reviewer 2.1 - microbial nutrition and metabolism

8/16/2019 Reviewer 2.1 - Microbial Nutrition and Metabolism

1/6

UNIVERSITY OF THE PHILIPPINES MANILA

COLLEGE OF ARTS AND SCIENCES

DEPARTMENT OF BIOLOGY

BIOLOGY 120 (General Microbiology)

Lecture 2.1 – Microbial Nutrition and Metabolism

By: Lani Manahan-Suyom, MSc

SS AY 2013-2014

Outline

1.0 Microbial Nutrition

1.1

Nutrition and Cell Chemistry

1.2

Nutrient Uptake1.3

Culture Media

2.0 Metabolism

Microorganisms require about ten elements in large quantities, because

they are used to construct carbohydrates, lipids, proteins, and nucleic acids.

Several other elements are needed in very small amounts and are parts of

enzymes and cofactors

Biochemical components of cells

Water: 80% of wet weight

Dry weight

o Protein 40-70%

o Nucleic Acid 13-34%

o

Lipid 9-15%o Also monomers, intermediates and inorganic ions

Macronutrients

Cells make proteins, nucleic acids and lipids

Macronutrients

o Macromolecules, metabolism

o CHON SP K Mg Fe

o Sources

Organic compounds

Inorganic salts

Micronutrients

Elements needed in trace quantities

o Co, Cu, Mn, Zn, V

o Enzymes

o Tap water

Most of them are part of enzymes

o Iron – cytochrome, carboxylases

Micronurients (trace elements) needed by microorganisms

Boron (B) Autoinducer for quorum sensing in bacteria also

found in some polketide antibiotics (creates biofilm) Chromium

(Cr)

Possible but not proven component for glucose

metabolism (necessary in mammals)

Cobalt (Co) Vitamin B12; transcarboxulase (only in propionic

acid bacteria)

Copper (Cu) In respiration, cytochrome oxidase; in

photosynthesis, plastocyanin, some superoxide

dismutases

Iron (Fe) Cytochromes; catalases; peroxidises; iron-sulfur

proteins; oxygenases; all nitrogenises

Manganese

(Mn)

Activator of many enzymes; component of certain

superoxide dismutases and of the water splitting

enzyme in oxygenis phototrophs (photosystem II)

Molybdenum

(Mo)

Certain flavin-containing enzymes; some

nitrogenises, nitrate reductases, sulphite oxidases,

DMSO-TMAO reductases; some formate

dehydrogenases

Nickel (Ni) Most hydrogenases; coenzymes F430 of

methanogens; carbon monoxide dehydrogenases;

urease

Selenium

(Se)

Dormate dehydrogenase; some hydrogenases; the

amino acid selenocysteine

Tungsten

(W)

Some formate dehydrogenases; oxotransferases of

hyperthermophiles

Vanadium(V) Vanadium nitrogenises; bromoperoxidase

Zinc (Zn) Carbonic anhydrase; alcohol dehydrogenase; RNA

and DNA polymerases and many DNA binding

proteins

A not every micronutrient listed is required by all cells some metals

listed are found in enzymes or cofactors present in only specific

microorganisms

B needed in greater amounts than other trace metals

Growth Factors

Biotin – Carboxylation (Leuconostoc)

Cyanocobalamin or Vit B12 – Molecular rearrangements (Euglena)

Folic Acid – one carbon metabolism (Enterococcus) Pantothenic Acid – fatty acid metabolism (Proteus)

Pyridoxine or Vit B6 – transamination (Lactobacillus)

Niacin – precursor of NAD and NADP (Brucella)

Riboflavin or Vit B2 – precursor of FAD and FMN (Caulobacter)

Thiamine or Vit B1 – aldehyde group transfer (Bacillus anthracis)

Groups of microorganisms: nutritional requirement

Energy Sources

Phototrophs Light

Chemotrophs Oxidation of organic/inorganic

compounds

Hydrogen and Electron Sources

Lithotrophs Reduced inorganic molecules

Organotrophs Organic molecules

Carbon Sources

Autotrophs CO2 sole or principal

biosynthetic carbon source

Heterotrophs Reduced, preformed, organic

molecules from other organisms

Major Nutritional

Types

Sources of Energy,

Hydrogen/Electrons

and Carbon

Representative

Microorganisms

Photolithotrophic

Autotrophy

Light energy

Inorganic

hydrogen/elect

ron donor CO2 carbon

source

Algae

Purple and

green sulphur

bacteria Blue-green

algae

(cyanobacteria)

