Lesson 5 - Chapter 5 Notes

chemoheterotrophs

an organism that uses organic molecules as a source of carbon and energy

chemotrophs

an organism that uses oxidation-reduction reactions as a primary energy source

substrate

any compound with which an enzyme reacts

Compare and contrast cyclic and noncyclic photophosphorylation.

cyclic photophosphorylation: the electrons eventually return to chlorophyll. noncyclic photophosphorylation: the electrons released from chlorophyll do not return to chlorophyll but become incorporated into NADPH

Identify the components of an enzyme.

enzymes contain a protein portion called an apoenzyme and a nonprotein component called a cofactor; together its referred to as a holoenzyme.

List the factors that influence enzymatic activity.

factors influencing enzymatic activity: temperature, pH, substrate concentration and inhibitors

green bacteria

gram-negative, nonproteobacteria; anaerobic and phototrophic, use reduced organic compounds as electron donors for CO2 fixation

feedback inhibition

inhibition of an enzyme in a particular pathway by the accumulation of the end-product of the pathway; also called end-product inhibition.

light reactions

light energy is used to convert ADP and phosphate to ATP.

Describe how lipids and proteins are prepared for glycolysis.

lipases breakdown fats into fatty acid and glycerol components. Proteases and peptidases breakdown proteins into their amino acid components.

Define amphibolic pathways

metabolic pathways that function in both anabolism and catabolism

fermentation test

method used to determine whether a bacterium or yeast ferments a specific carbohydrate; usually performed in a peptone broth containing the carbohydrate; a pH indicator, and an inverted tube to trap gas.

Compare and contrast oxidative phosphorylation and photophosphorylation.

oxidative phosphorylation, energy is released as electrons are passed to a series of electron acceptors (an electron transport chain) and finally to the ultimate electron acceptor - oxygen (or another inorganic compound). VS photophosphorylation (occurs only in photosynthetic cells like certain plants), energy in the form of light is trapped by chlorophyll, and electrons are passed through a series of electron acceptors. The electron transfer then releases energy used for the synthesis of ATP.

substrate-level (phosyphorylation)

the synthesis of ATP by direct transfer of a high-energy phosphate group from an intermediate metabolic compound of ADP

oxidative (phosphorylation)

the synthesis of ATP coupled with electron transport

carbon fixation

the synthesis of sugars by sing carbons from CO2

transamination

the transfer of an amino group from an amino acid to another organic acid

catabolism

all decomposition reactions in a living organism; the breakdown of complex organic compounds into simpler ones

Explain the overall function of biochemical pathways.

A series of enzymatically catalyzed chemical reactions called biochemical pathways store energy in and release energy from organic molecules. This is in lieu of a single burst type reaction. The overall function of metabolic pathways is the storage and release of this energy to be used by the cell.

Compare and contrast aerobic and anaerobic respiration.

Aerobic prokaryotes, 38 ATP molecules can be produced from complete oxidation of a glucose molecule in glycolysis, the Krebs cycle, and the electron transport chain. In eukaryotes, 36 ATP molecules are produced from complete oxidation of a glucose molecule (some energy is lost in the membrane transport of the mitochondrial organelle). Anaerobic respiration, the final electron acceptor includes NO3-, SO4-, and CO3- (you will notice that all electron acceptors are negatively charged). The total ATP yield is less than aerobic respiration because only part of the Krebs cycle operates under anaerobic conditions.

anabolism

all synthesis reactions in a living organism; the building of complex organic molecules from simpler ones

Compare and contrast the light and dark reactions of photosynthesis.

Light-dependent (light) reactions - light energy is used to convert ADP and phosphate to ATP. Light-independent (dark) reactions - the electrons are used along with energy from ATP to reduce carbon dioxide to sugar.

Describe the chemical reactions of, and list some products of, fermentation.

Fermentation releases energy from sugars or other organic molecules by oxidation. products of fermentation are lactic acid; ethanol and CO2

FAD

Flavin adenine dinucleotide; a coenzyme that functions in the removal and transfer of hydrogen ions (H+) and electrons from substrate molecules.

FMN

Flavin mononucleotide; a coenzyme that functions in the transfer of electrons in the electron transport chain

Describe the chemical reactions of glycolysis.

Glycolysis is the oxidation of glucose to pyruvic acid with the production of some ATP and energy containing NADH. It is the most common pathway for the oxidation of glucose. Two ATP and two NADH molecules are produced from one glucose molecule and pyruvic acid is the end product (important because it is the beginning product of both the Krebs cycle and fermentation).

entner-doudoroff pathway

an alternate pathway fro the oxidation of glucose to pyruvic acid

Provide an example of the use of biochemical tests to identify bacteria.

One example of a biochemical test is the detection of amino acid catabolizing enzymes involved in decarboxylation and dehydrogenation, another is a fermentation test. Fermentation tests are used to determine whether an organism can ferment a carbohydrate to produce acid and gas.

