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Carbon Dioxide: A colorless, odorless gas that can be formed by the body and is necessary for the respiration cycle of plants and animals.

The Carbon Cycle

JoVE 10933

Carbon is the basis of all organic matter on Earth, and is recycled through the ecosystem in two primary processes: one in which carbon is exchanged among living organisms, and one in which carbon is cycled over long periods of time through fossilized organic remains, weathering of rocks, and volcanic activity. Human activities, including increased agricultural practices and the burning of fossil fuels, has greatly affected the balance of the natural carbon cycle. All living things are composed of organic molecules that contain atoms of the element carbon. Carbon exists in the atmosphere as carbon dioxide gas, which reacts with water to form bicarbonate. During photosynthesis, primary producers (or autotrophs) convert carbon dioxide and bicarbonate into organic carbon-containing compounds, such as glucose, to provide energy for growth, maintenance and other processes. Heterotrophs receive organic carbon for growth and maintenance by consuming autotrophs. Through the process of cellular respiration, these organic molecules are broken down to release the energy stored within them. The byproducts of this process are water and carbon dioxide, which is released into the atmosphere through respiration, continuing the cycle. Carbon can also return to the environment as animal waste or as decaying material from dead organisms. Decomposers, such as bact

 Core: Ecosystems

Carbon and Nitrogen Analysis of Environmental Samples

JoVE 10012

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University


Elemental Analysis is a method used to determine elemental composition of a material. In environmental samples such as soils, scientists are particularly interested in the amounts of two ecologically important elements, nitrogen and carbon. Elemental analysis by …

 Environmental Science

Diffusion

JoVE 10700

Diffusion is the passive movement of substances down their concentration gradients—requiring no expenditure of cellular energy. Substances, such as molecules or ions, diffuse from an area of high concentration to an area of low concentration in the cytosol or across membranes. Eventually, the concentration will even out, with the substance moving randomly but causing no net change in concentration. Such a state is called dynamic equilibrium, which is essential for maintaining overall homeostasis in living organisms. Diffusion plays an integral role in biological processes such as respiration, the process by which organisms exchange gases with their environment. After breathing in air, the concentration of oxygen in the alveoli, air sacs of the human lung, is higher than the oxygen concentration in the blood. Consequently, oxygen diffuses down its concentration gradient into the blood. In order to get into body tissue, oxygen and other nutrients carried in the blood must diffuse into tissues down their concentration gradients. Metabolic waste such as carbon dioxide diffuses from tissues into capillaries where the carbon dioxide concentration is less than that inside body tissues. Blood carrying carbon dioxide is then pumped to the lungs where carbon dioxide readily diffuses into alveoli that have a lower concentration of the gas than blood. Carbon dioxide

 Core: Membranes and Cellular Transport

Cellular Respiration- Concept

JoVE 10567

Autotrophs and Heterotrophs

Living organisms require a continuous input of energy to maintain cellular and organismal functions such as growth, repair, movement, defense, and reproduction. Cells can only use chemical energy to fuel their functions, therefore they need to harvest energy from chemical bonds of biomolecules, such as sugars and lipids. Autotrophic organisms, namely…

 Lab Bio

Photosynthesis- Concept

JoVE 10565

Autotrophs

Almost all living organisms on Earth depend on photosynthesis, which is the process that converts sunlight energy into a simple sugar called glucose. This molecule can be used as a short-term energy source or to build more complex carbohydrates like starches for long-term energy storage. Autotrophs are organisms that capture light energy using photosynthesis. Also known …

 Lab Bio

Redox Reactions

JoVE 10671

Oxidation-reduction, or redox, reactions change the oxidation states of atoms via the transfer of electrons from one atom, the reducing agent, to another atom that receives the electron, the oxidizing agent. Here, the atom that donates electrons is oxidized—it loses electrons—and the atom that accepts electrons is reduced—it has a less positive charge because it gains electrons. The movement of energy in redox reactions is dependent on the potential of the atoms to attract bonding electrons—their electronegativity. If the oxidizing agent is more electronegative than the reducing agent, then energy is released. However, if the oxidizing agent is less electronegative than the reducing agent, the input of energy is required. Is oxidation a loss or gain of electrons? The terminology can be confusing. The acronym OIL RIG is commonly used to remember. It stands for oxidation is loss; reduction is gain. So, if an atom is oxidized, then it loses electrons. As a reducing agent, the oxidized atom transfers electrons to another atom, causing it to be reduced. With OIL RIG in mind, most questions about the members of a redox reaction can be answered. Redox reactions either produce or require energy. If an atom loses an electron to a more electronegative atom, then it is an energetically favorable reaction, and energy is released. This

