5 Microbial Metabolism

heterotrophs

(feeders on others) require an organic carbon source. -referred to as organotrophs -for carbon =must have a ready source of organic compounds for biosynthesis—the production of needed cellular components, usually from simpler molecules

reduction

(meaning that it has gained one or more electrons)

enzyme's substrate

(or substrates, when there are two or more reactants),

autotrophs

(self-feeders) use carbon dioxide, -get their own -referred to as lithotrophs (rock eating) -This requires both energy (ATP) and electrons (from the oxidation of NADPH).

metabolic pathways

(sequences of chemical reactions) are determined by its enzymes, which are in turn determined by the cell's genetic makeup. - involved in almost all biologically important chemical reactions: enzymes

steps of electron transport chain (system)

1..High-energy electrons transfer from NADH to FMN, the first carrier in the chain 2. FMNH2 passes 2H+ to the other side of the mitochondrial membrane (see Figure 5.16) and passes two electrons to Q 3..Electrons are passed successively from Q to cyt b,- last cyt a3 , passes its electrons oxygen (O2), which becomes negatively charged and picks up protons from the surrounding medium to form H2O. -FADH2 adds its electrons -at a lower level than NADH= chain produces about one-third less energy for ATP -important feature -FMN and Q, that accept and release protons and electrons cytochromes, that transfer electrons only =chain is accompanied at several points by the active transport (pumping) of protons from the matrix side-protons provides energy that the chemiosmotic mechanism uses to generate ADP.

glycolysis products

2 pyruvate, 2 ATP, 2 NADH = net

Photosynthesis can be summarized with the following equations

6CO2 + 6H2O + sunlight ---> C6 H12 O6 + 6O2 1. Plants, algae, and cyanobacteria use water as a hydrogen donor, releasing O2 - electrons are taken from hydrogen atoms, an energy-poor molecule, and incorporated into sugar, an energy-rich molecule. The energy boost is supplied by light energy,

saturation

; that is, its active site is always occupied by substrate or product molecules, and it's catalyzing a specific reaction at its maximum rate = further increase in substrate concentration will not affect the reaction rate because all active sites are already in use

Glycolysis (Embden-Meyerhof pathway)

= splitting of sugar oxidation of glucose to pyruvic acid -Most microorganisms use-occurs in most living cells. - 1. The enzymes of glycolysis catalyze the splitting of glucose, a six-carbon sugar, into two three-carbon sugars. These sugars are then oxidized, releasing energy, and their atoms are rearranged to form two molecules of pyruvic acid -during = NAD+ is reduced to NADH -net production of two ATP molecules -does not require oxygen -series of ten chemical reactions, each catalyzed by a different enzyme 2 basic stages, a preparatory stage and an energy-conserving stage -First, in the preparatory stage (steps 1-4) ATP are used as a six-carbon glucose molecule is phosphorylated, restructured, and split into two three-carbon compounds: glyceraldehyde 3-phosphate (GP) and DHAP=DHAP is readily converted to GP. - DHAP into GP means that from this point on in glycolysis, two molecules of GP are fed into the remaining chemical reactions. -second - energy-conserving stage (steps ), the two three-carbon molecules are oxidized in several steps to two molecules of pyruvic acid. In these reactions, two molecules of NAD+ are reduced to NADH, and four molecules of ATP are formed

Naming Enzymes

= usually end in ase -can be grouped into six classes, according to the type of chemical reaction they catalyze -Enzymes within each of the major classes are named according to the more specific types of reactions they assist

chlorophyll

A green pigment found in the chloroplasts of plants, algae, and some bacteria

coenzyme A (CoA,)

A molecule that is required for many cellular reactions and that is often transiently linked to other molecules, such as acetyl groups-carrier -important role in the synthesis and breakdown of fats and in a series of oxidizing reactions called the Krebs cycle.

chemiosmosis

A process for synthesizing ATP using the energy of an electrochemical gradient and the ATP synthase enzyme. -energy released when a substance moves along a gradient is used to synthesize ATP. The "substance" in this case refers to protons. - gradient yields energy. -ATP that is generated. O2 is the final electron acceptor. generate about 34 molecules of ATP from each molecule of glucose oxidized: approximately three from each of the ten molecules of NADH (a total of 30), and approximately two from each of the two molecules of FADH2 (a total of four).

atp

ATP is similar to a highly flammable liquid such as kerosene=easier to ignite and provides heat more quickly and conveniently

chemiosmotic mechanism of ATP generation

ATP synthesis using the electron transport chain is called chemiosmosis and it involves oxidative phosphorylation.

flavin mononucleotide (FMN)

Accepts electrons from NADH in Complex I -a coenzyme form of riboflavin, which functions in the electron transport chain -flavin coenzymes -are also electron carriers

in some instances, the waste products of one microorganism can be used as a carbon and energy source by another species.

