Chapter 6 - Metabolism

Energy and Metabolism

• Explain what metabolic pathways are and describe the two major types of metabolic pathways

• Discuss how chemical reactions play a role in energy transfer

• bioenergetics - concept of energy flow through living systems (like cells)

• metabolism - all chemical reactions that take place inside cells, including those that use energy and those that release energy

Metabolism of Carbohydrates

• Ex. of cellular processes
  • metabolism of sugar
• breakdown of glucose-- simple sugar
  • insert equation
• carbs consumed have origins in photosynthesis organisms like plants
  • plants use sunlight to convert to carbon dioxide gas into sugar molecules (like glucose)
• synthesis of glucose:
  • insert equation
• in chemical reactions of photosynthesis, primary energy currency in form of ATP-- adrenosine triphosphate
• sugar (glucose) is stored as starch or glycogen
• light energy is temporarily stored in ATP and NDPH (nicotinamide adenine dinucleotide phosphate)
  • stored energy is then used
  • sugar can be combined or converted into other types of sugar
  • once consumed, can make way to cells of organism
  • chemical reaction goal is to harvest energy in sugar molecules
  • energy needed to make one molecule of glucose from six molecules of carbon dioxide is 18 molecules of ATP and 12 molecules of NADPH

Metabolic Pathways

• metabolic pathways - series fo interconnected biochemical reactions that convert substrate molecule or molecules thorugha series of metabolic intermediates
• 2 metabolic pathways (sugar metabolism):
  • anabolic (building) pathway
  • synthesize sugar from smaller molecules (requires energy)
  • catabolic (breaking down) pathway
  • break sugar down into smaller molecules (produces energy)
• metabolism is composed of building (anabolism) and degradation (catabolism)

Anabolic Pathway

• require input of energy to synthesize complex molecules from simpler ones
  • ex. synthesizing sugar from co2, synthesis of large proteins from amino acid building blocks, synthesis of new DNA strands from nucleic acid building blocks

Catabolic Pathway

• ATP is important molecule for cells
  • stored sugar can provide ATP-- 36 to 38 molecules
• this pathway involves degration (breakdown) of complex molecules into simpler ones
• energy stored in bonds of molecules is released in this pathway and harvested to be used to produce ATP
• fats are also broken down through similar catabolic reactions to release energy and make ATP

Evolution of Metabolic Pathways

• all organisms harvest energy from their environment and convert it to ATP to carry out cell functions
• all branches of life share same metabolic pathways suggesting all organisms evolved from same ancient common ancestor
• organisms probably evolved anaerobic metabolism to survive

Potential, Kinetic, Free, and Activation Energy

• define ‘energy’
• explain difference between kinetic and potential energy
• discuss concepts of free energy and activation energy
• describe endergonic and exergonic reactions

energy - ability to do work

Types of Energy

• kinetic energy - energy associated with objects in motion
  • ex. speeding bullet, walking person, rapid movement of molecules, electromagnetic radiation
• potential energy - energy with potential to do work
  • ex. energy of water behind dam, person about to skydive out a plane
• chemical energy - potential energy within chemical bonds and released when bonds are broken
  • provide living cells with energy from food; release of energy is brought about by breaking molecular bonds within fuel molecules

Free Energy

• free energy - used to quantitate energy transfers; also called Gibbs free energy after Josiah Willard Gibbs (developed measurement)
  • review: second law of thermodynamics: all energy transfers involve loss of some amount of energy in unusable form like heat resulting in entrophy
  • this energy refers to energy associated with chemical reaction available after entrophy is accounted for; this is usable energy-- available to do work
• delta G - change in free energy
  • change can be calculated for any system that undergoes change like chemical reaction
  • to calculate, subtract amount of energy lost to entropy from total energy change of system
  • total energy change in system is called enthalpy
  • (insert formula)