 Core: Chemistry of Life

Free Energy

JoVE 10730

Free energy—abbreviated as G for the scientist Gibbs who discovered it—is a measurement of useful energy that can be extracted from a reaction to do work. It is the energy in a chemical reaction that is available after entropy is accounted for. Reactions that take in energy are considered endergonic and reactions that release energy are exergonic. Plants carry out endergonic reactions by taking in sunlight and carbon dioxide to produce glucose and oxygen. Animals, in turn, break down the glucose from plants using oxygen and make carbon dioxide and water. When a system is at equilibrium, there is no net change in free energy. In order for cells to keep metabolism running and stay alive, they must stay out of equilibrium by constantly changing concentrations of reactants and products The direction of energy flow through the system determines if the reaction is endergonic or exergonic. Systems with no net change in free energy are considered to be at equilibrium. Most chemical reactions are reversible—they can proceed in both directions. To stay alive, cells must stay out of equilibrium by constantly changing the concentrations of reactants and products so that metabolism continues to run. If a reaction requires an input of energy to move forward, then the change in free energy, or the ΔG of the reaction is positive and the re

 Core: Metabolism

Fermentation

JoVE 10745

Most eukaryotic organisms require oxygen to survive and function adequately. Such organisms produce large amounts of energy during aerobic respiration by metabolizing glucose and oxygen into carbon dioxide and water. However, most eukaryotes can generate some energy in the absence of oxygen by anaerobic metabolism.

Aerobic respiration proceeds through a series of oxidation-reduction reactions that end when oxygen–the final electron acceptor–is reduced to water. In the absence of oxygen, this reaction cannot proceed. Instead, cells regenerate NADH produced during glycolysis by using an organic molecule, such as pyruvate, as the final electron acceptor. The process of using an organic molecule to regenerate NAD+ from NADH is called fermentation. There are two types of fermentation based on the end products of the reaction: 1) lactic acid fermentation and 2) alcohol fermentation. In mammals, lactic acid fermentation takes place in red blood cells that cannot respire aerobically due to lack of mitochondria, as well as in skeletal muscles during strenuous exercise. It also occurs in certain bacteria, like those found in yogurt. In this reaction, pyruvate and NADH are converted to lactic acid and NAD+. Alcohol fermentation is a two-step process. In the first step, pyruvate is converted to carbon dioxide and acetaldehyde

 Core: Cellular Respiration

Second Law of Thermodynamics

JoVE 10727

The Second Law of Thermodynamics states that entropy, or the amount of disorder in a system, increases each time energy is transferred or transformed. Each energy transfer results in a certain amount of energy that is lost—usually in the form of heat—that increases the disorder of the surroundings. This can also be demonstrated in a classic food web. Herbivores harvest chemical energy from plants and release heat and carbon dioxide into the environment. Carnivores harvest the chemical energy produced by herbivores—with only a fraction of it representing the original radiant energy from the sun—and also release heat energy with carbon dioxide into their surroundings. As a result, the heat energy and other metabolic by-products released at each stage of the food web have increased its entropy. The Second Law of Thermodynamics states that entropy, or the amount of disorder in a system, increases each time energy is transferred or transformed. In every energy transfer, a certain amount of energy is lost in a form that is unusable—usually in the form of heat. This heat energy can temporarily increase the speed of molecules it encounters. As such, the more energy that a system loses to its surroundings, the less ordered and the more random it becomes. Similar to the First Law of Thermodynamics, the Second Law of Thermodynamics c

 Core: Metabolism

Gas Exchange and Transport

JoVE 10884

Gas exchange, the intake of molecular oxygen (O2) from the environment and the outflow of carbon dioxide (CO2) into the environment, is necessary for cellular function. Gas exchange during respiration occurs largely via the movement of gas molecules along pressure gradients. Gas travels from areas of higher partial pressure to areas of lower partial pressure. In mammals, gas exchange occurs in the alveoli of the lungs, which are adjacent to capillaries and share a membrane with them. When the lungs expand, the resultant decrease in pressure relative to the atmosphere draws oxygen into the lungs. Air entering the lungs from the environment has a higher oxygen concentration and a lower carbon dioxide concentration than the oxygen-depleted blood that travels from the heart to the lungs. Thus, oxygen diffuses from the alveoli to the blood in the capillaries, where it can be delivered to tissue. Carbon dioxide, by contrast, diffuses from the capillaries to the alveoli, where it can be expelled through exhalation. Gas flow is determined by the pressure gradient of each gas, with each gas moving down its gradient. The pressure exerted by an individual gas in a mixture of gases is its partial pressure, and each gas moves from a higher to a lower partial pressure. Thus, the movement of O2 and CO2 are not directly related

 Core: Circulatory and Pulmonary Systems

Physiology of the Circulatory System- Concept

JoVE 10625

Homeostasis

Conditions in the external environment of an organism can change rapidly and drastically. To survive, organisms must maintain a fairly constant internal environment, which involves continuous regulation of temperature, pH, and other factors. This balanced state is known as homeostasis, which describes the processes by which organisms maintain their optimal internal…

 Lab Bio

The Calvin Cycle

JoVE 10753

Oxygenic photosynthesis converts approximately 200 billion tons of carbon dioxide (CO2) annually to organic compounds and produces approximately 140 billion tons of atmospheric oxygen (O2). Photosynthesis is the basis of all human food and oxygen needs.