Acetobacter (ah-sēʹtō-BAK-ter) bacteria oxidize ethanol made by yeast. - Propionibacteria convert lactic acid to pyruvic acid in preparation for the Krebs cycle

The Integration of Metabolism

Actually, anabolic and catabolic reactions are joined through a group of common intermediates -Both anabolic and catabolic reactions also share some metabolic pathways, such as the Krebs cycle- not only participate in the oxidation of glucose but also produce intermediates that can be converted to amino acids

Fermentation

After glucose has been broken down into pyruvic acid, the pyruvic acid can be completely broken down in respiration -organic product in fermentation, whereupon NAD+ and NADP+ are regenerated and can enter another round of glycolysis 1.releases energy from sugars or other organic molecules, such as amino acids, organic acids, purines, and pyrimidines; 2.does not require oxygen (but can occur in its presence); 3.does not require the use of the Krebs cycle or an electron transport chain; 4.uses an organic molecule synthesized in the cell as the final electron acceptor; 5.produces only small amounts of ATP (only one or two ATP molecules for each molecule of starting material) because much of the original energy in glucose remains in the chemical bonds of the organic end-products, such as lactic acid or ethanol

Oxidation-reduction

Also known as redox; a chemical reaction in which the oxidizing agent is reduced (by losing oxygen) and the reducing agent is oxidized (by gaining oxygen). -An electron is transferred from molecule A to molecule B. In the process, molecule A is oxidized, and molecule B is reduced

they are linked

Although microbial metabolism can cause disease and food spoilage, many pathways are beneficial rather than pathogenic.

nicotinamide adenine dinucleotide (NAD+)

An energy carrier that accepts electrons and feeds them into the electron transport chain - derivatives of the B vitamin niacin (nicotinic acid) -function as electron carriers. -is primarily involved in catabolic (energy-yielding) reaction

flavin adenine dinucleotide (FAD)

An energy carrier that accepts electrons and feeds them into the electron transport chain -flavin coenzymes -are also electron carriers

Photoautotrophs

An organism that harnesses light energy to drive the synthesis of organic compounds from carbon dioxide. -They include photosynthetic bacteria (green and purple bacteria and cyanobacteria), algae, and green plants. - hydrogen atoms of water are used to reduce carbon dioxide, and oxygen gas is given off. -several other families of photosynthetic prokaryotes-classified according to the way it reduces CO2- some (they must have an anaerobic environment)- they are anoxygenic

fermentation test

Another biochemical test -The test medium contains protein, a single carbohydrate, a pH indicator, and an inverted Durham tube, which is used to capture gas -can use the protein or carbohydrate as a carbon and energy source -If they catabolize the carbohydrate and produce acid, the pH indicator changes color -produce gas as well as acid from carbohydrate catabolism-tube indicates gas formation

Lipid Biosynthesis

Because lipids vary considerably in chemical composition, they are synthesized by a variety of routes -glycerol portion of the fat is derived from dihydroxyacetone phosphate, an intermediate formed during glycolysis -Fatty acids, which are long-chain hydrocarbons (hydrogen linked to carbon), are built up when two-carbon fragments of acetyl CoA are successively added to each other -most important role of lipids is to serve as structural components of biological membranes, -function in energy storage. Recall that the breakdown products of lipids after biological oxidation feed into the Krebs cycle

Hydrolysis

Breaking down complex molecules by the chemical addition of water

polysaccharides

Carbohydrates that are made up of more than two monosaccharides

help each other

Catabolic reactions provide building blocks for anabolic reactions and furnish the energy needed to drive anabolic reactions -made possibible by atp

Purine and Pyrimidine Biosynthesis

Certain amino acids—aspartic acid, glycine, and glutamine—made from intermediates produced during glycolysis and in the Krebs cycle participate in the biosyntheses of purines and pyrimidines The carbon and nitrogen atoms derived from these amino acids form the purine and pyrimidine rings, and the energy for synthesis is provided by ATP.

Calvin-Benson cycle

Cyclic carbon-fixing pathway that builds sugars from CO2; the light-independent reactions of photosynthesis.

FADH2

During aerobic respiration, which of the following directly donates electrons to the electron transport chain at the lowest energy level

Endergonic vs. Exergonic

Endergonic - requires energy Exergonic - releases energy

activation energy,

Energy needed to get a reaction started -which is the amount of energy needed to disrupt the stable electronic configuration of any specific molecule so that the electrons can be rearranged.