Photoorganotrophic

Heterotrophy

Light energy

Organic

hydrogen/elect

ron donor

Organic carbon

source (CO2

may also be

used)

Purple non-

sulfur bacteria

Green non-

sulfur bacteria

Chemolithotrophic

Autotrophy

Chemical

energy source

(inorganic)

Inorganic

hydrogen/elect

ron donor

CO2 carbon

source

Sulfur oxidizing

bacteria

Hydrogenbacteria

Nitrifying

bacteria

Iron bacteria

Chemoorganotrophic

Heterotrophy

Chemical

energy source

(organic)

Organic

hydrogen/elect

ron donor

Organic carbon

source

Protozoa

Fungi

Most non-

photosynthetic

bacteria


2/6

Chemoorganotrophs are by definition heterotrophs.

Most chemolithotrophs and phototrophs are autotrophs.

Autotrophs are sometimes called primary producers

o they synthesize new organic matter from CO2

Virtually all organic matter on Earth has been synthesized by primary

producers, in particular, the phototrophs

Properties of Microbial Photosynthetic Systems

Property Cyanobacteria Green and Purple

Bacteria

Purple Nonsulfur

Bacteria

Photopigment Chlorophyll Bacteriochlorophyll Bacteriochlorophyll

O2

Production

Yes No No

Electron

Donors

H2O H2, H2S, S H2, H2S, S

Carbon

Source

CO2 CO2 Organic/CO2

PrimaryProducts of

Energy

Conversion

ATP + NADPH ATP ATP

Chemoautotroph

Bacteria Electron donor Electron

acceptor

Production

Alcaligens and

Pseudomonas

sp.

H2 O2 H2O

Nitrobacter NO2 O2 NO3, H2O

Nitrosomonas NH4 O2 NO2, H2O

Desulfovibrio H2 SO4 H2O, H2S

Thiobacillusdenitrificans

S, H2S NO3 SO4, N2

Thiobacillus

ferooxidans

Fe2+

O2 Fe3+

, H2O

Nitrifying Bacteria

Uptake of Nutrients

Nutrient molecules frequently cannot cross selectively permeable

plasma membranes through passive diffusion and must be transported

by one of three major mechanisms involving the use of membrane

carrier proteins

1.

Phagocytosis – Protozoa

2. Permeability absorption – most microorganisms

Simple transport

o Passive transport or simple diffusion

o Facilitated diffusion*

Group translocation**

ABC transporter**

*could transport agains or with the concentration gradient

**active transports against concentration gradient

Passive Diffusion

Passive diffusion is the process in which molecules move from a region

of higher concentration to one of lower concentration as a result of

random thermal agitation. A few substances, such as glycerol, can cross

the plasma membrane by passive diffusion

Facilitated Diffusion

The rate of diffusion across selectively permeable membranes is greatly

increased by the use of carrier proteins, sometimes called permeases,

which are embedded in the plasma membrane. Since the diffusion

process is aided by a carrier, it is called facilitated diffusion. The rate of

facilitated diffusion increases with the concentration gradient much

more rapidly and at lower concentrations of the diffusing molecule

than that of passive diffusion

Can be against or with concentration gradient

A Model of Facilitated Diffusion

The membrane carrier can change conformation after binding an

external molecule and subsequently release the molecule on the cellinterior. It then returns to the outward oriented position and is ready

to bind another solute molecule

Because there is no energy input, molecules will continue to enter only

as long as their concentration is greater on the outside

Symport and Antiport

Active Transport

Active transport is the transport of solute molecules to higher

concentrations, or against a concentration gradient, with the use of

metabolic energy input


3/6

Group Translocation

The best-known group translocation system is the

phosphoenolpyruvate: sugar phosphotransferase system (PTS), which

transports a variety of sugars into prokaryotic cells while

Simultaneously phosphorylating them using phosphoenolpyruvate

(PEP) as the phosphate donor

PEP + sugar (outside) pyruvate + sugar-P (inside)

