LECTURE PRESENTATIONS

For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION

Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark

ENVE 3003/ ENVE 3103

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology – Assist. Prof. Deniz AKGÜL
LAB
• Safety training and exam

• Safety rules in the lab!

• Attendance to lab: 80%

As an Environmental Engineer, in
which areas/processes do you need
Microbiology knowledge?
 Pathogens
• Disinfection
• Wastewater Treatment
– Activated sludge C removal
• Wastewater Treatment
– Biological Nutrient Removal C,N,P removal
• Sludge Digestion
• Composting
• Organic Waste and Leachate Stabilization in
Lanfills
• controlling water and waste quality
– every biological process is based on the action
of microorganisms
 LECTURE PRESENTATIONS
For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION
Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark

Chapter 1
Microorganisms and
Microbiology
© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology – Assist. Prof. Deniz AKGÜL
 I. Introduction to Microbiology
• 1.1 The Science of Microbiology
• 1.2 Microbial Cells
• 1.3 Microorganisms and Their Environments
• 1.4 Evolution and the Extent of Microbial Life
• 1.5 The Impact of Microorganisms on Humans

© 2012 Pearson Education, Inc.

1.1 The Science of Microbiology
• Microbiology revolves around two
themes:
1. Understanding basic life processes
• Microorganisms are excellent
models for understanding cellular
processes in organisms

2. Applying that knowledge to the

benefit of humans
• Microorganisms play important
roles in medicine, agriculture, and
industry

© 2012 Pearson Education, Inc.

1.1 The Science of Microbiology
• The Importance of Microorganisms
– Oldest form of life
– Largest mass of living material on Earth
– Carry out major processes for biogeochemical
cycles
– Can live in places unsuitable for other organisms
– Other life forms require microorganisms to survive

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1.2 Microbial Cells
• The Cell
– A dynamic entity that forms the fundamental
unit of life (Figure 1.2)

© 2012 Pearson Education, Inc.

 (a) (b) (c)

a) A bacterial community that developed in the depths of a lake, showing cells of various
phototrophic bacteria.

b) A bacterial community in a sewage sludge sample. The sample was stained with a
series of dyes, each of which stained a specific bacterial group.

c) A microbial community scraped from a human tongue.

Figure 1.2 Bacterial cells and some cell structures
Flagella

Nucleoid Membrane Wall

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1.2 Microbial Cells
• Characteristics of Living
Systems

– Metabolism: chemical
transformation of
nutrients

– Reproduction: generation
of two cells from one

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1.2 Microbial Cells
• Characteristics of Living
Systems (Figure 1.3)
– Differentiation: synthesis
of new substances or
structures that modify the
cell (only in some
microorganisms )
– Communication:
generation of, and
response to, chemical
signals (only in some
microorganisms)

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1.2 Microbial Cells
• Characteristics of Living
Systems (Figure 1.4)
– Movement: via self-
propulsion (only in some
microorganisms)

– Evolution: genetic changes

in cells that are transferred
to offspring

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1.2 Microbial Cells
• Functions of the cells as Catalysts and as
Coding Devices

1. Cells carry out chemical reactions

• Enzymes: protein catalysts of the cell that
accelerate chemical reactions

2. Cells store and process information that is eventually

passed on to offspring during reproduction through
DNA and evolution (Figure 1.4)
• Transcription: DNA produces RNA
• Translation: RNA makes protein
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Figure 1.4 The catalytic and genetic functions of the cell

Genetic Catalytic
functions functions

DNA Energy conservation:

ADP + Pi ATP
Replication Transcription Metabolism: generation
of precursors of macro-
molecules (sugars, amino
RNA acids, fatty acids, etc.)
Enzymes: metabolic catalysts
Translation

Proteins

Growth

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1.3 Microorganisms and Their
Environments all living organisms plus
physical and chemical
constituents of their
environment

environment in which a
microbial population lives

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1.3 Microorganisms and Their
Environments
• Diversity and abundances of
microorganisms are controlled
by resources (nutrients) and
environmental conditions (e.g.,
temp, pH, O2)

N
C P
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Figure 1.6 A summary of life on Earth through time and origin of the cellular domains

Mammals Humans
Vascular
plants
Shelly Origin of Earth
invertebrates
Present (4.6 bya)
 20% O2

1 Origin of
4
bya cellular life
bya

O2
Anoxygenic
Algal phototrophic
diversity bacteria
2 3 Anoxic
bya bya Earth

Earth
Modern is slowly
eukaryotes oxygenated Origin of
cyanobacteria

Bacteria
LUCA
© 2012 Pearson Education, Inc.
1.4 Evolution and the Extent of
Microbial Life
• The Extent of Microbial Life
– Microorganisms found in almost every
environment imaginable
– Global estimate of 5  1030 cells
• Most microbial cells are found in oceanic and
terrestrial subsurfaces
– Microbial biomass is significant and cells are key
reservoirs of essential nutrients (e.g., C, P, N)

© 2012 Pearson Education, Inc.

1.5 The Impact of Microorganisms on
Humans
• Microorganisms can be both
beneficial and harmful to humans
• harmful microorganisms =>infectious
disease agents, or pathogens

• Many more microorganisms are

beneficial than are harmful
• Ex: Nitrogen fixing bacteria => convert
atmospheric nitrogen into fixed N that the
plants use for growth

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Figure 1.8 Death rates for the leading causes of death in the United States: 1900 and today

1900 2000
Influenza and Heart disease
pneumonia
Tuberculosis Cancer
Gastroenteritis Stroke
Heart disease Pulmonary
disease
Stroke Accidents
Kidney disease Diabetes

Accidents Alzheimer’s
disease
Cancer Influenza and
pneumonia
Infant diseases Kidney disease
Diphtheria Septicemia Infectious disease
Nonmicrobial disease
Suicide

0 100 200 0 100 200

Deaths per 100,000 population Deaths per 100,000 population

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1.5 The Impact of Microorganisms on
Humans
• Microorganisms and Agriculture
– Many aspects of agriculture depend on
microbial activities (Figure 1.9)
• Positive impacts
– nitrogen-fixing bacteria
– cellulose-degrading microorganisms in the rumen
– regeneration of nutrients in soil and water
• Negative impacts
– diseases in plants and animals

© 2012 Pearson Education, Inc.