Enzyme Specificity and Efficiency

Enzyme Specificity and Efficiency -able to hydrolyze a peptide bond only between two specific amino acids -the three-dimensional shape of the specific amino acids of the active site fits the substrate somewhat as a lock fits with its key - the active site and substrate are flexible, and they change shape somewhat as they meet to fit together more tightly. -relatively few of the enzyme's amino acids make up the active site -certain compound can be a substrate for several different enzymes

three classes of carrier molecules in electron transport chains:

Flavoproteins , Cytochromes, Ubiquinones, or coenzyme Q (Q)

coenzyme

If the cofactor is an organic molecule -may assist the enzyme by accepting atoms removed from the substrate or by donating atoms required by the substrate.

for prokaryotes

In most prokaryotic cells, the plasma membrane does so. An electron transport chain also operates in photophosphorylation - 38 ATP molecules: 34 from chemiosmosis plus 4 generated by oxidation in glycolysis and the Krebs cycle = can use a nitrate ion (NO3 −) as a final electron acceptor;, (N2), sulfur-Anaerobic respiration by bacteria using nitrate and sulfate as final acceptors is essential for the nitrogen and sulfur cycles that occur in nature

Additional Pathways to Glycolysis

Many bacteria have another pathway in addition to glycolysis pentose phosphate pathway; another alternative is the Entner-Doudoroff pathway.

glucose electrons carriers

NAD to and FAD

Photosynthesis electron carriers

NADP+ to NADPH

amino group

NH2

heterolactic (or heterofermentative

Organisms that produce lactic acid as well as other acids or alcohols

oxidation-reduction (redox) reactions

Oxidation and reduction reactions are always coupled: each time one substance is oxidized, another is simultaneously reduced. The pairing of these reactions

oxidative phosphorylation

Part of the electron transport chain. A process occurring in the mitochondria that results in the formation of ATP from the flow of electrons across the inner membrane to bind with oxygen. -The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration. -electrons are transferred from organic compounds to one group of electron carriers (usually to NAD+ and FAD). Then the electrons are passed through a series of different electron carriers to molecules of oxygen (O2) or other oxidized inorganic and organic molecules

Phototrophs

Phototrophs use light as their primary energy source

Entner-Doudoroff pathway

Produces NADPH and ATP -without either glycolysis or the pentose phosphate pathway. -produces two molecules of NADPH and one molecule of ATP -found in some gram-negative bacteria Pseudomonas, Rhizobium, Agrobacterium

flavoproteins

Proteins to which a flavin is attached FAD, other flavins synthesized from riboflavin

kred #2

Pyruvic acid -cannot enter the Krebs cycle directly. In a preparatory step, it must lose one molecule of CO2 and become a two-carbon compound =called an acetyl group -attaches to coenzyme A -known as acetyl coenzyme A (acetyl CoA) - During this reaction, pyruvic acid is also oxidized, and NAD+ is reduced to NADH. each molecule of glucose, two molecules of CO2 are released, two molecules of NADH are produced, and two molecules of acetyl CoA are former =ready to enter the Krebs cycle. CoA detaches from the acetyl group. The acetyl group combines with oxaloacetic acid to form citric acid. -The formation of citric acid is thus the first step in the Krebs cycle several general categories; one of these is decarboxylation -All three carbon atoms in pyruvic acid are eventually released as CO2 by the Krebs cycle- all 6 in two turns of the Krebs cycle. Another general category of Krebs cycle chemical reactions is oxidation-reduction= -isocitric acid is oxidized. -Hydrogen atoms are also released -NAD+ picks up two electrons but only one additional proton=NADH -FAD picks up two complete hydrogen atoms and is reduced to FADH2. play a role in other pathways, especially in amino acid biosynthesis

phosphorylated

Referring to a molecule that has been the recipient of a phosphate group.

Metabolic Diversity among Organisms

Some microbes can sustain themselves on inorganic substances by using pathways that are unavailable to either plants or animals. -All organisms can be classified metabolically according to their nutritional pattern—

Amino Acid and Protein Biosynthesis

Some microbes contain the enzymes necessary to use starting materials, such as glucose and inorganic salts, for the synthesis of all the amino acids they need -Other microbes require that the environment provide some preformed amino acids. (a) Pathways of amino acid biosynthesis through amination or transamination of intermediates of carbohydrate metabolism from the Krebs cycle, b) Transamination, a process by which new amino acids are made with the amine groups from old amino acids.

catalysts

Substances that can speed up a chemical reaction without being permanently altered themselves

phosphorylation

The addition of p to a chemical compound

decarboxylation

The complete loss of a carboxyl group as carbon dioxide

Substrate-Level Phosphorylation

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

The Light-Independent Reactions: The Calvin-Benson Cycle

The light-independent reactions are so named because they don't require light directly. They include a complex cyclic pathway called the Calvin-Benson cycle, in which CO2 is "fixed"—that is, it's used to synthesize sugars

transamination

The process by which an amino group from one amino acid is transferred to a carbon compound to form a new amino acid. -amine group comes from a preexisting amino acid

Biosynthesis

The process by which living organisms produce larger molecules from smaller ones.

allosteric ("other space") inhibition

The process in which an enzyme's activity is changed because of binding to the allosteric site. - can activate an enzyme rather than inhibit it.

