Chapter 12: Metabolism and Bioenergetics Flashcards
Define metabolism
The entire set of chemical reactions occurring in a living system.
Define catabolism
The breaking down of large molecules into smaller ones.
–Example: degrading nutrients in our food such as fats, carbs, and proteins.
Name the characteristics of catabolism
→Catabolism is an oxidative process and releases energy that will be captured in the form of ATP.
These are via oxidizing molecules in what are known as degradative reactions.
Define anabolism
This is NOT necessarily the opposite of catabolism…
It is:
→The building of large molecules.
-These anabolic reactions are called synthetic reactions.
Name the characteristics of anabolism
→Anabolism is reductive and uses energy.
-Require reducing agents that will provide electrons for reduction
-Since we are building large molecules, covalent bonds are forming and this process consumes energy (ATP).
-We cannot store ATP, but it is estimated we turn over 1⁄2 our weight in ATP daily.
What is the chemical reaction for the digestion of proteins? How do we digest the macromolecules in our food?
Digestion is the hydrolysis of macromolecular nutrients into their corresponding components known as metabolic fuels
–proteins→amino acids
–polysaccharides→monosaccharides
–triacylglycerols→fatty acids
Which enzymes are involved in the digestion of proteins?
Proteins are hydrolyzed by proteases.
In this figure, the addition of water breaks the peptide bond.
There is the regeneration of a carboxy terminal and a new amino terminal.
What is the chemical reaction for the digestion of carbohydrates?
→Polysaccharides (carbohydrates) are hydrolyzed by amylases.
-There are 2 types of amylases:
→Salivary
→Pancreatic
→Hydrolysis of polysaccharides involves the breaking of glycosidic bonds.
This means digestion begins in the mouth where hydrolysis is already taking place!
Which enzymes are involved in the digestion of carbohydrates?
Amylases
There are 2 types of amylases:
→Salivary
→Pancreatic
In the chemical reaction for the digestion of triglycerides, which bond is broken?
Triacylglycerols (triglycerides) are hydrolyzed by lipases.
The bond being broken is the ester bond being hydrolyzed by H2O.
Only the two groups on the exterior can be lysed, not the middle ester since it is “protected” by the other two groups.
Which enzymes are involved in the digestion of triglycerides?
Lipases. Lipases are not highly specific; they are generally specific.
This is because triacylglycerols are a family with many different types of substrates, so lipases, being less specific, can recognize all of them.
What are fates of digestion products?
→Digestion products can be degraded or stored.
1. Digestion products can be degraded in catabolism
Or,
2. If we eat them in excess, we can store them.
–They are stored as LARGE molecules.
–Digestion products can be stored as large molecules which can be later mobilized as needed.
What is the storage form of glucose?
Glycogen
We can hydrolyze starch and release glucose, but if we eat starch in excess, it won’t be stored, but glycogen will be. We can’t store starch.
We have limited space for glycogen storage.
We store glycogen in the liver and muscles.
What is the reaction needed to remove glycogen and release glucose from storage?
This is called phosphorolysis;
A combination of hydrolysis and phosphorylation. When we are ready to make use of glucose, it will be removed from storage and degraded. Glycogen is broken down through phosphorolysis (not hydrolysis) in the liver and muscles.
Which cells store triglycerides?
adipocytes (fat cells)
How are the products of digestion of triglycerides transported?
Protein albumin or linked to cholesterol.
Stored fat (formed from fatty acids) can be hydrolyzed when needed, releasing fatty acids which are transported by the protein albumin or linked to cholesterol. Not all the fat will be hydrolyzed, only part of it.
What are metabolic pathways?
Metabolic pathways are series of consecutive reactions.
–a→b→c→d etc
-The product of the subsequent step becomes the substrate of the next step and they all have names.
i.e. Glycolysis and the citric acid cycle.
What is a metabolic pathway metabolite?
→Metabolic pathways involve mostly intermediates called metabolites
The pathways are mostly called metabolites.
They are intermediates that are only temporarily formed.
Metabolism is often called “intermediate metabolism” because it is composed mostly of intermediates.
What is a metabolic pathway precurser?
A few metabolites may be used as precursors to other things of intermediates.
Examples of precursors of metabolism
Pyruvate is the precursor of alanine.
Even more important: pyruvate and CO2 are the precursors to oxaloacetate! (Oxaloacetate is found in the citric acid cycle).
What is the relationship between the reduction state of a compound and the amount of energy released?
Reduced compounds have more energy.
How are coenzymes (cofactors) used as acceptors of electrons?
