Microbiology Lecture Notes: The Microbial World and You, Study notes of Microbiology

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Microbiology Lecture Notes

Module 1

Chapter 1: The Microbial World and You

Microbes in Our Lives

• Microorganisms are organisms that are too small to be seen with the unaided

eye

• Germ refers to a rapidly growing cell
• A fer are pathogenic (disease-causing)
• Decompose organic waste
• Are producers in the ecosystem by photosynthesis
• Product industrial chemicals such as ethanol and acetone
• Produce fermented foods such as vinegar, cheese and bread
• Product products used in manufacturing (cellulase) and disease treatment

(insulin)

Designer Jeans: Made by Microbes

• Stone washing: Trichoderma
• Cotton: Gluconacetobacter
• Debleaching: mushroom peroxidase
• Indigo: E. Coli
• Plastic: bacterial polyhydroxyalkanoate

Microbes in Our Lives

• Knowledge of microorganisms
• Allows humans to

o Prevent food spoilage

o Prevent disease occurrence

• Led to aseptic techniques to prevent contamination in medicine and in

microbiology laboratories

Naming and Classifying Microorganisms

• Linnaeus established the system of scientific nomenclature
• Each organism has two names: the genus and specific epithet

Scientific Names

• Are italicized or underlined

o The genus is capitalized; the specific epithet is lowercase

• Are “latinized” and used worldwide
• May be descriptive or honor a scientist
• After the first use, scientific names may be abbreviated with the first letter of the

genus and the specific epithet

- EXAMPLE:

o Escherichia Coli and Staphylococcus aureus are found in the human body

o E. coli is found in the large intestine , and S. aureus is on the skin

What is a correct scientific name?

a. Baker’s yeast

b. Saccharomyces cerevisiae

• Include:

o Methanogens

o Extreme halophiles

o Extreme thermophiles

Fungi

• Eukaryotes
• Chitin cell walls
• Use organic chemicals for energy
• Molds and mushrooms are multicellular,

consisting of masses of mycelia, which are composed of filaments called hyphae

• Yeasts are unicellular

Protozoa

• Eukaryotes
• Absorb or ingest organic chemicals
• May be motile via pseudopods, cilia, or flagella

Algae

• Eukaryotes
• Cellulose cell walls
• Use photosynthesis for energy
• Produce molecular oxygen and organic compounds

Viruses

• Acellular
• Consist of DNA or RNA core
• Core is surrounded by a protein coat
• Coat may be enclosed in a lipid envelope
• Are replicated only when they are in a living host cell

Multicellular Animal Parasites

• Eukaryotes
• Multicellular animals
• Parasitic flatworms and roundworms are called helminths
• Microscopic stages in life cycles

Classification of Microorganisms

Three domains

• Bacteria
• Archaea
• Eukarya

o Protists

o Fungi

o Plants

o Animals

A Brief History of Microbiology

• Ancestors of bacteria were the first life on Earth
• The first microbes were observed in 1673

The First Observations

• 1665: Robert Hooke reported that living things are composed of little boxes, or

cells

• 1858: Rudolf Virchow said cells arise from preexisting cells
• Cell theory : All living things are composed of cells and come from preexisting

cells

• 1673 – 1723: Anton van Leeuwenhoek described live microorganisms

The Debate over Spontaneous Generation

• Spontaneous generation : the hypothesis that living organisms arise from

nonliving matter; a “vital force” forms life

• Biogenesis : the hypothesis that living organisms arise from preexisting life

Evidence Pro and Con

1668: Francesco Redi filled 6 jars with decaying meat

Conditions:

Three jars covered with fine net

Results:

No maggots

Conditions:

Three open jars

Results:

Maggots appeared

Evidence Pro and Con

1745: John Needham put boiled nutrient broth into covered flasks

Conditions:

Nutrient broth heated, then placed in sealed flask

Results:

Microbial growth

Evidence Pro and Con

1765: Lazzaro Spallanzani boiled nutrient solutions in flasks

Conditions:

