Microbio Exam 1

Genome

comprises the total genetic information of an organism

Metagenome

collections of sequences from diverse populations of microbes taken directly from the environment.

Spontaneous Generation

A theory suggesting that living creatures could arise without parents

Pure Culture

lab growth of microorganisms that contains only a single species or strain

Agar

Gelling agent used to solidify a liquid culture medium. First used by Angelina and Walther Hesse.

Petri Dish

Developed by Julius Petri to culture bacteria

Edward Jenner

Deliberately infected patients with material he collected from cowpox. The basis for vaccination.

Alexander Fleming

Discovered that Penicillium mold could generate a substance to kill bacteria. Howard Florey and Ernst Chain used this information to create Penicillin, the first commercial version of this.

Antiseptic

an antimicrobial substance applied to living tissue, such as the skin. Ignaz Semmelweis ordered doctors to use these.

Aseptic

Completely free of microbes

Germ Theory of Disease

suggests that many diseases are caused by microbes

Florence Nightingale

Recognized the significance of disease in warfare and founded the science of medical statistics. Devised the polar area chart to display the deaths of soldiers and the causes.

Louis Pasteur

Produced data to refute the spontaneous generation theory using the swan-neck flask experiment. Also developed the first vaccines based on weakened strains of microbes. Discovered fermentation as well.

Swan Neck Flask Experiment

1. A broth was boiled to kill all microbes in a flask, while air could enter from the neck of the flask

2. After a year, there was no microbe growth at the based of the flask, only the neck.

3. The flask was tipped to allow the microbes to reach the base, allowing for microbe growth once again.

Koch’s Postulates

1. Suspected microbe is only present in all diseased hosts

2. Suspected microbe is grown in a pure culture outside the host.

3. The cultured microbe is introduced to healthy host, who become sick with the same disease as the original hosts.

4. The same suspected microbe can be isolated from the sick.

Bacilli

Rod Shaped Bacteria

Cocci

Sphere shaped Bacteria

Absorption

the photon’s energy is acquired by the absorbing object

Reflection

the wavefront bounced off the surface of an object

Refraction

the bending of light as it enters a substance that slows its speed

Scattering

the wavefront interacts with an object smaller than the wavelength of light

Wet Mount Preparation

observing microbes by placing them in a drop of water on a slide with a coverslip. This allows for the observation of cells in their natural state, but provides little contrast between the cell and the background. The sample may also dry out quickly

Flow Cell

Used to avoid overheating, fresh medium passes through the specimen allowing for observation of live microbes

Fixation

Where cells are made to adhere to a slide in a fixed position

Staining

Cells are given a distinct color. These have conjugated double bonds/aromatic rings, and one or more positive charges

Simple Stain

adds dark color to cells, but not the external medium or surrounding tissue (Methylene blue is commonly used)

Differential Stain

stains one kind of cell but not another. Gram stain is most famous but others include acid-fast, spore, and negative.

Fluorophore

a fluorescent chemical compound

Compound Microscopy

Uses a system of multiple lenses designed to compensate for aberration (flaws in the lens). Uses an ocular lens (the part you look through) and an objective lens (gathers light and focuses it into an image). The microscope must be parfocal (stay sharp when focal length or magnification is changed).

Electron Microscopy

The most important tool for observing the shapes of macromolecular structures. Allows electrons to behave like light waves and be absorbed by the sample (coated in heavy metal) for great resolution. During this process, the electron beam and sample are in a vacuum. In these microscopes, the lens are magnetic fields.

Transmission Electron Microscopy (TEM)

Electrons pass through the specimen, revealing internal structures. Specimen must be sliced.

Scanning Electron Microscopy (SEM)

Electrons scan the specimen’s surface, revealing external features in 3D.

Atomic Force Microscopy

An example of scanning probe microscopy, measures the van der Waals forces between electron shells of the adjacent atoms of the cell’s surface and the sharp tip of the probe (can be used to observe live bacteria

X-ray Crystallography

For samples that can be crystallized, X-ray diffraction makes it possible to fix the position of individual atoms in a molecule. In the process, a beam of X-rays is shot at a crystallized sample

Gram Stain

A type of differential stain, Gram-positive bacteria retain the crystal violet stain because of their

thicker cell wall. Gram-negative bacteria do not.

Fluorescence Microscopy

the specimen absorbs light of one wavelength (excitation) and then emits light of a lower energy (emission), creating a longer wavelength (used to view live marine bacteria/gut bacteria). The process requires a high-intensity light source.

Dark-field Microscopy

enable microbes to be visualized as halos of bright light against darkness (allows detection of objects unresolved by bright-field microscopy). Light shines at an angle where only light scattered by the sample reaches the objective.

