(5) Microbial Metabolism, Part 1

Lecture 9

in order to grow, cells must:

• incorporate nutrients from their environment

• transform them into precursor molecules

• then use them to construct new cells

metabolism =

the series of biochemical reactions by which cells break down or biosynthesize various metabolites

anabolism =

the synthesis of complex molecules from simpler ones together with the storage of energy

catabolism =

the breakdown of complex molecules to yield simpler molecules and energy

nutrients =

the supply of monomers (or precursors of monomers) required by cells for growth

macronutrients =

nutrients that are required in large amounts m

micronutrients =

nutrients required in minute amounts; includes trace metals and growth factors

just a handful of chemical elements predominant in living systems:

hydrogen, oxygen, carbon, nitrogen, phosphorous, sulfur, and selenium

chemical makeup of a cell

• ~75% of the wet weight of a microbial cell is water

• remainder primarule macromolecules (proteins, nucleic acids, lipids, and polysaccharides)

• building blocks: amino acids, fatty acids, nucleotides, and sugars

• protein dominate the macromolecular composition of a cell

• DNA comprises a very small percent of cell’s dry weight

ALL cells require

carbon and nitrogen in large amounts

most microbes (heterotrophs) require organic compounds as their source of carbon

obtain organic compounds from their breakdown of polymeric substances or from the direct uptake of their monomeric constituents

autotrophs can synthesize their own

organic compounds from carbon dioxide (CO2)

microbes nitrogen sources -

can use ammonia (NH3), nitrate (NO3-), organic nitrogen sources (amino acids), nitrogen gas (N2) (nitrogen-fixing bacteria)

microbes - oxygen and hydrogen are obtained from

water (also from O2)

microbes - phosphorous

phosphate

• used for nucleic acids and phospholipids

microbes - sulfur sources

sulfate, sulfide, or organic S compounds

• used in amino acids cysteine and methionine, and in several vitamins

potassium (K) -

required for the activity of several enzymes

magnesium (Mg) -

stabilizes ribosomes, membranes, and nucleic acids, and is required for activity of many enzymes

calcium (Ca) and sodium (Na) are

essential nutrients for only a few microorganism

trace metals

• microorganism require several metals in very small amounts

• function as cofactors of certain enzymes

growth factors

organic compounds required in small amounts by certain organisms

• vitamins, amino acids, purine, pyrimidines

transporting nutrients made difficult by

• impermeability of the cytoplasmic membrane

• concentration of nutrients in cytoplasm must often be higher than concentration in the environment

active transport =

how cells accumulate solutes against a concentration gradient

three basic mechanisms in prokaryotic cells

simple transport, group translocation, ABC transport systems

simple transport -

utilizes a transmembrane proteins

group translocation -

employs a series of proteins

ABC transport systems -

consists of three components (substrate-binding protein, transmembrane transport, and an ATP-hydrolyzing protein)

mechanisms of active transport are

energy driven

• may use proton motive force, ATP, or another energy-rick compound

active transport and transporters - transmembrane component is composed of

polypeptide with 12 transmembrane domains

• polypeptide weaves back and forth through the membrane to from a channel

• solute transported through the channel into the cell

transport is linked to a

conformational change in the transmembrane protein that occurs when it binds its specific solute

simple transporters

• energy from proton motive force

• responsible for transporting phosphate, sulfate, and other organic compounds

simple transporters can either be

symport reactions or anti port reactions

symport reactions -

solute and a protein are co-transported in the sam direction

• majority of transport events

antiport reactions -

solute and a proton are transported in opposite directions

group translocation - differs from simple transport in two ways

• substance transported is chemically modified during the transport process

• an energy-rich compound drives transport

ABC transport system

• require transmembrane protein, substrate binding protein, and ATP-hydrolyzing protein

• ATP hydrolysis drives uptake

ABC transport systems - gram-negative bacteria

employ periplasmic susbtrate-binding proteins

• characterized by very high substrate affinity → bind substrate even at very low concentrations

