Biology: Metabolism Vocab

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Metabolism

The chemical reactions that take place inside cells, including those that use energy and those that release energy.

Anabolic Pathway

Chemical reactions where smaller molecules are used to form larger molecules.

Catabolic Pathway

Chemical reactions where larger molecules are broken down into smaller molecules.

Energy

The ability to create a measurable change in something.

Work

Creating a measurable change in something.

Kinetic Energy

The energy in objects that are moving. The amount is proportional to the speed and mass of the object.

Potential Energy

Often referred to as stored energy. Has the ability to become useable energy.

Chemical Energy

Energy that is stored in the bonds that hold atoms together. This energy is released when the bonds are broken.

Gibbs Free Energy

The amount of useable energy that is available in the reactants and the products of chemical reactions.

Enthalpy

Total change of energy in a system.

Kelvin Scale

A system for measuring temperature that is exactly like the centigrade scale except zero degrees Kelvin is set at absolute zero. Absolute zero is the coldest temperature possible. To convert from centigrade to Kelvin just add 273 to degrees Celsius.

Endergonic Reactions

Chemical reactions that absorb useable energy. They are non-spontaneous because energy is needed to drive the reaction forward.

Exergonic Reactions

Chemical reactions that release useable energy. They are spontaneous reactions because the released energy can be used to overcome the activation energy needed to start the reaction.

Oxidation Reaction

Electrons are lost by the atom or molecule in this reaction.

Reduction Reaction

Electrons are gained by the atom or molecule in this reaction.

Activation Energy

All chemical reactions require an initial input of energy to get started. For example, fires are spontaneous reactions because the energy generated from the fire causes the fire to spread, but a fire will not start until you start the initial reaction with activation energy. Once started the fire provides its own activation energy to continue the reaction.

Catalyst

Something that speeds up a chemical reaction by lowering the activation energy required to start the reaction. Is not used up in the chemical reaction so it can continue to work speeding up reactions.

Enzyme

A biological catalyst, usually a protein, is a catalyst for biochemical reactions (metabolism). Can reduce the activation energy required for chemical reactions by bringing the reactants close together so they can react. It does this by binding itself to the reactants.

Enzyme Substrate

The reactants that bind to the enzyme. These molecules are attracted to specific parts of the enzyme causing them to bind to the enzyme.

Enzyme Active Site

This is the spot on the enzyme that attracts the substrates. Their shape conforms to the shape of the substrate and may also attract the substrate electrostatically (positive attracts negative).

Protein Denaturing

Proteins have specific shapes that give the proteins their unique properties. The natural shape of a protein can be altered with chemicals or with heat. the altered protein no longer has its natural shape and can no longer do the things it would normally be able to do. This altered protein is considered inactivated, and this is usually irreversible.

Lock and Key Method

Proteins can bind to substrates in this type of manner. Just like a keyhole is shaped to fit the key, parts of the protein are shaped to fit the protein’s substrates. The “keyhole” on the protein may also attract the substrate by relying on different chemical properties.

Induced Fit Model

The idea that the protein and substrate that binds to it will change shape slightly when they are bound together. This minor change in shape can make it easier for reactions to take place. The new shape may conform to other substrates better. The polarity or charge of the protein and substrate can change as well when bound together, making it easier or harder for polar interactions to occur.

Allosteric Site

An additional site on an enzyme that can be used to activate or inactivate the enzyme. Some enzymes are always active in their natural form and require the binding of an inhibitor to render it inactive. While some enzymes are inactive in their natural form and require an activator to bind to it to activate them. The binding of the activator or inactivator to the site changes the overall shape of the enzyme altering its behavior. The binding of the activator or inactivator can also change the polarity or charge of different regions on the enzyme.

Cofactor

Inorganic ions that bind to enzymes. The enzymes may not work or work poorly if it is not bound to it. The binding of these ions allows the enzyme to take the most optimal shape or charge needed for function.

Coenzyme

Organic helper molecules that bind to enzymes allowing the enzymes to function properly. They act much like cofactors. Many vitamins are this or turn into this later when they are needed.

Thermodynamics

The study of energy and energy transfer involving physical matter.

