Exam 1 MCB3020

Module 1: 1-52 Module 2: 53-78

Microbiology

The branch of biology that studies microbes.

Cellular organisms

Organisms made up of cells; examples include fungi, protists, bacteria, and archaea.

Acellular organisms

Not made of cells; includes viruses, viroids, satellites, and prions.

Virus

• Composed of protein and nucleic acids

• An infectious particle that requires a host cell to replicate.

Viroid

• Composed of RNA only

• infectious RNA lacking a protein coat.

Satellite

• Composed of nucleic acids

• Require helper viruses to replicate.

Prion

• Composed of proteins

• Protein-based infectious agent lacking nucleic acids.

Prokaryote

Organism lacking a nucleus and membrane-bound organelles.

Eukaryote

Organism with a nucleus and membrane-bound organelles.

Domain Archaea

• Prokaryotic

• single-celled

• no nucleus

• extreme environments

• single circular chromosome

• identified by Carl Woese.

Domain Bacteria

• Prokaryotic

• single-celled

• no nucleus

• single circular chromosome.

Domain Eukarya

• Eukaryotic domain

• Cells with organelles

• multiple linear chromosomes

• more complex morphology.

Carl Woese

Scientist who identified the Archaea domain using ribosomal RNA sequencing.

LUCA

Last Universal Common Ancestor; common to all three domains.

3.5 billion years ago

Earliest microbial fossils date to this time.

Central dogma

DNA stores genetic information and is transcribed to RNA, then translated to proteins.

RNA world hypothesis

Early self-replicating RNA used to store genetic information and catalyze cellular processes.

Francesco Stelluti

First to observe organisms (bees and weevils) under a microscope.

Robert Hooke

First to publish drawings of microorganisms (Micrographia, 1665).

Antony van Leeuwenhoek

First person to observe microorganisms accurately.

Aristotle

Proposed the idea of spontaneous generation.

Louis Pasteur

Disproved spontaneous generation; swan-neck flask; germ theory; pasteurization.

Joseph Lister

Father of modern surgery; developed antiseptic techniques.

Robert Koch

• Work on anthrax etiology

• Koch’s postulates: a set of four criteria used to establish whether a specific microorganism is the causative agent of a disease

Spontaneous generation

Discredited theory that living organisms arise from nonliving material.

Swan-neck flask

• Used swan neck flask, which has an
  entry tube that is bent to slow down spread of microbes from outside air.

• Meat broth was placed in the flask and applied heat to sterilize it
  removing all the microbes.

• One flask was left open to outside air and was found contaminated with microbes, while the one that was closed was not contaminated

Germ Theory of Disease

Idea that diseases are caused by microorganisms.

Pasteurization

Heating foods to kill unwanted organisms.

Koch’s Postulates

Four-step criteria linking a microorganism to a disease.

1. 1) Observe an unhealthy organism containing a microorganism
   2) Isolate the microorganism and grow it in pure culture.
   3) Re-infect a healthy organism with the isolated microorganism
   4) Observe the healthy organism turn sick (or die), and then re-
   isolate the harmful microorganism from the organism’s body

Second Golden Age of Microbiology

• Period of rapid microbiology advancements suggesting a new era of discovery.

• Genomics

Smallest microorganisms

Viruses.

Largest microorganisms

Eukaryotic protists.

Light microscope

Involves passing light through lenses to magnify a sample.

Electron microscope

Uses electrons instead of light for imaging; higher resolution.

Bright-field microscope

Dark image of the specimen against a bright background.

Dark-field microscope

Bright image against a dark background.

Phase-contrast microscope

Uses differences in density and refractive index to produce detailed images.

Fluorescence microscope

Uses fluorescent dyes to visualize cells under UV light.

Transmission Electron Microscope (TEM)

TEM produces images of internal details of cells.

Scanning Electron Microscope (SEM)

Produces images of details of cell surfaces.

Stain

A solution containing a chromophore that colors the specimen.

Fixation

Preserves specimens; methods include heat fixation and chemical fixation.

Simple stain

Application of a single dye to reveal morphology, size, and arrangement.

Differential stain

Use of two or more dyes to differentiate groups (e.g., Gram staining) or structures.

Gram staining

Differential stain distinguishing Gram-positive and Gram-negative bacteria.

Steps of Gram Staining

Gram-positive

Bacteria with a thick peptidoglycan layer; appear blue/purple after stain.

Gram-negative

Bacteria with a thin peptidoglycan layer and outer membrane; appear red/pink after stain.

Acid-fast stain

Differential stain for Mycobacterium with waxy cell walls.

Structural stains

Stains that highlight cell structures such as endospores, capsules, and flagella.

Capsule

Well-organized extracellular layer of polysaccharides; can resist phagocytosis and desiccation.

