microbio chs. 1, 2, 3

What is microbiology?

the study of small organisms that require the use microoganisms, also called microbes

What are the acellular forms studied in microbio?

• prions: proteinous infectious agents

• viruses: nonliving nucleic acid masses surrounded by protein coats. require a host to infect

What are the cellular prokaryotes studied in microbio?

• Archaea: single-celled organisms in extreme environments

• Bacteria: all non-archaeon prokaryotes

What are the eukaryotes studied in microbio?

• Helminths: umbrella term for parasitic worms such as roundworms and flatworms

• fungi: heterotrophic decomposers that vary in cell level (uni or multi)

• protozoa: single-celled, animal-like eukaryotes

What are the 6 types of microbiology?

1. medical: focuses on pathogens to humans and animals

2. public health/epidemiology: controls community spread and makes educational resources

3. immunology: makes protective substances in response to disease/cancer

4. industrial: safety of food, water, creation of biotechnology

5. agricultural: concerns crops and farm animals

6. environmental: involves aquatic, soil, astromicrobiology, and the crust

What is the order and rough timeline of the first cells?

• soon after Earth’s birth, the first ancient cells formed

• around 3.6bya, unicellular bacteria and archaea developed

• 2.1bya, eukaryotes emerged

Why should we not get rid of bacteria?

they have adapted to so many conditions on Earth and withstood the test of time. different species can be found ANYWHERE, and their longevity is useful

How do bacteria relate to photosynthesis?

• originators of the process, firstly anoxygenic

• then developed to being aerobic

• added oxygen to atmosphere and formed ozone layer

What does “eukaryote” actually mean?

true nucleus

How are human uses of bacteria found?

empirically: based on experience, not from experimenting

How do bacteria relate to biotechnology and bioremediation?

• biotech: manipulating microbes for industrial products (GMOs, recombinant DNA tech)

• bioremediation: introducing microbes to clean toxic pollutants (ex. oil spill)

What is a pathogen?

a microbe that causes disease in animals and plants

How do pathogens relate to infectious and communicability?

• all microbial diseases are infectious

• communicability (transfer from person to person) varies on the type of disease

Which microbes are unicellular and which are multicellular?

• uni: bacteria, archaea, protozoa

• multi: helminths, most fungi, some algae

What are the protists?

umbrella term for eukaryotes that can be photosynthetic (algae) or non-photosynthetic (protozoa)

What is the history of the microscope?

in the 1660s, Anton van Leeuwenhoek worked in textiles and created a ground glass microscope to magnify linen. this then evolved into him looking at tooth bacteria and observing small, moving “animalcules”

What did the Hooke family do?

began building early models of the compound microscope, which we still use today. Robert Hooke was responsible for drawing the structures he saw and inspired Leeuwenhoek.

What is spontaneous generation and how was it disproven?

• the belief that life magically appears from a life-giving force (abiogenesis)

• Louis Pasteur did his swan-neck flask experiment: two flasks contained clear broth, and when the neck was broken from them, microbes entered and made the broth cloudy. if the neck remained intact, though, the broth stayed clear and sterile.

What is the cell theory and who is responsible for it?

the belief that all living things are made of cells + cells reproduce. Schleiden and Schwann proved this

How were spores and sterilization discovered?

English physicist John Tyndall proved that some microbes are extremely resistant to heat and must be removed some other way than simply boiling them. the idea of something free of all microbes, including endospores, came from this

How were aseptic techniques developed?

surgeon Joseph Lister noticed infection in the maternity ward and wanted to reduce microbes as much as possible, along with preventing wound or disease infection. he introduced hand washing and disinfecting with chemicals

How did the germ theory of disease develop?

Robert Koch observed how introducing a bacteria to cattle directly causes anthrax in their systems + established postulates to verify which organisms cause which disease. he helped invent most of our laboratory techniques (5 I’s)

What is the scientific method and who laid the groundwork for it?

• started from Ibn al-Haytham in the 900s-1000s in Persia

• the method comes from developing a hypothesis to explain a natural phenomenon, then testing it through experimentation MANY times

What is deductive vs inductive reasoning?

• deductive: comes from applying general, established principles and applying them to individual cases

• inductive: discovering principles by examination of specific cases

How does the binomal nomenclature system work?

all organisms are written in Genus species order, with that exact capitalization.

How are organisms classified in taxonomy and what is the order?

based on their evolutionary relatedness amongst other organisms. the most specific level is typically the highest and/or smallest. it is organized as: Domain, Kingdom, Phylum, Class, Order, Family, Genus Species

What are the 3 domains?

Bacteria, Archaea, Eukarya

What are radioactive isotopes used for?

medical and research purposes. despite being dangerous, they are incredibly useful

What is the difference between shells and orbitals + what are the quantities?

