Energy in the Cell

1. Energy in the Cell • Energy is in two basic forms: • 1. potential energy, which is energy stored up, ready to use, like a coiled spring, the capacity to do work. 2. kinetic energy, which is energy of motion, actually doing work. • Food molecules contain potential energy in their chemical bonds. • “calories” are a measure of energy. Some foods contain more energy per gram than others, because their chemical bonds store more energy. For instance, carbohydrates and proteins store 4 calories per gram, while fats store 9 calories per gram. • Cells convert the chemical bond energy in food molecules to chemical bond energy stored in ATP molecules. • ATP energy is used to run metabolism and all other bodily processes.

2. Thermodynamics • First Law: the total mount of energy in the Universe is constant. Energy is neither created not destroyed, it just changes form. • When energy is expended, part of it goes to do useful work, and the rest ends up as heat. None of it is lost, but it changes forms. • Second Law: disorder (entropy) increases. Energy goes from useful forms to useless heat. • Every energy transformation step is inefficient (as a consequence of the Second Law), meaning that some of the energy is converted to waste heat at every step, and the amount of useful work decreases with every step. • Life is very orderly compared to non-living things. Living things are able to locally reverse the overall direction of entropy by using a lot of energy. • The energy of living cells comes from the Sun, and it ends up as waste heat.

3. ATP • In living cells, energy for immediate use is stored as molecules of ATP, adenosine triphosphate. When the energy is used, one of the phosphates attached to ATP is released, giving ADP, adenosine diphosphate. • The 3 phosphates each have a negative charge, and so they repel each other. When the bond holding them together is broken, the phosphates fly apart, like a spring being released. The cell can use this energy in many different ways.

4. Metabolic Reactions • A metabolic reaction is the conversion of one chemical compound into another one inside a living cell. • For every metabolic reaction, you start with reactants and convert them to products. An enzyme does the conversion. Each reaction uses a different enzyme. • The basic rule: reactions run downhill: more energetic reactants are converted to less energetic products. • If a reaction needs to run uphill, creating products that contain more energy than the reactants, energy in the form of ATP must be added. • Reactants are also called substrates.

5. Enzymes • Enzymes are proteins that cause specific chemical reactions to occur. • Enzymes act as catalysts: they help the reaction occur, but they aren’t used up in the reaction. • All reactions require an input of energy to get them started: the activation energy. Think of touching a match to a piece of paper to start a fire: the match is supplying the activation energy. • Enzymes work by lowering the activation energy for a reaction. The reaction occurs thousands or millions of times faster than without the enzyme. The little bit of activation energy needed is supplied by the collision of the molecules involved. • Enzymes are very specific for their substrates: they work on only a very limited number of similar molecules.

6. Enzyme-Substrate Interactions • Each enzyme has an active site, a special region that holds the substrates together and causes them to react • The active site promotes the reaction by orienting the substrates properly, straining their bonds so they break more easily, and by providing acidic or basic amino acids to help the reaction along. • Enzymes often use small accessory molecules called coenzymes to help carry out the reaction. Most vitamins are coenzymes. . • Enzymes often have small molecules that act as inhibitors or activators of their activity. These molecules alter the active site so the enzyme reacts differently to the substrate. • Enzyme activity is strongly influenced by temperature. They have an optimum temperature: to hot or too cold slows them down. Most of the enzymes in humans have an optimum temperature near body temperature. • pH and salt level also influence enzyme activity, with optimum values for each.

7. Generating ATP from Food • ATP (adenosine triphosphate) is made from ADP (adenosine diphosphate) plus a phosphate ion (symbolized by Pi). Making ATP requires energy, which comes form the potential energy stored in food molecules. • More specifically, electrons from glucose or other food molecules are passed through a series of steps, releasing part of their energy in each step, and ultimately ending up attached to oxygen. The energy from the electrons going down the energy hill is used to create ATP from ADP and phosphate. • Similarly, high energy electrons are carried by the molecule NADH. When NADH uses its high energy electrons, it is converted to NAD+. Electrons in the cell are often accompanied by an H (hydrogen).

