Unit 5: Metabolism, Enzymes, and Cellular Respiration
Metabolism refers to the sum total of every chemical reaction in every organism. Cells use enzymes and metabolic pathways to conduct these chemical reactions. It is essential to understand the reactions that comprise metabolism to learn how organisms acquire and use energy to survive. Since this process is quite complicated, we will explore it from several different angles in this unit.
Completing this unit should take you approximately 9 hours.
Upon successful completion of this unit, you will be able to:
- recognize and explain the difference between matter and energy;
- apply the laws of thermodynamics and conservation of matter to metabolism;
- describe the role of enzymes and how they function;
- explain the role of cellular respiration;
- account for the matter inputs and outputs to glycolysis, pyruvate oxidation (preparatory reaction) the Krebs/citric acid cycle, and the electron transport chain; and
- describe the source and fate of energy in glycolysis, pyruvate oxidation (preparatory reaction), the Krebs/citric acid cycle, and the electron transport chain.
5.1: Energy and Thermodynamics
Energy flows through all living systems. The chemical reactions that build and break down energy-containing compounds are vital to all living organisms. Biochemical pathways involve the building and breaking down through anabolism and catabolism, respectively. Notice that all of these pathways involve chemical reactions that require enzymes, which are the biological catalysts we will discuss in the next section.
Remember that the laws of thermodynamics state that energy is neither created nor destroyed, but transformed from one form to another. Biochemical reactions follow these same laws of thermodynamics which predict whether reactions will occur spontaneously, or without any energy required.
Watch these videos, which present the basic concepts of bioenergetics. Make sure you can distinguish between kinetic and potential energy and explain how energy is transformed from one form to another.
Watch this lab experiment demonstrating how the human body breaks down the sugar in a gummy bear into carbon dioxide, water, and energy.
5.2: Metabolic Pathways, Enzymes, and Regulation
Metabolism refers to all chemical reactions in the cell. Some reactions break down large molecules and release energy. Other reactions require energy to build up large molecules. These reactions are connected via metabolic pathways that must be regulated to conserve resources and energy.
Watch this video for an overview of the metabolic process. It describes the two major kinds of metabolic pathways, linear and cyclical. Pay attention to the descriptions for catabolic and anabolic pathways in cellular metabolism.
Note that catabolism breaks down molecules (creates energy), while anabolism assembles molecules (requires energy). You should also be able to define the components of a metabolic pathway: reactants (substrate molecules), intermediates (intermediate substrates), and the final products.
Watch this video, which reviews and builds on what we have learned so far about energy, including the first law of thermodynamics, the second law of thermodynamics, exergonic and endergonic chemical reactions, and how humans get energy. The presenter discusses how cells use ATP as an energy source.
An enzyme is a protein that serves as a biological catalyst. A catalyst is a substance that accelerates a chemical reaction without actually being a reactant in that reaction. In other words, a catalyst (and therefore an enzyme) does not get changed into another substance (a product). An enzyme interacts with reactants in such a way as to make it much more likely for those reactants to chemically react, turning them into products.
We call the reactants of a catalyzed reaction substrates. An enzyme operates by temporarily binding to substrates. The rate of the reaction (its speed) when an enzyme catalyzes it is typically at least one million times the rate without the help of an enzyme. This is why enzymes are absolutely vital. Without enzymes, the biochemical reactions of metabolism would occur much too slowly to support life. Importantly, since an enzyme does not get altered in a reaction in which it participates, it is reusable, and it can continue to catalyze the same sort of reaction if more substrate is present.
Watch this video, which discusses the characteristics and functions of enzymes. The presenter describes various factors that promote and affect enzyme activity, such as temperature, pH, concentrations, competitive inhibition, and allosteric regulation. Pay attention to the discussion on feedback inhibition and the regulatory mechanisms of catabolic pathways. Think about how this type of regulation benefits cells in terms of energy conservation.