Figure 1.9 Microorganisms in modern agriculture

Nitrogen fixing bacteria

N2 + 8H 2NH3 + H2 Soybean
plant

N-cycle S-cycle

Rumen
Grass Cellulose Glucose Microbial fermentation

Fatty acids CO2 + CH4

(Nutrition for animal) (Waste products)

© 2012 Pearson Education, Inc.

1.5 The Impact of Microorganisms on
Humans
• Microorganisms and Food
– Negative impacts
• Food spoilage by microorganisms requires
specialized preservation of many foods
– Positive impacts
• Microbial transformations (typically
fermentations) yield
– dairy products (e.g., cheeses, yogurt,
buttermilk)
– other food products (e.g., sauerkraut,
pickles, leavened breads, beer)
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1.5 The Impact of Microorganisms on
Humans
• Microorganisms, Energy, and the Environment

– Microorganisms are important in biofuels production

• Ex: methane, natural gas, ethanol, hydrogen

– The role of microorganisms in cleaning up pollutants

(bioremediation)
• Ex: consume spilled oil, solvents, pesticides, and
other environmentally toxic pollutants

© 2012 Pearson Education, Inc.

1.5 The Impact of Microorganisms on
Humans
• Microorganisms and Their Genetic Resources

– Microorganisms can be used for the

production of antibiotics, enzymes, and
various chemicals

– Genetic engineering use microorganisms to

generate products of value to humans, such
as insulin (biotechnology)

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II. Pathways of Discovery in
Microbiology
• 1.6 The Historical Roots of Microbiology
• 1.7 Pasteur and the Defeat of Spontaneous
Generation
• 1.8 Koch, Infectious Disease, and Pure
Culture Microbiology
• 1.9 The Rise of Microbial Diversity
• 1.10 The Modern Era of Microbiology

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1.6 The Historical Roots of Microbiology
• Microbiology began with the microscope
(Figure 1.12a)

Figure 1.12 Early microscopy

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1.6 The Historical Roots of Microbiology
• Robert Hooke (1635–1703): the first to
describe microorganisms
– Illustrated the fruiting structures of molds
(Figure 1.12b)

Figure 1.12 Robert Hooke and early microscopy

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1.7 Pasteur and the Defeat of
Spontaneous Generation
• Louis Pasteur (1822–1895) Spontaneous generation:
– Disproved theory of hypothesis that living
spontaneous generation organisms can originate
(Figure 1.16) from nonliving matter
• Led to the development of
methods for controlling the
growth of microorganisms: Aseptic technique:
aseptic technique using practices and
procedures to prevent
– Developed vaccines for contamination from
anthrax, fowl cholera, and pathogens
rabies

Pasteur’s Experiment

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Figure 1.16a

Steam, forced
out open end

Nonsterile liquid Neck of flask Liquid sterilized

poured into flask drawn out in flame by extensive heating

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Figure 1.16b

Dust and microorganisms

trapped in bend Open end

Long time

Liquid cooled Liquid remains

slowly sterile

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1.8 Koch, Infectious Disease, and the Rise
of Pure Cultures
• Robert Koch (1843–1910)
– Demonstrated the link between microorganisms
and infectious diseases
• Identified causative agents of anthrax and
tuberculosis

– Developed techniques (solid media) for obtaining

pure cultures of microorganisms

Koch’s Postulates

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Figure 1.19
KOCH’S POSTULATES

Diseased Healthy
The Postulates: Tools: animal animal

1. The suspected pathogen Microscopy, Red

must be present in all staining blood Observe
cases of the disease cell blood/tissue Red
and absent from healthy under the blood
Suspected microscope cell
animals.
pathogen

2. The suspected pathogen Laboratory Streak agar plate

No
must be grown in pure culture with sample
from either organisms
culture. diseased or present
Colonies of healthy animal
suspected
pathogen
Inoculate healthy animal with
cells of suspected pathogen

3. Cells from a pure Experimental

culture of the suspected animals
pathogen must cause
Diseased animal
disease in a healthy
animal.
Remove blood or tissue sample
and observe by microscopy

4. The suspected pathogen Laboratory Suspected Laboratory Pure culture

pathogen culture (must be
must be reisolated and reisolation
same
shown to be the same and culture
organism
as the original. as before)

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1.10 The Modern Era of Microbiology

• In the 20th century, microbiology developed

in three distinct directions:
– Applied microbiology
– Basic microbiology
– Molecular microbiology

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1.10 The Modern Era of Microbiology
• Applied Microbiology:
– Medical microbiology and immunology

– Agricultural microbiology and industrial

microbiology

– Aquatic microbiology and marine microbiology

– Microbial ecology

© 2012 Pearson Education, Inc.

1.10 The Modern Era of Microbiology
• Basic Microbiology
– Microbial systematics
• The science of grouping and classifying
microorganisms
– Microbial physiology
• Study of the nutrients that microorganisms require
for metabolism and growth and the products that
they generate
– Cytology
• Study of cellular structure

© 2012 Pearson Education, Inc.

1.10 The Modern Era of Microbiology
• Basic Science Subdisciplines in Microbiology
– Microbial biochemistry
• Study of microbial enzymes and chemical
reactions
– Bacterial genetics
• Study of heredity and variation in bacteria
– Virology
• Study of viruses

© 2012 Pearson Education, Inc.

1.10 The Modern Era of Microbiology
• Molecular Microbiology
– Biotechnology
• Manipulation of cellular genomes
• DNA from one organism can be inserted into a
bacterium and the proteins encoded by that DNA
harvested
– Genomics: study of all of the genetic material
(DNA) in living cells
• Transcriptomics: study of RNA patterns
• Proteomics: study of all the proteins produced by
cell(s)
• Metabolomics: study of metabolic expression in cells
© 2012 Pearson Education, Inc.
 LECTURE PRESENTATIONS
For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION
Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark

Chapter 2
A Brief Journey to
the Microbial World
© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
I. Seeing the Very Small
• 2.1 Some Principles of Light Microscopy
• 2.2 Improving Contrast in Light Microscopy
• 2.3 Imaging Cells in Three Dimensions
• 2.4 Electron Microscopy

© 2012 Pearson Education, Inc.