Endergonic Reactions and Exergonic Reactions

• exergonic reactions - reactions that have negative G and consequently release free energy
  • exergonic means energy exiting system
  • also known as spontaneous reactions
  • but not one that suddenly or quickly occurs
  • ex. rusting of iron; occurs over time
• endergonic reactions - reaction that requires input of energy instead of releasing energy
  • energy storing molecules, non-spontaneous
  • this reaction will not take place on its own w/o addition of free energy
• chemical reactions involved in anbolic processes are endergonic reactions; catabolic process of breaking sugar to simpler molecules release energy in series of exergonic reactions
  • sugar involves spontaneous reactions but not instantaneously
• chemical equilibrium
  • reactants in closed system will undergo chemical reactions in both directions until state of equilibrium is reached
  • state of equilibrium is one of lowest possible free energy and state of maximal entropy

Activation Energy

• activation energy - small amount of energy input necessary for all chemical reactions to occur
  • transition state - small energy input required to achieve contorted state; high-energy, unstable state
  • activation energy is always positive
• heat energy - speeds up motion of molecules, increasing frequency and force with which they collide; also moves atoms and bonds in molecule slightly, reaching transition state
  • cause chemical reactants in system to react more frequently
  • higher activation energy = slower chemical reaction

The Laws of Thermodynamics

• discuss concept of entropy

• explain first and second laws of thermodynamics

• thermodynamics - study fo energy and energy transfer involving physical matter

  • 2 types of systems: open or closed
  • open system is one where energy can be transferred between system and surroundings
    • ex. biological organisms; energy is exhchage between them and their surroundings
  • closed system is one that cannot transfer energy to surroundings

The First Law of Thermodynamics

• first law deals with total amount of energy in the universe; states that this total amount of energy is constant; there has always been and always will be exactly the same amount of energy in the universe
• energy may be transferred from place to place or transformed into different forms but cannot be created or destoryed
• ex. of work cells need to do: build complex molecules, transport material, powering beating motion of cilia, contract muscle fibers to create movement, reproduction

The Second Law of Thermodynamics

• heat energy - energy transferred from one system to another that is not doing work
  • ex. airplane flies through air; some energy of plane is lost
  • some energy is lost as heat energy during cell metabolic reactions
  • helps maintain body temp
  • no energy transfer is efficient because some energy is lost in unusable form
• order and disorder (randomness)
  • entropy - measure of randomness or disorder in system
  • high entropy means high disorder and low energy
• second law states every energy transfer or transformation increases entropy of universe
• entropy of universe is constantly increasing due to loss of usable energy with each energy transfer that occurs

ATP: Adenosine Triphosphate

• explain role of ATP as cellular energy currency

• describe how energy is released through hydrolysis of ATP

• adenosine triphosphate (ATP) - small relatively simple molecule; contains potential for quick burst of energy than can be harnessed to perform cell work

  • primary energy currency of cells
  • power majority of energy-requiring cell reactions

• adenosine is made of three phosphate groups: alpha, beta, gamma

  • these groups constitute energy powerhouse
  • adenosine is a nucleoside of nitrogenous base adenine and five-carbon sugar ribose
  • phosphoanhydride bonds - bonds that link phosphates
  • when broken, it release sufficient energy to power cell reactions and processes

• ATP is hydrolyzed into ADP

  • (insert formula)

• formation of ATP

  • (insert formula)

• ATP is a highly unstable molecule

Enzymes

• describe role of enzymes in metabolic pathways

• explain how enzymes function as molecular catalysts

• discuss enzyme regulation by various factors

• catalyst - substance that helps chemical reaction to occur

• enzymes - molecules that catalyze biochemical reactions

  • almost all enzymes are proteins, made of chains of amino acids
  • perform task of lowering activation energies of chemical reactions inside cell
  • enzymes bind to reactan molecules and hold them to make chemical bond breaking and bond forming processes take place readily
  • enzymes don’t change the (?) of a reaction; they don’t change if reaction is exergonic or endergonic because they don’t change free energy of reactants or products; only reduce activation energy required to reach transition state

Enzyme Active Site and Substrate Specificity

• substrates - chemical reactants to which enzyme binds
• active site - location in enzyme where substrate binds
  • where action happens
  • increasing environmental temp can increase reaction rates
• high temps will cause enzymes to denature - process that changes natural properties of substance