Coenzymes serve as hydrogen carriers for oxidation reactions that affect the energy nutrients in the citric cid cycle.
- NAD coenzyme acts as a hydrogen accepter in oxidation-reduction reactions. The ETC in cellular respiration is responsible for energy production and is an excellent illustration of NAD’s involvement in redox reactions.
How are cofactors recycled?
The components are called ETC carriers, because they accept electrons, move them, donate them, accept them, etc.
→ Reduced cofactors release electrons in the electron transport chain (ETC) through a process called oxidative phosphorylation.
Figure shoes the physical pathways of the ETC.
What are the steps of the outline of metabolism figure?
ADP is phosphorylated into ATP.
1. Biopolymers
2. Monomers
3. The citric acid cycle
4. Reduction of NADH,QH2
5. Electron (H-) transfer takes place
6. ADP can undergo oxidative phosphorylation to ATP
O2 can protonate to become H2O
NADH, QH2 can become NAD+, Q.
What are the characteristics of metabolic pathways?
→Metabolic pathways are all connected. Not a single reaction is isolated.
→All metabolic pathways are regulated.
→Not all metabolic pathways are found in all cells.
→Cells have a unique metabolic repertoire.
-The CO2 that is our waste is digested by plants. Then plants make starch that we eat.
In this way we are all interconnected
→Organisms may be metabolically interdependent.
What are the types of substances humans cannot make? Why these substances are called essential?
Essential means it is necessary to eat in our diet. Humans are unable to synthesize some important biomolecules. These substances are essential to have in our diet since we cannot produce them on our own.
Ex. Choline is found in eggs.
What is the role of vitamins in metabolism?
They arerequired as functional parts of enzymes involved in energy release and storage. This table shows a variety of vitamins, their corresponding coenzyme products, their biochemical functions, and what disease could be caused by their deficiency.
Characteristics and structure of niacin?
-Another name for vitamin B3
-A component of the coenzymes NAD+ and NADP+.
Characteristics and structure of thiamine?
- Vitamin B1
-It helps convert the 3-carbon intermediate to the 2-carbon intermediate.
-is a prosthetic group of some essential enzymes
-the first B vitamin discovered
What are the characteristics of free energy changes in metabolic reactions?
→Metabolic reactions are linked and not isolated.
→Free energy of metabolism (i.e. the entire system) is constantly changing.
→Free energy changes whenever a chemical reaction takes place in the system.
What is the relationship between equilibrium constant and standard free energy?
Free energy change depends on reactant concentrations. We use the concentrations at equilibrium.
What is the meaning of Standard (biochemically) free energy change?
Biochemical standard is ΔG°’
Chemical standard is ΔG°
→Free energy change is the driving force that reactants experience to reach their equilibrium.
“Driving force” could be called “the tendency” of a reaction to move in the forward or reverse reaction.
What are the biochemical standard state conditions?
–Temperature: 25 °C
–Pressure: 1 atm
–[Reactant]: 1 M
–pH: 7.0 ( [H+] = 10^-7M
–[H2O]: 55.5 M
How is the actual free energy change calculated?
This formula is how the actual free energy change or ΔG for biochemical reactions is calculated.
What are the components of ATP?
- coupled processes
- phosphoanhydride bonds
What is the meaning of “a coupled process”?
combining a favorable reaction with an unfavorable reaction.
What are the features of the ATP cycle?
Nutrients from our food proceed through the citric acid cycle to form ATP. Anabolism synthesizes large molecules.
What are the factors that explain the favorable hydrolysis of ATP?
The products of ATP hydrolysis are more stable than the reactants.
What is the meaning of “high” and “low” energy phosphorylated compounds?
Amount of energy released
What is the position of ATP in the table of “high” energy phosphorylated compounds?
ΔG°’= -30.5 Below phosphocreatine. ATP releases a significant amount of energy, but there are other compounds that release much more!
What is the position of ATP in the table of “low” energy phosphorylated compounds?
ΔG°’= -30.5. Above glucose -1-phosphate
Why does ATP have an intermediate position in the table?
PEP, 1,3-bisphosphoenolpyruvate and phosphocreatine can be used to make ATP. Everything listed below ATP can be made FROM ATP.
What is the phosphocreatine hydrolysis reaction?
When phosphocreatine is dephosphorylated, it becomes creatine.
What is the thioesters hydrolysis reaction?
The thioester wants to break.
Acetyl CoA, which is called the 2-carbon intermediate, is the one that enters the citric acid cycle which then releases energy as is shown on this slide.
Sulfur is the reactive group.