Confocal Microscopy

An advanced form of fluorescence microscopy, where a microscopic laser light source scans across the specimen

Phase Contrast Microscopy

Exploits differences in refractive index between the cytoplasm and the surrounding medium or between different organelles (can be used to view live cells and cellular organelles)

Passive Diffusion

movement of molecules from an area of high concentration to low without using energy

Osmosis

Passive diffusion of water

Active Transport

movement of molecules from an area of low concentration to high, requires energy

Gram Positive vs Gram Negative

Gram Positive bacteria contain a thick peptidoglycan layer. Gram negative bacteria lack this, but have a outer membrane

Capsule

Outermost layer of bacteria made of polysaccharide and glycoprotein, protects cells from phagocytosis

S-layer

An additional protective layer found in Gram positive and negative bacteria, a crystalline layer of thick subunits of protein or glycoprotein. Protects cell from osmotic stress

LPS (Lipopolysaccharide)

A large molecule containing lipid and carbohydrate components found in the outer membrane of gram negative bacteria. Contributes to structural integrity

Endotoxin

The toxic component of LPS, released when the bacterial cell dies and lyses, triggering an immune response in humans and animals

Periplasm

A gel-like matrix between the inner membrane and outer membrane of gram negative bacteria, crucial for binding, transport, and cell wall synthesis.

Replisome

Protein complex where DNA is synthesized by DNA polymerase, with help from accessory proteins

Polysome

a cluster of multiple ribosomes bound to a single messenger RNA (mRNA) molecule, working together to translate genetic instructions into proteins simultaneously

Nucleiod

non-membrane-bound area of the cytoplasm that contains the chromosome in the form of looped coils

Flagella

external filament whose rotary motor propels the cell

Stalk

membrane-embedded extensions of the cytoplasm

Pili

straight filaments of pilin protein used in attachment. sex pili is for conjugation

Chemotaxis

the movement of a bacterium in response to chemical gradients. Attractants cause Counterclockwise rotation, bundling of the flagella, and propulsion of the cell. Also called “Run.” Repellents (or absence of attractants) cause Clockwise rotation, loosening of the flagella bundle, end of motion and change of direction. Also called “Tumble.”

Phototrophs

obtain energy from chemical reactions triggered by light

Chemotrophs

obtain energy from oxidation-reduction reactions

Lithotrophs

use inorganic molecules as a source of electrons

Organotrophs

use organic molecules

Autotrophs

fix CO2 and assemble into organic molecules (mainly sugars)

Heterotrophs

use preformed organic molecules

Proton Motive Force

The electrochemical potential caused by the H+ gradient plus the charge difference

Nitrogen Fixation

The process of converting unreactive nitrogen gasses into usable chemical processes.

1. Nitrogenase fixes atmospheric N₂ into ammonia

2. Nitrifiers oxidize NH₄⁺ to create energy

3. Denitrifiers use oxidized forms as electron acceptors

Facilitated Diffusion

helps solutes move across a membrane from a region of high concentration to one of lower concentration. Does not use energy

ABC Transporters

Also known as the ATP-Binding cassette superfamily. They are powered by ATP and transport nutrients across the cell membrane.

Group Translocation

A process that uses energy to chemically alter the substrate during transport. An example is the phosphotransferase system (PTS) in bacteria, which use energy from phosphoenolpyruvate (PEP) to attach a phosphate to specific sugars.

Siderophores

Specialized molecules secreted to bind ion and transport it in the cell. This iron is released into the cytoplasm and reduced to a more useful form.

Symport

A coupled transport system where two molecules travel in the same direction

Antiport

A coupled transport system where the actively transported molecule moves int he direction opposite of the driving ion.

Phases of Bacterial Growth

1. Bacteria prepare their cell machinery for growth

2. Growth happens exponentially

3. Cells stop growing and shut down growth machinery while turning on stress responses to stay viable

4. Cells die as a negative exponential curve

Biofilms

Specialized, surface-attached communities that bacteria form when nutrients are plentiful. Can be constructed by one or multiple species and can form on a range of organic or inorganic structures.

Virion

The virus particle consisting of a viral genome

Virome

The sum of viral population sin an ecosystem

Capsid

The protein “shell” that the virion resides in

Prophage

A bacteriophage that integrates its genome into its bacterial host’s genome

Provirus

an integrated viral genome within a human cell

Viral Shunt

A process in which viruses infect marine microorganisms and causes them to burst, recycling their cellular material back into the ocean

Prions

Infections proteins with an abnormal structure that alters the conformation of other normal proteins