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 photosynthesis. -one of the three ways ATP is formed, and it occurs only in photosynthetic cells -light energy is absorbed by chlorophyll molecules in the photosynthetic cell, exciting some of the molecules' electrons. The chlorophyll principally used by green plants, algae, and cyanobacteria is chlorophyll a. It is located in the membranous thylakoids of chloroplasts -The excited electrons jump from the chlorophyll to the first of a series of carrier molecules, -protons are pumped across the membrane, and ADP is converted to ATP by chemiosmosis.

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 photosynthesis. -occurs only in photosynthetic cells, which contain light-trapping pigments such as chlorophylls.\-electron transport chain

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.

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.

electron transport chain (system)

The sequence of electron carriers used in oxidative phosphorylation -plasma membrane of prokaryotes and in the inner mitochondrial membrane of eukaryotes

cyclic photophosphorylation

The synthesis of ATP during photosynthesis, coupled to the cyclic passage of electrons to and from P700 / photo #1 , the specialized form of chlorophyll a which is involved in photosystem I, using a series of carrier molecules. - that dont have O as a biproduct -the electrons released from chlorophyll in photosystem 1 eventually return to chlorophyll -That is, the electrons in photosystem I remain in photosystem I.

chemiosmosis

The transfer of electrons from one electron carrier to the next releases energy, some of which is used to generate ATP from ADP through a process

Metabolic Pathways of Energy Production

To extract energy from organic compounds and store it in chemical form, organisms pass electrons from one compound to another through a series of oxidation-reduction reactions. -by a series of controlled reactions rather than in a single burst

Factors Influencing Enzymatic Activity

Two primary types are the control of enzyme synthesis -and the control of enzyme activity (how much enzyme is present versus how active it is)

Substrate Concentration

Under conditions of high substrate concentration, an enzyme is said to be in {saturation} -maximum rate can be attained only when substrate(s) is extremely high

nicotinamide adenine dinucleotide phosphate NADP+

a coenzyme form of niacin that functions as an electron carrier and can be reduced to NADPH during metabolism - derivatives of the B vitamin niacin (nicotinic acid) -function as electron carriers. -primarily involved in anabolic (energy-requiring) reactions

amination

addition of an amino group -Adding an amine group to pyruvic acid or to an appropriate organic acid of the Krebs cycle converts the acid into an amino acid

two types of respiration

aerobe, which uses oxygen, or anaerobe, which does not use oxygen and may even be killed by it.

collision theory

all atoms, ions, and molecules are continuously moving and colliding with one another. The energy transferred by the particles in the collision can disrupt their electron structures enough to break chemical bonds or form new bonds. states that atoms, ions, and molecules must collide in order to react - explains how chemical reactions occur and how certain factors affect the rates of those reactions.

holoenzyme

apoenzyme + cofactor -whole, active enzyme

Two of the most important coenzymes in cellular metabolism

are nicotinamide adenine dinucleotide (NAD ∙ ) and nicotinamide adenine dinucleotide phosphate (NADP ∙ )

Cytochromes

are proteins with an iron-containing group (heme) capable of existing alternately as a reduced form (Fe2+) and an oxidized form (Fe3+). The cytochromes involved in electron transport chains cyt c

Ubiquinones, or coenzyme Q (Q)

are small nonprotein carriers.

For their principal carbon source

autotrophs vs heterotrophs

anabolism,

building of complex organic molecules from simpler ones. -enzyme-regulated energy-requiring reactions -anabolic, or biosynthetic reactions - use dehydration synthesis reactions (reactions that release water) -endergonic (consume more energy than they produce). -ATP provides the energy for synthesis, and again some energy is given off as heat. - ATP breakdown

Metabolic Pathways of Energy Use

but about 45% of the energy of glucose is lost as heat -Cells use the remaining energy-in a variety of ways. - for the transport of substances across plasma membranes -some of their energy for flagellar motion -Most of the ATP, however, is used in the production of new cellular components.

oxidases

catalyze oxidation-reduction reactions involving oxygen

certain compound can be a substrate for several different enzymes

catalyze reactions at rates 108 to 1010 times (up to 10 billion times) higher than those of comparable reactions without enzymes.

produce energy from glucose

cellular respiration and fermentation - Both cellular respiration and fermentation usually start with the same first step, glycolysis -but different subsequent

(the catabolic reactions

chemical reactions that either produce energy

hydrolytic

cleavage of bonds by the addition of water

oxidizing

combine or become combined chemically with oxygen.

electron transport chain (system)

consists of a sequence of carrier molecules that are capable of oxidation and reduction - electrons are passed through the chain --- release of energy -- drive the chemiosmotic generation of ATP, - transport chain is contained in the inner membrane of mitochondria -Even a single bacterium may have several types of electron transport chains. ;

Flavoproteins

contain flavin a coenzyme derived from riboflavin (vitamin B2), and are capable of performing alternating oxidations and reductions. One important flavin coenzyme is flavin mononucleotide (FMN

Energy Production

convenient energy carrier. ATP="high-energy" bonds=unstable bonds= released quickly and easily.

enzyme poisons

cyanide and fluoride -because they permanently inactivate enzymes Cyanide can bind the iron -fluoride can bind calcium or magnesium

Inhibitors

decrease the activity of enzymes =are classified as either competitive or noncompetitive inhibitors -effective way to control the growth of bacteria

chemotrophs

depend on oxidation-reduction reactions of inorganic or organic compounds for energy.

parasites

derive nutrients from a living host.