Explain what is meant by oxidation-reduction.

Oxidation is the removal of one or more electrons from a substrate, and protons are often removed with the electrons. The loss of hydrogen atoms typically associated with oxidation reactions also gives the name "dehydration" to these reactions. The reduction of the substrate often refers to its gain of one or more electrons. Each time a substance is oxidized, another is simultaneously reduced.

Categorize the various nutritional patterns among organisms according to carbon source and mechanisms of carbohydrate catabolism and ATP generation.

Photoautotrophs (use light as their primary energy source) obtain energy by photophosphrylation and fix carbon from carbon dioxide via the Calvin-Benson cycle to synthesize organic compounds. Cyanobacteria are oxygenic Phototrophs, and green sulfur bacteria and purple sulfur bacteria are anoxygenic Phototrophs (their photosynthetic process does not produce oxygen). Photoheterotrophs use light as an energy source and an organic compound for their carbon source or electron donor. Photoheterotrophs cannot convert carbon dioxide to sugar. Chemoautotrophs use inorganic compounds as their energy source and carbon dioxide as their carbon source. Oxidation of the inorganic chemicals is used to generate the ATP, and is eventually stored. Chemoheterotrophs specifically use the electrons from hydrogen atoms in organic compounds as their energy source. Carbon is their energy source. Heterotrophs can be further classified by their source of organic material: saprophytes live on dead organic material (think of a compost pile), and parasites derive nutrients from a living host. Most bacteria, and all fungi, protozoa, and animals are chemoheterotrophs.

haloenzyme

an apoenzyme and a cofactor combine

Write a sentence to summarize energy production in cells.

Sunlight is converted to chemical energy in oxidation-reduction reactions carried on by phototrophs. Chemotrophs can use this chemical energy. In oxidation-reduction reactions, energy is derived from the transfer of electrons. To produce energy , a cell needs an electron donor (organic or inorganic), a system of electron carriers, and a final electron acceptor (organic or inorganic).

Explain the products of the Krebs cycle.

The Krebs cycle is the oxidation of acetyl (a derivative of pyruvic acid) to carbon dioxide, with the production of some ATP, energy containing NADH, and another released electron carrier, FADH2. The decarboxylation of the pyruvic acid produces one carbon dioxide molecule and one acetyl group. Two-carbon acetyl groups are oxidized in the Krebs cycle, and the electrons are picked up by NAD+ and FAD for the electron transport chain that will end the process. From one molecule of glucose, oxidation produces six molecules of NADH, two molecules of FADH2, and two molecules of ATP. Decarboxylation produces six molecules of CO2.

Describe the chemiosmotic model for ATP generation.

The mechanism of ATP synthesis using the electron transport chain is called chemiosmosis. Protons are pumped across the membrane to generate a proton motive force (gradient) as electrons move through a series of acceptors or carriers. Energy produced from the movement of protons back across the membrane is used by ATP synthase (-ase = enzyme as described earlier in the lesson) to make ATP from ADP and a phosphate group. In eukaryotes, electron carriers are located on the inner mitochondrial membrane (the cell's "power house"). In prokaryotes, the electron carriers are located in the plasma membrane. See the below diagram from your text to visualize chemiosmosis.

chemoautotrophs

an organism that uses an inorganic chemical as an energy source and CO2 as a carbon source

photoheterotrophs

an organism that uses light as its energy source and an organic carbon source

Define metabolism, and describe the fundamental differences between anabolism and catabolism.

The term metabolism refers to the sum of all chemical reactions within a living organism. Catabolism refers to chemical reactions that result in the breakdown of more complex organic molecules into simpler substances, usually releasing energy. Anabolism refers to chemical reactions in which simpler substances are combined to form more complex molecules, usually requiring energy.

photoautotrophs

an organism that uses light as its energy source and carbon dioxide (CO2) as its carbon source

ribozyme

an enzyme consisting of RNA that specifically acts on strands of RNA to remove introns and splice together the remaining exons

noncompetitive inhibition

an inhibitory chemical that does not compete with the substrate for an enzyme's active site

Identify the role of ATP as an intermediate between catabolism and anabolism.

