Chapter 11: Intro to Metabolism

Question 1

What is metabolism?

Answer 1

The series of chemical changes which take place in an organism, by means of which food is utilized, Bio molecules manufactured, and utilized and waste materials are eliminated.

Question 2

What is catabolism?

Answer 2

Breakdown of infested food for energy.

• These pathways are oxidative. Release energy.
• To capture energy released in breaking C-C bonds efficiently, metabolic pathways release energy in stages.

Question 3

What is anabolism?

Answer 3

Biosynthetic pathways that build molecules.

• These pathways are reductive, consume energy.
• Metabolic pathways use many chemical strategies to have enough free energy to make high energy, covalent C-C bonds.

Question 4

Stages of catabolism

Answer 4

Stage 1:

• Ingested food is broken down in the intestine
• Polymer —> monomer
• Little or no energy released

Stage 2:

• Monomer —> common metabolic intermediates, usually Acetyl CoA
• Usually occurs in the cytosol
• Small amounts of energy released

Stage 3:

• Acetyl CoA —> ATP
• Occurs in the mitochondria
• Build of energy released
• Consists of TCA cycle and oxidative phosphorylation (electron transport chain and ATP synthesis)

Question 5

Carbohydrates

Answer 5

• Glucose is the energy currency of the body as ATP is the energy currency of the cell.
• Blood glucose concentration is carefully regulated
• Glucose is stored in glycogen and is fundamental to metabolism of the cell.

Question 6

Proteins

Answer 6

• Breakdown of amino acids supplies energy to the cell in catabolic pathways
• Amino Acids are not stored, they are either catabolized to generate ATP or used to build new proteins.

Question 7

Lipids

Answer 7

• Long term storage for energy
• Most calories/gram
• Used for energy in the “fasting state” (e.g predominantly when glucose stores are depleted or running low).

Question 8

Nucleic Acids

Answer 8

• Nucleotides are not catabolized as a source of energy
• Most nucleotides are recycles as nitrogenous bases are difficult to excrete

Question 9

Four tissues involved in metabolic roles

Answer 9

Liver

Adipose

Muscle

Brain

Question 10

How does liver play a metabolic role?

Answer 10

The liver is known as the “self-less” metabolic clearinghouse of the body. -Buffers blood glucose: absorbs when glucose is high, releases when glucose is low

• Exports glucose and ketone bodies to peripheral tissues
• Responsible for urea synthesis and drug detoxification reactions

Question 11

How does adipose play a metabolic role?

Answer 11

TAG (fat) storage

Question 12

How does muscle play a metabolic role?

Answer 12

Consumer of energy in the form of glucose, fatty acids, and ketone bodies. Some glycogen stores but these stores are largely reserved for anaerobic glycolysis. So even with glycogen stores, muscle relies on nutrients in the blood to power metabolic needs.

Question 13

How does the brain play a metabolic role?

Answer 13

The brain relies only on circulation for metabolic input. Is a glucose “hog” but will switch to using ketone bodies if necessary.

Question 14

Types of metabolic pathways.

Answer 14

Catabolic (oxidative), anabolic (reductive) and amphibole (both catabolic and anabolic)

Question 15

Describe a catabolic pathway.

Answer 15

Glycolysis: glucose –> pyruvate

Glycogenesis: glycogen –> glucose

Beta-oxidation: fatty acid –> acetyl coA

Protein breakdown: amino acids –> carbon skeleton and urea

Question 16

Describe an anabolic pathway.

Answer 16

Gluconeogenesis: pyruvate –> glucose

Glycogen synthesis: glucose –> glycogen

Amino acid synthesis: amino group added to carbon skeletons

Fat synthesis: acetyl CoA and glycerol –> triacyl glycerols

Question 17

Describe an amphibolic pathway

Answer 17

TCA cycle aka citric acid cycle or Kreb’s cycle

• Central to all of metabolism
• Takes the products of all catabolic pathways and feeds into ATP synthesis machinery
• Intermediates of the cycle are used as substrates in anabolic pathways

Question 18

Futile Cycles

Answer 18

• Pathways are coordinated regulated to avoid FUTILE CYCLES which are energetically wasteful. Example:
  
  • Glycolysis and gluconeogenesis are never active at the same time in the same tissue
  • Glycogenolysis and glycogen synthesis never occur simultaneously in the same tissue.
• The same signal that turns off the forward pathway will also activate the reverse.
  