8. Oxidation • Energy from chemical bonds is transferred in the form of electrons. Oxidation means removing electrons. Its opposite is reduction, which is gaining electrons. LEO = Lose Electrons Oxidation; GER = Gain Electrons Reduction. • Some common forms of oxidation: burning and rusting. • Cells oxidize glucose to form carbon dioxide and water. The cell removes electrons from glucose (in a series of steps), which converts it to carbon dioxide. The energy stored in the electrons is used to make ATP. Finally, the electrons are given to oxygen molecules, converting them to water. • By passing the electrons through a series of steps before their final destination in water, the cell can harvest the energy efficiently. In contrast, burning releases the energy all at once, so it can’t be captured easily. • The electrons are often accompanied by a hydrogen (H), and they are usually carried in the cell by the molecule NADH (or its close relative NADPH).

9. Aerobic and Anaerobic Respiration • Respiration is generating energy by breaking down food molecules, converting the energy in their chemical bonds to ATP energy. • Before oxygen was present in the atmosphere, all cells used anaerobic respiration, which means generating energy in the absence of oxygen. • Many bacteria only have anaerobic respiration. Some are even poisoned by the presence of oxygen: the bacteria that cause gangrene, for example. • Most eukaryotes use aerobic respiration, generating energy with the use of oxygen , in addition to anaerobic respiration. We use anaerobic respiration to start the process, but finish it with aerobic. Aerobic respiration is much more efficient than anaerobic. • The anaerobic pathway is called glycolysis, which means “breaking down glucose”. It occurs in the cytoplasm. • The aerobic pathway occurs in the mitochondria.

10. Summary of Respiration • 1. glycolysis (anaerobic) breaks glucose (a 6 carbon chain) into 2 molecules of pyruvate (3 carbons each). This require 2 ATPs as input, and yields 4 ATPs. Glycolysis thus nets 2 ATPs for each glucose. • intermediate step between glycolysis and the Krebs cycle: conversion of pyruvate to acetyl CoA. • 2. Krebs cycle: acetyl CoA converted to carbon dioxide (aerobic). • 3. electron transport: high energy electrons converted to ATP (aerobic). • Aerobic respiration yields 34 more ATPs per glucose, giving a total of 36 ATPs generated from each glucose. All but 2 of them come from aerobic respiration.

11. Glycolysis • Occurs in the cytoplasm, not in mitochondria • Does not use oxygen. • Almost all living things use this pathway. • Basic process: add phosphates (from ATP) to each end of the glucose, then split it in half, using that chemical bond energy to generate 4 ATPs. Final 3-carbon products = pyruvate. • Also releases 2 electrons, which are carried by NADH. These electrons can be converted to energy if oxygen is present, but they cause problems if not. • What to do with excess electrons? Need to regenerate NAD+ so it can take up more electrons, so give the electrons back to pyruvate in some way: • In yeast, the pyruvate gets converted to ethanol when the electrons are added back. • In humans and many bacteria, pyruvate gets converted to lactate (lactic acid). Causes muscle pain during intense exercise when not enough oxygen gets to the muscle cells.

12. Aerobic Pathway • Requires oxygen, occurs in the mitochondria • Conversion of pyruvate (from glycolysis) to carbon dioxide, with generation of high energy electrons and ATP. • Preliminary steps before starting the Krebs cycle: 3 carbon pyruvate to 2 carbon acetyl CoA; third carbon lost as carbon dioxide. Generates high energy electrons carried by NADH. • Krebs cycle: add 2 carbon acetyl CoA to 4 carbon sugar, remove the 2 extra carbons one at a time as carbon dioxide, generate several high energy electrons on NADH plus some ATP.

13. Electron Transport • The final stage in aerobic respiration • Krebs cycle generates many high energy electrons (carried by NADH). Also some from glycolysis. These need to be converted to ATP so the cell can use them. • Electron transport pumps electrons from the inner compartment to the outer compartment of the mitochondria. • Electrons are passed from NADH through 3 proteins which use the electron energy to pump H+ ions through the membrane. Each protein pump drains energy from the electrons, so by the end of the process, the electrons are low energy. • The final protein pump adds the electrons (plus hydrogens) to oxygen, producing water. • The H+ level builds up between the membranes. It flows back into the inside through a special protein channel called ATP synthase, which uses the energy of their flow to combine ADP and Pi into ATP. This is the main way energy is generated in the cell. • Cyanide blocks electron transport chain—no more ATP is made • Brown fat runs electron transport chain without generating ATP, just to produce heat.