• shells are simply energy levels (elevator floor) of the atom

• orbitals are specific locations (hotel rooms) within a shell that contain 2 ELECTRONS ONLY.

• 1 orbital in 1st shell, 4 orbitals in second, 9 orbitals in third, 16 orbitals in fourth

What is a molecule vs compound?

molecules are more general and are only 2+ atoms, can be same element

compounds are 2+ DIFFERENT elements

What is ionization?

when a molecule with an ionic bond (ex. NaCl) is dissolved in liquid, the atoms dissociate into charged ions - makes them ELECTROLYTES

What are the 3 types of chemical reactions?

1. synthesis: A + B —> AB

2. decomposition: AB —> A + B

3. exchange: AB + XY —> AX + BY

What is concentration of a solution?

the amount of solute (solid, liquid, or gas) dissolved in a certain amount of solvent, also called molarity. remember that solutes won’t dissolve by just SETTLING

What is pH and neutralization?

• pH is a scale or equation (= -log[H+]) expressing how much hydrogen ion is released. it is LOGARITHMIC and moves tenfold

• acidic means there is more hydronium, basic means there is more hydroxyl

• neutralization occurs when solutions contain acids and bases and yield water and other neutral products

Inorganic vs organic chemicals?

• inorganic is anything that does not have both C and H

• organic means it has hydrocarbon bonds

What are carbohydrates and their unique names?

combinations of water and carbon in the quantity (CH2O)n

• monosaccharides have 3 to 7 carbons

• disaccharides have 2 monomers

• polysaccharide has 5+ monomers

What is the nature of carbohydrate bonds?

• monomers are joined through glycosidic bonds, where units are bonded to the same O

• occurs in a dehydration synthesis reaction - water is a byproduct

What is the function of polysaccharides?

provide structural support and serve as energy stores. in plants, the cell wall is strong from cellulose. in fungi, it is from chitin. in bacteria, it is from peptidoglycan or lipopolysaccharide

How are carbs stored in humans vs plants?

• stored as glycogen in humans

• starch in plants

What do all lipids have in common and what are the 4 classes?

all of them are nonpolar substances that are hydrophobic, so they will NOT dissolve in water. includes:

• triglycerides

• phospholipids

• steroids

• waxes

What is the structure and function of triglycerides?

• work as storage lipids, and include fats and oils

• composed of single glycerol connected to 3 fatty acid chains

• ester bond forms from carboxyl group on FA chains

What are saturated vs unsaturated fatty acids?

• saturated: all carbons are connected to other C and H through single bonds. typically exist as solids

• unsaturated: at least one C-C double bond in the chain. typically exist as liquids

What is the structure and function of phospholipids?

• made of a glycerol, 2 fatty acid chains, phosphate group

• major component of cell membranes due to their being permeable and fluid

• hydrophilic heads and hydrophobic tails

Why are steroids important?

they are also found in cell membranes and animal hormones. cholesterol is the most popular, which reinforces animal cell membranes

What is a wax?

a compound of a long chain alcohol and saturated FA. some natural things are waterproofed with this

What are the components of an amino acid?

ALL have an alpha carbon attached to a H, amine group, and carboxyl. the R group is what differentiates them

How does a peptide bond form?

comes from the amino group on one AA and the carboxyl on a different AA

What are peptides, polypeptides, and proteins?

• peptide is usually 2-4 AA

• polypeptide is 20+ AA

• proteins are at least 50 AA

What are the structure levels of protein explained?

• primary: type, number, and order of AA in the chain

• secondary: functional groups interact through H bonds —> alpha helix or beta sheets

• tertiary structure: more bonds between functional groups and other functional groups form, making a 3D structure

• quaternary: more than 1 polypeptide forms a large protein

What makes up a nucleotide?

pentose sugar, phosphate group, and nitrogenous base

What are the purines vs pyrimidines?

• purines=2 rings: alanine (A), guanine (G)

• pyrimidines=1 ring: thymine (T), cytosine (C), uracil (U)

What causes the double helix of DNA?

H bonds between complementary nitrogen bases

What are traits of RNA?

• single-stranded and has ribose sugar

• important for protein synthesis

• mRNA, tRNA, and rRNA

What is notable about ATP?

• serves as a high-energy compound released when bonds between phosphate groups are broken

• contains adenine, ribose, and 3 phosphates

• ADP can be reverted back to ATP

What are common traits of all cells?

• can be spherical, polygonal, cubical, or cylindrical

• their internal contents (protoplasm) are encased in a cell (cytoplasmic) membrane

• have chromosomes with DNA and ribosomes for protein synthesis

What is the difference between prokaryotes and eukaryotes?

eukaryotes have “true nuclei,” and includes organelles that split the cell into smaller components. organelles perform important functions for metabolism, growth, and nutrition.