  • Insulin to glucagon ratio regulates flux in metabolic pathways in all tissues -
  • Insulin signals the “fed” state, active “fed” state pathways, and inactivates “fasting” pathways
  • Pathways active in the fed state use ingested food for energy and store excess quantities for future use (in the form go glycogen and fat)
  • Glucagon and epinephrine signal the “fasting” state, activate “fasting” state pathways, and turn on “fating” pathways
  • Pathways active in the fasting state use fat and glycogen stores to provide energy

Question 19

Hormonal Regulation

Answer 19

• Different pathways are active in the FED and FASTED states.
  
  • Fed: after consumption of a meal so that freshly absorbed nutrients are being catabolized for energy and stored for future use.
  • Fasted: stored nutrients are used in catabolic pathways to power the cell (body).
• The switch between fed and fasted states are regulated by the insulin and glucagon ration.
  
  • insulin secretion is triggered when blood glucose rises after eating. high insulin to glucagon ratio activated the FED state pathways.
  • low insulin to glucagon ratio activates the FASTING state pathways.
• Levels of insulin and glucagon must depend on time since the last meal

Question 20

Regulatory Enzymes

Answer 20

• Typically, the insulin to glucagon ratio typically controls the FLUX through a pathway by altering the phosphorylation state of the enzyme which catalyzes the rate limiting step of the pathway to control the FLUX through the pathway.
  
  • Flux refers to the number of molecules that are processed by the metabolic pathway
  • Regulation of the enzyme catalyzing the rate limiting step acts as “on/off” switch for the entire pathway.
    
    • The rate limiting step is the “spigot” which controls how many molecules are processed by the pathway
    • Regulation may be at multiple levels (not just phosphorylation)
  • The rate limiting step is a subtype of regulatory enzyme
    
    • Regulatory enzymes are those whose rates of catalysis change
    • Although there may be more than 1 regulatory step, there is only 1 rate limiting step
    • Most enzymes are NOT regulatory (e.g. double arrows on metabolic map)
• Typically, the rate limiting step is:
  
  • The first step of the pathway
• A step with a large negative delta Go
  
  • Favorable reaction with high yield of product at equilibrium
  • This makes the step IRREVERSIBLE

Question 21

Feedback Inhibition and Covalent Modification

Answer 21

• In covalent modification, regulatory enzymes can be covalently bonded to different functional groups
  
  • The addition of a phosphate (or other group) changes the conformation of the enzymechange in enzyme activity
  • Phosphorylation and dephosphorylation requires kinases and phosphatases
  • This regulation is frequently downstream of insulin and glucagon signaling
• A common way to regulate the flux through a metabolic pathway is Feedback Inhibition. This is when excess product down-regulates the activity of the first or rate limiting step in the pathway.
  
  • Why make more product when there’s already an excess?
  • Feedback inhibition frequently works by allosterism

Question 22

Allosterism

Answer 22

• Many regulatory enzymes are allosteric enzymes which has several distinct advantages
  
  • 1) Allosteric enzymes have a characteristic sigmoidal shaped kinetics curve
    
    • The steeper curvegreater change in activity over a smaller change in [Substrate]
    • Typically, curve is steep over [S] seen in the cell
  • 2) Regulation is rapid
• Allosteric regulation is typically NOT a result of insulin or glucagon signaling
  
  • These hormones are extracellular and signal through membrane receptors
  • Allosteric effectors are intracellular and are typically metabolites that signal to more than one pathway

Note: most non-regulatory enzymes within a pathway exhibit Michaelis Menten kinetics

Question 23

Common Allosteric Effectors

Answer 23

• Pathway specific allosteric effectors
  
  • Product as a negative effector
  • Substrate as positive effector
• Common allosteric effectors that signal overall metabolic state of the cell
  
