Microbiology

What does the science of microbiology study?

Life forms too small to see with the unaided eye.

Antoni van Leeuwenhoek, 1673

• made first observations of bacteria and protozoa on microscopes, termed them “animalcules”

Nomenclature

• naming of organisms

• latin

• started with Carlos Linnaeus

• Genus species

  • G. species

• EX: Escherichia coli or E.coli

  • if handwriting, underline not italicized

Types of microorganisms:

• Bacteria

• Archaea

• Fungi

• Protozoa

• Algae

• Viruses (NOT living)

• other multicellular animal parasites

Bacteria

• prokaryote

• unicellular

• cell wall is peptidoglycan

• asexual reproduction

• obtains nutrition through organic molecules, photosynthesis, and inorganic substances

Archaea

• prokaryote

• unicellular

• Yes/No cell wall (no peptidoglycan)

• asexual reproduction

• extreme halophiles, thermophiles, and methanogens

Fungi

• eukaryotes

• uni/multicellular

• cell wall is chitin

• sexual and asexual reproduction

• obtain nutrition through absorption of organic compounds

Protozoa

• eukaryote

• unicellular

• yes/no cell wall (varies)

• sexual and asexual reproduction

• absorbs or ingests organic compounds from environment, some are parasites and some are photosynthetic

Algae

• eukaryote

• uni/multicellular

• cell wall is made of cellulose

• sexual and asexual reproduction

• nutrition through photosynthesis

Helminths

• eukaryotes

• multicellular

• n/a cell wall

• sexual reproduction

• obtain nutrition through absorption, ingestion, and phagocytosis

viruses

• n/a prokaryote or eukaryote

• acellular

• n/a cell wall

• n/a nutrition

• reproduction happens within the host

Robert Hooke, 1665

• coined the term “cells”

  • smallest living structural units

Cell Theory

1. All living things are composed of cells

2. All living things can arise only from preexisting living cells

Louis Pasteur, 1861

• S-shape flask experiment

• aseptic technique

• People believed in spontaneous generation, but Pasteur believed spoilage or mold must have come from something

• debunked spontaneous generation

• showed the difference between fermentation, souring, and spoiling

• contributed to Germ Theory of Disease

aseptic technique

prevent contamination by unwanted organisms

fermentation

process by which yeasts convert sugars into alcohol in the absence of air

souring and spoiling

process by which bacteria convert alcohol into acetic acid (vinegar) in the presence of air

pasteurization

process that utilizes just enough heat to kill most of the bacteria that cause spoilage (not sterile)

Joesph Lister

• applied germ theory to medical procedures by disinfecting surgical wounds with phenol (carbonic acid)

Robert Koch

• discovered cause of anthrax in cattle and sheep

• he identified rod shaped bacteria, cultured in media, injected into healthy animals, which then got sick from same bacteria.

• he took a blood sample from those then sick animals to re-isolate the bacteria and double check work

• Koch’s postulates

Edward Jenner

• inoculated a healthy volunteer with cowpox

• volunteer then became immune to smallpox

• similar to vaccinating

vaccine

cultures of avirulent microorganisms used for preventative inoculation

chemotherapy

• treatment of a disease using chemical substances

  • antibiotics: chemicals produced naturally by bacteria and fungi to act against other microbes

  • synthetic drugs: chemotherapeutic agents prepared from chemicals in the lab

Alexandar Flemming

• Penicillium mold contaminated plates inhibited bacterial growth

• fungus produced a chemical - penicillin

resistance

genetic changes in microbes that enables them to tolerate a certain amount of an antibiotic that would normally inhibit them

What role do microorganisms play in the environment?

• bioremediation and recycling

Which has a nucleus? - prokaryotes or eukaryotes

eukaryotes

Prokaryotes

• lack nucleus

• no histones

• organelles: not membrane-enclosed

• cell walls: peptidoglycan

• cell division: binary fission

• can read DNA and make protein

• bacteria and archaea

Eukaryotes

• have nucleus

• DNA: nuclear membrane, multiple chromosomes

• histones

• organelles: membrane-enclosed

• The cell wall won’t be peptidoglycan- if have one

• cell division: mitosis

What are external structures of bacterial cells?