2.1 Some Principles of Light Microscopy

• Compound light microscope uses visible light to

illuminate cells
• Many different types of light microscopy:
– Bright-field
– Phase-contrast
– Dark-field
– Fluorescence
https://images-na.ssl-images-
amazon.com/images/I/41arbIoqZlL._AC_SL230_.jpg

© 2012 Pearson Education, Inc.

2.1 Some Principles of Light Microscopy
• Bright-field scope (Figure 2.1a)
– Specimens are visualized because of differences
in contrast (density) between specimen and
surroundings (Figure 2.2)
• Two sets of lenses form the image (Figure 2.1b)
– Objective lens and ocular lens
– Total magnification = objective magnification 
ocular magnification
– Maximum magnification is ~2,000

© 2012 Pearson Education, Inc.

Figure 2.1a A light microscope

Ocular
lenses Specimen on
glass slide

Objective lens

Stage

Condenser

Focusing knobs

Light source

https://www.youtube.com/watch?v=SUo2fHZaZCU
© 2012 Pearson Education, Inc.
Figure 2.1b Path of light through a compound light microscope. Besides 10x, ocular lenses are available in
15–30x magnifications

no magnification

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.2 Bright-field photomicrographs of pigmented microorganisms

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.2 Improving Contrast in Light Microscopy
• Improving contrast results in a better final
image
• Staining improves contrast
– Dyes are organic compounds that bind to
specific cellular materials
– Examples of common stains are methylene
blue, safranin, and crystal violet

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.3 Staining cells for microscopic observation

I. Preparing a smear

Spread culture in thin Dry in air

film over slide

II. Heat fixing and staining

Pass slide through Flood slide with stain;

flame to heat fix rinse and dry

III. Microscopy

Slide Oil

Place drop of oil on slide;

examine with 100
objective lens

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.2 Improving Contrast in Light Microscopy
• Differential stains: the Gram stain
• Differential stains separate bacteria into groups
• The Gram stain is widely used in microbiology
(Figure 2.4a)
– Bacteria can be divided into two major groups:
gram-positive and gram-negative
– Gram-positive bacteria appear purple and gram-
negative bacteria appear red after staining
(Figure 2.4b)»

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Gram Staining:
• Aim is to identify the type of infecitous
bacteria to decide the treatment process or
medication.

• https://www.youtube.com/watch?v=Jvo6IGKT
vxA&t=189s
• See class notes
Figure 2.4a The Gram stain - Steps in the procedure
Step 1 Flood the heat-fixed
smear with crystal
Result: violet for 1 min
All cells purple

Step 2 Add iodine solution

for 1 min
Result:
All cells
remain purple

Step 3 Decolorize with

alcohol briefly
Result: — about 20 sec
Gram-positive
cells are purple;
gram-negative
cells are colorless

Step 4 G- Counterstain with

Result: safranin for 1–2 min
Gram-positive
(G+) cells are purple; G+
gram-negative (G-) cells
are pink to red

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.4b Microscopic observation of gram-positive (purple) and gram-negative (pink) bacteria

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.2 Improving Contrast in Light Microscopy
• Phase-Contrast Microscopy
– Improves the contrast of a sample without the
use of a stain
– Allows for the visualization of live samples
– Resulting image is dark cells on a light
background (Figure 2.5 b)

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.2 Improving Contrast in Light Microscopy
• Dark-Field Microscopy
– Image appears light on a dark background
(Figure 2.5 c)
– Excellent for observing motility

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.5 Cells visualized by different types of light microscopy. The same field of cells of the baker’s yeast
Saccharomyces cerevisiae visualized by (a) bright-field microscopy, (b) phase-contrast microscopy, and (c)
dark-field microscopy. Cells average 8–10 µm wide.

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.2 Improving Contrast in Light Microscopy
• Fluorescence Microscopy
– Used to visualize specimens that fluoresce
• Emit light of one color when illuminated
with another color of light (Figure 2.6)
– Cells either fluoresce naturally
(autofluorescence) or after they have been
stained with a fluorescent dye like DAPI
– Widely used in microbial ecology for
enumerating bacteria in natural samples

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.6 Fluorescence microscopy. Same cells are observed by bright-field microscopy in part a and by
fluorescence microscopy in part b. Cells fluoresce red because they contain chlorophyll a and other pigments.

Fluorescence photomicrograph of cells of Escherichia coli made fluorescent by staining with the
fluorescent dye DAPI.
© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.3 Imaging Cells in Three Dimensions
• Confocal Scanning Laser Microscopy (CSLM)
– Uses a computerized microscope coupled
with a laser source to generate a three-
dimensional image (Figure 2.8)

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.8 Confocal scanning laser microscopy

(a) Confocal image

of a microbial biofilm
community cultivated in the
laboratory.
The green, rod-shaped cells
are Pseudomonas aeruginosa
experimentally introduced
into the biofilm.
Other cells of different colors
are present at different
depths in the biofilm.
(b) Confocal image of a
filamentous cyanobacterium
growing in a soda lake. Cells
are about 5 µm wide.

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.4 Electron Microscopy
• Electron microscopes use electrons instead
of photons to image cells and structures
(Figure 2.9)
• Two types of electron microscopes:
– Transmission electron microscopes (TEM)
– Scanning electron microscopes (SEM)

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.9 The electron microscope

Electron
source

Evacuated
chamber
Sample
port

Viewing
screen

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2.4 Electron Microscopy
• Transmission Electron Microscopy (TEM)
– Enables visualization of structures at the
molecular level (Figure 2.10a and b)
– Specimen must be very thin (20–60 nm) and
be stained

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.10a Electron micrographs. (a) Micrograph of a thin section of a dividing bacterial cell, taken by
transmission electron microscopy (TEM). Note the DNA forming the nucleoid. The cell is about 0.8 µm wide.