The photosynthetic process can be divided into two sets of reactions that take place in different regions of plant chloroplasts: the light-dependent reaction and the light-independent or “dark” reactions. The light-dependent reaction takes place in the thylakoid membrane of the chloroplast. It converts light energy to chemical energy, stored as ATP and NADPH. This energy is then utilized in the stroma region of the chloroplast, to reduce atmospheric carbon dioxide into complex carbohydrates through the light-independent reactions of the Calvin-Benson cycle. The Calvin-Benson cycle represents the light-independent set of photosynthetic reactions. It uses the adenosine triphosphate (ATP) and nicotinamide-adenine dinucleotide phosphate (NADPH) generated during the light-dependent reactions to convert atmospheric CO2 into complex carbohydrates. The Calvin-Benson cycle also regenerates adenosine diphosphate (ADP) and NADP+ for the light-dependent reaction. At the start of the Calvin-Benson cycle, atmospheric CO2 enters the leaf throug

 Core: Photosynthesis

Energy-releasing Steps of Glycolysis

JoVE 10739

While the first phase of glycolysis consumes energy to convert glucose to glyceraldehyde 3-phosphate (G3P), the second phase produces energy. The energy is released over a sequence of reactions that turns G3P into pyruvate. The energy-releasing phase—steps 6-10 of glycolysis—occurs twice, once for each of the two 3-carbon sugars produced during steps 1-5.

The first energy-releasing step—considered the 6th step of glycolysis overall—consists of two concurrent events: oxidation and phosphorylation of G3P. The electron carrier NAD+ removes one hydrogen from G3P, oxidizing the 3-carbon sugar and converting (reducing) NAD+ to form NADH and H+. The released energy is used to phosphorylate G3P, turning it into 1,3-bisphosphoglycerate. In the next step, 1,3-bisphosphoglycerate converts ADP to ATP by donating a phosphate group, thereby becoming 3-phosphoglycerate. The 3-phosphoglycerate is then converted into an isomer, 2-phosphoglycerate. Subsequently, 2-phosphoglycerate loses a water molecule, becoming the unstable molecule 2-phosphoenolpyruvate, or PEP. PEP easily loses its phosphate group to ADP, converting it into a second ATP molecule and becoming pyruvate in the process. The energy-releasing phase releases two molecules of ATP and one molecule of NADH per converted sugar. Because

 Core: Cellular Respiration

Chemical Reactions

JoVE 10662

A chemical reaction is a process by which the bonds in the atoms of substances are rearranged to generate new substances. Matter cannot be created or destroyed in a chemical reaction—the same type and number of atoms that make up the reactants are still present in the products. Merely the rearrangement of chemical bonds produces new compounds.

A chemical reaction takes starting materials—the reactants—and changes them into different substances—the products. The identities of the elements are the same on both sides of the equation, but they are arranged in different substances after the reaction takes place. In chemical reactions, the bonds between the atoms are broken and reformed which means that the shared electrons among the atoms are rearranged. Reactions can be spontaneous, or they might only occur in the presence of an energy source—such as heat or light. Additionally, macromolecules can act as enzymes—catalysts that greatly speed up chemical reactions. Most biological reactions would take far too long to complete without enzymes. Some types of reactions will proceed irreversibly until all of the reactants are used up, while others are reversible, with the products able to be converted back into the reactants if conditions change. Certain types of chemical reactions, such as combustion reactions or precipitation r

 Core: Chemistry of Life

Biofuels: Producing Ethanol from Cellulosic Material

JoVE 10014

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University


In this experiment, cellulosic material (such as corn stalks, leaves, grasses, etc.) will be used as a feedstock for the production of ethanol. The cellulosic material is first pretreated (ground and heated), digested with enzymes, and then fermented with…

 Environmental Science

Metabolic Labeling

JoVE 5687

Metabolic labeling is used to probe the biochemical transformations and modifications that occur in a cell. This is accomplished by using chemical analogs that mimic the structure of natural biomolecules. Cells utilize analogs in their endogenous biochemical processes, producing compounds that are labeled. The label allows for the incorporation of detection and affinity tags, which can then be …

 Biochemistry

The Colonization of Land

JoVE 11016

Changes in the environment of the early Earth drove the evolution of organisms. As prokaryotic organisms in the oceans began to photosynthesize, they produced oxygen. Eventually, oxygen saturated the oceans and entered the air, resulting in an increase in atmospheric oxygen concentration, known as the oxygen revolution approximately 2.3 billion years ago. Therefore, organisms that could use oxygen for cellular respiration had an advantage. More than 1.5 years ago, eukaryotic cells and multicellular organisms also began to appear. Initially, all of these species were restricted to the oceans of Earth. The first organisms to live on land were photosynthetic prokaryotes that inhabited moist environments near ocean shores. Despite the lack of water, terrestrial environments offered an abundance of sunlight and carbon dioxide for photosynthesis. Around 500 million years ago, the ancestors of nowadays plants were able to colonize drier environments, but they required adaptations to prevent dehydration. They developed methods for reproduction that did not depend on water and protected their embryos from drying out. These early plants furthermore evolved a vascular system that included roots to acquire water and nutrients and a shoot to obtain sunlight and carbon dioxide. Plants and fungi appear to have colonized land at the same time. Their coevolution onto land

