Unit 3

Metabolism

The totality of an organism's chemical reactions, consisting of catabolic and anabolic pathways, which manage the material and energy resources of the organism.

Metabolic Pathways

A series of chemical reactions that either builds a complex molecule or breaks down a complex molecule into simpler compounds.

Catabolic Pathways

Metabolic pathways that release energy by breaking down complex molecules into simpler compounds.

Anabolic Pathways (Biosynthetic Pathways)

Metabolic pathways that consume energy to build complicated molecules from simpler ones.

Kinetic Energy

The energy an object has due to its motion

Potential Energy

Stored energy that results from the position or spatial arrangement (structure) of an object

Spontaneous Process

A process that can occur without an input of energy; without an overall input of energy; a process that is energetically favorable.

Free Energy

Measures the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell.

Free Energy Change

A measure of the change in free energy as a chemical reaction or physical change occurs

Exergonic Reaction

A spontaneous chemical reaction in which there is a net release of free energy; negative change in free energy

Endergonic Reaction

A non-spontaneous chemical reaction in which free energy is absorbed from the surroundings; positive change in free energy

Energy Coupling

In cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction.

Catalyst

Substance that speeds up the rate of a chemical reaction by lowering activation energy required.

Activation Energy

The minimum amount of energy required to start a chemical reaction

Active Site

A region on an enzyme that binds to a protein or other substance during a reaction. Each active site of an enzyme is specific, has its own shape and size, can have chemical charges or not, and its chemical properties must be compatible with its substrate.

Enzyme

• A type of protein that acts as a catalyst to bring about a specific biochemical reaction.

• These proteins retain a tertiary shape structure which is required for functionality; their structural characteristics make them reaction specific.

• They are reusable

• Can facilitate synthesis or digestion reactions.

• Their names tend to end in -ase.

Substrate

A specific reactant acted upon by an enzyme.

Primary Structure of Protein

The first level of protein structure; the specific sequence of amino acids making up a polypeptide chain.

Secondary Structure of Protein

Regions of repetitive coiling or folding of the polypeptide backbone of a protein due to hydrogen bonding between constituents of the backbone (not the side chains). This causes an alpha helix shape or beta pleated sheet.

Tertiary Structure of Protein

The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.

Denature

A change in the shape of a protein that destroys the characteristic properties of that protein. Can be caused by changes in temperature or pH (among other things). It is typically irreversible but in some cases it can be reversed.

pH

Measures hydrogen ion concentration on a logarithimic scale.

Chemical Reaction

The process by which one or more substances change to produce one or more different substances

Reactant

A chemical substance that is present at the start of a chemical reaction

Product

A substance that forms in a chemical reaction

Activators and Inhibitors

Substances that bind to an enzyme and either increase or decrease its activity

Cofactors

Any inorganic nonprotein molecule that helps with catalytic activity (ex. zinc, iron, copper)

Coenzyme

Organic, nonprotein catalytic helper (ex. vitamins)

Allosteric Regulation

The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site. Can include an allosteric activator and an allosteric inhibitor (noncompetitive).

Competitive Inhibition

Substance that resembles the normal substrate competes with the substrate for the active site (attaches to active site in place of substrate).

Noncompetitive inhibitor

A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing its conformation so that it no longer binds to the substrate.

Feedback Inhibition

A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.

ATP

• Adenosine Triphosphate

• Consists of 3 phosphate groups, ribose sugar, and the nitrogen base adenine

• Main energy source that cells use for most of their work

ADP

• Adenosine Diphosphate

• Consists of adenine, ribose sugar, and 2 phosphate groups

• The compound that remains when a phosphate group is removed from ATP, releasing energy.

Electron

A subatomic particle that has a negative charge

Proton

A subatomic particle that has a positive charge and that is found in the nucleus of an atom

H+

Hydrogen ion

Oxidation

The loss of electrons from a substance involved in a redox reaction.

Redox Reaction

A chemical reaction involving the transfer of one or more electrons from one reactant to another; also called oxidation-reduction reaction.

Reduction

The gain of electrons by a substance involved in a redox reaction; always accompanies oxidation.

Oxidizing Agent

The electron acceptor in a redox reaction.

Reducing Agent

The electron donor in a redox reaction.

Autotroph

An organism that makes its own food

Heterotroph

An organism that cannot make its own food.

Photosynthesis

Process by which plants and some other organisms use light energy to convert water and carbon dioxide into oxygen and high-energy carbohydrates such as sugars and starches

Chloroplast

An organelle found in plant and algae cells where photosynthesis occurs

Thylakoid

A flattened membrane sac inside the chloroplast, used to convert light energy into chemical energy. Its inside is called the lumen and stacks of thylakoids are referred to as Granum.

Stroma

The fluid of the chloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water. Site of the Calvin Cycle

Non-Cyclic Photosynthesis

The synthesis of ATP and reduced NADP involving photosystems I and II.

