Microbio 1

study glycolsis

microorganisms

are organisms that are too small to be seen with the unaided eye



bacteria,

fungi, protozoa, microscopic algae, and viruses

microbiome

adult human: 30 trillion body cells

* 40 trillion bacterial cells

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helps maintain good health

prevebt growth of pathogenic microbes

train immune system

normal microbiota

•the **collection** of acquired **microorganisms on or in a healthy human being**

•**acquired as newborns**

•**May colonize the body indefinitely**

•May **colonize the body fleetingly** (making them transient microbiota)

•Colonization can only **occur at body sites that provide nutrients and the right environment** for the microbes to flourish

Who established scientific nomenclature

Carolus Linnaeus in 1735

* genus and specific epithet
* genus is general

scientific names

italicized or undrlined

* genus is capitalized, epithet is lowercase
* latin name
* elephant-→ Loxodonta africana

**Escherichia coli**

•Honors the discoverer, Theodor Escherich

•Describes the bacterium’s habitat-the large intestine, or colon

**Staphylococcus aureus**

•Describes the clustered (staphylo-) spherical (coccus) cells

•Describes the gold-colored (aureus) colonies

•After the first use, scientific names may be abbreviated with the first letter of the genus and the specific epithet:



•Escherichia coli and Staphylococcus aureus are found in the human body



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

Types of Microorganisms

•Bacteria

•Archaea

•Fungi

•Protozoa

•Algae

•Viruses

•Multicellular Animal Parasites

Bacteria

•Prokaryotes

•“Prenucleus”

•Single-celled

•Bacteria are enclosed in cell walls composed largely of carbohydrate and protein complex – **Peptidoglycan**

•Divide via binary fission

•Derive nutrition from organic or inorganic chemicals or photosynthesis

•May “swim” by using moving appendages called flagella

Archaea

•Are prokaryotes

•Lack peptidoglycan cell walls

•May lack cell wall entirely

•Often live in extreme environments

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Include:

•Methanogens

•Extreme halophiles

•Extreme thermophiles

•Generally, not known to cause disease in humans

Fungi

•Eukaryotes

•Distinct nucleus surrounding DNA genetic material

•Chitin cell walls

•Absorb organic chemicals for energy

•Yeasts are unicellular

•Molds and mushrooms are multicellular

•Molds consist of masses of mycelia, which are composed of filaments called hyphae

Protozoa

•Eukaryotes

•Absorb or ingest organic chemicals

•May be motile via pseudopods, cilia, or flagella

•Free-living or parasitic (derive nutrients from a living host)

•Some are photosynthetic

•Reproduce sexually or asexually

Algae

•Eukaryotes

•Cellulose cell walls

•Found in freshwater, saltwater, and soil

•Use photosynthesis for energy

•Produces oxygen and carbohydrates

Sexual and asexual reproduction possible

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

•Inert outside living hosts

Multicellular Animal Parasites

•Eukaryotes

•Multicellular animals

•Not strictly microorganisms

•Parasitic flatworms and roundworms are called helminths

•Some microscopic stages in their life cycles

Classification of Microorganisms

•Bacteria



•Archaea



•Eukarya

▪Protists

▪Fungi

▪Plant

▪Animals

Normal Microbiota

•Microbes normally present in and on the human body are called **normal microbiota**

* Normal microbiota prevent growth of pathogens



* Normal microbiota produce growth factors such as vitamins B and K



•**Resistance** is the ability of the body to ward off disease

•**Resistance factors** include **skin, stomach acid, and antimicrobial chemicals**

Emerging Infectious Diseases

•When a pathogen invades a host and overcomes the host's resistance, disease results



•**Emerging infectious diseases (EIDs):** new diseases and diseases increasing in incidence

Viral Evolution and Adaptation

•Mutation rate of RNA viruses: 1 mutation per every 104 to 105 nucleotides

•Mutation rate of DNA viruses: 1 mutation per every 108 to 1011 nucleotides

•Influenza viruses: Antigenic drift

•Recombination

•Reassortment or gene swapping or antigenic shift (influenza viruses)

First observation of microbio

* 1665
* Robert hooke said how all living things are composed of boxes or cells--→ cell theory
* first microbes observed by Aton Van leeuwenhock
* saw animalcules with lenses

Cell theory

all living things are composed of cells

Spontaneous generation

•the hypothesis that life arises from nonliving matter; a “vital force” is necessary for life