  • Signals that indicate the cell needs more energy –> activation of catabolic / energy generating pathways
    
    • AMP, ADP
    • NADP
    • NAD+ (all of these are empty electron carriers)
    • empty electron carriers
  • Signals that inidicate the cell has plenty of energyactivation of anabolic / storage pathways
    
    • ATP
    • NADPH
    • NADH
    • Citrate (all of these are full carriers)
    • ** full carriers

Note: ATP and NADH/NADPH are the carriers for two forms of free energy (e.g. bond energy and redox potential energy).

Common allosteric effectors will signal metabolic state within the cell to simultaneously affect the activity of multiple enzymes

Question 24

Compartmentalization of Pathways

Answer 24

• One simple way to regulate pathways is compartmentalization and different pathways are often segregated into separate organelles.
• This prevents common metabolic intermediates in one pathway from being siphoned off into another, unintended pathway and avoids futile cycles
• Best example, is fatty acid oxidation and synthesis. Breakdown of fatty acids to acetyl-CoA occurs in the mitochondria (where ATP synthesis occurs) while synthesis of new fatty acids using acetyl- CoA occurs in the cytosol.

Question 25

Why Multiple Levels of Regulation?

Answer 25

* Each serves a different purpose * Insulin and glucagon are circulating hormones and they typically • Signal the metabolic state of the ENTIRE BODY using signal transduction pathways * Change enzyme activity through phosphorylation which is the “on / off” switch for enzyme activity * Universal allosteric activators and inhibitors are intracellular and typically * Are responsible for the CELLULAR RESPONSE and fine-tune metabolic pathways in response to cellular needs * More rapid than phosphorylation * Single effector can affect the flux through multiple pathways * Different levels of regulation work in conjunction to provide the needed amount of flux for each cell within the body

Question 26

Delta Go and Equilibrium Steps

Answer 26

* Most steps in pathways have DGo close to zero and are considered “equilibrium” reactions. * They will produce product without energy input * The reverse direction also proceed with no energy input * The amount of product and reactant at equilibrium are equal * This type of reaction indicated by double arrows on your metabolic map

Question 27

Steps with Negative delta Go

Answer 27

* Reactions with G \< 0 proceed unaided (e.g. without energy input) * These reactions yield more product than reactant at equilibrium * Steps with a large negative delta Go have special properties: * The reverse reaction (with a large + delta Go) will NOT proceed unaided (e.g. without energy input) * The reverse reaction usually occurs using different enzyme(s) Steps with Negative G * These steps tend to be REGULATED enzymes REGULATORY steps catalyzed by * These are good candidates for regulation as “turning off” the enzyme catalyzing the forward direction does not affect the reverse reaction

Question 28

Reactions with Positive delta G

Answer 28

* Some reactions MUST have a + delta G (e.g. the reverse of a reaction with a – delta G ) * These reactions will not occur at substantial rates because the energy of the products is greater than the energy of the reactants (G \> 0) * Cells can carry out many such necessary reactions by coupling it to a reaction that has a negative DG of larger magnitude * Use of energy in the form of ATP or another source of energy to drive the reaction forward is considered priming and priming reactions are those that involve the consumption of energy to prepare the substrate for the next step in the pathway * This linkage of reactions is permitted because FREE ENERGIES ARE ADDITIVE Note: Non-spontaneous = endothermic = unfavorable **Non-spontaneous = endothermic = unfavorable**

Question 29

ATP Hydrolysis

Answer 29

* Frequently, ATP hydrolysis is used to power reactions with a + G * ATP is the “energy currency of the cell” * Hydrolysis ATP phosphoanhydride bonds releases stored free energy * Phosphoanhydride bonds contain and store a large amount of free energy due to competing resonance * There are several activated energy carriers in addition to ATP include NADPH, NADH and Acetyl CoA.