 Core: Evolutionary History

Products of the Citric Acid Cycle

JoVE 10977

The cells of most organisms—including plants and animals—obtain usable energy through aerobic respiration, the oxygen-requiring version of cellular respiration. Aerobic respiration consists of four major stages: glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation. The third major stage, the citric acid cycle, is also known as the Krebs cycle or tricarboxylic acid (TCA) cycle. For every glucose molecule that undergoes cellular respiration, the citric acid cycle is carried out twice; this is because glycolysis (the first stage of aerobic respiration) produces two pyruvate molecules per glucose molecule. During pyruvate oxidation (the second stage of aerobic respiration), each pyruvate molecule is converted into one molecule of acetyl-CoA—the input into the citric acid cycle. Therefore, for every glucose molecule, two acetyl-CoA molecules are produced. Each of the two acetyl-CoA molecules goes once through the citric acid cycle. The citric acid cycle begins with the fusion of acetyl-CoA and oxaloacetate to form citric acid. For each acetyl-CoA molecule, the products of the citric acid cycle are two carbon dioxide molecules, three NADH molecules, one FADH2 molecule, and one GTP/ATP molecule. Therefore, for every glucose molecule (which generates two acetyl-CoA molecules), the citric acid cycle yiel

 Core: Cellular Respiration

Plant Diversity- Concept

JoVE 10598

From Water to Land

Kingdom Plantae first appeared about 410 million years ago as green algae transitioned from water to land. Though challenging, this transition benefited early colonizers in several ways. Initially, most living organisms (including plants and animals) were ocean dwelling, making aquatic environments crowded and highly competitive. In contrast, land was a relatively…

 Lab Bio

Cellular Respiration - Student Protocol

JoVE 10568

Quantifying Respiration using Microrespirometers
NOTE: In this experiment, you will measure the rate of cellular respiration for germinating seeds by measuring the rate of exchange for oxygen. As oxygen is consumed to provide energy, germinating seeds release carbon dioxide. This carbon dioxide is absorbed by potassium carbonate and thus the overall…

 Lab Bio

The Citric Acid Cycle

JoVE 10741

The citric acid cycle, also known as the Krebs cycle or TCA cycle, consists of several energy-generating reactions that yield one ATP molecule, three NADH molecules, one FADH2 molecule, and two CO2 molecules.

Acetyl CoA is the point-of-entry into the citric acid cycle, which occurs in the inner membrane (i.e., matrix) of mitochondria in eukaryotic cells or the cytoplasm of prokaryotic cells. Prior to the citric acid cycle, pyruvate oxidation produced two acetyl CoA molecules per glucose molecule. Hence, the citric acid cycle runs twice per glucose molecule. The citric acid cycle can be partitioned into eight steps, each yielding different molecules (italicized below). With the help of catalyzing enzymes, one acetyl CoA (2-carbon) reacts with oxaloacetic acid (4-carbon), forming the 6-carbon molecule citrate. Next, citrate is converted into one of its isomers, isocitrate, through a two-part process in which water is removed and added. The third step yields α-ketoglutarate (5-carbon) from oxidized isocitrate. This process releases CO2 and reduces NAD+ to NADH. The fourth step forms the unstable compound succinyl CoA from α-ketoglutarate, a process that also releases CO2 and reduces NAD+ to NADH. The fifth

 Core: Cellular Respiration

Dehydration Synthesis

JoVE 10681

Dehydration synthesis is the chemical process in which two molecules are covalently linked together with the release of a water molecule. Many physiologically important compounds are formed by dehydration synthesis, for example, complex carbohydrates, proteins, DNA, and RNA.

Sugar molecules can be covalently linked together by dehydration synthesis, also called condensation reaction. The resulting stable bond is called a glycosidic bond. To form the bond, a hydroxyl (-OH) group from one reactant and a hydrogen atom from the other form water, while the remaining oxygen links the two compounds. For each additional bond that is formed, another molecule of water is released, literally dehydrating the reactants. For example, individual glucose molecules (monomers) can undergo repeated dehydration synthesis to create a long chain or branched compound. Such a compound, with repeating identical or similar subunits, is called a polymer. Given the diverse set of sugar monomers, and variation in the location of the linkage, a virtually unlimited number of sugar polymers can be built. Plants produce simple carbohydrates from carbon dioxide and water in a process called photosynthesis. Plants store the resulting sugars (i.e., energy) as starch, a polysaccharide that is created from glucose molecules by dehydration synthesis. Cellulose is likewise buil