ABC-transport system - gram-positive bacteria and archaea

empty substrate-binding proteins on the external surface of their cytoplasmic membranes

ABC transport systems properties

• periplasmic substrate-binding protein has high affinity for the substrate

• membrane-spanning protein forms the transport channel

• cytoplasmic ATP-hydrolyzing protein supplies the energy for the transport event

once a microorganism has acquired the nutrients it needs,

it must obtain and conserve energy in order to grow

energy is obtained and conserved via

energy-yielding chemical reactions

microbes can be grouped into catabolic energy classes according tot the

chemical reactions they use to obtain and store energy (and how they obtain carbon)

chemotrophs

obtain/conserve energy from chemicals

chemoorganotrophs

obtain'/conserve energy fro organic chemicals; energy released during oxidation of organic compounds is conserved in the high-energy bonds of ATP

chemolithotrophs

obtain/conserve energy via oxidation of inorganic compounds; further divided into groups that utilize related compounds

phototrophs

use cholorphylls and other pigments to convert light energy into ATP

oxygenic phototrophs -

produce oxygen during photosynthesis

anqxygenic phototrophs -

do not produce oxygen during photosynthesis

heterotrophs obtain carbon from

organic compounds

autotrophs obtain carbon from

carbon dioxide

energy is defined as

the ability to do work

all chemical reactions are accompanied by

changes in energy; energy is either required or releases as the reaction proceeds

Gibbs free energy (G) =

energy available to do work

change in free energy during a reaction under a reaction under standard conditions is referred to as

ΔG0′ (change in standard free energy)

if the ΔG0′ for a reaction is negative (-ΔG0′), the reaction will

proceed with the release of energy

if the ΔG0′ for a reaction is positive, the reaction will

require an input of energy to proceed

to calculate the free-energy yield of a chemical reaction

we need to know the free energy inherent in the reactants and products

free energy of formation (Gf0)

the energy releases or required during formation of a given molecule from the elements

Gf0 of compounds is not zero; will be

positive or negative depending on whether formation of that compound required an input of free energy or released free energy

Gf0 of most compounds is

negative because most compounds form spontaneously

standard conditions include

• gases: 1 atm partical pressure

• pure liquids: total pressure of 1 atm

• solutes: concentration of 1 M

• solids: under 1 atm presure

why is ΔG is more accurate than ΔG0

• In some cases, the consumption of products is so aggressive
  that it can drive Keq values to <1, the log of which will be negative

• This can change the calculated ΔG such that reactions that might
  have been endergonic (+ ΔG, require an input of energy) under
  standard conditions can become exergonic (- ΔG, release
  energy) in natural habitats

only exergonic reactions yield/release

energy that can be conserved by the cell

catalysts function by lowering

the activation energy of a reaction to that supplied by kinetic energy, thereby increasing the reaction rate

catalysts do not affect

the energetics or equilibrium of a reaction (do not make the reaction more or less favorable)

the major catalysts in cells are

enzymes (proteins) and RNAs called ribozymes

enzymes are highly specific for the

reaction they catalyze

enzymes contain an active site =

3D pocket that exactly fits the substrates(s); enzyme combines with the reactant(s); enzyme combines with the reactant(s) in an enzyme-substrate complex

many enzymes contain

small non-protein, non-substrate molecules that participate in catalysis

enzymes - prosthetic groups:

bind tightly to their enzymes, usually bind covalently and permanently

coenzymes

• bind their enzymes loosely and transiently

• single molecule may associate with a number of different enzymes

• most are derivatives of vitamins

to catalyze a reaction,

the enzyme binds its substrate and positions it properly in the active sire

the enzyme-substrate complex aligns

reactive groups and puts strain on specific bonds → bonds broken or swapped to form bonds with a second substrate

for endergonic reactions,

free energy must be put into the reaction

• this is achieved by coupling the energy-reaction to an energy-yielding reaction so that together the reactions give a negative ΔG

theorhetically, all enzymes are

reversible; however, enzymes that catalyze highly exergonic or endergonic reactions typically function in only one direction