Cytoplasmic DNA
Septum Cell wall (nucleoid)
membrane

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.4 Electron Microscopy
• Scanning Electron Microscopy (SEM)
– Magnification range of 15–100,000

Figure 2.10c Scanning electron micrograph of bacterial cells. A single cell is about 0.75 µm wide.

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
II. Cell Structure and Evolutionary History
• 2.5 Elements of Microbial Structure
• 2.6 Arrangement of DNA in Microbial Cells
• 2.7 The Evolutionary Tree of Life

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.5 Elements of Microbial Structure
• All cells have the following in common:
– Cytoplasmic membrane
– Cytoplasm
– Ribosomes

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2.5 Elements of Microbial Structure
• Eukaryotic vs. Prokaryotic Cells
– Eukaryotes (Figures 2.11b and 2.12c)
• DNA enclosed in a membrane-bound nucleus
• Cells are generally larger and more complex
• Contain organelles
– Prokaryotes (Figures 2.11a and 2.12a and b)
• No membrane-enclosed organelles, no nucleus
• Generally smaller than eukaryotic cells

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.11b Internal structure of eukaryotic cells

Cytoplasmic
membrane
Endoplasmic
reticulum

Ribosomes
Nucleus

Nucleolus
Nuclear
membrane
Golgi
complex
Cytoplasm
Mitochondrion
Chloroplast
Eukaryote

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.12c Electron micrograph of sectioned eukaryotic cells

Eukaryote
Cytoplasmic
membrane
Nucleus

Cell
wall

Eukarya Mitochondrion

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.11a Internal structure of prokaryotic cells

Cytoplasm Nucleoid Ribosomes

Plasmid

Cytoplasmic
Cell wall
membrane
Prokaryote

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.12a Electron micrograph of sectioned prokaryotic cells

Prokaryotes Prokaryotes

(a) Bacteria Archaea

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.5 Elements of Microbial Structure
• Viruses
– Not considered cells
– No metabolic abilities of their own
– Rely completely on biosynthetic machinery of
infected cell
– Infect all types of cells
– Smallest virus is 10 nm in diameter

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.7 The Evolutionary Tree of Life
• Evolution
– The process of change over time that results in
new varieties and species of organisms

• Phylogeny : Evolutionary relationships between

organisms
– Ribosomal RNA (rRNA) is excellent for
determining phylogeny
– Relationships visualized on a phylogenetic tree

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.17 The phylogenetic tree of life as defined by comparative rRNA gene sequencing

BACTERIA ARCHAEA EUKARYA

Animals
Slime
Entamoebae
molds
Green nonsulfur Euryarchaeota
bacteria Fungi
Methanosarcina
Mitochondrion Methano- Plants
Extreme
Gram- Crenarchaetoa bacterium halophiles
Proteobacteria positive Thermoproteus
Methano- Ciliates
bacteria
Pyrodictium coccus Thermoplasma
Chloroplast
Cyanobacteria Thermococcus
Flavobacteria Flagellates
Marine Pyrolobus
Crenarchaeota Methanopyrus
Trichomonads

Thermotoga

Microsporidia
Thermodesulfobacterium
LUCA Diplomonads
Aquifex (Giardia)
(Last universal
common ancestor)

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.7 The Evolutionary Tree of Life
• Comparative rRNA sequencing has defined three
domains:
– Bacteria (prokaryotic)
– Archaea (prokaryotic)
– Eukarya (eukaryotic)
• Archaea and Bacteria are NOT closely related
(Figure 2.17)
• Archaea are more closely related to Eukarya than
Bacteria
• Eukaryotic microorganisms were the ancestors of
multicellular organisms (Figure 2.17)

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
III. Microbial Diversity
• 2.8 Metabolic Diversity
• 2.9 Bacteria
• 2.10 Archaea
• 2.11 Phylogenetic Analyses of Natural
Microbial Communities
• 2.12 Microbial Eukarya

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
 Classifications of microorganisms based upon how
they obtain energy:
Energy Sources

Chemicals Light

Chemotrophy Phototrophy

Organic Inorganic
chemicals chemicals
(glucose, acetate, etc.) (H2, H2S, Fe2+, NH4+, etc.)

Chemoorganotrophs Chemolithotrophs Phototrophs

(glucose + O2 CO2 + H2O) (H2 + O2 H2O) (light)

Figure 2.18 Metabolic options for conserving energy

2.8 Metabolic Diversity
• Chemoorganotrophs
– Obtain their energy from the oxidation of
organic molecules (Figure 2.18)
– Aerobes use oxygen to obtain energy
– Anaerobes obtain energy in the absence of
oxygen
• Chemolithotrophs
– Obtain their energy from the oxidation of
inorganic molecules (Figure 2.18)
– Process found only in prokaryotes

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.8 Metabolic Diversity
• Phototrophs
– Contain pigments that allow them to use
light as an energy source (Figure 2.18)
– Oxygenic photosynthesis produces oxygen
– Anoxygenic photosynthesis does not produce
oxygen

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.8 Metabolic Diversity
Organisms are also classified according to their
source of cell carbon for biosynthesis:

– Autotrophs
• Use carbon dioxide as their carbon source
• Sometimes referred to as primary producers
– Heterotrophs
• Require one or more organic molecules for their
carbon source
• Feed directly on autotrophs or live off products
produced by autotrophs

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.8 Metabolic Diversity
Extremophiles: Organisms that inhabit
extreme environments
Habitats include
– Boiling hot springs
– Glaciers
– Extremely salty bodies of water
– High-pH environments

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.9 Bacteria
• The domain Bacteria contains an enormous
variety of prokaryotes (Figure 2.19)
• All known pathogenic prokaryotes are Bacteria

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 2.19 Phylogenetic tree of some representative Bacteria

Spirochetes
Green sulfur Planctomyces
Deinococcus bacteria
Green nonsulfur Chlamydia
bacteria
Cyanobacteria
Thermotoga
Gram-positive
OP2 bacteria

Aquifex

Proteobacteria

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.10 Archaea

Examples:

Methanogens: degrade organic matter

anaerobically, produce methane (natural gas)

Extreme halophiles: require high salt

concentrations for metabolism and reproduction

Thermoacidophiles: grow in moderately high

temperatures and low-pH environments
© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.12 Microbial Eukarya
Figure 2.33a Microbial Eukarya – (a) Algae (b) Fungi (c) Protozoa
Figure 2.34 Lichens. (a) An orange-pigmented lichen growing on a rock, and (b) a yellow-pigmented lichen
growing on a dead tree stump,

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
2.12 Microbial Eukarya
• Eukaryotic microorganisms include:
* fungi
* algae
* protozoa
* slime molds

- Fungi are decomposers.