Nutrient broth placed in flask, heated, then sealed

Results:

No microbial growth

Evidence Pro and Con

1861: Louis Pasteur demonstrated that microorganisms are present in the air

Conditions:

Nutrient broth placed in flask, heated, NOT sealed

Results:

Microbial growth

Conditions:

Nutrient broth placed in flask, heated, then sealed

Results:

No microbial growth

The Theory of Biogenesis

• Pasteur’s S-shaped flask kept microbes out but let air in

The Golden Age of Microbiology

• Beginning with Pasteur’s work, discoveries included the relationship between

microbes and disease, immunity, and antimicrobial drugs

Fermentation and Pasteurization

• Pasteur showed that microbes are responsible for fermentation
• Fermentation is the conversion of sugar to alcohol to make beer and wine
• Microbial growth is also responsible for spoilage of food

Recombinant DNA Technology

• Microbial genetics : the study of how microbes inherit traits
• Molecular biology : the study of how DNA directs protein synthesis
• Genomics : the study of an organism’s genes; has provided new tools for

classifying microorganisms

• Recombinant DNA : DNA made from two different sources

o In the 1960s, Paul Berg inserted animal DNA into bacterial DNA, and the

bacteria produced an animal protein

• 1941: George Beadle and Edward Tatum showed that genes encode a cell’s

enzymes

• 1944: Oswald Avery, Colin MacLeod, and Maclyn McCarty showed that DNA is the

hereditary material

• 1961: François Jacob and Jacques Monod discovered the role of mRNA in protein

synthesis

Nobel Prizes for Microbiology Research

▪ * The first Nobel Prize in Physiology or Medicine

1901* von Bering Diphtheria antitoxin

1902 Ross Malaria transmission

1905 Koch TB bacterium

1908 Metchnikoff Phagocytes

1945 Fleming, Chain, Florey Penicillin

1952 Waksman Streptomycin

1969 Delbrück, Hershey, Luria Viral replication

1997 Prusiner Prions

2005 Marshall & Warren H. pylori & ulcers

2008 zur Hausen HPV & cancer

2008 Barré-Sinoussi & Montagnier HIV

Microbial Ecology

• Bacteria recycle carbon, nutrients, sulfur, and phosphorus that can be used by

plants and animals

Bioremediation

• Bacteria degrade organic matter in sewage
• Bacteria degrade or detoxify pollutants such as oil and mercury

Biological Insecticides

• Microbes that are pathogenic to insects are alternatives to chemical pesticides in

preventing insect damage to agricultural crops and disease transmission

• Bacillus thuringiensis infections are fatal in many insects but harmless to other

animals, including humans, and to plants

Biotechnology

• Biotechnology , the use of microbes to produce foods and chemicals, is

centuries old

• Recombinant DNA technology , a new technique for biotechnology, enables

bacteria and fungi to produce a variety of proteins, including vaccines and

enzymes

▪ Missing or defective genes in human cells can be replaced in gene

therapy

▪ Genetically modified bacteria are used to protect crops from insects and

from freezing

Normal Microbiota

• Bacteria were once classified as plants, giving rise to use of the term flora for

microbes

• This term has been replaced by microbiota
• Microbes normally present in and on the human body are called normal

microbiota

• Normal microbiotas prevent growth of pathogens
• Normal microbiotas produce growth factors, such as folic acid and vitamin K
• Resistance is the ability of the body to ward off disease
• Resistance factors include skin, stomach acid, and antimicrobial chemicals

Biofilms

• Microbes attach to solid surfaces and grow into masses
• They will grow on rocks, pipes, teeth, and medical implants

Infectious Diseases

• When a pathogen overcomes the host’s resistance, disease results
• Emerging infectious diseases (EIDs) : new diseases and diseases increasing

in incidence

Avian Influenza A

• Influenza A virus
• Primarily in waterfowl and poultry
• Sustained human-to-human transmission has not occurred yet

