?
1. Beer/wine
2. Bread
3. Cheese/yogurt
4. Pickles and sauerkraut

CHUNKYNESS!!!
Lactate dehydrogenase-1 is found mostly inside of heart cells. How can measuring LDH-1 indicate if someone had a heart attack?
Measure blood levels of LDH-1

*Elevated levels of LDH-1 in blood serum suggest hearts cells have been damaged and are leaking
How is the Cori Cycle used during exercise?

Four things to know...
1. During exercise, oxygen intake can't keep up w/ glycolysis
2. Pyruvate is converted to lactate by fermentation
3. During rest, lactate is converted back to glucose by gluconeogensis
4. Cycle between muscle and liver
What is "white meat?"

What is it specialized for?

Where does it obtain energy from?
White meat is fast twitch muscle

Specialized for short bursts of activity

Obtains energy through fermentation b/c lack of mitochondria
What is "dark meat?"

What is it specialized for?

Where does it obtain energy from?
Dark meat is slow twitch muscle

It's specialized for slow and steady contractions, i.e. quads

Obtains energy through oxidative phosphorylation b/c contains lots of mitochondria
What is the Pasteur effect?
In cells that rely on energy production through fermentation, the rate of glycolysis is increased
in order to counter balance the poor production of ATP
How do tumor cells obtain their energy?

Do they use glucose at all?
Tumors produce most of their chunky-beefy energy through fermentation

Tumors use lots of glucose (less efficient means)
How can tumors be found and why?
Use a PET

Look for abnormal usage of glucose which is indicative of a tumor (increased rate in glycolysis gives them away) *Pasteur effect
Why do we have the pentose phosphate pathway?

Four reasons...
1. Generation of NADPH
2. Generation of ribose (biosynthethic precursor for nucleotides)
3. Carbon fixation
4. Important pathway in actively dividing cells (high DNA/RNA metabolism)
What are two things NADPH is used for?
1. Biosynthethic reactions

2. Detoxifying oxidative damage
What are the two phases of the pentose phosphate pathway?
1. Oxidative phase

2. Non-Oxidative phase
What happens in the oxidative phase of the pentose phosphate pathway?

three things...
1. 1 of 6 carbons is oxidized to CO₂

2. A ribose 5-phosphate is created

3. 2 NADPH are created
What occurs during the non-oxidative phase of the pentose phosphate pathway?

Two things...
1. Unused ribose is converted back to glucose

2. Glucose is used in either glycolysis or for another pass through the pentose phosphate pathway
How many reaction are in the oxidative phase of the pentose phosphate pathway?

Are there any irreversible steps?
There are 4 reations in oxidative phase

There are 2 irreversible NADPH generating steps
What is the main irreversible step in the pentose phosphate pathway?

What enzyme is used in this step?

Why is this an irreversible, regulatory step?
Main irreversible step is converting glucose 6-Pi to 6-Phosphogluconon-δ-lactone

Enzyme: Glucose 6-phosphate dehydrogenase

The NADPH that is formed inhibits the enzyme (feedback inhibition)
Why do people with a defect in the enzyme G6PD become sick when they eat fava beans?
NADPH is needed to to remove toxic oxygen species

People w/ G6PD deficiencies are sensitive to oxygen radicals and become sick when they eat fava beans b/c the beans contain a compound that stimulates production of toxic oxygen radicals
What happens when a person has a defect in the enzyme G6PD?
A defect in this enzyme inhibits the pentose phosphate pathway and the production of NADPH
What is the second irreversible step the pentose phosphate pathway?

What enzyme is used?

What is formed?
The second, irreversible step is the conversion of 6-Phosphogluconate to
D-Ribulose 5-phosphate

Enzyme: 6-phosphogluconate dehydrogenase

Forms NADPH and CO₂ (by oxidizing C-1)
What is the net oxidative pentose phosphate reaction?

Products and reactants?
Reactants: Glucose-6 Pi, 2NADP, H₂O

Products: Ribose-5 Pi, 2NADPH, CO₂
What happens in the net non-oxidative pentose phosphate reaction?
It reversibly regenerates glucose-6 Pi from extra ribose-5 Pi
When is the non-oxidative phase of the pentose phosphate reaction used?