Biogenesis

the hypothesis that living cells arise only from preexisting living cellsFirs

First debate over spontaneous generation

•1668: Francesco Redi filled jars with decaying meat

* covered w net: no maggots
* open: maggots
* sealed: no maggots

demonstrated that new life does not come from spontaneous generatoin

thoery of biogensis

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

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* •Microorganisms originate in air or fluids, not mystical forces

The Golden Age of Microbiology

1857-1914

•Beginning with Pasteur's work, discoveries included the relationship between microbes and disease, immunity, and antimicrobial drugs



•Pasteur showed that microbes are responsible for fermentation



•Microbial growth is also responsible for spoilage of food and beverages

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•Bacteria that use air spoil wine by turning it to vinegar (acetic acid)

Fermentation

•microbial conversion of sugar to alcohol in the absence of air

Pasteurization

application of a high heat for a short time to kill harmful bacteria in beverages

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•Pasteur demonstrated that these spoilage bacteria could be killed by heat that was not hot enough to evaporate the alcohol in wine

The Germ Theory of Disease

•1835: Agostino Bassi showed that a silkworm disease was caused by a fungus



•1865: Pasteur showed that another silkworm disease was caused by a protozoan



•1840s: Ignaz Semmelweis advocated handwashing to prevent transmission of puerperal fever from one obstetrical patient to another

Antiseptics

•1860s: Applying Pasteur’s work showing that microbes are in the air, can spoil food, and cause animal diseases, Joseph Lister used a chemical antiseptic (phenol) to prevent surgical wound infections

Anthrax

•1876: Robert Koch discovered that a bacterium causes anthrax and provided the experimental steps, **Koch’s postulates,** to demonstrate that a specific microbe causes a specific disease



* he isolated the bacteria making the animals sick
* found that the bacteria was in the sick and not in healthy
* isolated→ cultured→ can infect other animals = is tied to the disease

Vaccination

•1796: Edward Jenner inoculated a person with cowpox virus, who was then immune to smallpox



•Vaccination is derived from the Latin word **vacca,** meaning cow



•The protection is called **immunity**

chemotherapy

•Treatment of disease with chemicals is called **chemotherapy**



•Chemotherapeutic agents used to treat infectious disease can be **synthetic drugs** or antibiotics

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•**Antibiotics** are chemicals produced by bacteria and fungi that inhibit or kill other microbes

first synthetic drugs

•Quinine from tree bark was long used to treat malaria

magic bullet

•Paul Ehrlich speculated about a “**magic bullet**” that could destroy a pathogen without harming the host



•1910: Ehrlich developed a synthetic arsenic drug, salvarsan, to treat syphilis

first antibiotic

•1928: Alexander Fleming discovered the first antibiotic (by accident)



•Fleming observed that Penicillium fungus made an antibiotic, penicillin, that killed ***S. aureus***

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* 1940 Penicillin was tested clinically and mass-produced

Problems with Antimicrobial Chemicals

•Overuse can lead to resistance



•Some drugs can be toxic to humans



•Especially antivirals

Research used to overcome these problems has ushered in a Third Golden Age of Microbiology from the late 1980s to the present

Bacteriology

study of bacteria

Mycology

study of fungi

Parasitology

study of protozoa and parasitic worms

Immunology

•study of immunity



•Vaccines and interferons are used to prevent and cure viral diseases



•A major advance in immunology occurred in 1933 when Rebecca Lancefield classified streptococci based on their cell wall components

Virology

•study of viruses



•Dmitri Iwanowski in 1892 and Wendell Stanley in 1935 discovered the cause of mosaic disease of tobacco to be a virus

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Electron microscopes have made it possible to study the structure of viruses in detai

Molecular Genetics

the study of how microbes inherit traits

Molecular biology

the study of how D N A directs protein synthesis

Genomics

study of an organism’s genes; has provided new tools for classifying microorganisms

Recombinant D N A

•**:** D N A made from two different sources



•In the 1960s, Paul Berg inserted animal D N A into bacterial D N A, and the bacteria produced an animal protein

Microbial ecology

•study of the relationship between microorganisms and their environment

Bacteria convert carbon, oxygen, nitrogen, sulfur, and phosphorus into forms used by plants and animal

Bioremediation

Using Microbes to Clean Up Pollutants

Insect Pest Control by Microorganisms

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



•Prevent insect damage to agricultural crops and disease transmission

Atoms and molecules

chemistry is the study of interactions between atoms and molecules



•The **atom** is the smallest unit of matter and cannot be subdivided into smaller substances



