Chapter 10: Introduction to Metabolism

microbial metabolism and its importance

the total of all chemical reactions in the cell, including both energy conserving reactions and energy requiring reactions

catabolism

• fueling reactions

• energy conserving reactions

• provide ready source or reducing power

• generate precursors for biosynthesis

anabolism

• synthesis of complex organic molecules from simpler ones

• requires energy from fueling reactions

chemoorganotroph

energy from organic molecules

chemolithotroph

energy from inorganic molecules

autotroph

carbon source from CO2

heterotroph

carbon source from organic molecules

organotroph

electron source from organic molecules

lithotroph

electron source from inorganic molecules

thermodynamics

• energy is the capacity to do work or to cause particular changes

• analyzes energy changes in a collection of matter called a system (cell)

• all other matter in the universe is called the surroundings

first law of thermodynamics

energy can be neither created or destroyed

second law of thermodynamics

physical and chemical processes proceed in such a way that the disorder of the universe (entropy) increases to the maximum possible

free energy

• changes in energy that can occur in chemical reactions are expressed by the equation ( delta G = delta H - T x delta S)

• change in free energy of a chemical reaction is directly related to the equilibrium constant of the reaction

free energy change (delta G)

amount of energy in a system that is available to do work

when delta G is negative

• The equilibrium constant is greater than one and the reaction goes to completion

• the reaction is said to be endergonic and requires energy (not spontaneous)

• exergonic reaction: Z → enzyme → X + Y + ENERGY

when delta G is positive

• The equilibrium constant is less than one and little product will be formed at equilibrium

• the reaction is said to be endergonic and requires energy (not spontaneous)

• endergonic reaction: ENERGY + X + Y → enzyme → Z

ATP

• high-energy molecule used to capture, store, and provide chemical energy

• hydrolysis of terminal phosphate negative delta G

  • strongly exergonic reaction that can be coupled with various endergonic reactions to facilitate their completion

• high phosphate group transfer

• formed from ADP and Pi (inorganic phosphate) by energy trapping processes

oxidation reduction reaction

• the release of energy during metabolic processes normally involves oxidation-reduction reactions

• involve the transfer of electrons from an electron donor to an electron acceptor

  • when electrons are transferred from an electron donor to an electron acceptor with a more positive reduction potential → free energy is released that can be used to form ATP

reduction potential (Eo)

• the equilibrium constant for an oxidation reduction reaction and is a measure of the tendency of the electron donor to lose electrons

  • the more negative the reduction potential, the better it is as an electron donor

  • greater difference between the reduction potential of the donor and the acceptor → more negative delta G

electron transport chain

• series of electron carriers each with a different redox potential → ordered from most negative to most positive Eo

• important in a variety of electron carriers organized into a chain

electron carriers

• located in plasma membranes of chemoorganotrophs in bacteria and archaeal cells and located in internal mitochondrial membranes in eukaryotic cells

• NAD+, NADP+, flavoproteins (FAD, FMN), quinones, iron-sulfur centers (ferredoxin), and cytochromes (hemes)

  • each differ in transporting electrons and impacts how they function in the ETC

enzymes

• protein catalysts with great specificity for the reaction

• may only be composed of a protein or it may be a holoenzyme

catalyst

substance that increases the rate of a reaction without being permanently altered

holoenzyme

consists of a protein component (apoenzyme) and a nonprotein component (cofactor)

coenzyme

a cofactor that is loosely attached to the apoenzyme

• may dissociate from the apoenzyme and carry one or more of the products of the reaction to another enzyme

prosthetic group

cofactor that is firmly attached to the apoenzyme

enzyme: oxidoreductase

oxidation reduction reactions

enzyme: transferase

reactions involving the transfer of chemical groups between molecules

enzyme: hydrolase

hydrolysis of molecules

enzyme: lyase

breaking of C-C, C-O, C-N, and other bonds by a means other than hydrolysis

enzyme: isomerase

reactions involving isomerizations

enzyme: ligase

joining of two molecules using ATP

enzyme reaction mechanism

enzymes increase the rate of a reaction bud do not alter the equilibrium constant (or the standard free energy change) of the reaction

enzymes lower the activation energy

required to bring the reacting molecules together correctly to form the transition state complex