(Two situations...)
1. Cell needs NADPH but not ribose, so they convert ribose back to glucose and oxidize it again to make more NADPH

2. Cells need ribose, but not NADPH, so a bypass of the oxidative pathway is provided
What are the key enzymes of the Non-oxidative branch of the pentose phosphate pathway?

Two of 'em...
1. Transaldolase

2. Transketolase
What does transaldolase do?
Transaldolase transfers a 3 carbon fragment and the reaction is similar to that of aldolase (condensation reaction)
What does transketolase do?

Three things...
1. Transfers 2 carbon fragments from a ketone donor to an aldose acceptor
2. Proceeds through an "activated acetaldehye"
3. Uses thiamin pyrophosphate (TPP) in a manner similar to pyruvate decarboxylase
What can a thiamin defeciency result in?
Beriberi

Beriberi is largely a deficiency in transketolase activity

Symptoms include weakness and neurological problems
What is thiamin?

What is it used for?
Thiamin is a cofactor

It's used in the cleavage of bonds adjacent to carbonyl groups

Also used in transfer of 2 carbon "active acetaldehyde units"
Where is glycogen is predominately found in our body?

Two places...
1. Liver

2. Muscles
What three enzymes make glycogen?
1. Glycogen synthase
2. Glycogen branching enzyme
3. Glucogenin
Glycogen:

What does glycogen synthase do?
Makes linear α1-4 linkages
Glycogen:

What does the glycogen branching enzyme do?
Makes the α1-6 branches
Glycogen:

What does glucogenin do?
It makes the starting glycogen primer
Glycogen:

What is the precursor for making glycogen?
UDP-glucose (high energy form of glucose)
Glycogen:

To initiate glycogen synthesis, what is glucose 6-phosphate converted into?

Using what enzyme??
Converted into glucose 1-phosphate

Enzyme: phosphoglucomutase
Glycogen:

What is glucose 1-phosphate converted into during a key step in glycogen biosynthesis?

Enzyme?
It's converted into UDP-glucose

Enzyme: UDP-glucose pyrophosphorylase
Glycogen:

What is UDP-glucose's role in the glycogen synthase reaction?
It is the immediate donor of glucose residues
Glycogen:

What occurs during the first reaction in glycogen synthesis in which glycogen synthase is the catalysis?

Two parts...
1. Enzyme transfers the glucose residue of UDP-glucose to the nonreducing end of a glycogen branch

2. Glycogen chain is elongated by glycogen synthase
Glycogen:

What must occur during glycogen synthesis in order for glycogen to branch?
Glycogen branching enzyme must make the bonds found at the branching points
Glycogen:

How does glycogen branching enzyme form the branches of glycogen?

Two things...
1. It catalyzes the transfer of terminal fragments to a more interior position of the chain

2. The residues transfered are six residues away from the nonreducing end
Glycogen:

What is necessary for the glycogen synthase to be active?
A short primer of at least 3 glucose molecules
Glycogen:

What is the fist linkage in the glycogenin reaction?
Transfer of glucose residue from UDP-glucose to hydroxyl group of Tyr of glycogenin

Catalyzed by glucosyltransferase activity
What is glycogenin?

Two things...
1. Intriguing protein

2. Both the primer on which new chains of glycogen are synthesized as well as the enzyme that catalyzes their assembly
Glycogen:

What happens after the first addition of glucose in the glycogenin reaction?

Two things...
1. Extend chain by adding seven more glucose residues derived from UDP-glucose

2. Glycogen synthase takes over
Glycogen:

What two enzymes are involved in glycogen degradation?
1. Phosphorylase

2. Debranching enzyme (hydrolase)
Glycogen:

What does phosphorylase do?
Splits the α1-4 bonds using phosphate as a nucleophile

*group transfer reactions
Glycogen:

What does the debranching enzyme (hydrolase) do?

Two steps...
1. Transfers linear segments after phosphorlyase hydrolyzes
2. Splits the α1-6 bonds at branch points using water as nucleophile

*group transfer reaction
Glycogen:

At what end of the glycogen molecule does degradation occur?
Degradation occurs at the nonreducing end
Glycogen:

What does phosphorylsis do in glycogen degradation?
Conserves energy in the glycosidic bond
Glycogen:

How far away from a branching point can Phosphorylase remove glucose units?
It can remove glucose residues within 4 glucose units of a branching point
Glycogen:

What do debranching enzymes do?