After watching this video, you should be able to describe how inhibitors regulate the activity of enzymes of metabolic pathways and explain how excess products inhibit pathways to prevent a cell from wasting chemical resources.
Read this section to review enzyme nomenclature. Notice how the names of the enzymes often relate to actions on substrates.
5.3: The Role of Cellular Respiration, Energy, and ATP
In this section, we explore cellular respiration, the metabolic pathway that breaks down our food in the form of glucose to produce oxygen, water, and ATP, which is the most usable energy source for the cell. This process takes place in the mitochondria within the cell. Aerobic respiration occurs in the presence of oxygen; anaerobic respiration occurs without oxygen and builds lactic acid.
Any living cell is able to extract energy from fuel and temporarily store that energy in the form of ATP, or a similar energy currency. The primary processing of fuel is called glycolysis. Only certain cells under the right conditions are able to continue where glycolysis leaves off, allowing much more usable energy to be extracted from the fuel.
That additional processing of energy is called cellular respiration. Glycolysis and cellular respiration both extract usable energy from fuel by undergoing oxidation/reduction (or redox) reactions.
Oxidation refers to the loss of electrons from a particle (such as a fuel molecule), whereas reduction is the gain of electrons. Since electrons are not destroyed in chemical reactions, oxidation occurs only if reduction also occurs. When something is oxidized (loses electrons), something else gets reduced (gains electrons).
Organisms extract energy from fuel molecules by oxidizing these fuel molecules. In cellular respiration, there is a substance (external to the process) that ultimately accepts the electrons that have been removed from the fuel. For aerobic organisms, that substance is oxygen, and when oxygen accepts those electrons (along with protons) from the fuel molecules, the oxygen gets reduced into water. Cellular respiration is important because it allows for maximal oxidation of fuels, which maximizes the amount of energy that can be extracted and stored as ATP.
Watch this video for an overview of cellular respiration. After you watch, you should be able to explain the role of cellular respiration.
Watch this video, which explores the concept of energy chemical systems. The presenter explains how molecules move back and forth between a low energy state (more stable) to a high energy state (more unstable). Pay attention to the description of endergonic and exergonic reactions. The presenter explains the movement of energy between ADP and ATP, and NAD+ and NADH, FAD, and FAD2.
Watch this lecture to review the role of the ATP molecule and its importance for cells. It will help you understand the phosphate functional group and how the hydrolysis of ATP releases energy.
At this point, you should be able to explain the catabolic and anabolic pathways in cellular metabolism, describe the structure and function of ATP, explain how ATP performs cellular work, and distinguish between consumers, producers, and decomposers of nutrition.
5.4: Glycolysis
Living organisms perform an important catabolic pathway that breaks down organic compounds to yield energy in the form of ATP. The molecules are completely broken down aerobically through cell respiration. Scientists have defined three primary stages in cell respiration, which we will review in detail: glycolysis, the citric acid cycle, and oxidative phosphorylation.
Glycolysis is the first step in the process of cellular respiration. It involves the partial breakdown of glucose into two pyruvate molecules. Glycolysis is the first step in harvesting potential energy from the bond of glucose. Notice that glycolysis, a multi-step biochemical pathway, produces a small amount of energetic resources.
Any living cell can extract energy from fuel and temporarily store that energy in the form of ATP, or a similar energy currency. This primary processing of fuel is called glycolysis. Only certain cells under the right conditions can continue where glycolysis leaves off, allowing much more usable energy to be extracted from the fuel. This additional processing of energy is called cellular respiration. Glycolysis and cellular respiration both extract usable energy from fuel by undergoing oxidation/reduction (or redox) reactions. Read this brief introduction to glycolysis.
Watch this overview of the process of glycolysis and its ingredients. Glycolysis has two main steps: energy-requiring and energy-releasing.
Watch this video, which provides more details about glycolysis.
At this point, you should be able to describe how the carbon skeleton of glucose changes as it proceeds through glycolysis, the structure of ATP, the investment phase that requires ATP, the payoff phase that produces ATP, and the products of glycolysis.