Which steps are regulated in a metabolic pathway?
Steps with large free energy changes (-).
Dam example:
When you subtract the large from the small, it gives a negative value. A large, -ΔG is irreversible and regulated.
“The tendency to GO is GREAT.”
The little waves on the right side cannot be regulated, because they are very small, therefore ΔG is close to 0.
What does this picture represent?
Glucose stored as glycogen
What do adipocytes (fat cells) store?
Triacylglycerols
What are the transport proteins of lipids?
lipoproteins
What happens in the phosphorolysis (not hydrolysis) in the liver and muscles?
Phosphorolysis is the reaction needed to remove glycogen and release glucose from storage
All the sets of chemical reactions that take place in a living system, whether that be unicellular organisms or human beings is the definition of which concept?
Metabolism
There are so many metabolic reactions, so it is convenient to divide them into what 2 major types?
Catabolism and Anabolism
In this figure, free energy in the form of ATP is involved
In this figure, free energy in the form of ATP is involved as macromolecules are degraded into smaller units.
Macromolecules are not necessarily degraded into building blocks; that’s more to do with anabolism.
Name the chemical reaction and the bond broken
Hydrolysis of polysaccharides (carbohydrates) involves the breaking of glycosidic bonds.
In this figure, the alpha(1→4) is broken.
Due to the “…” on either side of this diagram, the compounds shown are likely starches.
Glycogen is broken down through
phosphorolysis (NOT hydrolysis)
What do these images represent?
→Glucose being stored as glycogen
– Glycogen is highly branched
Name this reaction
Phosphorolysis. Glycogen is broken down through phosphorolysis. In this figure, the phosphate group is breaking the bond between alpha(1→4) and phosphorylating (adding the phosphate group) to the carbon #1 on what is now glucose- 1-phosphate.
What happens in phosphorolysis?
Glycogen is broken down through phosphorolysis. In this figure, the phosphate group is breaking the bond between alpha(1→4) and phosphorylating (adding the phosphate group) to the carbon #1 on what is now glucose- 1-phosphate. It can be very easily converted to glucose-6-phosphate.
Name this cell and its function
Adipocytes (fat cells) which store triacylglycerols.
Fatty acids must be transported through the bloodstream via the protein
Albumin. Fatty acids are not free floaters in the body since they would lower the pH.
They must be transported through the bloodstream via the protein albumin.
Albumin has [ ] binding sites and will carry [ ] fatty acids to cholesterol.
Albumin:
This protein has 7 binding sites and will carry 7 fatty acids to cholesterol.
Cholesterol’s carboxyl group bonds to the fatty acid to form an ester.
In this figure, cholesteryl stearate is shown, with the cholesteryl ester attached.
The cholesteryl esters and some intact fats combine with proteins to form the
lipoproteins.
Define lipoproteins
Lipoproteins are the transport proteins of lipids.
-Apolipoproteins form lipoproteins.
Define Apolipoproteins
Apolipoproteins are proteins that bind lipids to form lipoproteins. They transport lipids in blood, cerebrospinal fluid, and lymph. The lipid components of lipoproteins are insoluble in water.
→Metabolic pathways are series of consecutive [ ]
–a→b→c→d etc
-The product of the [ ] becomes the [ ] of the next step and they all have names.
I.e. Glycolysis and the citric acid cycle.
→Metabolic pathways are series of consecutive reactions.
–a→b→c→d etc
-The product of the subsequent step becomes the substrate of the next step and they all have names.
I.e. Glycolysis and the citric acid cycle.
Which cycle is oxaloacetate found in?
Oxaloacetate is found in the citric acid cycle
What is the net reaction of pyruvate as a precursor?
Pyruvate→Oxaloacetate is [ ] or in equilibrium like in Pyruvate→Alanine. It is [ ], which means it can be [ ].
The enzyme catalyzing this step is a regulatory enzyme, indicating it is [ ].
Pyruvate→Oxaloacetate is NOT reversible or in equilibrium like in Pyruvate→Alanine. It is IRREVERSIBLE, which means it can be REGULATED.
The enzyme catalyzing this step is a regulatory enzyme, indicating it is ALLOSTERIC.
The enzymes in metabolism that are regulatory and catalyze reversible steps are called
allosteric. If we consume excess protein and don’t use all of it, it gets degraded back into pyruvate.
What does this image represent?
This image shows how the common intermediates glyceraldehyde-3-phosphate, pyruvate and Acetyl-CoA are involved in several metabolic pathways.
Some metabolic pathways share a few common [ ].
intermediates.
