Chapter 12: Metabolism and Bioenergetics

Question 1

Define metabolism

Answer 1

The entire set of chemical reactions occurring in a living system.

Question 2

Define catabolism

Answer 2

The breaking down of large molecules into smaller ones.
–Example: degrading nutrients in our food such as fats, carbs, and proteins.

Question 3

Name the characteristics of catabolism

Answer 3

→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.

Question 4

Define anabolism

Answer 4

This is NOT necessarily the opposite of catabolism…
It is:
→The building of large molecules.
-These anabolic reactions are called synthetic reactions.

Question 5

Name the characteristics of anabolism

Answer 5

→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.

Question 6

What is the chemical reaction for the digestion of proteins? How do we digest the macromolecules in our food?

Answer 6

Digestion is the hydrolysis of macromolecular nutrients into their corresponding components known as metabolic fuels
–proteins→amino acids
–polysaccharides→monosaccharides
–triacylglycerols→fatty acids

Question 7

Which enzymes are involved in the digestion of proteins?

Answer 7

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.

Question 8

What is the chemical reaction for the digestion of carbohydrates?

Answer 8

→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!

Question 9

Which enzymes are involved in the digestion of carbohydrates?

Answer 9

Amylases
There are 2 types of amylases:
→Salivary
→Pancreatic

Question 10

In the chemical reaction for the digestion of triglycerides, which bond is broken?

Answer 10

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.

Question 11

Which enzymes are involved in the digestion of triglycerides?

Answer 11

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.

Question 12

What are fates of digestion products?

Answer 12

→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.

Question 13

What is the storage form of glucose?

Answer 13

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.

Question 14

What is the reaction needed to remove glycogen and release glucose from storage?

Answer 14

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.

Question 15

Which cells store triglycerides?

Answer 15

adipocytes (fat cells)

Question 16

How are the products of digestion of triglycerides transported?

Answer 16

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.

Question 17

What are metabolic pathways?

Answer 17

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.

Question 18

What is a metabolic pathway metabolite?

Answer 18

→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.

Question 19

What is a metabolic pathway precurser?

Answer 19

A few metabolites may be used as precursors to other things of intermediates.

Question 20

Examples of precursors of metabolism

Answer 20

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).

Question 21

What is the relationship between the reduction state of a compound and the amount of energy released?

Answer 21

Reduced compounds have more energy.

Question 22

How are coenzymes (cofactors) used as acceptors of electrons?

Answer 22

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.

Question 23

How are cofactors recycled?

Answer 23

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.

Question 24

What are the steps of the outline of metabolism figure?

Answer 24

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.

Question 25

What are the characteristics of metabolic pathways?

Answer 25

→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.

Question 26

What are the types of substances humans cannot make? Why these substances are called essential?

Answer 26

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.

Question 27

What is the role of vitamins in metabolism?

Answer 27

 They are required 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.

Question 28

Characteristics and structure of niacin?

Answer 28

-Another name for vitamin B3 -A component of the coenzymes NAD+ and NADP+.

Question 29

Characteristics and structure of thiamine?

Answer 29

- 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

Question 30

What are the characteristics of free energy changes in metabolic reactions?

Answer 30

→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.

Question 31

What is the relationship between equilibrium constant and standard free energy?

Answer 31

Free energy change depends on reactant concentrations. We use the concentrations at equilibrium.

Question 32

What is the meaning of Standard (biochemically) free energy change?

Answer 32

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.

Question 33

What are the biochemical standard state conditions?

Answer 33

--Temperature: 25 °C --Pressure: 1 atm --[Reactant]: 1 M --pH: 7.0 ( [H+] = 10^-7M --[H2O]: 55.5 M

Question 34

How is the actual free energy change calculated?

Answer 34

This formula is how the actual free energy change or ΔG for biochemical reactions is calculated.

Question 35

What are the components of ATP?

Answer 35

- coupled processes - phosphoanhydride bonds

Question 36

What is the meaning of “a coupled process”?

Answer 36

combining a favorable reaction with an unfavorable reaction.

Question 37

What are the features of the ATP cycle?

Answer 37

Nutrients from our food proceed through the citric acid cycle to form ATP. Anabolism synthesizes large molecules.

Question 38

What are the factors that explain the favorable hydrolysis of ATP?

Answer 38

The products of ATP hydrolysis are more stable than the reactants.

Question 39

What is the meaning of “high” and "low" energy phosphorylated compounds?

Answer 39

Amount of energy released

Question 40

What is the position of ATP in the table of “high” energy phosphorylated compounds?

