microbiology test 1

Why do we care about microbes?

We care about microbes because of disease. Microbes are everywhere, but not all microbes are bad. Some microbes are the base of food chains, important for nutrient cycling, global photosynthesis, and agriculture. The are more microbial cells than human cells in the body.

commensals or mutualists

microbes that discourage pathogens and contribute to health

extremophiles

microbes that live in extreme environments

microbiology

the study of microscopic organisms (includes bacteria, viruses, archaea, fungi, and parasites)

Robert Hooke

made the first microscopic observations of molds and fungi in 1655

Antoni van Leeuwenhoek

discovered bacteria and protozoa and is credited as the developer of microbiology

spontaneous generation

the belief that the decay of organic matter generates microbes (this is an old theory)

abiogenesis

the belief that life can originate from non-living material

biogenesis

the belief that life can only arise from living things

Louis Pasteur

Disproved the idea of spontaneous generation and developed vaccines (TB, cholera, anthrax, and rabies). He disproved spontaneous generation by studying how beverages spoil which resulted in pasteurization.

inductive reasoning

make observations and develop an explanation or hypothesis

deductive reasoning

take an explanation for a phenomenon (hypothesis) and make observations to determine whether that explanation is supported

smallpox

extreme symptoms (fever, rash, shock) caused by a virus

Edward Jenner

Invented the smallpox vaccine. He noticed dairymaids got cowpox (mild symptoms) and then were immune to smallpox. He generated a hypothesis, ran an experiment, and developed the vaccine.

germ theory

microorganisms are the causative agent of diseases

Robert Koch and his postulates

Koch’s postulates are used to determine if a microbe causes disease.

1) suspected pathogen must be present in all diseased animals and absent from healthy animals

2) suspected pathogen must be isolated in a pure culture

3) the pure culture should be able to be used to infect and cause disease in a healthy host

4) the suspected pathogen must be re-isolated from the new host

refraction

The bending/changing of the angle of light passing through a lens. Occurs as light passes through the convex surface of a glass lens.

compound microscope

A microscope with two lenses. It has a light to illuminate the sample and a condenser to focus the light.

resolving power

the ability to distinguish two points from each other

numerical aperture

mathematical constant that is defined by the physical properties of the lens (higher NA=higher RP)

What is the visible light spectrum?

400 nm - 750 nm

bright field microscope

most common, image forms when light is transmitted through a specimen, generally requires a form of contrast (like a stain)

dark field microscope

Adapted from bright field by adding a stop which only allows peripheral light through. The light reflects off the sides of a specimen, the field is dark, and it is generally used when samples are sensitive to heat or drying.

phase contrast and interference microscope

Used to produce images with high levels of contrast. This is useful for observing internal structures and small differences in light waves passing through different parts of a specimen will be observed as different light intensities.

differential interference contrast microscope

adds more detail to image, including 3D

fluorescent microscopy

uses UV light, samples must be stained with dyes that fluoresce under UV and produce visible light

confocal microscopy

constructs a 3D image from multiple 2D scans of a specimen with a laser (also uses fluorescent stains)

scanning electron microscopy

Allows us to see very small specimens in detail. Can magnify a sample up to 5 million x

transmission electron microscopy

electrons are transmitted through the specimen so samples must be very thin (used to look at viruses and cell structure)

chromophore

what causes a stain’s color

auxochrome

what causes a stain’s charge

basic stains

positively charged, attracted to the cell components, stains the cell

negative stains

negatively charged, repelled by the cells, stains the background, used when cells are too sensitive to be heat fixed

differential stains

two different colored dyes are used to distinguish between cell types (ex: gram stain)

structural stains

stains with special properties are used to observe a specific cell

prokaryotes

single celled (can be arranged as chains or clusters), no true organelles, usually (not always) smaller

ex: bacteria and archaea

eukaryotes

single celled or multicellular, compartmentalized into special organelles, macro or microscopic

Hadean era

about 4-4.6 bya, this is when the earth formed and the first cells appeared

What are the requirements for life?

heredity, reproduction, growth, development, metabolism, responsiveness, and transport

Archaean era

2\.5-4 bya, bacteria and archaea diverge, origin of photosynthesis, era ends with the great oxygenation event (cyanobacteria in oceans started producing oxygen through photosynthesis)

Proterozoic era

.54-2.5 bya, great oxygenation event, eukaryotes emerge, cambrian explosion (a wide variety of animals burst into the evolution scene)

What are the four main macromolecules?

carbohydrates, lipids, proteins, and nucleic acids

carbohydrates

contain carbon, hydrogen, and oxygen (CH2O)n

saccharide

simple carbohydrates (monosaccharide, disaccharide, and polysaccharide)

What’s the role of carbohydrates in the cell?

