Bio 301 - Ch 4 Book Notes

microbial nutrition

• a limiting factor to microbial growth is the finite supply of nutrients in the environment

• essential nutrients are compounds that microbes must have but cannot make

  • these nutrients must be found from the surrounding environment

  • if this nutrient is depleted, the microbe will not grow

• all microorganisms require a minimum set of macronutrients and micronutrients

  • common macronutrients include C, N, P, H, O & S

  • there are also macronutrient cations that serve as cofactors: Mg2+, Fe2+, K+

  • Ca2+ acts as a regulatory signaling molecule

  • common micronutrients include Co, Cu, Mn, Mo, Ni & Zn

• all cells require nutrients to increase in biomass and gain energy

microbes build biomass through autotrophy or heterotrophy

• all Earth’s life forms are based on carbon which is a limited resource that must be recycled to maintain life

• the survival and metabolism of any one group of organisms depend on the survival of other groups of organisms

• the carbon cycle involves two counterbalancing metabolism: heterotrophy & autotrophy

• heterotrophy breaks down multi-carbon nutrients and harvests the C to make cell constituents & some is converted into CO2 as a waste product

• autotrophy takes the CO2 molecules discarded as waste by heterotrophs and reassembles them into multi-carbon nutrients like glucose

  • the glucose is then used as a C source for the heterotrophs

• organotrophy

  • a form of heterotrophy in which organic sources are broken down in ways that harvest carbon for growth and give energy (oxidation)

  • these organisms convert a generous amount of organic carbon source to CO2 which is then released into the atmosphere

• autotrophs assimilate CO2 gas as a carbon source via CO2 fixation which reduces CO2 to generate a complex, organic component of C, H, and O

  • autotrophs are classified as photoautotrophs or chemolithoautotrophs based on how they obtain their energy

• photoautotrophs use light energy to fix CO2 into biomass but chemolithoautotrophs fix CO2 using chemical reactions

  • chemolithoautotrophs gain energy by oxidizing inorganic substance like iron or ammonia & they do not use light

microbes obtain energy through phototrophy or chemotrophy

• macronutrients provide the essential building blocks that are needed to synthesize proteins & other cell structures

• a source of energy is required — absorption of light or from redox reactions

• chemotrophs

  • capture the energy difference to do work

• two categories of chemotrophs use different sources of electron donors

  • lithotrophs: oxidize inorganic chemical for energy

  • organotrophs: oxidize organic compounds for energy

microorganisms that can use a mix of different sources of energy and carbon are mixotrophs

• Rhodospirillum rubrum grows by photoheterotrophy when light is available and oxygen is absent, but it can switch to organotrophy and respiration, without absorbing light, when O2 is available

• the amount of energy harvested from oxidizing a compound depends on the compound’s reduction state

  • the more reduced the compound is, the more electrons it has to give up and the higher potential energy yield

  • a highly reduced compound can donate electrons to a less reduced compound
    

energy is stored for later use

• once energy is obtained, it must be converted to a useful form that the cell can use; this might be electrochemical or chemical energy

• energy stored by an electrical potential across the membrane is called membrane potential

  • this is generated when chemical energy is used to pump protons, Na+, or K+ to the outside of the cell & makes the cation conc greater on the outside of the cell compared to the inside

  • an example is membrane proteins such as cytochrome oxidases use energy from respiration to pump protons across the cell membrane and out of the cell, generating a proton gradient

• the proton gradient (delta P) plus the charge difference (voltage potential) across the membrane forms an electrochemical potential

  • when this electrochemical potential includes a proton gradient, it also has proton potential or proton motive force

  • the energy stored in the PMF can be used by specific transport proteins to move nutrients into the cell, to directly drive motors that rotate flagella & to drive the synthesis of ATP production by ATP synthase

ATP synthase components & function mechanism

• the membrane-embedded F-ATP synthase, also called F1Fo ATP synthase, provides most of the ATP for aerobic respiring cells

• ATP synthase is a complex of many different proteins

  • the enzyme includes a channel (Fo) which allows protons to move across the membrane & drive the rotation of the ATP c-ring

  • the rotation of the c-ring causes changes in the F1 complex that mediate formation of ATP

• some bacteria living in alkaline environments use a different form of ion motive form involving Na+ (sodium motive force)

The Nitrogen Cycle

• N is an essential component of proteins, nucleic acids, and other cell constituents

• 79% of the Earth’s atmosphere is composed of N2 gas which is an inaccessible form of N for most organisms

  • nitrogen-fixing bacteria have the ability to convert diatomic nitrogen into ammonium

  • these bacteria may be free-living in the soil or in water or they may form symbiotic associations with plants

  • the product ammonium is then used by all microbes to make amino acids and other nitrogen-containing compounds

• nitrogen-fixing bacteria that form symbiotic relations include the following:

  • Rhizobium, Sinorhizobium, and Bradyrhizobium species are nitrogen-fixing symbionts of leguminous plants such as soybeans, chickpeas, and clover

  • although symbionts are most widely known nitrogen-fixing bacteria, the majority of nitrogen in soil & aquatic environment is fixed by free-living bacteria and archaea

• various groups of organisms collaborate to recycle ammonium ions and nitrate ions into nitrogen gas & collect energy in the process of converting reactants to products and biologically useful forms of N

• in nitrification, nitrifiers gain energy by converting or oxidizing ammonia in two steps to form nitrate

  • this process is a form of lithotrophy

• denitrification is a process that uses nitrate and related inorganic forms of nitrogen as terminal electron acceptors for certain electron transport chains

  • these bacteria reduce nitrate to N2 which sends N gas back into the atmosphere which roughly balances the amount removed by nitrogen fixation

Nutrient Uptake

• a microbe must find means of motility to access nutrients and move those nutrients across the membrane into the cytoplasm

  • the cell membrane is selectively permeable to the nutrients that the cell can use

• selective permeability can be achieved in the following ways:

  • membrane-spanning protein channels or pores that differentiate between substrates of certain sizes or chemical composition; permits the entry of those substances (facilitated diffusion)

  • substrate-specific carrier proteins, permeases, that span the cytoplasmic membrane and transport substrates into the cell

  • nutrient-binding proteins that sample the external environment (Gram-positive bacteria) or the periplasmic space (Gram-negative bacteria) for specific nutrients & then those pass those nutrients to specific permeases in the membrane

• microbes must overcome the issue of low nutrient concentrations in the natural environment

  • if the intracellular concentration of a nutrient never rose higher than the extracellular concentration, the cell would starve in low-nutrient environments

  • to surpass this issue, most organisms have evolved efficient transport systems that concentrate nutrients inside the cell relative to outside

  • moving molecules against a concentration gradient requires some form of energy input

  • environments where nutrients are available but exist at low concentrations & are composed in form that cannot be transported into the cell

  • to combat this, many microbes unlock the nutrients by secreting digestive enzymes that break down the complex carbs or other molecules into smaller compounds that are easier to transport

facilitated diffusion