Examples:
◼ glyceraldehyde-3-phosphate to alanine to triacylglycerols
◼ pyruvate to oxaloacetate to amino acids
◼ acetyl-CoA to fatty acids or CO2.
What type of reactions are involved in metabolic pathways?
Many metabolic pathways involve oxidation-reduction reactions. This figure shows methane getting oxidized to CO2. →In CH4, C is in its most reduced form. (Most hydrogens bonded)
→In CO2, C is in its most oxidized form. (This releases a lot of energy and heat). This is a redox reaction; most metabolic pathways involve redox reactions.
Do reduced compounds have more or less energy?
reduced compounds have more energy
Carbons in fatty acids and carbohydrates are oxidized to
CO2.
This figure shows methylene groups in a chain of fatty acids.
The carbons are fully saturated and reduced fatty acids will provide a lot of energy.
They are fully oxidized in our cells to CO2.
Polyhydroxylated.
They are partially reduced with the OH attached, with the potential to release energy when fully reduced.
→Carbons that are reduced or partially reduced represent a form of stored free energy.
Which coenzyme (cofactors) are used as acceptors of electrons?
-NAD+
-NADP+
-Ubiquinone
***Ubiquinone has 3 other names: Q, CoQ and Coenzyme Q.
Cofactors are [ ] molecules.
They can be prosthetic groups or cosubstrates. Coenzymes are NAD+, NAD, FAD and acetyl CoA. All have [ ].
Cofactors are organic molecules.
They can be prosthetic groups or cosubstrates. Coenzymes are NAD+, NAD, FAD and acetyl CoA. All have adenosine.
Reduced cofactors release electrons in [ ] through a process called [
].
These are the physical pathways of the ETC.
Not all metabolic pathways are found in all cells. The only cells that have all the metabolic pathways are in the [ ].
The [ ] also has lots of [ ] that are unique to it, that cannot be found elsewhere in digestion.
Not all metabolic pathways are found in all cells. The only cells that have all the metabolic pathways are in the liver.
The liver also has lots of enzymes that are unique to it, that cannot be found elsewhere in digestion.
The brain cells cannot make [ ], so it is dependent on other organs to
produce energy for it to use.
glucose
We are unable to make about half of the amino acids on our own.
These are the larger amino acids. For instance, it takes [ ] to make [ ], and our bodies are not capable of making it.
We are unable to make about half of the amino acids on our own.
These are the larger amino acids. For instance, it takes 16 steps to make tryptophan, and our bodies are not capable of making it.
classify vitamins into two groups:
→water soluble
→fat soluble
Vitamin deficiencies can cause
disease
Water soluble vitamins are precursors for [ ]?
enzymes.
Example: Folic acid is a vitamin with lipoamide as its coenzyme product. Folic acid’s biochemical function is as a cofactor for one-carbon transfer reactions. A deficiency in folic acid can cause anemia.
An excess of fat-soluble vitamins can be toxic because
they are stored in the adipose (fat) tissues.
-ΔG means the reaction is
favorable
+ΔG means the reaction is
unfavorable
This table shows the standard state conditions for biochemicals.
The difference between chemical and biochemical standard is the [ ].
This means the reactant concentration will be affected by the [ ].
The concentration of the metabolites is [ ] relative to the solvent [ ], so we consider [ ] to be a [
] concentration: 55.5 M.
The difference between chemical and biochemical standard is the pH.
This means the reactant concentration will be affected by the pH.
The concentration of the metabolites is so small relative to the solvent (water), so we consider water to be a super high concentration: 55.5 M.
What is often involved in coupled processes?
ATP
What type of bonds participate in ATP?
phosphoanhydride bonds
Why does ATP hydrolysis release energy?
The products of ATP hydrolysis are more stable than the reactants.
The products of ATP hydrolysis are [ ] than the reactants.
The products of ATP hydrolysis are more stable than the reactants.
Why are the products of ATP hydrolysis more stable than the reactants?
1.Unfavorable electrostatic repulsion is lowered in products. 4 negatively charged oxygens is a lot of electrostatic repulsion. This is relieved when the bond is hydrolyzed.
2.There are more resonance forms in the products. Resonance=stability
3.The products are better hydrated. Surrounded by water makes them more stable.
Draw how resonance makes Pi more stable than ATP
Acetyl-CoA contains
Adenosine
What type of reaction is shown in the figure?
Decarboxylation reaction is defined as a chemical reaction that eliminates a carboxyl group and liberates carbon dioxide (CO2). Pyruvate being converted into acetyl-CoA is the MOST HIGHLY REGULATED reaction in the cells. It requires 5 cofactors.