 Core: Macromolecules

C4 Pathway and CAM

JoVE 10754

Some plants, like sugar cane and corn, that grow in hot conditions, use an alternative process called the C4 pathway to fix carbon. The cycle begins with CO2 from the atmosphere entering mesophyll cells where it is used to generate oxaloacetate—a four-carbon molecule—from phosphoenolpyruvate (PEP). Oxaloacetate is then converted to malate and transported to bundle sheath cells, where the oxygen concentration is low. There, CO2 is released from malate and enters the Calvin Cycle where it is converted into sugars. The CAM pathway is carried out in plants like cacti that also need to conserve water during the day. CAM plants let CO2 into the leaves at night and produce malate that is stored in vacuoles until the following day. The malate is then released from vacuoles and processed in the Calvin Cycle. The C4 pathway separates the different processes locally, while the CAM pathway separates them chronologically. Some plants, like corn and sugarcane, have evolved alternative ways to fix carbon that help avoid water loss in hot, dry environments. One such method is the C4 pathway. In the first step, CO2 enters mesophyll cells, and the enzyme phosphoenolpyruvate (PEP) carboxylase adds it to the 3-carbon compound PEP to form the 4-carbon compound oxaloacetate. Oxaloacetate is then converted

 Core: Photosynthesis

Algae Enumeration via Culturable Methodology

JoVE 10154

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - Arizona University
Demonstrating Author: Bradley Schmitz


Algae are a highly heterogeneous group of microorganisms that have one common trait, namely the possession of photosynthetic pigments. In the environment, algae can cause problems for swimming pool owners by growing …

 Environmental Microbiology

Potential Energy

JoVE 10729

Potential energy is a stored form of energy that has the potential to do work, and therefore, to be converted into kinetic energy. Gravitational energy, for example, is the potential energy found within gravitational force. Chemical energy is the potential energy stored within molecules by virtue of the bonds between their atoms. Weak bonds have high potential energy, whereas strong bonds have low potential energy. Energy can be stored in the form of chemical bonds. Some bonds are weak, and therefore have high potential energy. For example, hydrogen bonds found between water molecules or those that form between guanine (G) and cytosine (C) nucleotides in a DNA double helix. Strong bonds, on the other hand, have less potential energy. For example, NaCl molecules contain ionic bonds formed from the electrostatic attraction of sodium cations and chloride anions. Covalent bonds are another example that form from the mutual attraction of molecules for a shared pair of electrons. For example, hydrogen molecules form through the covalent bonding of two hydrogen atoms. Food has energy stored in the form of the chemical bonds between atoms. When animals ingest sugars, weak bonds between carbon and oxygen as well as those between hydrogen and other carbon atoms are broken to make carbon dioxide and water, which have much stronger chemical bonds. This proc

 Core: Metabolism

Climate Change- Concept

JoVE 10609

The certainty of climate change remains a public controversy despite the consensus among approximately 97% of active climate researchers, who not only agree that the Earth’s climate is changing but also state that this change is intensified by human activity, predominantly carbon emissions 1. The disconnect between the public and the experts is partly due to poor understanding of the…

 Lab Bio

What is Photosynthesis?

JoVE 10748

Photosynthesis is a multipart, biochemical process that occurs in plants as well as in some bacteria. It captures carbon dioxide and solar energy to produce glucose. Glucose stores chemical energy in the form of carbohydrates. The overall biochemical formula of photosynthesis is 6 CO2 + 6 H2O + Light energy → C6H12O6 + 6 O2. Photosynthesis releases oxygen into the atmosphere and is largely responsible for maintaining the Earth’s atmospheric oxygen content. Photosynthetic reactions occur in chloroplasts, specialized membrane-enclosed compartments in the plant cell. Chloroplasts consist of coin-like stacks of thylakoids. One such stack is called a granum. The thylakoid membranes are enriched with chlorophyll, a green pigment that gives plants and especially their leaves their green color. The chlorophyll molecule absorbs light energy in the form of photons from violet-blue, and orange and red wavelengths. The photons initiate a cascade that powers the reactions of Photosystem II and Photosystem I that produce ATP and NADPH. These two molecules are then used to power the light-independent reactions of the Calvin Cycle that take place in the stroma of the chloroplast to produce complex carbohydrates. Some plants, like corn and cacti that grow in dry, hot climates, use modi

 Core: Photosynthesis

Gas Absorber

JoVE 10436

Source: Michael G. Benton and Kerry M. Dooley, Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA


Gas absorbers are used to remove contaminants from gas streams. Multiple designs are used to accomplish this objective1. A packed bed column uses gas and liquid streams running counter to each other in a column…

 Chemical Engineering

Degassing Liquids with Freeze-Pump-Thaw Cycling

JoVE 5639

Source: Laboratory of Dr. Neil Branda — Simon Fraser University


Degassing refers to the process by which dissolved gases are removed from a liquid. The presence of dissolved gases such as oxygen or carbon dioxide can impede chemical reactions that utilize sensitive reagents, interfere with spectroscopic measurements, or can…

 Organic Chemistry

What is Cellular Respiration?

JoVE 10976

Organisms harvest energy from food, but this energy cannot be directly used by cells. Cells convert the energy stored in nutrients into a more usable form: adenosine triphosphate (ATP).