First Law of Thermodynamics

Conservation of energy. The energy in the universe is constant. Energy cannot be created or destroyed, it can only move from one place to another and change forms.

Second Law of Thermodynamics

There is always energy loss in the form of unusable energy, usually as heat. The amount of usable energy in the universe is always decreasing.

Adenosine Triphosphate (ATP)

A high energy molecule that living things use to drive metabolic reactions. The phosphate bond is an unstable high energy bond. This unstable bond releases useable energy when it breaks. It is unstable and breaks apart spontaneously soon after it is formed. This is why it is generated only when it is required to drive certain metabolic reactions.

Adenosine Diphosphate (ADP)

A low energy molecule that is formed when the high energy phosphate bond in ATP is broken. It is recycled back into ATP during cellular respiration and the light dependent cycle of photosynthesis.

NADH

This is a coenzyme that carries electrons that are released during the oxidation of molecules broken down during metabolic processes. It releases these electrons to feed the electron transport chain in the mitochondria which uses the energy to produce ATP.

FADH2

This is also a coenzyme similar to NADH. It also carries electrons released during the oxidation of molecules and transports them to the electron transport chain.

Photosynthesis

A metabolic pathway that produces sugars from sunlight, carbon dioxide, and water.

Chloroplast

A cellular organelle that is the site for photosynthesis.

Chlorophyll

A pigment molecule that absorbs light during photosynthesis. It reflects green light and gives plants their green color.

Thylakoid

A small membranous disk structure that is found in the chloroplast. It is the site for the light dependent reactions of photosynthesis. Their membrane contains proteins embedded with the light sensitive pigment molecule chlorophyll. Their membrane also contains the proteins that are involved in the electron transport chain of the light dependent reactions.

Granum

A stack of thylakoid discs.

Stomata

Openings on the surface of the plant that allow air to enter the plant. Plants can open and close this to prevent moisture from escaping through them.

Light Dependent Reactions

The stage of photosynthesis that depends on light to drive the reactions. Light energy is stored in high energy molecules like ATP and NADPH. H2O and light are needed in this stage of photosynthesis. Light strikes the chlorophyll molecules located in proteins embedded in the thylakoid membrane. Chlorophyll absorbs the light using it to energize electrons. The electrons are energized and power other proteins in the thylakoid membrane. The energy from the light is used to break water into protons, electrons, and oxygen gas in a process called photolysis.

Light Independent Reactions

The stage of photosynthesis that does not require light to happen. The chemical reactions in the reactions are driven by the energy from ATP and NADPH. Carbon Dioxide is taken in and used to produce the materials needed to make sugar.

ATP Synthase

A transmembrane protein that catalyzes the phosphorylation of ADP to produce ATP. This is an enzyme that uses the energy of protons moving through an electrochemical gradient set up in the lumen of the thylakoid by a process called photolysis.

Calvin Cycle

Also known as the light independent reactions. It consists of 3 stages. Fixation, reduction, and regeneration. During fixation, carbon dioxide is bonded or “fixed” to an organic compound called RuBP. Carbon fixation is catalyzed by an enzyme called Rubisco. During the reduction phase 3-PGA is phosphorylated by ATP and reduced by NADPH. The reactants are regenerated in the end so that the cycle can be repeated. The regeneration phase uses additional ATP.

Phosphorylation

The addition of phosphate to a molecule. When this occurs to ADP, it becomes ATP.

Dephosphorylation

The removal of a phosphate from a molecule. When this occurs to ATP, it becomes ADP.

Cellular Respiration and Fermentation

Living things need to be able to utilize the energy that is stored in the chemical bonds of molecules in order to survive. They are chemical pathways that allow organisms to transfer the energy that is stored in these bonds to high energy molecules like ATP that can be used directly to power metabolic reactions.

Glycolysis

The first step of cellular respiration and fermentation. Glucose is broken down into two pyruvate molecules. Glucose is a 6-carbon molecule, pyruvate is a 3-carbon molecule. Two ATP molecules are required to phosphorylate glucose twice. The phosphorylated glucose is unstable and splits into 3 carbon molecules. The 3 carbon molecules undergo a series of oxidation reactions that reduce NAD+ to NADH. The 3-carbon molecule then donates 2 phosphates to 2 ADP molecules turning them into ATP. It produces a net of 2 molecules of ATP and 2 molecules of NADH. The NADH is sent to the electron transport chain to produce more ATP.