Mechanism of the phosphotransferase system of E. Coli

o For glucose uptake, the system consists of five proteins:

Enzyme (Enz) I, Enzymes IIa, IIb, and IIc, and HPr. A phosphate

cascade occurs from phosphoenolpyruvate (PE-P) to Enzyme

IIc and the latter actually transports and phosphorylates the

sugar. Proteins HPr and Enz I are nonspecific and transportany sugar. The Enz II components are specific for each

particular sugar

ABC Transporter

ABC stands for ATP binding cassette

ABC transporters exist for the uptake of organic compounds (sugars

and amino acids, inorganic nutrients such as sulfate and phosphate,

and trace metals)

Proteins involved

o Periplasmic binding protein – high affinity to substrate even

at low concentration (less than 1 micromolar)

o Membrane spanning transporter – forms the transport

channel

o ATP hydrolyzing protein – supply energy

Has high affinity for to the molecule it needs to transport (even ifmolecule level is really low)

Simple Comparison of Transport Systems

Culture Media – nutrient solutions used to grow microorganisms

mostly for chemotroph organism

Despite the fact that microbiologists have been growing

microorganisms in laboratory cultures for over 125 years, most

microorganisms in nature have yet to be cultured, leaving many

challenges to the microbiologist today

Major Classes of Media

Defined

o Precise amounts of highly purified inorganic or organic

chemicals

o Exact composition (in both qualitative and quantitative sense)

is known

Complex

o Employ digests of microbial, animal or plant products, such as

casein (milk protein), beef (beef extract), soybeans (tryptic

soy broth), yeast cells (yeast extract), or any of a number of

other highly nutritious yet impure substances

Other Classification of Media

According to use

o Enriched

o Selective

o Differential

o General purpose

Fluidity

o Solid

o Semi solid

o Liquid

Development of Solid Medium

Before agar

o

Liquid medium

Potato slices

o Robert Koch (1881) used boiled potato, sliced

o Not all bacteria grew well

Gelatin

o Frederick Loeffler

o Meat extract medium + gelatine

o But gelatine liquid at RT

Agar

o Fannie Hesse (1882)

o Agar used for jams and jelly

o Generally not metabolized by microbes

o Liquefies at 100C, solidifies at 40C

Anaerobic Condition for Growth

Reducing media

o Contain chemicals (thioglycollate of oxyrase) that combine O2

o Heated to drive off or use up O2

Anaerobic Jar

Types of Anaerobic Bacteria

Facultative anaerobes

Obligate anaerobes

Microaerophyllic anaerobes – certain amount of oxygen tolerated

Anaerobic Chambers/Incubators

Anaerobic Jars

o

with anaerobic pack (releases CO2 and H and produceswater)

o gas generators

o candle jar – usually more effective in microaerophyllic (flame

uses up all the oxygen and flame dies)


4/6

An Overview of Metabolism

Metabolism

total of all chemical reactions occurring in the cell

A simplified view of cell metabolism depicts how catabolic degradative

reactions supply energy needed for cell functions and how anabolic

reactions bring about the synthesis of cell components from nutrients

Note that in anabolism, nutrients from the environment or those

generated from catabolic reactions are converted to cell components,

whereas in catabolism, energy sources from the environment are

converted to waste products

Enzymes

Biological catalyst

o Lowers activation energy of a reaction

Enzymes are generally much larger than the substrates

Present in small amount because they are reusable

Active site – the portion of the enzyme to which the substrate binds

Catabolism

Fermentation

o Anaerobic catabolism

o Organic compound is both an electron donor and an electron

acceptor

o ATP is produced by substrate level phosphorylation

Respirationo Catabolism in which a compound is oxidized

o O2 (or an O2 substitute) as the terminal electron acceptor

o Usually accompanied by ATP production by oxidative

phosphorylation

more ATP is produced in respiration than in fermentation and thus

respiration is the preferred choice. But many microbial habitats lack O2

and in such habitats, fermentation is the only option for energy

conservation by chemoorganotrophs

Glycolysis (Embden-Meyerhof-Parnas pathway)