• glycocalyx

• flagella

• axial filaments

• fimbriae

• pili

Glycocalyx

• “sugar coat”

• viscous, gelatinous polymer surrounding cell wall

• would be termed a “capsule” or “slime layer”

  • Capsule: organized and firmly attached to cell, virulence factor that resists phagocytosis

  • Slime layer: unorganized and loosely attached, biofilm formation

• source of energy and dehydration process

Flagella

• Arrangements:

  • atrichous

  • peritrichous

  • polar:

    • monotrichous

    • lophotrichous

    • amphitrichous

• Basic parts:

  • filament

  • hook

  • basal body

Flagella- movement

• Motility: ability of an organism to move by itself

  • runs and tumbles

  • swarming

• Taxis: ability to move toward or away from a stimulus

  • chemotaxis

  • phototaxis

• H antigen: flagellar protein useful for serotyping

  • ex: E. coli O157:H7

Axial filament

• utilized by spirochetes for movement

• bundles of fibrils at the ends of the cell beneath an outer sheath

• Not all spiral-shaped bacteria are spirochetes, but all spirochetes are spiral-shaped bacteria

Fimbriae

• short, straight, thin projections

• used for attachment

• very numerous

Pili

• longer than fimbriae

• used for DNA transfer

• 1-2 per cell

Shapes and Size of Bacteria:

Size: from .2-2.0 um diameter x 2-8 um length

Shape:

• coccus/cocci

• bacillus/bacilli

• spiral

  • Vibrio: curved rods

  • Spirilla: helical shape, rigid body

  • Spirochetes: helical shape, flexible

• monomorphic: maintain shape

• pleomorphic: environmental conditions or genetics can alter shape

Bacterial Arrangement:

Arrangement:

• Singles

• Diplococci or Diplobacilli

• Streptococci or Streptobacilli

• Tetrads

• Sarcinae

• Staphylococci (clusters)

• Coccobacilli

Cell wall

• peptidoglycan: repeating disaccharide attached with polypeptides

• made of sugars and proteins (NAM+NAG mono’s)

Gram Positive Cell Wall

• thick, multilayers of peptidoglycan

• teichoic acids

  • linkers

  • bind/regulate cationic movement across cell

Gram Negative Cell Wall

• thin, single layer of peptidoglycan

• outer membrane:

  • lipopolysaccharides, lipoproteins, phospholipids

    • Lipid A portion of LPS can cause fever, vasodilation, inflammation, shock, and blood clotting

  • may impede treatment of disease

Bacteria w/o cell walls

• often mistaken for viruses due to small size and lack cell wall (Mycoplasma)

• have other features of prokaryotic cells such as ribosomes

Atypical Cell Walls

• Mycobacterium: Acid-fast cell wall, Mycolic acid

  • Mycolic Acid: hydrophobic waxy lipid, prevents uptake of dyes (gram stain), slow transmission of nutrients/wastes across cell, meaning they grow slowly

• Archaea: Prokaryotes that are NOT bacteria, either lack cell walls or have cell walls w/o peptidoglycan

Structures Internal to the Cell Wall:

• plasma membrane

• cytoplasm

• nucleoid

• ribosomes

• inclusions

• endospores

Plasma Membrane

• phospholipid bilayer

  • composed of lipids and associated proteins (integral and peripheral proteins)

  • Fluid Mosaic Model: dynamic arrangement of phospholipids and proteins

  • Functions:

    • energy storage

    • selectively permeable

    • passive and active process

Cytoplasm

• cytosol

  • liquid portion of cytoplasm

  • mostly water

  • contains cell’s DNA in region called nucleoid

Nucleoid

• region of cell containing chromosome

• chromosome: long, circular, double-stranded DNA containing genetic info

• Plasmid:

  • small circular, dsDNA

  • extrachromosomal genetic elements

    • may be gained/lost w/o harm to cell

    • replicated independently of chromosome

Inclusions

• Act as storage centers

• reserve deposits

  • metachromatic granules

  • polysaccharide granules

  • lipid inclusions

  • etc

• EXTRA stuff in a cell

Endospores

• resting state that forms when nutrients are depleted

• durable, dehydrated, thick wall

• can survive extreme conditions (heat, radiation, chemicals)

• sporulation and germination

• terminally, subterminally, or centrally located

Ribosomes

• sites of protein synthesis

• composed of polypeptides and ribosomal RNA

• small 30S subunit and Large 50S subunit = 70S

Cytoskeleton

• composed of three or four types of protein fibers

• functions:

  • cell division

  • cell shape

  • segregate DNA molecules

  • move through environment

Archaea vs Bacteria

Bacteria vs Archaea vs Eukaryotes

In ___ reactions, the energy released in downhill reactions drives energy-dependent uphill reactions

Coupled

Bacteria live the lives of scavengers, fluctuating between periods of nutrients readily available and meager periods when they are scarce. Which structure minimizes the negative effects of the periods of starvation?

Inclusions

What is the name of the process used by cells to make protein from mRNA template?

Translation

What allows for the passage of polar molecules and ions across the plasma membrane?

Integral proteins

Which phase is the rate of cell death equivalent to the rate of the new cell formation?

• Exponential phase

• Lag phase

• Stationary phase

Stationary phase

What structure contributes to the spread of antibiotic resistance through the transfer of genetic information from one bacterial cell to another?

Conjugation pili

What is the role of pyruvate in fermentation?

It removes electrons directly from NADH to regenerate NAD+

Which molecules possesses the energy liberated after completion of glycolysis and Krebs cycle?