Answer 40

ΔG°’= -30.5 Below phosphocreatine. ATP releases a significant amount of energy, but there are other compounds that release much more!

Question 41

What is the position of ATP in the table of “low” energy phosphorylated compounds?

Answer 41

ΔG°’= -30.5. Above glucose -1-phosphate

Question 42

Why does ATP have an intermediate position in the table?

Answer 42

PEP, 1,3-bisphosphoenolpyruvate and phosphocreatine can be used to make ATP. Everything listed below ATP can be made FROM ATP.

Question 43

What is the phosphocreatine hydrolysis reaction?

Answer 43

When phosphocreatine is dephosphorylated, it becomes creatine.

Question 44

What is the thioesters hydrolysis reaction?

Answer 44

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.

Question 45

Which steps are regulated in a metabolic pathway?

Answer 45

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.

Question 46

What does this picture represent?

Answer 46

Glucose stored as glycogen

Question 47

What do adipocytes (fat cells) store?

Answer 47

Triacylglycerols

Question 48

What are the transport proteins of lipids?

Answer 48

lipoproteins

Question 49

What happens in the phosphorolysis (not hydrolysis) in the liver and muscles?

Answer 49

Phosphorolysis is the reaction needed to remove glycogen and release glucose from storage

Question 50

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?

Answer 50

Metabolism

Question 51

There are so many metabolic reactions, so it is convenient to divide them into what 2 major types?

Answer 51

Catabolism and Anabolism

Question 52

In this figure, free energy in the form of ATP is involved

Answer 52

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.

Question 53

Name the chemical reaction and the bond broken

Answer 53

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.

Question 54

Glycogen is broken down through

Answer 54

phosphorolysis (NOT hydrolysis)

Question 55

What do these images represent?

Answer 55

→Glucose being stored as glycogen -- Glycogen is highly branched

Question 56

Name this reaction

Answer 56

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.

Question 57

What happens in phosphorolysis?

Answer 57

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.

Question 58

Name this cell and its function

Answer 58

Adipocytes (fat cells) which store triacylglycerols.

Question 59

Fatty acids must be transported through the bloodstream via the protein

Answer 59

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.

Question 60

Albumin has [ ] binding sites and will carry [ ] fatty acids to cholesterol.

Answer 60

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.

Question 61

Define lipoproteins

Answer 61

Lipoproteins are the transport proteins of lipids. -Apolipoproteins form lipoproteins.

Question 62

Define Apolipoproteins

Answer 62

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.

Question 63

→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.

Answer 63

→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.

Question 64

Which cycle is oxaloacetate found in?

Answer 64

Oxaloacetate is found in the citric acid cycle

Question 65

What is the net reaction of pyruvate as a precursor?

Answer 65

Question 66

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 [ ].

Answer 66

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.

Question 67

The enzymes in metabolism that are regulatory and catalyze reversible steps are called

Answer 67

allosteric. If we consume excess protein and don’t use all of it, it gets degraded back into pyruvate.

Question 68

What does this image represent?

Answer 68

This image shows how the common intermediates glyceraldehyde-3-phosphate, pyruvate and Acetyl-CoA are involved in several metabolic pathways.

Question 69

Some metabolic pathways share a few common [ ].

Answer 69

intermediates. Examples: ◼ glyceraldehyde-3-phosphate to alanine to triacylglycerols ◼ pyruvate to oxaloacetate to amino acids ◼ acetyl-CoA to fatty acids or CO2.

Question 70

What type of reactions are involved in metabolic pathways?

Answer 70

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.

Question 71

Do reduced compounds have more or less energy?

Answer 71

reduced compounds have more energy

Question 72

Carbons in fatty acids and carbohydrates are oxidized to

Answer 72

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.

Question 73

Which coenzyme (cofactors) are used as acceptors of electrons?

Answer 73

-NAD+ -NADP+ -Ubiquinone ***Ubiquinone has 3 other names: Q, CoQ and Coenzyme Q.

Question 74

Cofactors are [ ] molecules. They can be prosthetic groups or cosubstrates. Coenzymes are NAD+, NAD, FAD and acetyl CoA. All have [ ].

Answer 74

Cofactors are organic molecules. They can be prosthetic groups or cosubstrates. Coenzymes are NAD+, NAD, FAD and acetyl CoA. All have adenosine.

Question 75

Reduced cofactors release electrons in [ ] through a process called [ ].

Answer 75

These are the physical pathways of the ETC.

Question 76

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.

Answer 76

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.

Question 77

The brain cells cannot make [ ], so it is dependent on other organs to produce energy for it to use.