ATP stores energy in chemical bonds that can be quickly released when needed. Cells produce energy in the form of ATP through the process of cellular respiration. Although much of the energy from cellular respiration is released as heat, some of it is used to make ATP. During cellular respiration, several oxidation-reduction (redox) reactions transfer electrons from organic molecules to other molecules. Here, oxidation refers to electron loss and reduction to electron gain. The electron carriers NAD+ and FAD—and their reduced forms, NADH and FADH2, respectively—are essential for several steps of cellular respiration. Some prokaryotes use anaerobic respiration, which does not require oxygen. Most organisms use aerobic (oxygen-requiring) respiration, which produces much more ATP. Aerobic respiration generates ATP by breaking down glucose and oxygen into carbon dioxide and water. Both aerobic and anaerobic respiration begin with glycolysis, which does not require oxygen. Glycolysis breaks down glucose into pyruvate, yielding ATP. In the absence of oxygen, pyruvate ferments, producing NAD+ for continued glycoly

 Core: Cellular Respiration

Threats to Biodiversity

JoVE 10951

There have been five major extinction events throughout geological history, resulting in the elimination of biodiversity, followed by a rebound of species that adapted to the new conditions. In the current geological epoch, the Holocene, there is a sixth extinction event in progress. This mass extinction has been attributed to human activities and is thus provisionally called the Anthropocene. In 2019 the human population reached 7.7 billion people and is projected to comprise 10 billion by 2060. Indicative of our impact, by biomass (the actual mass of a particular species), humans make up 36% of Earth’s mammals, livestock 60%, and wild mammals only 4%. Approximately 70% of all birds are poultry, so only 30% are wild. To minimize human impact on biodiversity and climate, we have to understand which of our activities are problematic and balance the needs of human civilization and progress with a sustainable plan for future generations. Some of the major threats to biodiversity include habitat loss due to human development, over-farming, and increased carbon dioxide emissions from factories and vehicles. A case study in human impact on the weather can be found in the 1930s event known as the Dust Bowl. In the 1920s and 30s, a large number of farmers moved to the Great Plains and clear cut the land, removing the native ground covering plants in order to

 Core: Biological Diversity

Pyruvate Oxidation

JoVE 10740

After glycolysis, the charged pyruvate molecules enter the mitochondria via active transport and undergo three enzymatic reactions. These reactions ensure that pyruvate can enter the next metabolic pathway so that energy stored in the pyruvate molecules can be harnessed by the cells.

First, the enzyme pyruvate dehydrogenase removes the carboxyl group from pyruvate and releases it as carbon dioxide. The stripped molecule is then oxidized and releases electrons, which are then picked up by NAD+ to produce NADH, forming acetate. Finally, coenzyme A—a sulfur-containing compound derived from a B vitamin—attaches to the acetate via its sulfur atom to create acetyl coenzyme A, or acetyl CoA. Acetyl CoA then moves into the citric acid cycle where it will be further oxidized.

 Core: Cellular Respiration

Dye-sensitized Solar Cells

JoVE 10328

Source: Tamara M. Powers, Department of Chemistry, Texas A&M University


Today's modern world requires the use of a large amount of energy. While we harness energy from fossil fuels such as coal and oil, these sources are nonrenewable and thus the supply is limited. To maintain our global lifestyle, we must extract energy from…

 Inorganic Chemistry

Electron Carriers

JoVE 10744

Electron carriers can be thought of as electron shuttles. These compounds can easily accept electrons (i.e., be reduced) or lose them (i.e., be oxidized). They, therefore, play an essential role in energy production because cellular respiration is contingent on the flow of electrons.

Over the many stages of cellular respiration, glucose breaks down into carbon dioxide and water. Electron carriers pick up electrons lost by glucose in these reactions, temporarily store the electrons and input them into the electron transport chain. Two such electron carriers are NAD+ and FAD, which are both derived from B vitamins. The reduced forms of NAD+ and FAD, NADH and FADH2, respectively, are produced during earlier stages of cellular respiration (glycolysis, pyruvate oxidation, and the citric acid cycle). The reduced electron carriers NADH and FADH2 pass electrons into complexes I and II of the electron transport chain, respectively. In the process, they are oxidized to form NAD+ and FAD. Additional electron carriers in the electron transport chain are flavoproteins, iron-sulfur clusters, quinones, and cytochromes. With the assistance of enzymes, these electron carriers eventually transfer the electrons to oxygen molecules. The electron carriers become oxidized as they donate electrons and reduc

 Core: Cellular Respiration

Conditions on Early Earth

JoVE 11015

Around 4 billion years ago, oceans began to condense on earth while volcanic eruptions released nitrogen, carbon dioxide, methane, ammonia, and hydrogen into the primordial atmosphere. However, organisms with the characteristics of life were not initially present on earth. Scientists have used experimentation to determine how organisms evolved that could grow, reproduce, and maintain an internal environment. In the 1920s, the scientists Oparin and Haldane proposed the idea that simple biological compounds could have formed on the early earth. More than 30 years later, Stanley Miller and Harold Urey at the University of Chicago tested this hypothesis by simulating the conditions of the early earth's atmosphere and oceans in a laboratory apparatus. Using electricity as an energy source, the Miller-Urey experiment generated amino acids and other organic molecules, showing that the environment of early earth was conducive to the formation of biological molecules. More recent experiments have yielded comparable results and suggest that amino acids may have formed near areas of volcanic activity or hydrothermal vents in the ocean. Amino acids and small organic molecules may then have self-assembled to form more complex macromolecules. For instance, dripping amino acids or nucleotides into hot sand can result in the formation of the corresponding polymer

 Core: Evolutionary History

Cofactors and Coenzymes

JoVE 10975

Enzymes require additional components for proper function. There are two such classes of molecules: cofactors and coenzymes. Cofactors are metallic ions and coenzymes are non-protein organic molecules. Both of these types of helper molecule can be tightly bound to the enzyme or bound only when the substrate binds.