Two things...
1. They transferase activity of debranching enzyme

2. They glucosidase activity of debranching enzyme
What peptide hormones released by the pancreas regulate blood sugar level?

Two of 'em...
1. Insulin

2. Glucogon
What do elevated levels of insulin signal?

What does this stimulate?
Blood glucose is high

*Stimulates glycogen synthase
What do elevated levels of glucogon signal?

What does this stimulate?
Blood glucose levels are low

*Activates phosphorylase
What protein modification regulates glycogen synthase and phophorylase?
Protein Phosphorylation
What three amino acids can be phosphorylated?
1. Serine

2. Tyrosine

3. Threonine
What do kinases do?
Kinases add a phosphate by a group transfer usually from ATP
What do phosphatases do?
Phosphotases remove phosphate by hydrolysis
Glycogen:

What regulates glycogen synthase?

Three things...
1. Inhibited by phophorylation (glycogen synthase kinase III)

2. Activity is stimulated by protein phosphatase I

3. Insulin activates activity
What 3 things regulate phosphorylase?
1. Inhibited by phophorylase (a phosphatase)

2. Activity is stimulated by phosphorylation (phosphorylase B kinase)

3. Glycogon stimulates it
What are the four sub compartments of the mitochondria?
1. Outer membrane (relatively permeable)
2. Inner membrane (selectively permeable)
3. Inter-membrane space
4. Matrix
Where does pyruvate dehydrogenase and the citric acid cycle occur?
In the mitochondrial matrix

CHUNKY BEEFYNESS.
What are two other names for the citric acid cycle?
1. Krebs Cycle

2. Tricarboxylic Acid Cycle (TCA)
How is Acetyl-CoA formed?

Two things..
1. Converts pyruvate (oxidative decarboxylation)

2. Catalyzed by pyruvate dehydrogenase complex
What is Coenzyme A?
*High energy handle*
It's a coenzyme, notable for its role in the synthesis and oxidization of fatty acids, and the oxidation of pyruvate in the citric acid cycle.

It is adapted from β-mercaptoethylamine, panthothenate and ATP
What is the structure of Coenzyme A?

Three parts...
1. Nucleotide
2. Vitamin
3. β-Mercapto-ethylene that has reactive thiol group on end
How are acyl groups linked to coeznyme A?
Acyl groups are covalently linked to the thiol group forming thioesters
What does pyruvate dehydrogenase complex consist of?
3 enzymes
&
5 cofactors
What are the five cofactors in the pyruvate dehydrogenase complex?
1. TPP
2. FAD
3. CoA
4. NAD
5. Lipoate
What is important about the structure of lipoate?
Lipoate has two thiol groups that can undergo reversible oxidation to a disulfide bond
Because of its structure, what can lipoic acid act as?

Two beefy ways...
1. Electron acceptor
and
2. Molecular tether (acyl carrier)
What are the three enzymes of the pyruvate dehydrogenase complex?
E1: Pyruvate dehydrogenase

E2: Dihydrolipoyl transacetylase

E3: Dihydrolipoyl dehydrogenase
What does E1 of the pyruvate dehydrogenase complex do?

Three things...
1. Decarboxylates pyruvate using TPP
2. Oxidizes the active acetaldehyde
3. Transfers both electrons and acetyl group to lipoic acid on E2
What does E2 of the pyruvate dehydrogenase complex do?
Acetyl group is oxidized and transfered to CoA to make acetyl Coa
What does E3 of the pyruvate dehydrogenase complex do?

Two things...
1. Regenerates oxidized lipoic acid on E2

2. Passes the electrons to NAD+ via FADH2
How does the structure of pyruvate dehydrogenase facilitate substrate channeling?
Have a direct passage b/c all are linked (no intermediates leaves until Acetyl-CoA is made)
What is the structural role of lipoate?
Lipoate couples the reaction sites of E1 with E2
What is substrate channeling?
No intermediates leave until product is made so you can have efficient and direct passage of intermediates
What are the two critical steps in pyruvate dehydrogenase?
1. Allosteric regulation

2. Covalent Modification
What three things repress pyruvate dehydrogenase through allosteric regulation?
1. End products (aceytl CoA)
2. High Energy (ATP, NADH)
3. Fatty acids
What activates pyruvate dehydrogenase through allosteric regulation?