Acetyl-CoA is the starting material of fatty acids.
–It can also be converted into cholesterol, amino acids, or CO2.
What are the intermediates of glucose (also known as intermediates of glucose catabolism)?
ΔG is favorable in the [ ] direction
irreversible (-) ΔG
Glyceraldehyde-3-phosphate:
Becomes the [ ], which acts as a
[ ] to triacylglycerols and is a reaction [
].
Glyceraldehyde-3-phosphate: Becomes the glycerol backbone, which acts as a
precursor to triacylglycerols and is a reaction intermediate.
Pyruvate is the product of [ ]
glycolysis. It can be taken out of the pathway or can continue down its typical (aerobic) “fate” (pathway) into acetyl-CoA.
Glucose is [ ] considered a [ ] because it’s what we start with, but subsequent steps are [ ].
Glucose is NOT considered a metabolite, because it’s what we start with, but subsequent steps are metabolites (intermediates).
Pyruvate is a classic example of a [ ]. It is composed of [ ], from the pathway glycolysis.
The classic example of a precursor.
It is composed of 10 steps, from the pathway glycolysis.
Acetyl-CoA: the starting material of [ ]. Can be converted into cholesterol, amino acids, or CO2.
Acetyl-CoA: the starting material of fatty acids. Can be converted into cholesterol, amino acids, or CO2.
NAD+
The most common electron [ ] in metabolism.
Oxidation involves [ ] of electrons, and those electrons need to be captured by different cofactors.
–contains adenosine
NAD+
The most common electron acceptor in metabolism.
Oxidation involves the release of electrons, and those electrons need to be captured by different cofactors.
–contains adenosine
Ubiquinone is reduced to
ubiquinol
Ubiquinone or Q or CoQ or coenzyme Q accepts [ ] in each of the [ ].
Ubiquinone or Q or CoQ or coenzyme Q accepts 2 electrons (one at a time) in each of the two steps.
–Q implies the oxidized form; ready to accept electrons.
Q is embedded in the lipid bilayer, where it transfers electrons.
–QH2 implies the reduced form, when electrons have already been accepted.
This is part of the electron transport chain.
Other names for Ubiquinone
Q or CoQ or coenzyme Q
What type of reaction do some cofacters undergo?
oxidation-reduction. The coenzymes NAD+ and NADP+ accept electrons in the form of a hydride ion (A hydride ion is a hydrogen with 2 electrons).
When the coenzyme NAD+ accepts the electrons it is reduced and becomes
NADH.
This is participating in catabolism (degrading the nutrients we eat).
When the coenzyme NAD(P)+ accepts electrons it becomes
NADPH. This is going to be used in anabolism.
NAD+ is [ ] of electrons
NAD+ is an acceptor of electrons
NADPH is a reducing agent in biosynthesis since it will be the [ ].
The electrons are used to make covalent bonds, which build molecules. This means that we ALWAYS need a reducing agent in synthesis, or else what would make the bonds that build up the molecule?
NADPH is a reducing agent in biosynthesis since it will be the donor of electrons.
The electrons are used to make covalent bonds, which build molecules. This means that we ALWAYS need a reducing agent in synthesis, or else what would make the bonds that build up the molecule?
The hydride ion is what moves the [ ] between [ ].
Represented as H- or H*- (radical).
the hydride ion is what moves the electrons between molecules.
Represented as H- or H*- (radical).
Coupled processes have
2-high energy bonds
Why are coupled processes high energy?
When hydrolyzed, they release a significant amount of energy.
These high-energy bonds are called phosphoanhydride bonds.
When they were added, water was removed. Therefore, to break them, we can add water.
In some cases, we can have MIXED anhydride bonds, where one of the P’s is replaced by a C. They are still high energy.
This hydrolysis is favorable.
The bond that will be hydrolyzed is the one on the LEFT.
Is this reaction favorable or unfavorable?
highly favorable
Is this reaction favorable or unfavorable?
highly unfavorable
ATP hydrolysis provides the energy for
glucose phosphorylation. The net reaction is the result of the coupling of two reactions.
If the sum of the two is negative, then the reaction can proceed because it is favorable. The sign indicates the direction of the reaction.
What are the characteristics of the table of phosphorylated compounds?
They are all phosphorylated substances.
From the red arrow up = high energy.
From the red arrow down = low energy.
They’re all negative, which means they are all favorable.
PEP (phosphoenolpyruvate) is the highest energy.
1,3-bisphosphoglycerate contains the mixed phosphoanhydrous bonds previously described.