Cofactors are present in ~30% of mature proteins. They are frequently incorporated into an enzyme as it is folded and are involved in the enzyme’s catalytic activity. Magnesium is an essential cofactor for over 300 enzymes in the human body, including DNA polymerase. In this case, the magnesium ion aids in the formation of the phosphodiester bond on the DNA backbone. Iron, copper, cobalt, and manganese are other common cofactors. Many vitamins are coenzymes, as they are nonprotein, organic helper molecules for enzymes. For example, biotin—a type of B vitamin—is important in a variety of enzymes that transfer carbon dioxide from one molecule to another.  Biotin, vitamin A and other vitamins must be ingested in our diet, as they cannot be made by human cells.

 Core: Metabolism

Anatomy of the Circulatory System

JoVE 10885

The human circulatory system consists of blood, blood vessels that carry blood away from the heart, around the body, and back to the heart, and the heart itself, which acts as a central pump. The systemic circuit supplies blood to the whole body, the coronary circuit supplies blood to the heart, and the pulmonary circuit supplies blood flow between the heart and lungs.

Blood travels from the right atrium to the right ventricle of the heart through the tricuspid valve, then from the right ventricle to the pulmonary artery through the pulmonary valve. Pulmonary veins then carry the blood to the left atrium of the heart, from which it is carried to the left ventricle through the mitral valve. Finally, the left ventricle pumps blood to the aorta (the largest artery in the body) through the aortic valve. Arteries, which carry blood away from the heart, split and get progressively smaller, becoming arterioles and eventually a series of capillaries, the sites of gas exchange. Capillaries converge to become larger venules, and eventually merge into veins, which bring blood back to the heart. Humans have a double circulatory system, in which blood travels through the heart twice via the pulmonary and systemic circuits. First, the heart receives deoxygenated blood in its right side and then pumps it to the nearby pulmonary circuit, the capillaries that ar

 Core: Circulatory and Pulmonary Systems

The Respiratory System

JoVE 10881

The respiratory system is comprised of the organs that enable breathing. Air enters the nostrils and mouth, followed by the pharynx (throat) and larynx (voice box), which lead to the trachea (windpipe). In the thoracic cavity, the trachea splits into two bronchi that allow air to enter the lungs. The bronchi split into progressively smaller bronchioles and terminate in small groups of tiny sacs in the lungs called alveoli, where gas exchange occurs. Air is cleansed in the nasal cavity, but anything that passes those defenses or enters through the mouth can be caught in the lungs. The lungs produce mucus that traps foreign particles, and the bronchi and bronchioles are lined with cilia that beat mucus and debris upward toward the throat for disposal (i.e., swallowing). Smoking damages the cilia, making removal of the excess mucus produced by smoking more difficult. This is one of the reasons smokers are more susceptible to respiratory infections. The trachea is a 10-12 cm long tube located in front of the esophagus that allows air to enter and exit the lungs. Its C-shaped hyaline cartilage keeps the trachea open. When the smooth muscle of the trachea contracts, the diameter of the trachea decreases and exhaled air is pushed out with great force (e.g., coughing). In cases of damage to the throat or mouth that blocks breathing, a tracheostomy, a surgica

 Core: Circulatory and Pulmonary Systems

The Blood-brain Barrier

JoVE 10841

The blood-brain barrier (BBB) refers to the specialized vasculature that provides the brain with nutrients in the blood while strictly regulating the movement of ions, molecules, pathogens, and other substances. It is composed of tightly linked endothelial cells on one side and astrocyte projections on the other. Together they provide a semipermeable barrier that protects the brain and poses unique challenges to the delivery of therapeutics. The BBB is made up of a variety of cellular components, including endothelial cells and astrocytes. These cells share a common basement membrane and together regulate the passage of components between the circulation and the interstitial fluid surrounding the brain. The first type of cellular component, specialized endothelial cells, make up the walls of the cerebral capillaries. They are connected by extremely tight and complex intercellular junctions. These junctions create a selective physical barrier, preventing simple diffusion of most substances, including average to large-sized molecules such as glucose and insulin. A second cell type, astrocytes, are a type of glial cell of the central nervous system which influences endothelial cell function, blood flow, and ion balance in the brain through interaction and close association with cerebral vasculature. They provide a direct link between the vasculature

 Core: Nervous System

What is Metabolism?