14. Energy from Other Foods • Glucose is the primary food molecule • Carbohydrates are broken down into glucose in the stomach. It enters the blood through the small intestine. • Cells absorb glucose and trap it inside by adding a phosphate to it. • It is then either used directly or converted into starch, to be used later. • Fats are the primary energy storage molecules, containing more than twice as much energy per gram as carbohydrates or proteins. The fatty acids are converted to acetyl CoA (preliminary steps of aerobic metabolism). From there they enter the Krebs cycle. The glycerol molecules go into glycolysis. • The liver converts excess starch into fat. • Proteins are mostly broken down into amino acids which become parts of new proteins. • When proteins are used for energy, their carbon backbones enter glycolysis or Krebs cycle at various points. The amino group becomes ammonia, which is poisonous. Ammonia gets converted to urea, which is a lot less toxic, and then gets excreted in urine.

15. Photosynthesis • Photosynthesis means taking energy from sunlight and converting it to a form usable by living cells. • Green plants do photosynthesis; so do many bacteria and protists (which are single celled eukaryotes). • Two parts to photosynthesis: • 1. the light-dependent reactions, in which sunlight is used to extract high energy electrons from water. These high energy electrons are then used to make ATP. Oxygen from the water is released into the atmosphere. • 2. the light-independent reactions (or dark reactions, or Calvin cycle), in which that ATP energy is used to convert carbon dioxide into glucose. • In plants, all of these reactions occur in the chloroplast, an organelle that contains its own DNA and is thought to be derived from an ancient symbiosis between a free-living photosynthetic bacterium and a primitive eukaryote (just like the mitochondria). • All the food we animals eat comes from these reactions.

16. Light and Pigments • Visible light is a form of electromagnetic radiation, along with X-rays, ultraviolet, infrared, microwaves, radio waves, etc. The only difference between these forms of radiation is the wavelength. • Visible light is all frequencies between 400 and 700 nanometers, with blue light at the 400 end and red at the 700 end. • White light is a mixture of all these wavelengths; colors appear when only some wavelengths are present. • Chlorophyll is green because it absorbs the red and blue wavelengths, reflecting only the green wavelengths. • Other plant pigments absorb different wavelengths, so they have different colors. • Absorbing light puts chlorophyll into a high energy state. This energy is then harvested by a series of metabolic reactions.

17. Light-Dependent Reactions • The chlorophyll molecules are arranged in groups of 200-300, called photosystems. Each photosystem acts like an antenna—any of the molecules can capture a photon of sunlight, but then that energy is transferred to a central “reaction center” molecule, which passes the energy (excited electrons) out of the photosystem. • In green plants, there are 2 separate ways of extracting electrons. The more heavily used pathway needs 2 photons to boost electrons up to a high enough energy to be bound to the plant cell’s energy carrying molecule, NADPH. The electrons on NADPH are then passed to the light-independent reactions to generate glucose. • The electrons are initially extracted from water, carried along with the hydrogens. The waste product is oxygen, which goes into the atmosphere. This is the source of all the oxygen in the atmosphere.

18. Light-Independent Reactions • The energy from sunlight is captured in the form of excited electrons, which are bound to the electron-carrying molecule NADPH. • To form glucose, carbon dioxide (which has 1 carbon atom) is attached to a 5-carbon sugar, then processed through a series of intermediates called the “Calvin cycle”. • The Calvin cycle goes around 6 times to create the 6-carbon glucose from carbon dioxide. Each turn regenerates all the necessary intermediates. The cycle uses electrons from NADPH, and also energy from ATP. • After glucose is synthesized, it is converted to starch for storage, and then the starch is converted to sucrose (a disaccharide) for transport to other parts of the plant.