Cyclic Phosphorylation

Only produces ATP, no NADPH phosphorylation; no electron acceptors, electrons loop back and are recharged. Happens when CO2 is low

Light Reactions

The first of two major stages in photosynthesis (preceding the Calvin cycle). These reactions, which occur on the thylakoid membranes of the chloroplast or on membranes of certain prokaryotes, convert solar energy to the chemical energy of ATP and NADPH, releasing oxygen in the process.

Photosystem

Cluster of chlorophyll and proteins found in thylakoids

Chlorophyll

Green pigment in plants that absorbs light energy used to carry out photosynthesis

Electron Carriers

Proteins arranged in chains on the membrane to allow the transfer of electrons from one carrier to another.

Electron Transport Chain in Photosynthesis

Electrons move through several transmembrane proteins that are responsible for pumping H+ ions across the membrane creating the chemical gradient across the chloroplast membrane. This proton gradient powers ATP synthase and the ETC itself helps generate NADPH. Energy source is captured light. Part of the light reactions.

NADP+

Carrier molecule that transfers high-energy electrons from chlorophyll to other molecules

NADPH

An electron carrier involved in photosynthesis. Light drives electrons from chlorophyll to NADP+, forming NADPH, which provides the high-energy electrons for the reduction of carbon dioxide to sugar in the Calvin cycle.

In photosynthesis, water is

Oxidized; an electron and H donor

Photophosphorylation

The process of generating ATP from ADP and phosphate by means of a proton-motive force generated by the thylakoid membrane of the chloroplast during the light reactions of photosterm-68ynthesis.

Calvin Cycle

Reactions of photosynthesis in which energy from ATP and NADPH is used to build high-energy compounds such as sugars

Calvin Cycle Overview

Second step of photosynthesis occurring in the stroma; CO2 from the air is incorporated into organic molecules in chloroplasts (carbon fixation), fixed carbon reduced to carbs via NADPH which adds electrons and ATP from the earlier light reaction:

ATP + NADPH + CO2 ------> C6H12O6 + ADP + Pi + NADP+

ETC in photosynthesis vs cellular respiration

Similarities

• Both use excited electrons to power transport of H+

• Creation of proton gradient by ATP synthase

Differences

• Products: Photo makes ATP and NADPH while CellResp makes NAD+, 2FADH, and ATP

• Source of excited electrons, i.e. light photon vs NADH

Photorespiration

A metabolic pathway that consumes oxygen, releases carbon dioxide, generates no ATP, and decreases photosynthetic output; generally occurs on hot, dry, bright days, when stomata close and the oxygen concentration in the leaf exceeds that of carbon dioxide.

C3 Plants

A plant that uses the Calvin cycle for the initial steps that incorporate CO2 into organic material, forming a three-carbon compound as the first stable intermediate.

C4 Plants

A plant that prefaces the Calvin cycle with reactions that incorporate CO2 into four-carbon compounds, the end product of which supplies CO2 for the Calvin cycle.

CAM Plants

Plants close their stomata during the day, collect CO2 at night, and store the CO2 in the form of acids until it is needed during the day for photosynthesis

Cellular Respiration

Process that releases energy by breaking down glucose and other food molecules in the presence of oxygen

Fermentation

A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid.

Lactic Acid Fermentation

The chemical breakdown of carbohydrates that produces lactic acid as the main end product

Aerobic

Process that requires oxygen

Anaerobic

Process that does not require oxygen

Glycolysis

First step in releasing the energy of glucose, in which a molecule of glucose is broken into two molecules of pyruvic acid

NAD+/NADH

An organic molecule that serves as an electron carrier by being oxidized (losing electrons) to NAD+ and reduced (gaining electrons) to NADH.

Pyruvate

Organic compound with a backbone of three carbon atoms. Two molecules form as end products of glycolysis

Pyruvate Oxidation

Conversion of pyruvate to acetyl CoA and CO2 that occurs in the mitochondrial matrix in the presence of O2.

Krebs Cycle

Second stage of cellular respiration, in which pyruvic acid is broken down into carbon dioxide in a series of energy-extracting reactions

FADH2

During aerobic respiration, which of the following directly donates electrons to the electron transport chain at the lowest energy level? (hint: electron carrier produced during the Krebs cycle)

Oxidative Phosphorylation

The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.

Substrate-Level Phosphorylation

The enzyme-catalyzed formation of ATP by direct transfer of a phosphate group to ADP from an intermediate substrate in catabolism.

ATP Synthase

Large protein that uses energy from H+ ions to bind ADP and a phosphate group together to produce ATP

Electron Transport Chain in Cellular Respiration

• Occurs along the cristae in the inner membrane of mitochondria

• Produces 32-24 ATP

• H+ ions pumped across inner mitochondrial membrane to create an H+ gradient

• At the end H+ diffuse through ATP synthase (ADP —> ATP)

• Oxygen is the final electron acceptor in the form of water

Chemiosmosis

A process for synthesizing ATP using the energy of an electrochemical gradient and the ATP synthase enzyme.