Question 30

Direct coupling: Couples reactions and equilibrium constants

Answer 30

* Sequential steps in a metabolic pathway may be coupled without the involvement of an energy carrier. * Reaction A is endergonic: [X] \> [Y] at equilibrium * Reaction B is exergonic: [Z] \> [Y] at equilibrium * Coupled reaction is spontaneous: * Once a molecule of Y is made in reaction A, it is immediately consumed in Reaction B. This siphoning of Y into Reaction B deprives the reverse Reaction A of it’s substrate. Thus, there is little possibility of Y --\> X and Reaction A is “pulled” forward. * Examples of Direct Coupling: * Redox reactions * Steps 6 and 7 of glycolysis

Question 31

Standard delta G vs delta Go and Concentration

Answer 31

* Delta Go is fixed quantity * This is the free energy under standard conditions * The equilibrium constant can be determined if DGo is known (G = 0 at equilibrium) * When evaluating chemical reactions, the standard free energy Delta Go is quoted * This standard energy provides a reference with which to evaluate all reactions DG is variable quantity and is the free energy of the reaction within cells * Delta G us variable quantity and is the free energy of the reaciton within cells * Cells almost never have the standard concentrations of reactants and therefore the G of a reaction at any given moment may be substantially different from the standard Go * Why? When assessing the ΔG, the actual [products] and [reactants] are used in a ratio for “Keq term” * This means that the ΔG of the reaction (but not ΔGo) can change * Natural log (ln) of a numbers greater than 1 are positive while ln of a number less than 1 is negative. * When this number is added to the ΔGo, the value of ΔG varies

Question 32

Delta G vs Delta Go in Coupled Reactions

Answer 32

Question 33

Redox Reactions in Metabolism

Answer 33

* Energy yielding (catabolic) reactions break down biomolecules by oxidizing them to release the free energy stored in their C-C bonds * Energy contained in glucose is oxidized to CO2 and H2O. * Energy consuming (anabolic) biosynthetic reactions reduce biomolecules to form energy containing C-C bonds * Biosynthesis of fats requires the formation of many C-C bonds and hence stores a lot of energy * Energy “stored” in structures at right decrease as oxidation occurs

Question 34

Redox Reactions

Answer 34

* Oxidation-reduction reactions (redox) * involve transfer of electrons * Seen in many metabolic processes including Catabolism, Photosynthesis, Electron transport chain in mitochondria * In general chemistry, redox reactions are usually written with metals and are relatively easy to recognize because they involve a change in charge of metal ions * Redox reactions are a coupled reaction in which energy may be transferred * If one atom or molecule is oxidized during a chemical reaction then another molecule must be reduced

Question 35

Redox Coenzymes Carry e-

Answer 35

* e- are never “free floating”. Carriers shuttle electrons through the cell. The most commonly seen carriers are: NADH, NADPH, FMN, FADH2 * Energy contained in high energy e- stored in NADH or FADH2 is harvested to make ATP in mitochondria (via a coupled reaction) * Energy stored in high energy e- on NADPH typically used directly in biosynthetic reactions

Question 36

Structure of NADH and NADPH

Answer 36

* NADH and NADPH hold electrons on their nicotinamide ring. This conjugated ring system easily accommodates the extra electrons. * The only structural difference between NADH and NADPH is a single phosphate on the ribose ring. However, NADPH is used in biosynthetic reactions while NADH is used in catabolic reactions.

Question 37

Forms of Free Energy and Carriers

Answer 37

* 3 forms of free energy will be seen in metabolism: * Bond energy (e.g. ATP, C-C bonds in glucose, etc.). The energy carrier here is ATP. * Redox potential energy. Several energy carriers will transport these high energy electrons (e.g. NADPH, NADH, FADH2) * Electrochemical potential energy. There is no “carrier” here because free energy must be stored across a membrane and is therefore not mobile * With respect to free energy, catabolism can be described as converting bond energy (e.g. glucose) into redox potential energy (e.g. NADH), and then to electrochemical potential energy (seen in the electron transport chain or ETC). The energy stored in the ETC is used to make ATP or bond energy.

Question 38

Chapter Summary

Answer 38