- Protists include algae and protozoa:

•The algae are phototrophic (Figure 2.33a)
•Protozoa NOT phototrophic (Figure 2.33c)
- Algae and fungi have cell walls, whereas protozoa
and slime molds do not
2.12 Microbial Eukarya
• Lichens are a mutualistic relationship
between two groups of protists
– Fungi and cyanobacteria
– Fungi and algae

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
 LECTURE PRESENTATIONS
For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION
Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark

Chapter 3
Cell Structure and
Function in Bacteria
and Archaea
© 2012 Pearson Education, Inc.
 I. Cell Shape and Size
• 3.1 Cell Morphology
• 3.2 Cell Size and the Significance of
Smallness

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
3.1 Cell Morphology
• Morphology = cell shape

• Major cell morphologies (Figure 3.1)

– Coccus (pl. cocci): spherical or ovoid
– Rod: cylindrical shape
– Spirillum: spiral shape
• Cells with unusual shapes
– Spirochetes, appendaged bacteria, and filamentous
bacteria
© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 3.1 Representative cell morphologies of prokaryotes

Coccus Spirochete

Coccus cells may also exist as short chains

or grapelike clusters

Rod Budding and

appendaged bacteria

Spirillum

Filamentous bacteria

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
3.1 Cell Morphology
• Morphology typically does not predict physiology1,
ecology and phylogeny2, etc. of a prokaryotic cell
• Selective forces may be involved in setting the
morphology
– Optimization for nutrient uptake (small cells and
those with high surface-to-volume ratio)
– Swimming motility in viscous environments or
near surfaces (helical or spiral-shaped cells)
– Gliding motility (filamentous bacteria)

1
functions and activities of living organisms and their parts
2
the evolutionary history of a group of organisms
© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
3.2 Cell Size and the Significance of
Smallness
Advantages to being small (Figure 3.3)
• Small cells have more surface area relative to
cell volume than large cells (i.e., higher S/V)
– support greater nutrient exchange per unit
cell volume
– tend to grow faster than larger cells

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 3.3 Surface area and volume relationships in cells

r = 1 m

S/V = ?

r = 2 m

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 3.3 Surface area and volume relationships in cells

r = 1 m
r = 1 m Surface area (4r2) = 12.6 m2
4
Volume ( 3 r3) = 4.2 m3

Surface
=3
Volume

r = 2 m
r = 2 m
Surface area = 50.3 m2
Volume = 33.5 m3

Surface
= 1.5
Volume

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
II. The Cytoplasmic Membrane and
Transport
• 3.3 The Cytoplasmic Membrane
• 3.4 Functions of the Cytoplasmic Membrane
• 3.5 Transport and Transport Systems

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
3.3 The Cytoplasmic Membrane in
Bacteria and Archaea
• Cytoplasmic membrane:
Cytoplasmic membrane = Cell membrane= plasma membrane

– Thin structure (thickness: 6-8 nm) that surrounds the

cell
– Vital barrier that separates cytoplasm from
environment
– Highly selective permeable barrier
– Enables specific metabolites and excretion of
waste products
© 2012 Pearson Education, Inc.
3.3 The Cytoplasmic Membrane
• Composition of Membranes
– General structure is phospholipid bilayer
(Figure 3.4)
• Contain both hydrophobic and
hydrophilic components

Animation: Membrane Structure

https://www.youtube.com/watch?v=UQGQQyW7zyM

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 3.4 Phospholipid bilayer membrane
Glycerol

Fatty acids

Phosphate
Ethanolamine

Hydrophilic General architecture

region of a bilayer
Hydrophobic
membrane; the blue
Fatty acids balls depict glycerol
region
with phosphate and
Hydrophilic
region
(or) other hydrophilic
groups.
Glycerophosphates

Fatty acids
Figure 3.5 Structure of the cytoplasmic membrane

peripheral
membrane
proteins Out
Hydrophilic
Phospholipids groups

6–8 nm
Hydrophobic
groups

In

Integral
membrane Phospholipid
proteins molecule

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
3.3 The Cytoplasmic Membrane
Membrane Proteins

Integral membrane proteins Peripheral membrane proteins

Integral membrane proteins: channeling

or transporting molecules across the
membrane.

Outer surface proteins => bind

substrates or process large molecules for
transport

Inner surface proteins => involved in

energy-yielding reactions and other
important cellular functions
• Difference of Archaeal Membranes
Archaea: Ether linkages in phospholipids

Bacteria and Eukarya: ester linkages in phospholipids

Archaea: Phytanyl side

chain (instead of fatty
acid).
Can exist as lipid
monolayers, bilayers, or
mixture.
Figure 3.7d,e Membrane structure in Archaea may be bilayer or monolayer (or a mix of both)

Out

Glycerophosphates
Phytanyl

Membrane protein

In
Out

Lipid bilayer

Biphytanyl

In

Lipid monolayer

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
3.4 Functions of the Cytoplasmic
Membrane (Figure 3.8)

• Permeability Barrier
– Transport proteins accumulate solutes against
the concentration gradient
• Protein Anchor
– Holds transport proteins in place
• Energy Conservation

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 3.8 The major functions of the cytoplasmic membrane.