Aerobic Respiration

This pathway takes place after glycolysis if oxygen is available. The pyruvate that was produced in glycolysis is decarboxylated (loses a carbon dioxide molecule) and is converted into acetyl-CoA, a 2-carbon molecule attached to a coenzyme named coenzyme A. Acetyl-Coa proceeds to the citric acid cycle and some of the products from the citric acid cycle continues to the electron transport chain to undergo oxidative phosphorylation.

Acetyl-CoA

A 2-carbon molecule attached to coenzyme A. This molecule is important because several amino acids and fats can be converted into this and enter the citric acid cycle for ATP production. This is the common point where the metabolic pathways for carbohydrates, fats, and proteins come together. Some of the more complex amino acids will be converted into other molecules found in the citric acid cycle.

Citric Acid Cycle

Also known as the Kreb Cycle. Acetyl-CoA is broken down into carbon dioxide in a series of chemical reactions that produces NADH, FADH2, and ATP. First acetyl-CoA combines with a 4-carbon molecule named oxaloacetate to form a 6-carbon molecule citrate. Citrate undergoes a few conformational changes and then breaks down into a 5-carbon molecule releasing a carbon dioxide molecule. The energy released from this catabolic reaction is captured by converting NAD+ to NADH. The 5-carbon molecule loses another carbon dioxide resulting in a 4-carbon molecule and another NADH. This 4-carbon molecule undergoes a series of conformational changes turning it back into oxaloacetate so that the citric acid cycle can continue. GTP a high energy molecule similar to ATP is formed from the energy released in this process. One turn of this cycle consumes one acetyl-CoA molecule and produces 3 NADH, 1FADH2, 1 GTP, and 2 carbon dioxide molecules.

Oxidative Phosphorylation

This step occurs in the folds of the inner mitochondrial membrane. An electron transport chain uses electrons from NADH and FADH2 to produce ATP. ATP synthase which is also found in the light dependent cycle of photosynthesis is used to phosphorylate ADP to form ATP during oxidative phosphorylation. The protons that drive the ATP synthase accumulate in the intermembrane space of the mitochondria. The energy from the protons as they are pushed through the ATP synthase drives the phosphorylation of ADP. It is called this because it requires oxygen. Each NADH molecule produces 2 to 3 ATP molecules while each FADH2 molecule produces 1 to 2 ATP molecules when they unload their electrons into the electron transport chain.

Anaerobic Respiration

This process is very similar to aerobic respiration. This uses a different molecule as a substitute for oxygen. Some prokaryotes that live in oxygen poor environments have adapted to use sulfates and nitrates instead of oxygen to produce ATP.

Fermentation

An alternative pathway to cellular respiration that occurs when there no oxygen is available. This process is anaerobic and is not considered respiration because the electron transport chain is not involved. During fermentation ATP is only produced in the glycolysis step. The reactions in this pathway after glycolysis only occur to regenerate the molecules needed to continue glycolysis. The products from this differ depending on the type of cells that are undergoing this. Lactic acid is the product that is produced in our muscles in the absence of oxygen. Alcohol is produced by many microorganisms that undergo this. Because the electron transport chain is not involved in this, very few ATP molecules are produced in this pathway. The byproducts of this may be reprocessed and turned into ATP later when oxygen becomes available.

Protein & Lipid Metabolism

Proteins and Lipids can enter the citric acid cycle to produce ATP in various ways. Proteins are broken down into amino acids that can be converted to pyruvate, acetyl-CoA, or other components of the citric acid cycle depending on the structures of the amino acids. Fatty acids are long hydrocarbon chains, so they can be broken down into 2 carbon molecules that can be made into acetyl-CoA.

Autotroph

Organisms that are able to produce their own energy using the energy from non-living things. Chemoautotrophs produce energy by using inorganic molecules while photoautotrophs produce their energy using light.

Heterotroph

Organisms that must obtain energy that is produced by other living things.