Noncompetitive inhibitors

do not compete with the substrate for the enzyme's active site; instead, they interact with another part of the enzyme - causes the active site to change its shape, making it nonfunctiona --can be either reversible or irreversible

NAD+

electron carrier involved in glycolysis

ETCs

electron transport chain -but their ETCs are not all identical

In many cellular oxidations

electrons and protons (hydrogen ions, H+) are removed at the same time - biological oxidations involve the loss of hydrogen atoms, they are also called dehydrogenation reductions

steps

electrons are transferred (along with protons) from reduced coenzymes (NADH, NADPH) to pyruvic acid or its derivatives -Those final electron acceptors are reduced to the end-products shown -function of the second stage of fermentation is to ensure a steady supply of NAD+ and NADP+ so that glycolysis can continue. -end-products depend on the particular microorganism-Chemical analyses of these end-products are useful in identifying microorganisms

A Summary of Energy Production Mechanisms

energy passes from one organism to another in the potential energy contained in the bonds of chemical compounds. - retained by oxidation reactions -To obtain energy -must have an electron (or hydrogen) donor=initial energy source -Electron donors are diverse=pigments, glucose -transferred to electron carriers,- -electron acceptors in further oxidation-reduction reactions, producing more ATP.

The Generation of ATP

energy released during oxidation-reduction reactions is trapped within the cell by the formation of ATP.- an inorganic phosphate group, i, is added to ADP with the input of energy to form AT

In living systems

enzymes increase the reaction rate without raising the temperature -enzyme lowers the activation energy of the reaction (see arrows). Thus, more molecules of reactant AB are converted to products A and B because more molecules of reactant AB possess the activation energy needed for the reaction.

lipases

enzymes that break down lipids

Microbial Metabolism

even the most structurally simple organism involve a large number of complex biochemical reactions -reactions that are unique to bacteria are fascinating because they allow microorganisms to do things we cannot do-live on cellulose -allows some microorganisms to grow in or on the human body as

Competitive inhibitors

fill the active site of an enzyme and compete with the normal substrate for the active site. -shape and chemical structure are similar to substrate -Some competitive inhibitors bind irreversibly to amino acids in the active site -Increasing the substrate concentration can overcome reversible competitive inhibition -Another type can operate on enzymes that require metal ions for their activity

Kreds cycle outcomes

four molecules of CO2 - six molecules of NADH -two molecules of FADH2 - two molecules of ATP -A molecule of guanosine triphosphate (GTP), (Humans produce CO2 from the Krebs cycle in most cells of the body and discharge it through the lungs during exhalation. NADH and FADH2 are the most important - most enegy

The product of glucose phosphorylation

glucose 6-phosphate - process involves the expenditure of energy

Monosaccharides

glucose, fructose, galactose

fermentation

glycolysis has taken place, the pyruvic acid is converted different products, depending on the type of cell. These products might include alcohol (ethanol) and lactic acid. =no Krebs cycle or electron transport chain -atp only from glycolosis

anoxygenic photoautotrophs

green and purple bacteria.

pH

have an optimum pH at which they are most active -When the H+ concentration (pH) in the medium is changed drastically, the protein's three-dimensional structure is altered. - can cause denaturation -alter a protein's three-dimensional structure because the H+ (and OH−) compete with hydrogen and ionic bonds in an enzyme, resulting in the enzyme's denaturation.

How do organisms use oxidation-reduction reactions?

in catabolism to extract energy from nutrient molecules.-degrade them from highly reduced compounds (with many hydrogen atoms) to highly oxidized compounds -glucose that have many hydrogen atoms are highly reduced compounds, containing a large amount of potential energy. -cell oxidizes a molecule of glucose (C6H12O6)

phosphate group

inorganic

Anaerobic Respiration

inorganic substance other than oxygen (O2). Because only part of the Krebs cycle operates under anaerobic conditions -ex= (N2), sulfur -and because only some of the carriers in the electron transport chain participate in anaerobic respiration - ATP yield is never as high as in aerobic respiration. =anaerobes tend to grow more slowly than aerobes.

Pathways can be categorized

into two general types—catabolic and anabolic.

Cellular Respiration

is defined as an ATP-generating process in which molecules are oxidized and the final electron acceptor comes from outside the cell and is (almost always) an inorganic molecule

Metabolism

is the buildup and breakdown of nutrients within a cell. These chemical reactions provide energy and create substances that sustain life. -key players in metabolism are enzymes and the molecule adenosine triphosphate (ATP).