Permeability barrier: Protein anchor: Energy conservation:

Prevents leakage and Site of many proteins that Site of generation and use
Functions as a gateway participate in transport, of the proton motive force
for transport of bioenergetics,
nutrients into, and chemotaxis
and wastes out of,
the cell

Although structurally weak, the cytoplasmic membrane has

many important cellular functions.
3.5 Transport and Transport Systems

https://www.youtube.com/watch?v=3k7Y6NcXe6s
Figure 3.9 Transport versus diffusion.

Rate of solute entry

Transporter saturated
with substrate

Transport

Simple diffusion

External concentration of solute

III. Cell Walls of Prokaryotes

• 3.6 The Cell Wall of Bacteria: Peptidoglycan

• 3.7 The Outer Membrane
• 3.8 Cell Walls of Archaea

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
3.6 The Cell Wall of Bacteria:
Peptidoglycan
Peptidoglycan (Figure 3.16)
– Rigid layer that provides strength to cell wall
– Polysaccharide composed of
• N-acetylglucosamine and N-acetylmuramic acid
• Amino acids
• Lysine or diaminopimelic acid (DAP)
• Cross-linked differently in gram-negative
bacteria and gram-positive bacteria (Figure
3.17)

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 3.16 Cell walls of Bacteria. (a, b) Schematic diagrams of gram-positive
and gram-negative cell walls.
3.6 The Cell Wall of Bacteria:
Peptidoglycan
• Gram-Positive Cell Walls (Figure 3.18)
– Can contain up to 90%
peptidoglycan
Gram-Positive Cell Walls vs Gram-Negative Cell Walls
3.7 Gram-Negative Bacteria:
The Outer Membrane
• Total cell wall contains ~10% peptidoglycan
(Figure 3.20a)

• Most of cell wall composed of outer membrane

(lipopolysaccharide [LPS] layer)

• Structural differences between cell walls of gram-

positive and gram-negative Bacteria are
responsible for differences in the Gram stain
reaction
Gram Positive vs Gram Negative Bacteria

• https://www.youtube.com/watch?v=Jvo6I
GKTvxA
3.8 Cell Walls of Archaea

• No peptidoglycan
• Typically no outer membrane
• Some archaea have cell wall of Pseudomurein*

*Polysaccharide similar to peptidoglycan

Composed of N-acetylglucosamine and N-acetyltalosaminuronic
acid. Found in cell walls of certain methanogenic Archaea

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
IV. Other Cell Surface Structures and
Inclusions
• 3.9 Cell Surface Structures
• 3.10 Cell Inclusions
• 3.11 Gas Vesicles
• 3.12 Endospores

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
3.9 Cell Surface Structures
• Capsules and Slime Layers
– Polysaccharide layers (Figure 3.23)
• May be thick or thin, rigid or flexible
– Assist in attachment to surfaces
– Protect against phagocytosis
– Resist desiccation

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 3.23
Bacterial capsules. Capsules of Acinetobacter species
observed by phase-contrast
microscopy after negative staining of
cells with India ink. India ink does not
penetrate the capsule, so the capsule
appears as a light area surrounding
the cell, which appears black.

Transmission electron micrograph of

a thin section of cells of
Rhodobacter capsulatus with
capsules (arrows) clearly evident;
cells are about 0.9 µm wide.

Cell Capsule

Transmission electron micrograph of

Rhizobium trifolii stained with
ruthenium red to reveal the capsule.
The cell is about 0.7 µm wide.
3.9 Cell Surface Structures
• Fimbriae: Enable organisms to stick to surfaces or form
pellicles (film)

Flagella

Fimbriae
 3.9 Cell Surface Structures
• Pili
– Typically longer than fimbriae
– Assist in surface attachment
– Facilitate genetic exchange between cells
(conjugation)
– May be involved in motility

Virus-
covered
pilus

The pilus on an Escherichia coli cell that is undergoing conjugation (a form of genetic transfer).
3.10 Cell Inclusions
• Carbon storage polymers
– Glycogen: glucose polymer
– Poly--hydroxybutyrate (a lipid) and other
polyhydroxyalkanoates (Figure 3.26)

• Polyphosphates: accumulations of inorganic

phosphate
• Sulfur globules: composed of elemental sulfur
• Magnetosomes: magnetic storage inclusions

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 3.26 Poly-β-hydroxyalkanoates.

Polyhydroxyalkanoate

Electron micrograph of a thin section of cells of a bacterium containing

granules of PHA. Nile red–stained cells of a PHA-containing bacterium.
3.12 Endospores
• Endospores
– Highly differentiated cells
resistant to heat, harsh
chemicals, and radiation
(Figure 3.32)

– Only present in some gram-

positive bacteria

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
Figure 3.32 The bacterial endospore.

Terminal Subterminal Central

spores spores spores

Phase-contrast photomicrographs illustrating endospore morphologies

and intracellular locations in different species of endospore-forming
bacteria. Endospores appear bright by phase-contrast microscopy.

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
 V. Microbial Locomotion
• 3.13 Flagella and Motility
• 3.14 Gliding Motility
• 3.15 Microbial Taxes

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
3.13 Flagella and Motility

• Flagellum (pl. flagella): structure that assists

in swimming
– Helical in shape
3.14 Gliding Motility

• Gliding Motility
– Flagella-independent motility
– Slower and smoother than swimming
– Requires surface contact

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
3.15 Microbial Taxes
• Taxis: directed movement in response to chemical
or physical gradients
– Chemotaxis: response to chemicals
– Phototaxis: response to light
– Aerotaxis: response to oxygen
– Osmotaxis: response to ionic strength
– Hydrotaxis: response to water

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology
 LECTURE PRESENTATIONS
For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION
Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark

Chapter 4
Nutrition, Culture,
Lectures by
and Metabolism of
John Zamora
Middle Tennessee State University Microorganisms
© 2012 Pearson Education, Inc.
I. Nutrition, Culture, and Metabolism
of Microorganisms
• 4.1 Nutrition and Cell Chemistry
• 4.2 Culture Media

• 4.3 Laboratory Culture

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology –
4.1 Nutrition and Cell Chemistry
• Metabolism
– Metabolism is the series of biochemical reactions
by which the cell breaks down or biosynthesizes
various metabolites.
– The sum of all chemical reactions that occur in a
cell
• Catabolic reactions (catabolism)
– Energy-releasing metabolic reactions
• Anabolic reactions (anabolism)
– Energy-requiring metabolic reactions

© 2012 Pearson Education, Inc. Marmara University – Enve3003 Env. Eng. Microbiology –
4.1 Nutrition and Cell Chemistry
4.1 Nutrition and Cell Chemistry
• Nutrients
– Supply of monomers required by cells for
growth
• Macronutrients
– Nutrients required in large amounts
• Micronutrients
– Nutrients required in trace amount

© 2012 Pearson Education, Inc.

