Bacterial Classification


Bacterial Groups



The classification of organisms based upon phylogenetic relationships

Phylogenetic relationships are evolutionary relationships


A group of interbreeding organisms


Five Kingdom System




Protoza (Protista)

Bacteria (Monera)


Three Domains (or kingdoms)

Archea (ancient bacteria; prokaryotic)

Eubacteria (true bacteria; prokaryotic)

Eukaryotes (true cells


Archeabacteria include:

Methanogens - strict anaerobes; CH4  from CO2 and H2

Extreme Halophiles - grow in high concentrations of salt

Thermoacidophiles - hot (often > 80 deg) acidic environments


Scientific Nomenclature

Binomial nomenclature

Geneus species name

Bergy’s Manual


Taxonomic Hierarchy









Major groups of bacteria

Unusual cell walls (Archea)

Thick Gram+ cell walls (Actinomycetes, Lactobacillaaceae, Micrococcaceae)

Wall-less bacteria (Mycoplasmas)

Thin, Gram- cell walls ( Psudomondaceae, Enterobacteriaceae, Spirochetes, etc.)


Methods of Classification


Differential staining

Biochemical tests


Phage typing

DNA sequence analysis


Culture Characteristics


Media Components

Carbon Source

Nitrogen Source

Minor Nutrients

Solid Support  

If not liquid media


Carbon Sources

Usually sugars

Alternatives include:

Fats or lipids

Proteins or amino acids

Fix CO2


Nitrogen Sources

Usually ammonium ion

Alternatives include:

Nitrate ion

Nitrite ion

Amino acids

Nucleic acids

Other compounds containing nitrogen


Minor Nutrients





Other metals

Some organisms very particular

Solid Support


Melts near room temperature

Digested by proteases which are produced by many bacteria

Agar derived from algal polysaccharide


Bacterial Metabolism



Energy Production

Bacterial Catabolism




Metabolism - sum of all chemical reactions in cell

Anabolism - reactions that synthesize or “build up” e.g. protein synthesis

Catabolism - reactions that digest or “break down” e.g. starch to glucose


Enzyme Introduction

Enzyme Components

Enzyme Mechanism

Factors Influencing Enzymes

Bacterial Metabolism

Enzyme Introduction

Enzymes are biological catalysts

Catalyst are agents which speed up a reaction

Enzymes are very specific

Enzymes are proteins

Catalysts work by lowering the activation energy of a reaction


Enzymes work to lower activation energy (diagram)


Enzyme Components

Cofactor - nonprotein component that is part of enzyme, e.g. Fe, NAD+, biotin

Apoenzyme - protein portion of enzyme

Holoenzyme - Cofactor plus apoenzyme


Enzyme Mechanism

Substrate binds to active site; lock & key specificity

Formation of enzyme-substrate complex

Catalytic activity; localized acid or base or induced fit


Factors Influencing Enzymes



Salt concentration


Competitive (active site)

NonCompetitive (allosteric)

Feedback Inhibition


Energy Production

Oxidation / Reduction reactions

Role of ATP






Oxidation / Reduction

Oxidation - loss of electrons

Reduction - gain of electrons

Redox reactions always coupled

Oxidations of carbon tend to be energetically favorable


Role of ATP

ATP  -->  ADP + Pi

Energy intermediate or “currency”

Hydrolysis of ATP “coupled” to energetically unfavorable reactions



Substrate - direct transfer of phosphate from an organic molecule to ADP

Oxidative - ATP generated via chemiosmosis (“proton pump”) and ATP synthase

Photo - light energy from photosynthesis, a modification of chemiosmosis


Bacterial Catabolism

Carbohydrate catabolism has two functions:

energy production and/or storage

generation of chemical intermediates

Cellular respiration and fermentation

Includes three processes:


Kreb’s or Tricarboxylic Acid (TCA) cycle

Electron transport /oxidative phosphorylation


Bacterial Catabolism - Glycolysis

splitting” of sugar

Glucose to pyruvate

Substrate phosphorylation

10 reactions / two phases


Energy Production

Evolution - probably oldest


Bacterial Metabolism - Kreb’s Cycle

Pyruvate to Acetyl-CoA & CO2 + NADH2

Acetyl-CoA & OAA to Citrate (6C)

Oxidation to 4C acid

Substrate phosphorylation

Oxidation to OAA

Production of 5 NADH2 & 1 ATP for every pyruvate


Bacterial Catabolism - Electron transport

Uses NADH2 from Kreb’s Cycle and glycolysis

Generates 3 ATP for each NADH2

Uses O2 as final electron acceptor

Generates 2 ATP for each FADH2



Glycolysis - Includes:



ATP Synthesis

NADH2 Production



splitting” of sugar

Glucose to pyruvate

Substrate phosphorylation

10 reactions / two phases


Energy Production

Evolution - probably oldest


Summary of glycolysis

1 Glucose to 2 pyruvate

2 NADH2 produced

2 ATP consumed

2 ATP for each 3C molecule produced

Net yield of 2 ATP


Anaerobic Fermentation

NADH2 must be recycled for glycolysis to continue to produce ATP

Pyruvate to lactate

Pyruvate to ethanol & CO2

Pyruvate to propionate



Bacterial Catabolism

Krebs’ Cycle - Includes:

CO2 production

Oxidation of organic acids

Subtrate ATP Synthesis

NADH2 Production

FADH2 Production

Regeneration of beginning material


Krebs’ Cycle Summary

4 NADH2 produced per pyruvate; 8 per glucose

1 FADH2 produced per pyruvate; 2 per glucose

1 GTP produced per pyruvate; 2 per glucose

3 CO2 per pyruvate; 6 per glucose



Oxidative Phosphorylation


Oxidative phosphorylation - Includes:

uses oxygen as final electron acceptor

oxidizes NADH and FADH

ATP Synthesis

Uses membrane potential


Oxidation of NADH & FADH

regenerates NAD & FAD for Kreb’s cyccle

3 ATP’s produced for each NADH

2 ATP’s produced for each FADH


10 NADH (2 from glycolysis and 8 from Kreb’s cycle) yield 30 ATP per glucose

2 FADH (from Kreb’s cycle) yields 4 ATP

2 ATP from Kreb’s cycle

2 ATP from Glycolysis

38 ATP produced per molecule of glucose oxidized