Oxidation

is the removal of electrons (e−) from an atom or molecule, a reaction that often produces energy. -Molecule A has undergone oxidation (meaning that it has lost one or more electrons), molecule B has undergone reduction

Photosynthesis takes place in two stages

light dependent reactions and independent (dark) reactions

dependent (light) reactions

light energy is used to convert ADP and to ATP. In addition, in the predominant form of the light-dependent reactions, the electron carrier NADP+ is reduced to NADPH take - H2O release - ATP , O2, NADPH

photosystems

light-collecting units of the chloroplast -proteins in the thylakoid membrane organize chlorophyll and other pigments into clusters -Chlorophyll and other pigments are packed into thylakoids of chloroplasts Photosystem II = most likely the first photosystem to evolve, it was the second one discovered- It contains chlorophyll that is sensitive to wavelengths of light of 680 nm. Photosystem I contains chlorophyll that is sensitive to wavelengths of light of 700 nm

Saprophytes (decomposers)

live on dead organic matter

dehydrogenation reaction

loss of hydrogen atoms - most biological oxidations involve this organic molecule is oxidized by the loss of two hydrogen atoms, and a molecule of NAD+ is reduced. Remember that NAD+ assists enzymes by accepting hydrogen atoms that have been removed from the substrate, in this case the organic molecule -NAD+ accepts two electrons and one proton. One proton (H+) is left over and is released into the surrounding medium. The reduced coenzyme, NADH, contains more energy than NAD+. This energy can be used to generate ATP in later reactions. -one hydrogen atom and two electrons, and one proton is released into the medium. NAD+ is reduced to NADH, which is a more energy-rich molecule.

Demature

loss of its characteristic three-dimensional structure (tertiary configuration) -breakage of hydrogen bonds and other noncovalent bonds -some cases, denaturation is partially or fully reversible denatured by concentrated acids, bases, heavy-metal ions (such as lead, arsenic, or mercury), alcohol, and ultraviolet radiation

Alcohol fermentation

lycolysis of a molecule of glucose to yield two molecules of pyruvic acid and two molecules of ATP. In the next reaction, the two molecules of pyruvic acid are converted to two molecules of acetaldehyde and two molecules of CO2 - then reduced by two molecules of NADH to form two molecules of ethanol. low-energy-yield process -most of the energy contained in the initial glucose molecule remains in the ethanol, the end-product. bacteria and yeasts.

coenzyme

may assist the enzyme by accepting atoms removed from the substrate or by donating atoms required by the substrate. -act as electron carriers, removing electrons from the substrate and donating them to other molecules in subsequent reactions -Many coenzymes are derived from vitamins

amphibolic pathways

metabolic pathways that have both catabolic and anabolic functions -are dual-purpose. For example, NAD+ is involved in catabolic reactions, whereas NADP+ is involved in anabolic reactions

Lipid and Protein Catabolism

microbes also oxidize lipids and proteins, and the oxidations of all these nutrients are related -Microbes produce extracellular enzymes called lipases that break fats down into their fatty acid and glycerol components -Each component is then metabolized separately / fatty acids and glycerol-Krebs cycle functions in the oxidation of both -Whereas beta-oxidation (fatty acid oxidation Proteins, carbohydrates, and lipids can all be sources of electrons and protons for respiration. These food molecules enter glycolysis or the Krebs cycle at various points.

homolactic (or homofermentative).

microbes produce only lactic acid, -Lactic acid fermentation can result in food spoilage. However, the process can also produce yogurt from milk, sauerkraut from fresh cabbage, and pickles from cucumbers.

Lactic Acid Fermentation

molecule of glucose is oxidized to two molecules of pyruvic acid This oxidation generates the energy that is used to form the two molecules of ATP. In -the next step, the two molecules of pyruvic acid are reduced by two molecules of NADH to form two molecules of lactic acid =most of the energy produced by the reaction remains stored in the lactic acid -yields only a small amount of energy. - lactic acid bacteria are Streptococcus and Lactobacillus

Adenosine triphosphate (ATP)

molecule that cells use to manage energy needs -ATP consists of an adenine, a ribose, and three phosphate groups

cofactor

nonprotein component - Ions of iron, zinc, magnesium, or calcium

anoxygenic

not producing molecular oxygen in photosynthesis

organotrophs

obtain electrons from organic compounds

pentose phosphate pathway (or hexose monophosphate shunt)

operates simultaneously with glycolysis and provides a means for the breakdown of five-carbon sugars (pentoses) as well as glucose -produces important intermediate pentoses used in the synthesis of (1) nucleic acids, (2) glucose from carbon dioxide in photosynthesis, and (3) certain amino acids. - important producer of the reduced coenzyme NADPH from NADP+. -net gain of only one molecule of ATP -Bacillus subtilis (SU-til-us), E. coli,

photosynthesis

organic molecules, especially sugars, are synthesized with the energy of light from the energy-poor building blocks, carbon dioxide and water.

oxygenic

oxygen producing = photosynthesis

Photosynthesis

photo means light, and synthesis refers to the assembly of organic compounds. synthesize complex organic compounds from simple inorganic substances. The major mechanism for such synthesis -conversion of light energy from the sun into chemical energy. -chemical energy is then used to convert CO2 to -carried out by plants and many microbes. -more reduced carbon compounds, primarily sugars

chlorophyll

principal pigment of plants and other photosynthetic organisms

Protein Catabolism

produce extracellular proteases and peptidases, enzymes that break down proteins into their component amino acids -which can cross the membranes. -Proteins are too large -before amino acids can be catabolized-converted to other substances -enter the Krebs cycle= = deamination -Other conversions involve decarboxylation (the removal of —COOH) and desulfurization (removal of —SH).