MRSA

• Methicillin-resistant Staphylococcus aureus
• 1950s: Penicillin resistance developed
• 1980s: Methicillin resistance
• 1990s: MRSA resistance to vancomycin reported

o VISA: vancomycin-intermediate-resistant S. aureus

o VRSA: vancomycin-resistant S. aureus

West Nile Encephalitis

• Caused by West Nile virus
• First diagnosed in the West Nile region of Uganda

in 1937

• Appeared in New York City in 1999
• In nonmigratory birds in 47 states

Bovine Spongiform Encephalopathy

• Caused by a prion

o Also causes Creutzfeldt-Jakob disease (CJD)

• New variant CJD in humans is related to cattle that have been fed sheep offal for

protein

Escherichia coli O157:H

• Toxin-producing strain of E. coli
• First seen in 1982
• Leading cause of diarrhea worldwide

m, ion,oAr tmomol,eicounle,oAr molecule B

O

H

2H = 2 × 1 = 2

O = 16

MW = 18

1 mole weighs 18 g

B

Ionic Bonds

• The number of protons and electrons is equal in

an atom

• Ions are charged atoms that have gained or lost electrons
• Ionic bonds are attractions between ions of opposite charge

▪ One atom loses electrons, and other gains electrons

Covalent Bonds

• Covalent bonds form when two atoms share one or more pairs of electrons

Hydrogen Bonds

• Hydrogen bonds form when a hydrogen atom that is covalently bonded to an O

or N atom is attracted to another N or O atom in another molecule

Molecular Weight and Moles

• The sum of the atomic weights in a molecule is the molecular weight
• One mole of a substance is its molecular weight in grams

Chemical Reactions

• Chemical reactions involve the making or breaking of bonds between atoms
• A change in chemical energy occurs during a chemical reaction
• Endergonic reactions absorb energy
• Exergonic reactions release energy

Synthesis Reactions

• Occur when atoms, ions, or molecules combine to form new, larger molecules
• Anabolism is the synthesis of molecules in a cell

Combinesto form

A (^) + B AB

Atom, ion,oAr tmomol,eicounl,eoAr molecNuelewBmoleculeAB

Decomposition Reactions

• Occur when a molecule is split into smaller molecules, ions, or atoms
• Catabolism is the decomposition reactions in a cell

Breaksdown into

A

A + B

New moleculeAABto

Exchange Reactions

• Are part synthesis and part decomposition

NaOH + HCl NaCl + H2O

Reversible Reactions

• Can readily go in either direction
• Each direction may need special conditions

A +

B

Heat

AB

Water

Important Biological Molecules

• Organic compounds always contain carbon and hydrogen
• Inorganic compounds typically lack carbon

Water

• Inorganic
• Polar molecule
• Solvent

▪ Polar substances dissociate, forming solutes

- H

and OH

− participate in chemical reactions

R—R + H O ⟶ R—OH + H—R

Maltose + H O ⟶ Glucose + Glucose

• H b on

d s absorb heat

▪ Makes water a temperature buffer

Acids

• Substances that dissociate into one or more H

▪ HCl ⟶ H

**+

• Cl**

−

Bases

• Substances that dissociate into one or more OH

−

▪ NaOH ⟶ Na

**+

• OH**

−

• Part of membranes

Proteins

• Are essential in cell structure and function
• Enzymes are proteins that speed chemical reactions
• Transporter proteins move chemicals across membranes
• Flagella are made of proteins
• Some bacterial toxins are proteins

Amino Acids

• Proteins consist of subunits called amino acids
• Exist in either of two stereoisomers : D or L
• L-forms are most often found in nature

Peptide Bonds

• Peptide bonds between amino acids are formed by dehydration synthesis

Levels of Protein Structure

• The primary structure is a polypeptide chain
• The secondary structure occurs when the amino acid chain folds and coils in a

regular helix or pleats

• The tertiary structure occurs when the helix

folds irregularly, forming disulfide bridges, hydrogen bonds, and ionic bonds

between amino acids in the chain

• The quaternary structure consists of two or more polypeptides
• Conjugated proteins consist of amino acids and other organic molecules