Figure 4.1 Elemental and macromolecular composition of a bacterial cell

© 2012 Pearson Education, Inc.

4.1 Nutrition and Cell Chemistry
• Carbon
– Required by all cells
– Typical bacterial cell ~50% carbon (by dry weight)
– Major element in all classes of macromolecules
– Heterotrophs use organic carbon
– Autotrophs use inorganic carbon

© 2012 Pearson Education, Inc.

4.1 Nutrition and Cell Chemistry
• Nitrogen
– Typical bacterial cell ~12% nitrogen
(by dry weight)
– Key element in proteins, nucleic acids, and
many more cell constituents

© 2012 Pearson Education, Inc.

4.1 Nutrition and Cell Chemistry
• Other Macronutrients
– Phosphorus (P)
• Synthesis of nucleic acids and phospholipids
– Sulfur (S)
• Sulfur-containing amino acids (cysteine and
methionine)
• Vitamins (e.g., thiamine, biotin, lipoic acid) and
coenzyme A
– Potassium (K)
• Required by enzymes for activity

© 2012 Pearson Education, Inc.

4.1 Nutrition and Cell Chemistry
• Other Macronutrients (cont’d)
– Magnesium (Mg)
– Calcium (Ca)
– Sodium (Na)
4.1 Nutrition and Cell Chemistry
Micronutrients: microorganisms require several
metals in very small amounts relative to
macronutrients.

•Iron: plays a major role in cellular respiration

– Under anoxic conditions, generally ferrous
(Fe2+) form; soluble
– Under oxic conditions: generally ferric (Fe3+)
form; exists as insoluble minerals

© 2012 Pearson Education, Inc.

4.1 Nutrition and Cell Chemistry
• Organic Micronutrients: Growth Factors
– Organic compounds required in small
amounts by certain organisms
• Examples: vitamins, amino acids, purines,
pyrimidines
– Vitamins
• Most commonly required growth factors
• Most function as coenyzmes (assist certain
enzymes in catalysis)

© 2012 Pearson Education, Inc.

Table 4.1 Micronutrients (trace elements) needed by microorganisms

© 2012 Pearson Education, Inc.

4.2 Culture Media
• Culture Media
– Nutrient solutions used to grow
microorganisms in the laboratory
• Two broad classes
– Defined media: precise chemical composition
is known
– Complex media: composed of digests of
chemically undefined substances (e.g., yeast
and meat extracts)

© 2012 Pearson Education, Inc.

4.2 Culture Media
• Selective Media
– Contains compounds that selectively inhibit growth
of some microorganisms but not others
• Differential Media
– Contains an indicator, usually a dye, that detects
particular chemical reactions occurring during
growth
4.2 Culture Media
• For successful cultivation of a microorganism, it
is important to know the nutritional
requirements and supply them in proper form
and proportions in a culture medium
4.3 Laboratory Culture
• Pure culture: culture containing only a single kind of
microorganism
• Contaminants: unwanted organisms in a culture
• Cells can be grown in liquid or solid culture media
– Solid media are prepared by addition of a gelling
agent (agar or gelatin)
– When grown on solid media, cells form isolated
masses (colonies)

Agar: a gelatinous substance obtained from marine algae

4.3 Laboratory Culture
• Microorganisms are everywhere
– Sterilization of media is critical
– Aseptic technique should be followed
(Figure 4.4)

Animation: Aseptic technique

https://youtu.be/bRadiLXkqoU?si=WRgYc0QSAvt-6yfi

© 2012 Pearson Education, Inc.

Figure 4.4 Aseptic transfer

Loop is heated until Tube is uncapped. Tip of tube is run

red hot and cooled in through the flame.
air briefly.

Sample is removed on The tube is reflamed The tube is recapped.

sterile loop for transfer Loop is reheated
to a sterile medium. before being taken out
© 2012 Pearson Education, Inc. of service.
4.3 Laboratory Culture
• Pure culture technique
– Streak plate (Figure 4.5)
– Pour plate
– Spread plate

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Figure 4.5 Making a streak plate to obtain pure cultures

Isolated colonies Confluent growth at

at end of streak beginning of streak

Loop is sterilized
and a loopful of
inoculum is
removed from
tube.

Streak is made and spread out on Appearance of a well-streaked plate after

a sterile agar plate. Following the incubation, showing colonies of the bacterium
initial streak, subsequent streaks Micrococcus luteus on a blood agar plate. It is
are made at angles to it, the loop from such well-isolated colonies that pure
being resterilized between streaks. cultures can usually be obtained.

https://youtu.be/0heifCiMbfY?si=OI29yL3pzSp0VRlJ
© 2012 Pearson Education, Inc.
II. Energetics, Enzymes and Redox
Catalysis and Enzymes
• Activation energy: energy required to bring all
molecules in a chemical reaction into the reactive
state (Figure 4.6)
– A catalyst is usually required to breach
activation energy barrier
4.5 Catalysis and Enzymes
• Catalyst: substance that
– Lowers the activation energy of a reaction
– Increases reaction rate
– Does not affect energetics or equilibrium
of a reaction

© 2012 Pearson Education, Inc.