Aerobic respiration among eukaryotes

produces a total of only 36 molecules atp -fewer ATPs than in prokaryotes because -energy is lost when electrons are shuttled across the mitochondrial membranes - inorganic substance oxygen (O2).

apoenzyme

protein portion of an enzyme -Apoenzymes are inactive by themselves; they must be activated by cofactors

increase the reaction rate

raise its temperature. By causing the molecules to move faster, heat increases both the frequency of collisions and the number of molecules that attain activation energy. -collisions also increases when pressure is increased or when the reactants are more concentrated

Temperature

rate increases a temperature increases. -heat = more movement= more energy -elevation beyond a certain temperature (the optimal temperature) drastically reduces the rate of reaction - 35°C and 40°C for bacteria in our body -declines beyond the optimal temperature because of the enzyme's denaturation

light-independent (dark)

reactions, these electrons are used along with energy from ATP to reduce CO2 to sugar

desulfurization

removal of SH

enzymes

serve as biological catalysts - in living cells -each enzyme acts on a specific substance, called the enzyme's substrate -each catalyzes only one reaction pof part (a), the enzyme changes shape slightly to fit together more tightly with the substrate.

end-product

several steps are required for the synthesis of a particular chemical compound -similar to an assembly line,-by a separate enzyme

enzyme's ability to accelerate a reaction without the need for an increase in temperature is crucial to living systems

significant temperature increase would destroy cellular proteins = its job =speed up biochemical reactions at a temperature that is compatible with the normal functioning of the cell.

allosteric site

site on the enzyme other than the substrate's binding site

apoenzyme

some enzymes consist entirely of proteins, most consist of both apoenzyme, and cofactor.

active site.

specific region of the surface of the enzyme

Chemoheterotrophs

specifically use the electrons from hydrogen atoms in organic compounds as their energy source - further classified according to their source of organic molecules. -Saprophytes - parasites Most bacteria, and all fungi, protozoa, and animals, are chemoheterotrophs.-Bacteria and fungi can use a wide variety of organic compounds for carbon and energy sources energy and carbon sources because they occur as separate entities. However, in chemoheterotrophs, the distinction isn't as clear because the energy and carbon sources are usually the same organic compound—glucose

step 3

substrate molecule is transformed by the rearrangement of existing atoms, the breakdown of the substrate molecule, or in combination with another substrate molecule. then it releases the new product bc it dont fit and moves on

green bacteria,

such as Chlorobium (KLO-rō-bē-um), use sulfur (S), sulfur compounds (such as hydrogen sulfide, H2S), or hydrogen gas (H2) to reduce carbon dioxide and form organic compounds. -or oxidize hydrogen gas to water (H2O)

purple bacteria

such as Chromatium (krō-MĀ-shum), also use sulfur, sulfur compounds, or hydrogen gas to reduce carbon dioxide. They are distinguished from the green bacteria by their type of chlorophyll, location of stored sulfur, and ribosomal RNA

carbon fixation

synthesis of sugars by using carbon atoms from CO2 gas - Earth depends on the recycling of carbon in this way

influence the activity of an enzyme

temperature, pH, substrate concentration, and the presence or absence of inhibitors.

enzyme-substrate complex

temporary intermediate compound forms - while enzyme orients the substrate into a position that increases the probability of reaction

deamination

the amino group of an amino acid is removed and converted to an ammonium ion (NH4 +), which can be excreted from the cell.

Carbohydrate Catabolism

the breakdown of carbohydrate molecules to produce energy, is therefore of great importance in cell metabolism\- btw-Most microorganisms oxidize carbohydrates as their primary source of cellular energy. -Glucose is the most common carbohydrate -lso catabolize various lipids and proteins for energy production