1. Apply primary stain Crystal Violet – will turn all cells purple

2. Apply a mordant Iodine – Fixes stain in the cells, still purple

3. Apply decolorizer Alcohol or Acetone – removes dye from gram-
   negative cells but not the gram-positive

4. Apply counterstain Safranin – turns gram-negative cells a red/pink color
   and leaves gram-positive as is

Bacterial Shapes of Cocci, Bacilli, Vibrio, Spirilla, and Spirochete

• Cocci - Spherical

• Bacilli – Rods

• Vibrio - Comma

• Spirilla – Spiral with rigid helices

• Spirochete – Corkscrew helices

What are the three layers of the cell envelope? (internal to external)

• Cell envelope: Consists of the plasma membrane

• cell wall

• layers outside of the cell wall (Glycocalyx)

Describe the 3 layers of the cell envelope

• Plasma membrane: Selective permeable barrier that controls what substances enter and leave the cell; fluid mosaic model

• Cell Wall: Maintains cell shape, protects against osmotic stress, and
  sometimes plays a role in pathogenicity

• Glycocalyx: Additional layer outside of the cell wall that consists of
  carbohydrates, proteins, and lipids; has a capsule and slime layer.

Fluid Mosaic Model

Made up of a bilayer that consists of a sea of phospholipids with proteins floating in it.

Two Kinds of Proteins within the cell membrane

• Peripheral proteins: Loosely associated with the outside of the cell membrane; easily removed

• Integral proteins: Cross into the hydrophobic portion of the bilayer, so they are not easily removed; can be called a transmembrane protein when it crosses the entire membrane

Hopanoids

Steroid-like molecules that strengthen prokaryotic cell membranes

What compound in the cell wall is only found in bacteria?

Peptidoglycan

What are the major differences between gram+ and gram- bacteria that
causes them to stain differently?

• Gram-positive: Primarily made of a thick peptidoglycan; Some have teichoic acid – add rigidity to cell wall; Have a layer of proteins on the outer surface of peptidoglycan; periplasmic space between plasma membrane and cell wall

• Gram-negative: Thin peptidoglycan layer; Have an additional membrane called outer membrane that plays role in defense and immunity

What is the periplasmic space of bacteria?

Space between the plasma membrane and cell wall in Gram-positive bacteria

What is the S-layer?

• The extracellular portion of the cell wall commonly found in bacteria and archaea.

• Has a number of functions including protection from host defenses, adhesion to surfaces, and protection against osmotic stress, predations, and ion and pH fluctuations

Glycocalyx

• Additional extracellular polymers.

• Typically made up of polysaccharides

• Facilitate the formation of the biofilm

Two examples of glycocalyx structures and their roles

• Capsule – well-organized extracellular layer of polysaccharides that can sometimes be visible using a light microscope; Makes the cell resistant to phagocytosis, it excludes viruses and detergents, and protects against desiccation.

• Slime Layer – Similar to capsule except it is diffuse, less organized, and more easily removed; Aids in cell motility

Biofilm

Sticky substance that acts as a defensive structure for the immune system

Cytoplasm

Consists of everything inside the cell envelope, including the cytoskeleton, intracytoplasmic membranes, inclusions, ribosomes, the nucleoid, and plasmids

Three examples of bacterial cytoskeleton

1. FtsZ in cell division

2. MreB determines cell shape in rod-shape bacteria

3. CreS creates curve shape in Caulobacter crescentus bacteria

What is an inclusion

An aggregate of organic or inorganic substances stored in the cell for later use

Three types of Inclusions with definition

1. Storage Inclusion: Store carbon, glycogen, amino acids, and other nutrients.

2. Microcompartments: Serve as other functions beside storage

3. Gas Vacuoles: Regulate buoyancy in bacterial cell

Ribosome

Complexes of RNA and protein that serve as the site of protein synthesis within the cell.

Ribosome sizes for the three domains

• Bacteria and Archaeal ribosomes = 70S with a 50S large subunit and 30S small subunit

• Eukaryotic ribosomes = 80S with a 60S large subunit and 40S small subunit

Nucleoid

Where the single, circular, double-stranded chromosome and associated proteins aggregate within the cell

Plasmid

Small, double-stranded, extrachromosomal DNA molecules found in
bacteria, archaea, and some fungi

Role of R Plasmid, Conjugative Plasmid, Col Plasmids, Virulence Plasmids, and Metabolic Plasmids

a. R Plasmid – Carry antibiotic resistance genes

b. Conjugative Plasmid – Form a sex pilus and transfer DNA

c. Col Plasmids – destroy closely related species

d. Virulence Plasmids – Virulence genes

e. Metabolic Plasmids – Carry genes for enzymes involved in metabolism

Three types of External Structures

• Fimbria and Pili: Interchangeable terms; fine, thin, hair like appendages that assist in attachment to surfaces, aid in motility and electron transport.

• Flagella: thin, rigid, threadlike appendages that are involved in motility,

  swarming behavior, attachment to surfaces, and virulence.

Chemotaxis

A process in which bacteria move toward an attractant and away from a repellent

What is the most common type of cell wall in archaea?

S- layer

Name and Describe two external structures unique to archaea

• Cannulae: hollow, tubelike structures

• Hami: Look like tiny grappling hooks and may be used for adhesion