4.5 Catalysis and Enzymes
• Enzymes
– Biological catalysts
– Typically proteins (some RNAs)
– Highly specific
– Generally larger than substrate
– Typically rely on weak bonds
• Examples: hydrogen bonds, van der Waals
forces, hydrophobic interactions
– Active site: region of enzyme that binds substrate
Oxidation–Reduction and Energy-
Rich Compounds
• 4.6 Electron Donors and Electron Acceptors
• 4.7 Energy-Rich Compounds and Energy
Storage

© 2012 Pearson Education, Inc.

4.6 Electron Donors and Electron
Acceptors
• Energy from oxidation–reduction (redox) reactions
is used in synthesis of energy-rich compounds (e.g.,
ATP)
• Redox reactions occur in pairs (two half reactions;
Figure 4.8)
Electron donor: the substance oxidized in a
redox reaction
Electron acceptor: the substance reduced in a
redox reaction
© 2012 Pearson Education, Inc.
Figure 4.8 Example of an oxidation–
reduction reaction
4.6 Electron Donors and Electron
Acceptors
• Substances can be either electron donors or
acceptors under different circumstances (redox
couple)

© 2012 Pearson Education, Inc.

Example: Oxidation of Glucose

➢ The electron donor (Carbon in glucose) is oxidized to

CO2.
➢ Oxygen is the electron acceptor, it is reduced to water.
4.7 Energy-Rich Compounds and
Energy Storage

• Chemical energy released in redox reactions

is primarily stored in certain phosphorylated
compounds
– ATP; the prime energy currency
– Others (phosphoenolpyruvate, glucose 6-
phosphate)
• Chemical energy also stored in coenzyme A

© 2012 Pearson Education, Inc.

4.7 Energy-Rich Compounds and
Energy Storage
• Long-term energy storage involves insoluble
polymers that can be oxidized to generate ATP
– Examples in prokaryotes
• Glycogen
• Poly--hydroxybutyrate and other
polyhydroxyalkanoates
• Elemental sulfur
– Examples in eukaryotes
• Starch
• Lipids (simple fats)
© 2012 Pearson Education, Inc.
Catabolic Diversity
• Microorganisms demonstrate a wide range of
catabolic mechanisms:
Catabolic Diversity

• Phototrophy: uses light as energy source

– Photophosphorylation: light-mediated ATP synthesis

➢ Photoautotrophs: use ATP for assimilation of CO2 for

biosynthesis

➢ Photoheterotrophs: use ATP for assimilation of

organic carbon for biosynthesis

* Most phototrophs are autotrophs, also known as

photoautotrophs.
Catabolic Diversity
• Chemolithotrophy
– Uses inorganic chemicals as electron donors
• Examples include hydrogen sulfide (H2S),
hydrogen gas (H2), ferrous iron (Fe2+),
ammonia (NH3)

– Typically aerobic

– Most chemolithotrophs are autotrophs

(chemolithoautotrophs): uses CO2 as carbon
source

© 2012 Pearson Education, Inc.

Catabolic Diversity
• Chemoorganotrophy
– Uses organic chemicals as electron donors
• Examples include proteins, polysaccharides,
and lipids
– Chemoorganotrophs are heterotrophs, using
organics as carbon sources. (By contrast, most
chemolithotrophs and phototrophs are
autotrophs.)

– Can be aerobic or anaerobic

© 2012 Pearson Education, Inc.

Glycolysis
• A series of reactions in which glucose is oxidized to
pyruvate.

• Glycolysis is a nearly universal pathway for the

catabolism of glucose. It is the preceding step for
different processes:
➢ fermentation
➢ aerobic cellular respiration
➢ anaerobic cellular respiration

• In most organisms, it occurs in the cytosol (liquid part

of cell). Glycolysis doesn't require oxygen.
Glycolysis

• Is the first step in the breakdown of glucose to

extract energy.

• In glycolysis;
–Glucose consumed
–2 ATPs produced

© 2012 Pearson Education, Inc.

• Aerobic Respiration

- A series of reactions that converts glucose to

CO2 and allows the cell to recover significant
amounts of energy

- Higher ATP yield than anaerobic respiration

- Characteristic of many bacteria, fungi,

protozoa, animal cells

cytosol
mitochondria
• Aerobic Respiration
- Oxidation using O2 as the terminal electron
acceptor

- The steps include:

➢ Glycolysis
➢ Citric acid cycle (Krebs cycle)
➢ Electron transport chain

cytosol
mitochondria
• Aerobic Respiration steps

cytosol mitochondrion
The Electron Transport Chain
Electron transport carriers and enzymes are embedded in
➢ the cell membrane in prokaryotes
➢ on the inner mitochondrial membrane in eukaryotes
• Energized electrons are carried by electron carriers to the top
of the chain. The electrons are passed from protein to protein
within the membrane, slowly releasing their energy in steps.

• Some of that energy is used directly to form ATP.

• The final electron acceptor at the bottom of the chain is

oxygen, which reacts with four hydrogen ions (4H+) and four
electrons to form two molecules of H2O.

• Overall, the electron transport chain add 32 ATP molecules.

Aerobic process of ATP is very effective.
The Proton Motive Force

• Electron transport system oriented in cytoplasmic

membrane so that electrons are separated from protons
• During electron transfer, several protons are released on
outside of the membrane
• Results in generation of pH gradient and an
electrochemical potential across the membrane: the
proton motive force
– The inside becomes electrically negative and alkaline
– The outside becomes electrically positive and acidic

https://youtu.be/3y1dO4nNaKY?si=si-T4VlmoOb7Or8j
• Anaerobic Respiration
– The use of electron acceptors other than
oxygen
• Examples include nitrate (NO3−), ferric
iron (Fe3+), sulfate (SO42−), carbonate
(CO32−), certain organic compounds

– Less energy released compared to aerobic

respiration

– Involves glycolysis, the Krebs cycle, and the

electron transport chain
• Fermentation

- Incomplete oxidation of glucose

- Oxygen is not required

- Organic compounds are final electron

acceptors

Examples of
fermentation
products:
Figure 4.22 Catabolic diversity

© 2012 Pearson Education, Inc.