When complex molecules are split apart (catabolism), some of the energy is transferred to and trapped in ATP, and the rest is given off as heat. When simple molecules are combined to form complex molecules (anabolism), ATP provides the energy for synthesis, and again some energy is given off as heat.

aerobe

an organism requiring molecular oxygen (O2) for growth.

parasites

an organism that derives nutrients from a living host.

anaerobe

an organism that does not require molecular oxygen (O2) for growth

saprophytes

an organism that obtains its nutrients form dead organic matter

heterotrophs

an organism that requires an organic carbon source; also called organotroph

alcohol fermentation

a catabolic process, beginning with glycolysis that produces ethyl alcohol to reoxidize NADH

lactic acid fermentation

a catabolic process, beginning with glycolysis, that produces lactic acid to reoxidize NADH

denaturation

a change in the molecular structure of a protein, usually making it nonfunctional

competitive inhibitors

a chemical that competes with the normal substrate for the active site of an enzyme

NADP+

a coenzyme similar to NAD+

CoA

a coenzyme that functions in decarboxylation

NAD+

a coenzyme that functions in the removal and transfer of hydrogen ion (H+) and electrons from substrate molecules

ubiquinones

a low-molecular weight, nonprotein carrier in an electron transport chain; also called coenzyme Q

chemiosmosis

a mechanism that uses a proton gradient across a cytoplasmic membrane to generate ATP

pentose phosphate pathway

a metabolic pathway that can occur simultaneously with glycolysis to produce pentoses and NADH without ATP production; also called hexose monophosphate shunt.

enzymes

a molecule that catalyzes biochemical reactions in a living organism, usually a protein

autotrophs

a mutant microorganism with a nutritional requirement that is absent in the parent

coenzyme

a nonprotein substance that is associated with and that activates an enzyme

krebs cycle

a pathway that converts two-carbon compounds to CO2, transferring electrons to NAD+ and other carriers; also called tricarboxylic acid (TCA) or critic acid cycle

amphibolic pathways

a pathway that is both anabolic and catabolic

flavoproteins

a protein containing the coenzyme Flavin; functions as an electron carrier in electron transport chains

cytochromes

a protein that functions as an electron carrier in cellular respiration and photosynthesis

active site

a region on an enzyme that interacts with the substrate

electron transport chain

a series of compounds that transfer electrons from one compound to another, generating ATP by oxidative Phosphorylation

cellular respiration

a series of redox reactions in a membrane that generates ATP; the final electron acceptor is usually an inorganic molecule.

catalysts

a substance that increases the rate of a chemical reaction but is not altered itself

Define ribozyme.

a unique kind of enzyme. Ribozymes are enzymatic RNA molecules that cut and splice RNA in eukaryotic cells.

phototrophs

an organism that uses light as its primary source of energy

anaerobic respiration

respiration in which the final electron acceptor in the electron transport chain is an inorganic molecule other than molecular oxygen (O2)for example, a nitrate ion or CO2

aerobic respiration

respiration in which the final electron acceptor in the electron transport chain is molecular oxygen (O2)

List and provide examples of three types of phosphorylation reactions that generate ATP.

substrate-level Phosphorylation: a high-energy phosphate from an intermediate in catabolism is added to ADP. oxidative Phosphorylation: energy is released as electrons are passed to a series of electron acceptors (an electron transport chain) and finally to the ultimate electron acceptor - oxygen (or another inorganic compound). Photophosphorylation: (occurs only in photosynthetic cells like certain plants), energy in the form of light is trapped by chlorophyll, and electrons are passed through a series of electron acceptors. The electron transfer then releases energy used for the synthesis of ATP.

purple bacteria

such as chromatium, use sulfur, sulfur compounds or hydrogen gas to reduce carbon dioxide

phosphorylation

the addition of a phosphate group to an organic molecule

amination

the addition of an amino group

reduction

the addition of electrons to a molecule

carbohydrate catabolism

the breakdown of carbohydrate molecules to produce energy

saturation

the condition in which the active site on an enzyme is occupied by the substrate or product at all times

photosynthesis

the conversion of light energy from the sun into chemical energy; the light-fueled synthesis of carbohydrate from carbon dioxide (CO2)

dark reactions

the electrons are used along with energy from ATP to reduce carbon dioxide to sugar.

fermentation

the enzymatic degradation of carbohydrates in which the final electron acceptor is an organic molecule, ATP is synthesized by substrate-level Phosphorylation and O2 is not required

calvin-benson cycle

the fixation of CO2 into reduced organic compounds used by autotrophs

reaction rate

the frequency of collisions containing sufficient energy to bring about a reaction

dehydrogenation

the loss of hydrogen atoms from a substrate

glycolysis

the main pathway for the oxidation of glucose to pyruvic acid; also called the Embden-Meyerhof pathway

activation energy

the minimum collision energy required for a chemical reaction to occur

cofactor

the nonprotein component of an enzyme

collision theory

the principle that chemical reactions occur because energy is gained as a particles collide

allosteric inhibition

the process in which an enzyme's activity is changed because of binding to the allosteric site.

apoenzyme

the protein portion of an enzyme which required activation by a coenzyme

decarboxylation

the removal of CO2 from an amino acid

deamination

the removal of an amino group from an amino acid from ammonia

oxidation

the removal of electrons from a molecule

metabolism

the sum of all the chemical reactions that occur in a living cell