Induced Fit and Enzyme Function

• induced fit - expanpds upond lock and key model of enzyme substrate by describing a more dynamic interaction between enzyme and substrate
  • interaction cause mild shift in enzyme’s structure that confirms ideal binding arrangement between enzyme nad substrate
  • this binding maximizes enzyme’s ability to catalyze its reaction
• when exzyme binds its substrate, enzyme-substrate complex is formed; complex lowers activation energy of reaction and promotes rapid progression:
  • on basic level, enzymes promote chemical reactions that involve more than one substrate by bringing substrates together in optimal orientation
  • another way is creating optimal environment in active site for reaction to occur

Summary

• activation energy required for many actions include energy involved in manipulating or slightly contorting chemical bonds so that they can break and allow others to reform
  • enzymatic action aid this process
• enzyme-substrate complex can lower activation energy by controting substrate molecules to facilitate bond breaking, help reach transition state
• enzymes can lower activation energies by taking part in chemical reaction itself
• amino acid residue provide ions or chemical groups that form covalent bonds with substrate molecules as a step of reaction process
  • enzymes remain ultimately unchanged by reactions they catallyze
  • after enzyme si done catalyzing a reaction, it releases its product

Control of Metabolism Through Enzyme Regulation

• relative amounts and functioning of variety of enzymes in cell ultimately determine which reactions will proceed and at which rates
  • in some cell environments, enzyme activity is partly controlled by environmental factors like pH and temp

Regulation of Enzymes by Molecules

• enzymes can be regulated in ways that either promote or reduce their activity
• ex.
  • an inhibitor molecule is similar to a substrate that it can bind to active site and simply block substrate from binding
  • when this happens, enzyme is inhibited through competitive inhibition
  • in noncompetitive inhibition, inhibitor molecule bidns to enzyme in location other than allosteric site and manage to block substrate binding to active site
• allosteric inhibition - inhibitor molecules bind to enzymes in location where binding induces conformational change that reduces affinity of enzyme for its substrate
  • allosteric activators bind to locations on enzyme away from active site, inducing conformational change that increases affinity of enzyme’s active sites for its substrates
• 2 helper molecules: cofactors and coenzymes
  • binding to these promotes optimal conformational and function for their respective enzymes
  • cofactors - inorganic ions like iron and magnesium
  • ex. enzyme that builds DNA molecules, DNA polymerase
  • coenzymes - organic helper molecules with a basic atomic structure made up of carbon and hydrogen
  • ex. dietary vitamins

Enzyme Compartmentalization

• in eukaryotic cells, molecules like enzymes are compartmentalized into different organelles
  • allows for another level of regulation of enzyme activity
  • ex. of enzyme regulation based on location and proximity
  • enzymes involved in latter stages of cellular respiration (in mitochondria)
  • enzymes involved in digestion of cellular debris and foreign materials (in lysosomes)

Feedback Inhibition in Metabolic Pathways

• cells evolved to use products of their own reaction product to regulate its own further production
  • cell responds to abundance of specific products by slowing down production during anbolic or catabolic reactions
• production of amino acids and nucleotides is controlled through feedback inhibition
  • ATP is allosteric regulator of some enzymes involved in catabolic breakdown fo suagr
  • when ATP is abundant, cell can prevent further production
  • ATP is also unstable molecule that can spontaneously dissociate into ADP

Chapter Summaries

6.1 Energy and Metabolism

Cells perform the functions of life through various chemical reactions. A cell’s metabolism refers to the chemical reactions that take place within it. There are metabolic reactions that involve breaking down complex chemicals into simpler ones, such as breaking down large macromolecules. Scientists refer to this process as catabolism, and we associate such reactions an energy release. On the other end of the spectrum, anabolism refers to metabolic processes that build complex molecules out of simpler ones, such as macromolecule synthesis. Anabolic processes require energy. Glucose synthesis and glucose breakdown are examples of anabolic and catabolic pathways, respectively.