to provide structural support (cellulose and peptidoglycan), nutrient and energy storage (starch for plants, glycogen or animals), and adhesion

hydrolysis

digestion of carbohydrate polymers

lipids

a group of substances made of long hydrocarbon chains that are hydrophobic that are not soluble in polar solvents like water (ex: triglycerides, phospholipids, steroids)

What is the function of lipids in the cell?

storage (triglycerides) and structure (phospholipids)

proteins

made of amino acids

peptide

short amino acid chain

polypeptide

amino acid chain of 20+ amino acids

primary protein structure

amino acid sequence

secondary protein structure

more complex structure of amino acids, hydrogen bonds form between amino acids located near each other, alpha helix or beta sheets are formed

tertiary protein structure

complex 3D structure of a protein (fully functional)

quaternary protein structure

two or more polypeptides interact to form a protein complex

What is the nucleic acid structure?

nitrogenous base, pentose sugar, and phosphate

purines

adenine and guanine (two ring structure)

pyrimidine

thymine and cytosine (single ring structure)

phylogeny

the evolutionary history and relationships between organisms

What are the three domains of life and how do we know this?

bacteria, eukarya, and archaea, and we know this due to DNA sequencing

taxonomy

the classification and organization of organisms (arranged into these hierarchical groups: kingdom, phylum, class, order, family, genus, and species)

bacteria

Considered the least complex of all living things on earth but they are the most diverse. Only 1% of those organisms can be cultured, the rest we know through DNA sequencing.

bacteria flagella

allow cells to move in aqueous environments using propeller like motions

phototaxis

movement in response to a light signal

magnetotaxis

movement in response to a magnetic field

chemotaxis

movement in response to a chemical signal

run movement

bacteria flagella move counterclockwise (straight projection)

tumble movement

bacteria flagella move clockwise (random reorientation)

fimbriae

short, bristle-like attachment appendages on bacteria cells that are numbers on cell surface and allows attachment to surfaces and/or cell hosts

pilli

Longer attachment appendages on bacteria that allow attachment to surfaces and/or other cells. They can also have specialized functions like transfer of DNA between cells.

bacterial glycocalyx

coating of macromolecules that protects the cell

bacteria slime layer

loose shield that protects from dehydration and serves as a way for cells to adhere to surfaces

bacteria capsule

tightly bound layer that has a sticky consistency and protects bacteria from immune cells because the capsule prevents phagocytosis

What is the bacterial cell wall made of?

peptidoglycan

peptidoglycan

Make up the bacterial cell wall, comprised of glycan chains cross-linked by peptide fragments. Different bacteria have different amounts of peptidoglycan in their cell walls to prevent lysis (when cell membrane is destroyed in order to release intracellular materials)

lysozyme

an enzyme that can break the bonds in glycan chains and cause bacterial cell walls to break down (found in tears, salival, nasal and sinus fluids)

gram + cell wall

thick layer of peptidoglycan, teichoic acids embedded in peptidoglycan, loosely bound to the cell membrane, periplasmic space

gram - cell wall

comprised of a thinner layer of peptidoglycan and an outer membrane, lipopolysaccharides are imbedded in the peptidoglycan, contains outer membrane proteins (porins and structural proteins), more flexible due to thin layer of peptidoglycan, bigger periplasmic space

non-specific porins

allows small, hydrophilic molecules to pass through

specific porins

allows large, hydrophobic molecules (vitamins) to pass through

What are the key terms and characteristics of the cell membrane?

phospholipid bilayer, selective permeability, and fluid mosaic model

simple diffusion

going down a concentration gradient

facilitated diffusion

going down a concentration gradient through a membrane protein

active transport

going against a concentration gradient via membrane pump that requires energy

In prokaryotes, the chromosome is ___ and there is ___.

circular, one

plasmids

Small, extrachromosomal circular pieces of DNA found in prokaryotes. Not all cells of a species will have them and they contains genes that are not necessary for cellular function.

prokaryotic ribosomes

primary function is protein synthesis, made up of individual subunits (proteins and rRNA), smaller than eukaryotic ribosomes

halophile

extremophiles that like elevated salt

thermophile

extremophiles that like a high temperature

psychrophile

extremophiles that like low temperature

acidophile

extremophiles that like low pH (less than 6)

barophile

extremophiles that like high pressure

alkaliphile

extremophiles that like high pH (greater than 8)

xerophile

extremophiles that like dry conditions

symbiotic relationships

close associations formed between pairs of species (ex: mutualism, amensalism, commensalism, neutralism, and parasitism

mutualism

symbiotic relationship where both populations benefit

amensalism

symbiotic relationship where one population is harmed and the other isn’t affected

commensalism

symbiotic relationship where one population benefits and the other is not affected

neutralism

symbiotic relationship where neither population is affected

parasitism

symbiotic relationship where one population benefits and the other is harmed