JoVE 10725

Metabolism represents all of the chemical activity in a cell, including reactions that build molecules (anabolism) and those that break molecules down (catabolism). Anabolic reactions require energy, whereas catabolic reactions provide it. Thus, metabolism describes how cells transform energy through a variety of chemical reactions, which are often made more efficient with the help of enzymes. Metabolism is the management of energy in cells and provides three key functions: converting food into energy to run various cellular processes, producing energy to build cell components, and removing waste products. To produce energy, macromolecules from food must be broken down into smaller molecules—through a catabolic pathway. This, in turn, provides energy to construct larger molecules from smaller building blocks—through an anabolic pathway. In other words, the potential energy in food—comprised of the chemical energy stored in the bonds between atoms—can be converted into kinetic energy that can be used for cellular reactions. Enzymes are essential molecular tools in metabolic pathways, as they greatly speed up many chemical reactions by reducing the amount of required energy. Catabolism is the breakdown of macromolecules for any purpose. This inc

 Core: Metabolism

pH

JoVE 10669

The potential for a solution to donate or accept hydrogen ions determines whether it is an acid or a base. Acidic solutions donate protons, whereas bases or alkaline solutions can accept protons. Pure water has equal numbers of hydrogen ions to give protons and hydroxide ions to receive them, making it a neutral solution.

pH is a measure of the acidity or basicity of a water-based solution, determined by the concentration of hydrogen ions. In one liter of pure water, there are 1x10-7 moles of hydrogen ions. However, the extensive range of hydrogen ion concentrations present in water-based solutions makes measuring pH in moles cumbersome. Thus, a pH scale was developed in which moles of hydrogen ions are converted using the negative of the base 10 logarithm. The pH of pure water, then, is 7, representing a neutral solution. Most solutions have a pH between 0 and 14, but some solutions, like carborane (with a pH of -18), exceed this. One liter of carborane has 1x1018 moles of hydrogen ions. When free, unbound hydrogen ions accumulate, as with carborane, the solution is acidic, and the pH value falls below 7. Coffee, lemon juice, and gastric acid (digestive juices) are acidic solutions, with pHs around 4.5, 2.5, and 1.5, respectively. Solutions with pH values above 7 have lower hydrogen ion concentrations and are alkaline. In

 Core: Chemistry of Life

Raman Spectroscopy for Chemical Analysis

JoVE 5701

Source: Laboratory of Dr. Ryoichi Ishihara — Delft University of Technology


Raman spectroscopy is a technique for analyzing vibrational and other low frequency modes in a system. In chemistry it is used to identify molecules by their Raman fingerprint. In solid-state physics it is used to characterize materials, and more specifically …

 Analytical Chemistry

Sustainable Development

JoVE 10995

As the human population continues to grow and use resources, we must be mindful of our planet’s natural limits. Sustainable development provides a pathway to maintain and improve human life now while also ensuring that future generations will have the resources that they need. The long-term success of sustainability efforts rests on understanding the interplay between human actions and ecological systems. The oceans are one important focus of global conservation efforts. Overfishing, pollution, and effects of climate change, such as ocean acidification and rising sea levels, are just a few of the major concerns that must be addressed in order to protect the world’s oceans. In addition to providing vast amounts of food for humans, the oceans are an important source of atmospheric oxygen and provide a carbon sink for CO2 gas. They also help regulate the climate and influence weather patterns all over the globe. One major focus of sustainable development is ocean fishing. Modern fishing methods allow the collection of large numbers of fish at once, which is efficient in the short term but also causes local depletion of fish populations, which can have effects across the ocean food web. Current large-scale fishing methods also result in the deaths of other animals, such as dolphins and sea birds, which are caught in nets along with the int

 Core: Biological Diversity

Respiratory Exam I: Inspection and Palpation

JoVE 10028

Source: Suneel Dhand, MD, Attending Physician, Internal Medicine, Beth Israel Deaconess Medical Center


Disorders of the respiratory system with a chief complaint of shortness of breath are among the most common reasons for both outpatient and inpatient evaluation. The most obvious visible clue to a respiratory problem will be whether the…

 Physical Examinations I

Ideal Gas Law

JoVE 5537

Source: Laboratory of Dr. Andreas Züttel - Swiss Federal Laboratories for Materials Science and Technology


The ideal gas law describes the behavior of most common gases at near-ambient conditions and the tendency of all chemical matter in the dilute limit. It is a fundamental relationship between three measurable macroscopic system…

 General Chemistry

Working with Hot and Cold Sources

JoVE 10366

Source: Robert M. Rioux & Suprita Jharimune, Pennsylvania State University, University Park, PA


Working with extreme temperatures, both high and low, is an integral part of many laboratory operations. For many, mentioning a laboratory instantly evokes the mental picture of a Bunsen burner. Bunsen burners and hot plates are used…

 Lab Safety

Le Châtelier's Principle

JoVE 10138

Source: Laboratory of Dr. Lynne O'Connell — Boston College


When the conditions of a system at equilibrium are altered, the system responds in such a way as to maintain the equilibrium. In 1888, Henri-Lewis Le Châtelier described this phenomenon in a principle that states, "When a change in temperature, pressure, or…

 General Chemistry
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