Catabolic Reactions

the breakdown of complex organic compounds into simpler ones -catabolic, or degradative, reactions -enzyme-regulated chemical reactions that release energy are generally the ones involved -usually hydrolytic reactions (reactions which use water and in which chemical bonds are broken), - are exergonic (produce more energy than they consume) -some of the energy is transferred to and trapped in ATP, and the rest is given off as heat. - ATP synthesis

aerobic respiration

the final electron acceptor is O2

anaerobic respiration

the final electron acceptor is an inorganic molecule other than O2 or, rarely, an organic molecule = Krebs cycle

feedback inhibition (end-product inhibition)

the final product acts as a noncompetitive inhibitor of the first generally enzyme , which shuts down the pathway - This control mechanism stops the cell from making more of a substance than it needs and thereby wasting chemical resources - inhibiting the first enzyme in the pathway, the cell also keeps metabolic intermediates from accumulating = As the cell uses up the existing end-product, the first enzyme's allosteric site remains unbound more frequently, and the pathway resumes activity.

reaction rate

the frequency of collisions containing sufficient energy to bring about a reaction -/the rate at which reactants change into products over time =depends on the number of reactant molecules at or above the activation energy level -

turnover number

the number of substrate molecules an enzyme can convert into product per second -between 1 and 10,000 and can be as high as 500,000. For example, the enzyme DNA polymerase =15 rate at which enzymes switch between active and inactive forms is determined by the cellular environment.

NADH

the reduced form of NAD+; an electron-carrying molecule that functions in cellular respiration

nutritional pattern

their source of energy and their source of carbon.

cellular respiration

three principal stages: glycolysis, the Krebs cycle, and the electron transport chain (system). - CO2 from krebs cycle 1= Glycolysis is the oxidation of glucose to pyruvic acid with the production of some ATP and energy-containing NADH. 2=The Krebs cycle is the oxidation of acetyl CoA (a derivative of pyruvic acid) to carbon dioxide, with the production of some ATP, energy-containing NADH, and another reduced electron carrier, FADH2 3= The Krebs cycle is the oxidation of acetyl CoA (a derivative of pyruvic acid) to carbon dioxide, with the production of some ATP, energy-containing NADH, and another reduced electron carrier, FADH2 -oxidation-reduction reactions involving a series of additional electron carriers-Energy from these reactions is used to generate a considerable amount of ATP.-ATP is generated in the third step. =long series of oxidation-reduction reactions, - thought of as involving a flow of electrons from the energy-rich glucose molecule to the relatively energy-poor CO2 and H2O -glycolysis and the Krebs cycle generate a small amount of ATP and also supply the electrons that generate a great deal of ATP at the electron transport chain stage.

metabolism

to refer to the sum of all chemical reactions within a living organism. - chemical reactions either release or require energy, metabolism can be viewed as an energy-balancing act. divided into two classes of chemical reactions:

Krebs cycle

tricarboxylic acid (TCA) cycle or citric acid cycle =Oxidation of acetyl CoA produces NADH, FADH2, and ATP, and liberates CO2 as waste -the large amount of potential chemical energy stored in acetyl CoA is released -series of oxidations and reductions -transfer that potential energy, in the form of electrons, to electron carrier coenzymes, chiefly NAD+ and FADH - pyruvic acid derivatives are oxidized; the coenzymes are reduced.

Ribozyme

unique type of RNA =Like protein enzymes, ribozymes function as catalysts, have active sites that bind to substrates, and are not used up in a chemical reaction. Ribozymes cut and splice RNA and are involved in protein synthesis at ribosomes

he anabolic reactions

use energy

lithotrophs

use inorganic molecules as a source of electrons

Photoheterotrophs

use light as a source of energy but cannot convert carbon dioxide to sugar; rather, they use organic compounds, such as alcohols, fatty acids, other organic acids, and carbohydrates, as sources of carbon -green nonsulfur bacteria, such as Chloroflexus and purple nonsulfur bacteria, such as Rhodopseudomonas

Chemoautotrophs

use the electrons from reduced inorganic compounds as a source of energy, and they use CO2 as their principal source of carbon. They fix CO2 in the Calvin-Benson Cycle -energy for these organisms include hydrogen sulfide (H2S) , sulfur (S),NO2 -The energy derived from the oxidation of these inorganic compounds is eventually stored in ATP, which is produced by oxidative phosphorylation = The cells use these compounds as both the carbon source and the energy source.

Biochemical Tests and Bacterial Identification

used to identify bacteria and yeasts because different species produce different enzymes -used to identify bacteria that cause disease -All aerobic bacteria use the electron transport chain but their ETCs are not all identical

factors determine whether a collision will cause a chemical reaction

velocities of the colliding particles, their energy, - and their specific chemical configurations - even if colliding particles possess the minimum energy needed for reaction, no reaction will take place unless the particles are properly oriented toward each other

First considering the energy source

we can generally classify organisms as phototrophs or chemotrophs

noncyclic photophosphorylation

which is used in oxygenic organisms, both photosystems are required. The electrons released from the chlorophyll in photosystem II and photosystem I do not return to chlorophyll but become incorporated into NADPH -electrons lost from chlorophyll are replaced by electrons from H2O. To summarize: the products of noncyclic photophosphorylation are ATP (formed by chemiosmosis using energy released in an electron transport chain), O2 (from water molecules), and NADPH (carrying electrons from chlorophyll and protons derived ultimately from water