Bacterial Classification
Phylogeny
Bacterial
Groups
Taxonomy
The
classification of organisms based upon phylogenetic
relationships
Phylogenetic
relationships are evolutionary relationships
Species
A
group of interbreeding organisms
Five
Kingdom System
Animals
Plants
Fungi
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
Kingdom
Division
Class
Order
Family
Genus
Species
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
Morphology
Differential
staining
Biochemical
tests
Serology
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
Sulfur
Phosphate
Iron
Magnesium
Other
metals
Some
organisms very particular
Solid
Support
Gelatin
Melts
near room temperature
Digested
by proteases which are produced by many bacteria
Agar
derived from algal polysaccharide
Bacterial Metabolism
Introduction
Enzymes
Energy
Production
Bacterial
Catabolism
Introduction
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
Temperature
pH
Salt
concentration
Inhibitors
Competitive
(active site)
NonCompetitive (allosteric)
Feedback
Inhibition
Energy
Production
Oxidation
/ Reduction reactions
Role
of ATP
Phosphorylation
Substrate
Oxidative
Photo-
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
Phosphorylation
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:
Glycolysis
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
Activation
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:
Activation
Oxidation
ATP
Synthesis
NADH2
Production
Glycolysis
“splitting” of sugar
Glucose
to pyruvate
Substrate
phosphorylation
10
reactions / two phases
Activation
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