MCB3020 (UF) Bacusmo Exam 1

Microbiology

The branch of biology that studies microbes.

How does microbiology differ from other fields of biology?

It can be distinguished from other fields based on:

1. The size of the organisms studied

2. The techniques used to study them

Cellular Organisms

made up of cells

a. include fungi, protists, bacteria, and archaea

Acellular Organisms

Not made of cells

a. Include Viruses, Viroids, Satellites, and Prions

What are the viruses composed of?

Protein and Nucleic Acids

What are the viroids composed of?

RNA only

What are the satellites composed of?

Nucleic Acids

What are the prions composed of?

Proteins

What are prokaryotes?

Prokaryotes are organisms made up of a single cell lacking membrane-bound organelles and a nucleus.

What are eukaryotes?

Eukaryotes are organisms with cells that have DNA in a membrane-bound organelle, called a nucleus, and have other true membrane-bound organelles.

Domain Eukarya

Eukaryotic; Have cells and organized structures called Organelles; have Multiple Linear chromosomes; more complex morphology

Domain Archaea

Prokaryotic; Single-celled organisms with no nucleus or organelles; Have a single and circular chromosome; Found in extreme conditions; Identified by Carl Woese

Domain Bacteria

Prokaryotic; Single-celled organisms with no nucleus or organelles; Have a single and circular chromosome

What scientist identified that the phylogenetic tree is composed of these three domains of life? How did this scientist discover this?

Carl Woese identified the domain Archaea from Bacteria by using ribosomal RNA sequencing data.

Which domain is found in extreme environments?

Archaea

What does LUCA stand for and what branch is it found on?

Last Universal Common Ancestor - common ancestor of all three domains of life. States domains Achaea and Eukarya diverged from common ancestry and Bacteria evolved independently.

How far back do the earliest fossils of microbial life date back to?

3.5 billion years ago

What is the central dogma?

States that deoxyribonucleic acid (DNA) contains genetic information that is transcribed into messenger ribonucleic acid (mRNA) then translated to make proteins.

DNA-->(Transcription)-->mRNA-->(Translation)--> Protein

What is the RNA world hypothesis?

States the earliest self-replicating entity used RNA both to store genetic information and to conduct cellular processes.

Francesco Stelluti

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

Robert Hook

First to publish drawings of microorganisms in book Micrographic in 1665

Antony van Leeuwenhoek

First person to observe microorganisms accurately

Aristotle

Proposed idea of Spontaneous generation

Louis Pasteur

Disproved Spontaneous generation with his "swan-neck flask experiment" and came up with Germ Theory of disease; also came up with idea of pasteurization

Joseph Lister

Known as "father of modern surgery" because he developed antiseptic techniques and surgery systems to prevent microorganisms from entering wounds.

Robert Koch

Known for work with etiology of anthrax and established a list of criteria called Koch's Postulates.

Spontaneous Generation

The discredited theory that living organisms arise from nonliving material

Swan-Neck flash experiment

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

Concept that human and animal diseases are caused by microorganisms

Pasteurization

a method to eliminate unwanted organisms in food products

Koch's Postulates

Set of criteria used to link a microorganism to a disease

**4 steps:

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

Rapid advancements have led some to believe we are in a "second golden age of microbiology"

What is the smallest microorganism?

Viruses

What is the largest microorganism?

Eukaryotic Protists

Light microscope

Involves passing light through one or more lenses to create a magnified view of the sample

Electron microscope

Uses electrons rather than light

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 different densities and refractive indices of cellular components to produce a detailed image

Fluorescence microscope

Uses fluorescent dyes to visualize cells under UV light.

Transmission Electron Microscopes (TEM)

Produce an image of the details of the inside of the cell

Scanning Electron Microscopes (SEM)

Produce an image of the details of the cell surface.

Why do scientist stain specimens?

Allows scientist to increase the specimen's visibility, accentuate specific morphological features, and preserve the specimen

Why do we fix specimens to the slide? What are the two ways to do this?

To ensure the specimen is in position and to preserve the specimen's internal and external structures. The two ways are: heat fixation and chemical fixation

Stain

A solution containing a solute called chromophore, which gives the solution its color

Simple Stain

involves the application of a single dye and provides information about the morphology, size, and arrangement of bacterial cells

Differential Stain

Involves the application of two or more dyes and allows scientist to divide microorganisms into groups based on their staining properties (gram-positive vs gram-negative), or to detect certain structures (endospores, capsules, and flagella).

a. Example = Gram staining

What are the steps of gram staining?

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

What are the color identifications for gram-positive bacteria?

blue/purple

What are the color identifications for gram-negative bacteria?

red/pink

Acid-fast stain

Type of differential stain that uses a harsh acid to identify members of the genus Mycobacterium, which has a thick waxy-coated cell wall.

Structural stains

Used to identify and highlight the structures of a bacterial cell.

What are the three types of structural stains?

Endospore stains, Capsule stain, and Flagellar stain.

What is the bacterial shape of cocci?

Spherical

What is the bacterial shape of bacilli?

rods

What is the bacterial shape of vibrio?

comma

What is the bacterial shape of spirilla?

spiral with rigid helices

What is the bacterial shape of spirochete?

corkscrew helices

What are the three layers of the cell envelope?

Consists of the plasma membrane, cell wall, and layers outside of the cell wall (Glycocalyx)

What is the plasma membrane role in the cell envelope?

Selective permeable barrier that controls what substances enter and leave the cell; fluid mosaic mode

What is the cell walls role in the cell envelope?

Maintains cell shape, protects against osmotic stress, and sometimes plays a role in pathogenicity

What is the Glycocalyx role in the cell envelope?

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

What are the two kinds of protein within the cell membrane?

Peripheral proteins and integral proteins

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 causes gram-positive to stain differently than gram-negative?

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

What causes gram-negative to stain differently than gram-positive?

Thin peptidoglycan layer; Have an additional membrane called outer membrane that plays role in defense and immunity; peri

1. 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 and facilitate the formation of the biofilm

What are the two examples of glycocalyx structures?

Capsule and slime layer

What is the role of capsules in Glycocalyx?

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

What is the role of the slime layer in Glycocalyx?

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

What are the three examples of bacterial cytoskeleton?

-FtsZ in cell division

-MreB determines cell shape in rod-shape bacteria

-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

Name three types of inclusions

Storage inclusions, Microcompartments, and Gas Vacuoles

Storage inclusion

Store carbon, glycogen, amino acids, and other nutrients

Microcompartments

Serve as other functions beside storage

Gas Vacuoles

Regulate buoyancy in bacterial cells

Ribosome

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

Bacteria and Archaeal ribosome sizes

70S with a 50S large subunit and 30S small subunit

Eukaryotic ribosomes

80S with a 60S large subunit and 40S small subunit

Nucleiod

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

R Plasmid role

Carry antibiotic resistance genes

Conjugative Plasmid role

Form a sex pilus and transfer DNA

Col Plasmid role

destroy closely related species

Virulence Plamid role

virulence genes

Metabolic Plasmid role

Carry genes for enzymes involved in metabolism

What are the three types of external structures?

Fimbria, Pili, and Flagella

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

What are the two external structures unique to archaea?

Cannulae and Hami