6.2 Potential, Kinetic, Free, and Activation Energy

Energy comes in many different forms. Objects in motion do physical work, and kinetic energy is the energy of objects in motion. Objects that are not in motion may have the potential to do work, and thus, have potential energy. Molecules also have potential energy because breaking molecular bonds has the potential to release energy. Living cells depend on harvesting potential energy from molecular bonds to perform work. Free energy is a measure of energy that is available to do work. A system's free energy changes during energy transfers such as chemical reactions, and scientists refer to this change as ∆G.

A reaction's ∆G can be negative or positive, meaning that the reaction releases energy or consumes energy, respectively. A reaction with a negative ∆G that gives off energy is an exergonic reaction. One with a positive ∆G that requires energy input is an endergonic reaction. Exergonic reactions are spontaneous because their products have less energy than their reactants. Endergonic reactions' products have a higher energy state than the reactants, and so these are nonspontaneous reactions. However, all reactions (including spontaneous -∆G reactions) require an initial energy input in order to reach the transition state, at which they will proceed. This initial input of energy is the activation energy.

6.3 The Laws of Thermodynamics

In studying energy, scientists use the term “system” to refer to the matter and its environment involved in energy transfers. Everything outside of the system is the surroundings. Single cells are biological systems. We can think of systems as having a certain amount of order. It takes energy to make a system more ordered. The more ordered a system, the lower its entropy. Entropy is a measure of a system's disorder. As a system becomes more disordered, the lower its energy and the higher its entropy.

The laws of thermodynamics are a series of laws that describe the properties and processes of energy transfer. The first law states that the total amount of energy in the universe is constant. This means that energy cannot be created or destroyed, only transferred or transformed. The second law of thermodynamics states that every energy transfer involves some loss of energy in an unusable form, such as heat energy, resulting in a more disordered system. In other words, no energy transfer is completely efficient, and all transfers trend toward disorder.

6.4 ATP: Adenosine Triphosphate

ATP is the primary energy-supplying molecule for living cells. ATP is comprised of a nucleotide, a five-carbon sugar, and three phosphate groups. The bonds that connect the phosphates (phosphoanhydride bonds) have high-energy content. The energy released from ATP hydrolysis into ADP + Pi performs cellular work. Cells use ATP to perform work by coupling ATP hydrolysis' exergonic reaction with endergonic reactions. ATP donates its phosphate group to another molecule via phosphorylation. The phosphorylated molecule is at a higher-energy state and is less stable than its unphosphorylated form, and this added energy from phosphate allows the molecule to undergo its endergonic reaction.

6.5 Enzymes

Enzymes are chemical catalysts that accelerate chemical reactions at physiological temperatures by lowering their activation energy. Enzymes are usually proteins consisting of one or more polypeptide chains. Enzymes have an active site that provides a unique chemical environment, comprised of certain amino acid R groups (residues). This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, scientists call substrates, into unstable intermediates that they call transition states. Enzymes and substrates bind with an induced fit, which means that enzymes undergo slight conformational adjustments upon substrate contact, leading to full, optimal binding. Enzymes bind to substrates and catalyze reactions in four different ways: bringing substrates together in an optimal orientation, compromising the bond structures of substrates so that bonds can break down more easily, providing optimal environmental conditions for a reaction to occur, or participating directly in their chemical reaction by forming transient covalent bonds with the substrates.

Enzyme action must be regulated so that in a given cell at a given time, the desired reactions catalyze and the undesired reactions are not. Enzymes are regulated by cellular conditions, such as temperature and pH. They are also regulated through their location within a cell, sometimes compartmentalized so that they can only catalyze reactions under certain circumstances. Enzyme inhibition and activation via other molecules are other important ways that enzymes are regulated. Inhibitors can act competitively, noncompetitively, or allosterically. Noncompetitive inhibitors are usually allosteric. Activators can also enhance enzyme function allosterically. The most common method by which cells regulate the enzymes in metabolic pathways is through feedback inhibition. During feedback inhibition, metabolic pathway products serve as inhibitors (usually allosteric) of one or more of the enzymes (usually the first committed enzyme of the pathway) involved in the pathway that produces them.