NADH, FADH2, and ATP

What is the benefit of using an mRNA intermediate in the flow of genetic info in a eukaryotic cell?

Connection of distant compartments, amplification of info, and genome protection

Which molecule contribute most to the selectivity of the cell membrane?

Phospholipids

What is the function of oxygen in oxidative phosphorylation?

It acts as the final electron acceptor in the ETC

Which molecules are considered part of the cells savings account, because of their role in storing energy for the cell?

Lipids and carbohydrates

A cell that contains a nucleus us called _____ cell.

Eukaryotic

A microorganism has the following characteristics: its cells have a nucleus and cell walls, it is multicellular, and it grows in long filaments. What is its general classification?

• parasitic worm

• bacterium

• fungus

• protozoan

fungus

Which of the following individuals pioneered the use of chemicals to reduce the incidence of infections during surgery?

Lister

What is the correct order for the application of Koch’s postulates?

1. Inoculated suspect agent into test subject and observe that subject develops disease of interest.

2. Isolate and culture suspect agent in the lab.

3. Find suspect agent is every case of disease of interest but not in healthy host.

4. Recover and isolate suspect agent from test subject.

3, 2, 1, 4

How are the bacteria and archaea different from all the other cellular microbes?

they have no nucleus

Antoni van Leeuwenhoek was the first person in history to ___

view microorganisms and record these observations

Work by ___ laid the foundations of immunology with the development of vaccines

Jenner and Pasteur

Louis Pasteur demonstrated that fermentation of sugar to produce alcohol is caused by

facultative anaerobes

Microbiologists study parasitic worms because

they cause diseases that are diagnosed by finding microscopic eggs in clinical specimens

The term for the use of microorganisms to restore damaged environments is

bioremediation

Which of the following are paired incorrectly?

• Gram : cholera

• Jenner: smallpox

• Enrlich: syphilis

• Koch: anthrax

Gram: cholera

Which of the following is NOT a characteristic of viruses?

• they are visible with a light microscope

• they are composed of genetic material and protein

• they are obligatory parasites

• they are acellular

• they are typically smaller than prokaryotic cells

they are visible with a light microscope

which of the following techniques could be used to produce yeast capable of making viral proteins?

• genome sequencing

• bioremediation

• gene therapy

• recombinant DNA technology

recombinant DNA technology

Which of the following is an incorrect pairing?

• algae: aquatic and marine habitats

• viruses: acellular parasites

• protozoa: multicellular

• prokaryotes: no nuclei

• fungi: cell walls

Protozoa: multicellular

Which of the following is not a characteristic of protozoa?

• most exhibit asexual reproduction

• they are eukaryotic organisms

• they are all photosynthetic

• they frequently posses cilia or flagella

• they are single celled organisms

they are all photosynthetic

Bacterial protein synthesis can begin before the reading of the gene is complete.

T/F

T

Which of the following bacterial cell structures plays an important role in the creation of biofilms?

• glycocalyces

• flagella

• pili

• fimbriae

• fimbriae and glycocalyces

• fimbriae and glycocalyces

Which of the following are FALSE about pili?

• not all bacteria have pili

• pili are longer than fimbriae and flagella

• pili are a special type of fimbriae

• pili facilitate the transfer of DNA among bacterial cells

• pili are longer than fimbriae and flagella

which of the following chemical substances contributes to the unique characteristics of acid-fast bacteria?

• mycolic acid

• lipoteichoic acid

• endtoxin

• peptidoglycan

mycolic acid

Peptidoglycans are composed of sugars and ____

amino acids

One chain of alternating NAGs and NAMs is connected to another via____

tetrapeptides

Within the peptidoglycan layer, the cross bridges that connect the chains of alternating sugar molecules extend between ____

two N-acetylmuramic acid molecules

What role do the teichoic acids play within the cell wall of Gram-positive bacteria?

they serve to stabilize the cell wall and hold it in place

bacterial ___ are sites of metabolic storage

inclusions

a bacterial cell stains with the acid fast stain, which of the following is FALSE?

• it may be a member of the genus Mycobacterium

• it has a cell wall that contains waxy lipids

• it will be difficult to stain this cell with the Gram stain

• it has a cell wall that contains endotoxins

it has a cell wall that contains endotoxins

which of the following would NOT be found in the cytoplasm of the bacterial cell?

• ribosomes

• nucleoid

• endospores

• porins

porins

Metric system of measurement- micro

Examples:

2.3 m = 2300000 um

6.4 um = 0.0064 mm

Ocular lens

remagnifies the image formed by the objective lens

Body

transmits the image from the objective lens to the ocular lens using prisms

Objective lenses

primary lenses that magnify the specimens

Stage

holds the microscope slide in position

condenser

focuses light through specimens

illuminator

light source

coarse focusing knob

moves the stage up and down to focus the image

fine focusing knob

slightly moves the stage up and down for focusing

total magnification

objective lens x ocular lens

EX: 40x x 10 = 400x