•Atoms interact to form **molecules**

protons and electrons

same amount in atom

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atomic number = proton number

atomic mass= protons + neutrons

chemical bonds

•Atoms form molecules by combining to fill their outermost shells



•The number of missing or extra electrons in the outermost shell is known as the **valence**



•Molecules hold together because the valence electrons of the combining atoms form attractive forces, called **chemical bonds,** between the atomic nuclei



compound is 2 or more kinds of atoms

Atomic bonds

•The number of protons and electrons are 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

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



•Covalent bonds are stronger and more common in organisms than ionic bonds

**Hydrogen bonds**

**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

organic vs inorganic

•**Organic compounds** always contain carbon and hydrogen; typically structurally complex



•**Inorganic compounds** typically lack carbon; usually small and structurally simple

carbs

energy source

sugar and starch

isomers

•Molecules with same chemical formula, but different structures

Monosaccharidesv

•are simple sugars with three to seven carbon atoms



•Glucose and deoxyribose are examples of common monosaccharides

Disaccharides

•are formed when two monosaccharides are joined in a dehydration synthesis



•can be broken down by **hydrolysis**

Lipids

Proteins

Amino Acids

•Proteins consist of subunits called **amino acids**



•Amino acids contain an alpha-carbon that has an attached:

Nucleic Acids

•Consist of **nucleotides**



•Nucleotides consist of 



•A five-carbon (pentose) sugar



•Phosphate group



•Nitrogen-containing (**purine** or **pyrimidine**) base



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**Nucleosides** consist of

•Pentose

•Nitrogen-containing base

D N A

**Deoxyribonucleic acid**



•Contains deoxyribose



•Exists as a double helix



•**Adenine** hydrogen bonds with **Thymine**



•**Cytosine** hydrogen bonds with **Guanine**



Order of the nitrogen-containing bases forms the genetic instructions of the organism

RNA

•**Ribonucleic acid**



•Contains ribose



•Is single-stranded



•**Adenine** hydrogen bonds with **Uracil**



•**Cytosine** hydrogen bonds with **Guanine**



•Several kinds of R N A play a specific role in protein synthesis

ATP

•**Adenosine triphosphate**



•Made of ribose, adenine, and three phosphate groups

List the units used to measure microorganisms.

• Microorganisms are measured in micrometers
(μm) and nanometers (nm)
• 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

•Diagram the path of light through a compound microscope.

begins with the illuminator, then passes through the condenser, the specimen, the objective lens, then then the ocular lens.

total magnification

ability of the lenses to distinguish fine detail and structure

Explain how electron microscopy differs from light microscopy.

they produce an image of a specimen by using a beam of electrons rather than a beam of light.

prokaryote

•One circular chromosome, not in a membrane



•No histones



•No organelles



•Bacteria: peptidoglycan cell walls



•Archaea: pseudomurein cell walls



•Divides by binary fission

eukaryote

Paired chromosomes, \n in nuclear membrane



Histones

* like a wardrobe



Organelles



Polysaccharide cell walls, when present



Divides by mitosis

Size, Shape, and Arrangement of Bacterial Cells

Average size is .2 to 2 pm

•Most bacteria are monomorphic (single shape)



•A few are pleomorphic (many shapes)

shapes of bacteria

insert pic from slide

•Bacillus (rod-shaped)



•Coccus (spherical-shaped)



•Spiral



•Vibrio



•Spirillum



•Spirochete



•Star-shaped



•Rectangular

Glycocalyx of prokaryote

•External to the cell wall



•Viscous and gelatinous



•Made of polysaccharide and/or polypeptide



•Two types

* **Capsule:** neatly organized and firmly attached
* **Slime layer:** unorganized and loose

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•Contribute to **virulence**



•Capsules **prevent phagocytosis**



•Extracellular polymeric substance **helps form biofilms**

Flagella in prokaryotes

•Filamentous appendages external of the cell



•**Propel bacteria**



•Made of **protein flagellin**





•Three parts:

•Filament: outermost region

•Hook: attaches to the filament

•Basal body: consists of rod and pairs of rings; anchors flagellum to the cell wall and membrane





•Flagella allow bacteria to move toward or away from stimuli (**taxis**)



•Flagella rotate to “run” or “tumble”



•Flagella proteins are H antigens and distinguish among **serovars** (e.g., **Escherichia** coli O157:H7)

Archaella

•Archaella are whip-like structures on the surface of many archaea



•They are like flagella in bacteria.