What are the 5 I’s?

1. inoculation

2. incubation

3. isolation

4. inspection

5. identification

What is inoculation?

putting a small sample of bacteria (called a culture) onto a nutrient medium to grow; uses sterile instruments

What is incubation?

placing container in a temp-controlled chamber to encourage growth (and atmospheric gases are controlled), can be days or weeks. growth visible to our eyes occurs as colonies or turbidity

What are the physical states of media?

• liquid: water-based with solute called a broth

• semisolid: clot-like consistency to determine motility (agar or gelatin)

• solid: discrete colonies form and isolating

What are the chemical contents of media?

• defined: exact composition known (pure compounds), useful if exact nutrient needs are known

• complex: at least 1 component in the media is unknown (cell tissue, blood, yeast)

What is the “general” functional type of media?

its purpose is to grow as much life as possible. shows complexity and variety of life

What is the enriched function of media?

applies to complex organic substances (blood, serum, growth factors). bacteria are called fastidious if they require these things

What is the selective function of media?

certain microbes are inhibited, but not others. important when there are many species

What is the differential function of media?

allowing multiple organisms to grow, but with visible differences between them. there will be a change in color, size, bubbles, precipitates based on the type of chemicals in the media. dyes are used for pH indications

What is the reducing function of media?

introducing a substance (thioglycolic acid or cystine) that absorbs oxygen, specifically for anaerobic species

What is the transport function of media?

when specimens need to be maintained for a long period

What is the assay function of media?

used to determine effectiveness of antimicrobial drugs

What is the enumeration function of media?

for counting the number of organisms in milk, water, food, or soil. has applications in industrial and environmental microbiology

What is isolation and the methods?

inoculating a small number of cells into an expansive area so that a colony appears. can be a streak plate, pour plate, or spread plate

How is a streak plate performed?

a small drop is spread with an inoculating loop in a pattern - creates sections on the surface in the dish

How is a pour plate performed?

inoculated in a successive way to dilute the number of cells in following tubes, then poured into sterile dishes to solidify. results in decreased number of cells per volume. some colonies grow deep in medium

What is a pure culture and how is it created?

also called axenic: defined as growing only 1 type of bacteria and is completely sterile. done by subculturing an already well-isolated colony

What are the methods in identification?

biochemical tests (nutrient needs, growth products); genotypic testing of DNA and RNA; immunologic testing against known antibodies

Rank the microbes in terms of size:

1. prions

2. viruses

3. yeast

4. protozoa

How are simple and compound microscopes different?

• simple has single lens (magnifying glass, Leeuwenhoek microscope)

• compound has 2 lens systems with a lamp in the base

What is magnification and how is it determined?

• how much can we expand an image

• ocular x objective

What is resolution?

minimum distance required to separate 2 objects from one another - oil immersion makes this distance 0.2 microns

What is a compound brightfield microscope’s application?

• most cells require staining, or else they appear clear

• typically dead cells on slides (preserved)

• can also be alive if they are in a hanging drop

Application of compound darkfield microscope?

• only shows reflected light

• living cells that would be distorted with heat or stain

Application of phase-contrast microscope?

• internal structures of eukaryotes!!

• edges of cells

• endospores, granules, cilia

• uses polarized light to make sure brightness/color is accounted for

Application of fluorescent microscope?

• UV light

• stained with fluorescent dyes to emit a strong color (purple, green, red)

Application of confocal microscope?

• cell physiology: mitosis, muscle contraction

• overcomes issue of a structure being too thick

• fluorescent dyes with laser light

Applications of transmission electron microscope?

• membranes, organelles, viruses in great detail

• must be sectioned and sliced

• requires special training

• specimen prep and staining takes a week

Applications of scanning electron microscope?

• dramatic and realistic images

• 3D images of SURFACES - no cuts

Applications of atomic force microscope?

seeing molecules at the smallest level - DNA, CO2

How are live specimens prepared?

1. wet mount: put drop on slide and mount right on top. susceptible to drying or damage

2. hanging drop: concave slip to suspend drop and jelly to seal edges

How is a stained specimen prepared and chemically why?

1. positive: dye sticks directly onto specimen and colors it

2. negative: dye is in peripheral and makes silhouette. india ink or nigrosin is the black background

b/c bacteria cell walls are negative and that impacts how the dye will interact w/ them

Simple vs differential stains?

• simple: only 1 dye used

• differential: primary dye with a counterstain

What are the key types of differential stains?

1. Gram stain (cell wall): purple positive

2. acid fast (mycolic acid): fuchsia for AF

3. endospore: dye is forced in by heat

What is a special stain and the main types?

used to investigate certain structures

1. capsule staining: protective layer in bacteria and fungi

2. flagellar staining: coat then stain bacteria to see filaments