▪ Glycoproteins

▪ Nucleoproteins

▪ Lipoproteins

Nucleic Acids

• Consist of nucleotides
• Nucleotides consist of

▪ Pentose

▪ Phosphate group

▪ Nitrogen-containing ( purine or pyrimidine ) base

• Nucleosides consist of

▪ Pentose

▪ Nitrogen-containing base

DNA

• Deoxyribonucleic acid
• Has deoxyribose
• Exists as a double helix
• A hydrogen bonds with T
• C hydrogen bonds with G

RNA

• Ribonucleic acid
• Has ribose
• Is single-stranded
• A hydrogen bonds with U
• C hydrogen bonds with G

ATP

• Adenosine triphosphate
• Has ribose, adenine, and three phosphate groups

• Is made by dehydration synthesis
• Is broken by hydrolysis to liberate useful energy

for the cell

Chapter 3: Observing Microorganisms Through a Microscopes

Units of Measurement

• 1 μm = 10
  • 6 m = 10 - 3 mm
• 1 nm = 10
  • 9 m = 10 - 6 mm
• 1000 nm = 1 μm
• 0.001 μm = 1 nm

Microscopy: The Instruments

• A simple microscope has only one lens

Light Microscopy

• The use of any kind of microscope that uses visible light to observe specimens
• Types of light microscopy

▪ Compound light microscopy

▪ Darkfield microscopy

▪ Phase-contrast microscopy

▪ Differential interference contrast microscopy

▪ Fluorescence microscopy

▪ Confocal microscopy

Compound Light Microscopy

• In a compound microscope , the image from the objective lens is magnified

again by the ocular lens

• Total magnification = objective lens × ocular lens
• Resolution is the ability of the lenses to distinguish two points
• A microscope with a resolving power of 0.4 nm

can distinguish between two points ≥ 0.4 nm

• Shorter wavelengths of light provide greater resolution
• The refractive index is a measure of the

light-bending ability of a medium

• The light may bend in air so much that it misses

the small high-magnification lens

• Immersion oil is used to keep light from bending

Brightfield Illumination

• Dark objects are visible against a bright background
• Light reflected off the specimen does not enter the objective lens

Darkfield Illumination

• Light objects are visible against a dark background
• Light reflected off the specimen enters the objective lens

Phase-Contrast Microscopy

• Accentuates diffraction of the light that passes through a specimen

Differential Interference Contrast Microscopy

• Accentuates diffraction of the light that passes through a specimen; uses two

beams of light

Fluorescence Microscopy

• Uses UV light
• Fluorescent substances absorb UV light and emit visible light
• Cells may be stained with fluorescent dyes (fluorochromes)

Confocal Microscopy

• Used to distinguish between bacteria

▪ Gram stain

▪ Acid-fast stain

Gram Stain

• Classifies bacteria into gram-positive

or gram-negative

▪ Gram-positive bacteria tend to be killed by penicillin and detergents

▪ Gram-negative bacteria are more resistant to antibiotics

Color of

Gram-

Positive Cells

Color of

Gram-

Negative

Cells

Primary

Stain:

Crystal

Violet

Purple Purple

Mordant:

Iodine

Purple Purple

Decolorizin

g Agent:

Alcohol-

Acetone

Purple Colorless

Countersta

in:

Safranin

Purple Red

Acid-Fast Stain

• Stained waxy cell wall is not decolorized by

acid-alcohol

• Mycobacterium
• Nocardia

cells

▪ Capsule stain

▪ Endospore stain

▪ Flagella stain

Negative Staining for Capsules

• Cells stained
• Negative stain

Endospore Staining

Special Stains

• Used to distinguish parts of
• Primary stain: malachite green, usually with heat
• Decolorize cells: water
• Counterstain: safranin

Flagella Staining

• Mordant on flagella
• Carbolfuchsin simple stain

Color of

Acid-Fast

Color of

Non–Acid-

Fast

Primary

Stain:

Carbolfuchs

in

Red Red

Decolorizin

g Agent:

Acid-

alcohol

Red Colorless

Counterstai

n:

Methylene

Blue

Red Blue

Motile Cells

• Rotate flagella to run or tumble
• Move toward or away from stimuli ( taxis )
• Flagella proteins are H antigens

( E. coli O157:H7)

Axial Filaments

• Also called endoflagella
• In spirochetes
• Anchored at one end of a cell
• Rotation causes cell to move

Fimbriae and Pili

• Pili

▪ Facilitate transfer of DNA from one cell to another

▪ Gliding motility

▪ Twitching motility

The Cell Wall

• Prevents osmotic lysis
• Made of peptidoglycan (in bacteria)

Peptidoglycan

• Polymer of disaccharide:

▪ N-acetylglucosamine (NAG)

▪ N-acetylmuramic acid (NAM)

Peptidoglycan in Gram-Positive Bacteria

• Linked by polypeptides

Gram-Positive Cell Wall

• Thick peptidoglycan
• Teichoic acids

▪ Lipoteichoic acid links to plasma membrane

▪ Wall teichoic acid links to peptidoglycan

• May regulate movement of cations
• Polysaccharides provide antigenic variation
• 2-ring basal body
• Disrupted by lysozyme
• Penicillin sensitive

Gram-Negative Cell Wall

• Thin peptidoglycan
• Outer membrane
• Periplasmic space
• 4-ring basal body
• Endotoxin
• Tetracycline sensitive

Gram-Negative Outer Membrane

• Lipopolysaccharides, lipoproteins, phospholipids
• Forms the periplasm between the outer membrane and the plasma membrane
• Protection from phagocytes, complement, and antibiotics
• O polysaccharide antigen, e.g., E. coli O157:H
• Lipid A is an endotoxin
• Porins (proteins) form channels through membrane

The Gram Stain Mechanism

• Crystal violet-iodine crystals form in cell

• Gram-positive

▪ Alcohol dehydrates peptidoglycan

▪ CV-I crystals do not leave

• Gram-negative

▪ Alcohol dissolves outer membrane and leaves holes in peptidoglycan

▪ CV-I washes out

Atypical Cell Walls

• Acid-fast cell walls

▪ Like gram-positive cell walls

▪ Waxy lipid ( mycolic acid ) bound to peptidoglycan

▪ Mycobacterium

▪ Nocardia

• Mycoplasmas

▪ Lack cell walls

▪ Sterols in plasma membrane

• Archaea

▪ Wall-less, or

▪ Walls of pseudomurein (lack NAM and D-amino acids)

Damage to the Cell Wall

• Lysozyme digests disaccharide in peptidoglycan
• Penicillin inhibits peptide bridges in peptidoglycan
• Protoplast is a wall-less cell
• Spheroplast is a wall-less gram-positive cell

▪ Protoplasts and spheroplasts are susceptible to osmotic lysis

• L forms are wall-less cells that swell into irregular shapes

The Plasma Membrane

• Selective permeability allows passage of some molecules
• Enzymes for ATP production
• Photosynthetic pigments on folding’s called chromatophores or thylakoids
• Damage to the membrane by alcohols, quaternary ammonium (detergents),

and polymyxin antibiotics causes leakage of cell contents

▪ Phospholipid bilayer

▪ Peripheral proteins

▪ Integral proteins

▪ Transmembrane Proteins

▪ Sterols

▪ Glycocalyx carbohydrates

• Endocytosis

▪ Phagocytosis: pseudopods extend and engulf particles

▪ Pinocytosis: membrane folds inward, bringing in fluid and dissolved

substances

Fluid Mosaic Model

• Membrane is as viscous as olive oil
• Proteins move to function
• Phospholipids rotate and move laterally

Movement of Materials across Membranes

• Simple diffusion : movement of a solute from an area of high concentration to

an area of low concentration

• Facilitated diffusion : solute combines with a transporter protein in the

membrane