•Archaeal motility structure



•Made of glycoproteins archaellins



•Anchored to the cell



•Archaella (singular: archlaellum) rotate like flagella

Axial Filaments

Also called **endoflagella**



•Found in spirochetes



•Anchored at one end of a cell



•Rotation causes cell to move like a corkscrew

Fimbriae and Pili

**Fimbriae**

•Hairlike appendages that allow for attachment

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**Pili**

•Involved in motility (**gliding** and **twitching** motility)

•**Conjugation pili** involved in D N A transfer from one cell to another

 acquisition of new genetic information through

conjugation

cell wall

•Prevents osmotic lysis and protects the cell membrane



•Made of **peptidoglycan** (in bacteria)



•Contributes to pathogenicity

Composition and Characteristics

•Peptidoglycan



•Polymer of a repeating disaccharide in rows:



•N-acetylglucosamine(N A G)

•N-acetylmuramicacid (N A M)

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Rows are linked by polypeptides

Gram-Positive Cell Walls

•Thick peptidoglycan



•Teichoic acids

Gram-Negative Cell Walls

•Thin peptidoglycan



•Outer membrane



•Periplasmic space

Gram-positive Cell Walls

•Teichoic acids



•Lipoteichoic acid links cell wall to plasma membrane

•Wall teichoic acid links the peptidoglycan

•Carry a negative charge

•Regulate movement of cations



•Polysaccharides and teichoic acids provide antigenic specificity

Gram-Negative Cell Walls

•Periplasm between the outer membrane and the plasma membrane contains peptidoglycan



•Outer membrane made of polysaccharides, lipoproteins, and phospholipids





•Protect from phagocytes, complement, and antibiotics



•Made of **lipopolysaccharide (L P S)**



•**O polysaccharide** functions as antigen (e.g., **E.** coli O157:H7)

•**Lipid A** is an endotoxin embedded in the top layer



•**Porins** (proteins) form channels through membrane

Cell Walls and the Gram Stain Mechanism

•Crystal violet-iodine crystals form inside cell



•Gram-positive



•Alcohol dehydrates peptidoglycan



•C V - I crystals do not leave



•Gram-negative



•Alcohol dissolves outer membrane and leaves holes in peptidoglycan



•C V - I washes out; cells are colorless



•Safranin added to stain cells

Gram-Positive Cell Walls

•2 rings in basal body of flagella



•Produce exotoxins



•High susceptibility to penicillin



•Disrupted by lysozyme

Gram-Negative Cell Walls

•4 rings in basal body of flagella



•Produce endotoxins and exotoxins

Low susceptibility to penicillin

Atypical Cell Walls

•Acid-fast cell walls



•Like gram-positive cell walls



•Waxy lipid (**mycolic acid**) bound to peptidoglycan



•**Mycobacterium**



•**Nocardia**

Stain with carbolfuchsinv

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•Mycoplasmas



•Lack cell walls



•Sterols in plasma membrane



•Archaea



•Wall-less, or

Walls of pseudomurein (lack N A M and D - a mi n oacids

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•Mycoplasmas



•Lack cell walls



•Sterols in plasma membrane



•Archaea



•Wall-less, or

Walls of pseudomurein (lack N A M and D - a mi n oacids

Plasma Membrane

cytoplasmic membrane



•Phospholipid bilayer that encloses the cytoplasm



•Peripheral proteins on the membrane surface



•Integral and transmembrane proteins penetrate the membrane

Fluid mosaic model

•Membrane is as viscous as olive oil



•Proteins move freely for various functions



•Phospholipids rotate and move laterally



•Self-sealing

plasma membrane’s **selective permeability**

•allows the passage of some molecules, but not others



•Contain enzymes for A T P production



•Some membranes have photosynthetic pigments on foldings called **chromatophores**

Damage to the membrane

alcohols, quaternary ammonium (detergents), and polymyxin antibiotics break plasma membrane and causes leakage of cell contents

Passive processes vs Active

processes

•Passive processes: substances move from high concentration to low concentration; no energy expended



•Active processes: substances move from low concentration to high concentration; energy expended

Simple diffusion

passive process



•movement of a solute from an area of high concentration to an area of low concentration



•Continue until molecules reach equilibrium

Facilitated diffusion

passive process

•solute combines with a transporter protein in the membrane



•Transports ions and larger molecules across a membrane with the concentration gradient