Watch this lecture for another overview of the process of glycolysis.
5.5: The Krebs Cycle (Citric Acid Cycle)
The Krebs cycle (also called the citric acid cycle and TCA cycle) is a cyclical biochemical pathway that begins the completion of the oxidation of glucose. While it forms a small amount of ATP via substrate-level phosphorylation, its main role is the formation of energetic electron carriers that are needed for the electron transport chain.
In this section, we look at the chemical reactions involved in this cycle in greater detail. Notice that there are multiple names for this cycle in biology: scientists use the three names (the Krebs cycle, citric acid cycle, and TCA cycle) interchangeably since they all refer to the same process.
Watch this lecture for a tour of the Krebs/citric acid cycle.
After you watch, you should be able to identify where the Krebs Cycle takes place in the mitochondria, describe the process of the Krebs Cycle, list the products of the citric acid cycle, and explain why we call it a cycle.
Read this section to review the next steps in the breakdown of glucose in aerobic cellular respiration. The citric acid cycle and oxidative phosphorylation are the two processes that lead to the complete oxidation of glucose.
After you read, you should be able to describe where pyruvate is oxidized to acetyl CoA, how the oxidation of pyruvate links glycolysis to the citric acid cycle, and what a cycle is and the products of the citric acid cycle.
5.6: Oxidative Phosphorylation: Electron Transport Chain and Chemiosmosis
Oxidative phosphorylation is the final stage of cellular respiration and is made up of two closely connected components: the electron transport chain and chemiosmosis. In the electron transport chain, electrons are passed from one molecule to another: the energy released during these electron transfers is used to form an electrochemical gradient. In chemiosmosis, the energy stored in the gradient is used to produce ATP.
The electron transport chain is a collection of proteins located in the inner membrane of the mitochondria known for its role in creating a proton gradient that is necessary for oxidative phosphorylation. These proteins are part of the final step of cellular respiration where glucose is completely oxidized by oxygen. The electrons, which are temporarily carried by previous redox electron carriers, move through the chain and reduce oxygen gas.
Watch this video, which outlines the final steps in cellular respiration. Pay close attention to the creation of ATP by the specialized protein complexes found in the mitochondria’s inner membrane.
After you watch, you should be able to describe the proteins that are a part of the electron transport chain, explain the movement of electrons down the electron transport chain is coupled production of ATP by chemiosmosis, explain where and how the respiratory electron transport chain creates a proton gradient, and distinguish the electron transport chain from the ATP synthase.
Watch this video, which tabulates the amount of energy cellular respiration generates.
Watch this lecture for another tour of the electron transport chain.
Read this text, which reviews what we have learned about oxidative phosphorylation and chemiosmosis. This process involves the coupling of the proton motive force initiated by the oxidation of the electron carriers NADH and FADH2. Hydrogen ions flow from the intermembrane space back to the matrix of the mitochondria through the ATP synthase. This chemiosmosis of hydrogen ions is coupled to the endergonic formation of ATP.
After you read, you should be able to distinguish between substrate-level phosphorylation and oxidative phosphorylation, explain the endergonic production of ATP by chemiosmosis through ATP synthase, and illustrate the production of ATP yield from the oxidation of a glucose molecule.
Watch this lecture to review the entire process of cellular respiration, from glycolysis to ATP generation, and the role of oxidation-reduction reactions in biological systems.
5.7: Anaerobic Cellular Respiration: Fermentation
Organic molecules are partially broken down when they lack oxygen. Some organisms use the process of fermentation to break glucose down when oxygen is not available following the electron transport chain.
Read this text to review the process of fermentation.
After you read, you should be able to describe the purpose of fermentation, distinguish alcohol fermentation and lactic acid fermentation, and compare the processes of fermentation and anaerobic cellular respiration.
Watch this video, which offers another explanation of anaerobic cellular respiration and its byproducts lactic acid and ethanol.
Unit 5 Assessment
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Take this assessment to see how well you understood this unit.
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