Stage 1 – preparatory reactions

o These are not redox reactions and do not release energy

o Lead to the production of a key intermediate of the pathway

Stage 2 – production of NADH, ATP and Pyruvate

o Redox reactions

o Energy is conserved in the form of ATP, and two molecules of

pyruvate are formed

o Redox balance has not yet been achieved

o Pyruvate formed here

Stage 3 – consumption of NADH and production of Fermentation

products

o

Redox reactions occur once againo Fermentation products are formed

Kreb Cycle (Citric Acid Cycle)

NADH – produces 2-3 ATPs

Respiration and Electron Transport

Respiration in which molecular oxygen or some other oxidant serves as

the terminal electron acceptor

The discussion of respiration deals with both the carbon and electron

transformations

o (1) The biochemical pathways involved in the transformation

of organic carbon to CO2

o (2) The way electrons are transferred from the organic

compound to the terminal electron acceptor, driving ATP

synthesis at the expense of the proton motive force


5/6

Electron Transport

Electron transport systems are composed of membrane associated

electron carriers. These systems have two basic functions

o (1) to accept electrons from an electron donor and transfer

them to an electron acceptor

o (2) to conserve some of the energy released during electron

transfer for synthesis of ATP

In bacteria – ETC happens in plasma membrane not mitoch. membrane

Types of Oxidation-reduction enzymes involved in electron transport

1. NADH dehydrogenases

2.

Riboflavin containing electron carriers generally called flavoproteins3. Iron sulphur proteins

4. Cytochromes

*in addition, one class of nonprotein electron carriers is known, the lipid

soluble quinines

ATP and Cell Yield

The amount of ATP produced by an organism has a direct effect on cell

yield

Cell yield is directly proportional to the amount of ATP produced

Energy costs for assembly of macromolecules are much the same for all

microorganisms

Production of ATP is specific to a strain which is related to its cell yield

Energy Storage

Most microorganisms produce insoluble polymers that can later be

oxidized for the production of ATP

Importance of polymer formation

o Potential energy is stored in a stable form

o Insoluble polymers have little effect on the internal osmotic

pressure of cells

*Storage polymers make possible the storage of energy in a readily

accessible form that does not interfere with other cellular processes

The Proton Motive Force

Carriers in the Electron Transport Chain (ETC) are

o Arranged in increasing positive reduction potential

o

Oriented in such a way that as e- are transported, protons are

separated from e-

o The final donating the electrons plus protons to a terminal

electron acceptor such as O2

o H+ are extruded to the outer surface of the membrane

o H+ originate from two sources

NADH

Dissociation of water into H and OH2??

o The extrusion of H+ to the environment results in the

accumulation of OH2 on the inside of the membrane

o As a result the two sides of the membrane differ in both

charge and pH

o Formation of an electrochemical potential across the

membrane = PMF

ATP Synthase (ATPase)

The use of PMF to generate ATP

Catalyzed a reversible reaction between ATP and ADP + P

Two components

o F1 complex – carries out the chemical functions

o F0 complex – ion translocating functions

Composition

o F1 complex - α3β 3γδε

o F0 complex - a,b2, c12

F0 generates the torque that is transmitted to F1

Assignment: Read Similarities of the ATP Synthesis via ATPase and

flagellar locomotion

Anabolism: biosynthesis

Sugar

Amino Acids


6/6

Fatty Acids

Regulation of the Activity of Enzymes: Feedback Inhibition

Reaction shut off because of an excess of the end product

Allosteric enzymes has 2 binding sites, the active site (where substrate

binds) and the allosteric site, where the end product of the pathwaybinds

Allosteric Site

With 2 protein binding sites

Without end product in the environment - active site can accept a

substrate, so chemical production will proceed

If end product is in excess – it will bind to the allosteric site and prevent

substrate from binding to active site

Regulation of the Activity of Enzymes: Covalent Modification

A) when cells are grown with excess ammonia, glutamine synthetase is

covalently modified by adenylylation as many as 12 AMP groups can be

added. When cells are ammonia-limited, the groups are removed,

forming ADP

B) Adenylylated GS subunits are catalytically inactive so the overall GS

activity decreases progressively as more subunits are adenylylated.

If end product is present, it will bind to the enzyme but when it binds,

the enzyme activity will just go down

The more product that binds, the less active the enzyme activity will be

Activity of enzyme not totally shut down

reviewer 2.1 - microbial nutrition and metabolism

Documents