• once the translation state has been reached, the reaction can proceed rapidly

enzymes bring substrates together

at the activation site to form an enzyme substrate complex

• this can lower activation energy in several ways

  • local concentrations: increased at the active site of the enzyme

  • molecules at the active site are oriented properly

environmental effects on enzyme activity

• amount of substrate present affects the reaction rate

• increase substrate = increase in activity

• UNTIL SATURATION → no further increase in reaction rate occurs with increases in substrate concentration, a reaction proceeding at maximal velocity (V max)

michaelis constant (Km)

• substrate concentration required for the reaction to reach ½ V max

• used to measure the affinity of an enzyme for its substrate

• lower Km the more tightly bound the enzyme is to the substrate

enzyme activity is affected by environment

• pH and temperature

  • each enzyme has a specific pH and temperature optima

enzyme inhibition

• competitive inhibition

• noncompetitive inhibition

competitive inhibition

• inhibitor binds at the active site and competes with the substrate

• can be overcome by adding excess substrate

noncompetitive inhibition

• inhibitor binds at another location and changes the conformation of the active site

• inactive or less active

• cannot be overcome by the addition of excess substrate

ribozymes

catalytic RNA molecules → act on RNA substrate molecules

posttranslational regulation of enzyme activity

• allosteric regulation

• covalent modification of enzyme

• feedback inhibition

allosteric regulation

• an effector or modulator binds reversibly and noncovalently to a regulatory site on the enzyme

• regulatory site is distinct from the catalytic site

• effect can be positive or negative

covalent modification of enzyme

• reversible covalent addition or removal of a chemical group (like phosphate, methyl group, adenylic acid)

• effect can be positive or negative

feedback inhibition

• every pathway has at least one pacemaker enzyme that catalyzes the slowest reaction in the pathway → often the first reaction in a pathway

• the end product of the pathway inhibits the pacemaker enzyme

prepatory stage

• 2 ATP are used

• glucose is split to form two molecules of glyceraldehyde 3-phosphate

energy conserving stage

• two glyceraldehyde-3-phosphate molecules are oxidized to 2 pyruvic acid molecules

• 4 ATP are produced

• 2 NADH are produced

glycolysis (embden meyerhof pathway)

• the oxidation of glucose to pyruvic acid produces 2 ATP and 2 NADH

  • preparatory stage

  • conservation stage

• this is one of three glycolytic pathways used to catabolize glucose to pyruvate

  • aerobic respiration

  • anaerobic respiration

  • fermentation

aerobic respiration

electon accepted by NAD+ are transferred to the electron transport chain and accepted by O2

anaerobic respiration

electron accepted by NAD+ are transferred to the membrane and accepted by inorganic molecules (NO3-, SO4-, CO3-)

fermentation

electron accepted by NAD+ are donated to endogenous acceptor (pyruvate)

glycolysis pathway

glucose + 2 ATP + 2 ADP + 2 PO4- + 2 NAD+ → 2 pyruvic acid + 4 ATP + 2 NADH + 2 H+

• overall net gain of two molecules of ATP for each molecule of glucose oxidized

kreb’s cycle

• pyruvic acid (from glycolysis) is oxidized decarboxylation (loss of CO2) occurs

• resulting in two carbon compound attaches to coenzyme A, forming acetyl CoA and NADH

• oxidation of acetyl CoA produced NADH, FADH2, and ATP and liberates CO2 as waste

chemiosmosis

• electrons (from NADH) pass down the electron transport chain while protons are pumped across the membrane

  • establishes proton gradient (proton motive force)

• protons in higher concentration on one side of the membrane diffuse through ATP synthase

  • releases energy to synthesize ATP