Answer 77

glucose

Question 78

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.

Answer 78

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.

Question 79

classify vitamins into two groups:

Answer 79

→water soluble →fat soluble

Question 80

Vitamin deficiencies can cause

Answer 80

disease

Question 81

Water soluble vitamins are precursors for [ ]?

Answer 81

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.

Question 82

An excess of fat-soluble vitamins can be toxic because

Answer 82

they are stored in the adipose (fat) tissues.

Question 83

-ΔG means the reaction is

Answer 83

favorable

Question 84

+ΔG means the reaction is

Answer 84

unfavorable

Question 85

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.

Answer 85

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.

Question 86

What is often involved in coupled processes?

Answer 86

ATP

Question 87

What type of bonds participate in ATP?

Answer 87

phosphoanhydride bonds

Question 88

Why does ATP hydrolysis release energy?

Answer 88

The products of ATP hydrolysis are more stable than the reactants.

Question 89

The products of ATP hydrolysis are [ ] than the reactants.

Answer 89

The products of ATP hydrolysis are more stable than the reactants.

Question 90

Why are the products of ATP hydrolysis more stable than the reactants?

Answer 90

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.

Question 91

Draw how resonance makes Pi more stable than ATP

Answer 91

Question 92

Acetyl-CoA contains

Answer 92

Adenosine

Question 93

What type of reaction is shown in the figure?

Answer 93

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.

Question 94

What are the intermediates of glucose (also known as intermediates of glucose catabolism)?

Answer 94

Question 95

ΔG is favorable in the [ ] direction

Answer 95

irreversible (-) ΔG

Question 96

Glyceraldehyde-3-phosphate: Becomes the [ ], which acts as a [ ] to triacylglycerols and is a reaction [ ].

Answer 96

Glyceraldehyde-3-phosphate: Becomes the glycerol backbone, which acts as a precursor to triacylglycerols and is a reaction intermediate.

Question 97

Pyruvate is the product of [ ]

Answer 97

glycolysis. It can be taken out of the pathway or can continue down its typical (aerobic) “fate” (pathway) into acetyl-CoA.

Question 98

Glucose is [ ] considered a [ ] because it’s what we start with, but subsequent steps are [ ].

Answer 98

Glucose is NOT considered a metabolite, because it’s what we start with, but subsequent steps are metabolites (intermediates).

Question 99

Pyruvate is a classic example of a [ ]. It is composed of [ ], from the pathway glycolysis.

Answer 99

The classic example of a precursor. It is composed of 10 steps, from the pathway glycolysis.

Question 100

Acetyl-CoA: the starting material of [ ]. Can be converted into cholesterol, amino acids, or CO2.

Answer 100

Acetyl-CoA: the starting material of fatty acids. Can be converted into cholesterol, amino acids, or CO2.

Question 101

NAD+ The most common electron [ ] in metabolism. Oxidation involves [ ] of electrons, and those electrons need to be captured by different cofactors. --contains adenosine

Answer 101

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

Question 102

Ubiquinone is reduced to

Answer 102

ubiquinol

Question 103

Ubiquinone or Q or CoQ or coenzyme Q accepts [ ] in each of the [ ].

Answer 103

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.

Question 104

Other names for Ubiquinone

Answer 104

Q or CoQ or coenzyme Q

Question 105

What type of reaction do some cofacters undergo?

Answer 105

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).

Question 106

When the coenzyme NAD+ accepts the electrons it is reduced and becomes

Answer 106

NADH. This is participating in catabolism (degrading the nutrients we eat).

Question 107

When the coenzyme NAD(P)+ accepts electrons it becomes

Answer 107

NADPH. This is going to be used in anabolism.

Question 108

NAD+ is [ ] of electrons

Answer 108

NAD+ is an acceptor of electrons

Question 109

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?

Answer 109

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?

Question 110

The hydride ion is what moves the [ ] between [ ]. Represented as H- or H*- (radical).

Answer 110

the hydride ion is what moves the electrons between molecules. Represented as H- or H*- (radical).

Question 111

Coupled processes have

Answer 111

2-high energy bonds

Question 112

Why are coupled processes high energy?

Answer 112

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.

Question 113

Is this reaction favorable or unfavorable?

Answer 113

highly favorable

Question 114

Is this reaction favorable or unfavorable?

Answer 114

highly unfavorable

Question 115

ATP hydrolysis provides the energy for

Answer 115

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.

Question 116

What are the characteristics of the table of phosphorylated compounds?

Answer 116

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.