Three items...
1. Low energy (AMP, NAD+)
2. CoA
3. Ca++
What inactivates pyruvate dehydrogenase through covalent modification?
It is inactivated by phophorylation through a specific kinase
What activates pyruvate dehydrogenase through covalent modification?
It is activated by DEphosphorylation through a specific phosphatase
What are people given during a heart attack to stimulate oxidation of carbohydrates?
Dichloroacetate
Citric Acid Cycle:

What does the citric acid cycle generate?

Three things...
1. NADH
2. FADH2
3. Biosynthetic precursors
Citric Acid Cycle:

What two findings suggested that the citric acid cycle is a cyclic pathway?
1. Adding glucose to cellular extracts was coupled to oxygen uptake

2. Adding any of the three carbon acids (succinate, fumarate, or oxaloacetate) stimulated O uptake in a catalytic manner (CHUNKY!)
Citric Acid Cycle:

What does the rate of flow in a linear pathway depend upon?
The concentration of the starting substrate

The more substrate you add, the greater the yield and ratio of product as long as the enzymes aren't saturated
Citric Acid Cycle:

What does the flow rate in a cyclic pathway depend upon?
The concentration of the reaction intermediates

*Only adding more reaction intermediates (not SM) increases rate of conversion
Citric Acid Cycle:

What do reaction intermediates serve as in cyclic pathways?
Catalysts (cuz they don't get used up)
Citric Acid Cycle:

What is the big picture of the citric acid cycle? (3 points)
1. 8 reactions
2. Start with 2 acetyl-CoA
3. Produce 4CO₂, 2GTP, 6NADH, and 2FADH₂
Citric Acid Cycle:

What are the eight intermediates (in order) of the citric acid cycle?
1. Oxaloacetate
2. Citric Acid
3. Isocitrate
4. α-Ketoglutarate
5. Succinyl CoA
6. Succinate
7. Fumarate
8. Malate
Citric Acid Cycle:

Describe reaction 1, citrate synthase
Start with acetyl-CoA and oxaloacetate and form citrate
*Irreversible, control point

Citrate synthase is enzyme
WTF Synthase, mate?
Assembles C-C bonds without ATP
Citric Acid Cycle:

Describe reaction 2, aconitase
Citrate to Isocitrate
-Isomerization reaction

Aconitase is enzyme

Change non-oxidizable tertiary alcohol to oxidizable secondary alcohol
Citric Acid Cycle:

What is important about the structure of iconistase?
Contains an Iron/Sulfur center
-This center binds citrate and make the -OH group on citrate a better leaving group
Citric Acid Cycle:

What is interesting about how citrate functions?
Citrate functions asymmetrically even though it is symmetric, which makes positioning important

The -OH group will only move to the oxaloacetate C
Citric Acid Cycle:

What makes citrate a "pro-chiral" molecule?

Two reasons...
1. One step away from chirality

2. Its active sites have complementary binding points
Citric Acid Cycle:

Describe reaction 3, isocitrate dehydrogenase
Form α-ketoglutarate
*Irreversible, control point

Oxidative decarboxylation

Make molecule of NADH

-Isocitrate dehydrogenase is enzyme
Citric Acid Cycle:

Describe reaction 4,
α ketoglutarate dehydrogenase
Form succinyl-CoA
CoA returns!
*Irreversible, control point

α ketoglutarate dehydrogenase is enzyme

Reaction & enzyme are nearly identical to that catalyzed by pyruvate dehydrogenase
Citric Acid Cycle:

Describe reaction 5, succinyl CoA synthetase
Succinyl-CoA is converted to succinate

Substrate level phosphorylation

*Only reaction that directly makes high energy molecule

-Succinyl CoA synthetase is enzyme
What is a Synthetase?
A synthetase makes carbon bonds in an ATP dependent manner

*Through condensation reactions