Microbiology Test 1

Miller-Urey Experiment

Mimicked early earth’s atmosphere and created life abiotically using lightning to demonstrate the potential origins of life on earth

Lucretius(1st century)

One of the first to believe that “invisible creatures” caused disease

Robert Hooke(17th century)

First to describe mold

Leeuwenhoek(17th century)

First to observe bacteria through a microscope he created. Called them “wee beasties”

Edward Jenner(18th century)

Developed the smallpox vaccine, pioneering the field of immunization.

Lady Mary Wortley Montague

Introduced variolation for smallpox prevention based on her observations of Turkish practices.

Semmelweis

introduced hand-washing as a way to prevent disease

Lister

pioneered antiseptic surgery, significantly reducing infection rates.

Nightingale

pioneered modern nursing practices and emphasized sanitation in hospitals.

Louis Pasteur(19th century)

a French microbiologist who developed the germ theory of disease and created vaccines for rabies and anthrax.

Robert Koch(19th century)

Created Koch’s postulates to determine which pathogen causes which disease

Sergei Winogradsky

Discovered chemoautotrophy. Known as the father of environmental microbiology

Ehrlich & Fleming

Pioneered chemotherapy

Carl Woeses(20th century)

Developed the three-domain system of classification, highlighting Archaea, Bacteria, and Eukarya. Responsible for RNA world hypothesis

Which categories of organisms are studied by microbiologists? Which are cellular? Acellular? Prokaryotic? Eukaryotic?

Cellular: fungi, protists, bacteria, archaea

Acellular: viruses, viroids, satellites, prions

Prokaryotes: bacteria, archaea

Eukaryotes: fungi, protists

Why do we study microorganisms and how do they affect us?

Studying them helps us understand basic life processes. They’re easy to study as they’re simple, reproduce quickly, and grow densely. We can apply that knowledge to benefit humans. They cause disease, help us digest food, synthesize nutrients, decompose things, and contribute to soil health

What is the typical size and mass of a microbe?

Under 5 microns and weigh 1×10^-15kg

Why can we claim that microorganisms have dominated Earth throughout its history?

Microfossils have been found from ~3.8GYA

What are the key characteristics of life?

• Growth: converting chemicals and energy into cells

• Evolution: has genes that can mutate

• Metabolism: cells are open systems exchanging w the environment

How old is Earth?

About 4.5GYA

When did life first arise and what is the evidence?

Life arose around 4.1GYA. Biomarkers and stable isotope anomalies are evidence of this

What are stromatolites?

Fossilized microbial mats dating back ~3.5GYA

What are the basic steps in the origin of life?

Life originated either from lightning or a meteorite. The Miller-Urey experiment recreated Earth’s early atmosphere and found that lightning would have been able to create amino acids abiotically, and life could have began from there

What is the rationale behind the RNA world hypothesis?

RNA would make sense for the first life forms as it can preform basic functions such as regulate gene expression, make protein(ribosomes), energy(ATP), store info and catalyze reactions(ribozymes)

What are the characteristics of LUCA?

• anaerobic

• prokaryote

• thermophile

• used hydrogen for energy

• chemolithotroph

• got carbon from CO₂

What is the difference between variolation and vaccination?

Variolation referred to inoculating someone with a small amount of smallpox matter, usually by rubbing it into a cut. Vaccination was injecting someone with cowpox. Vaccination was safer, as it didn’t leave the person contagious.

Explain Pasteur’s experiment.

Pasteur sterilized broth in a swan neck flask. No life developed, but when the neck was broken or the flask was tilted, growth occurred. This suggested that there was something in the air that caused life to grow rather than spontaneous generation.

What are Koch’s postulates?

• Suspected pathogen must be present in the diseased animal but not in healthy animals

• Suspected pathogen must be isolated and cultured

• When introduced to a healthy animal, it must contract the disease

• The same suspected pathogen must be isolated from the newly diseased animal

In terms of mortality per age group, how do the 1918 flu and covid differ?

Flu had higher mortality in young children, whereas covid had higher mortality in older individuals.

What are the basic parts of a bright field microscope?

• Ocular lens/eyepiece

• Objective lens

• Stage

• Coarse/fine adjustment knobs

• Condenser(under stage)

• Light source

What is the difference between resolution and magnification?

Magnification is how big something is, while resolution is how well you can distinguish one thing from another

Why do we use oil for the 100x lens?

The oil has the same density as the glass, so the light does not scatter. This results in better resolution

Why do we stain cells?

To improve contrast, and sometimes for identification

What are the three types of stains and what are they used for?

1. Gram stain: differentiate between gram negative and gram positive cells

2. Acid-fast stain: stains mycobacterium pink and other cells blue

3. Endospore stain: stains spores green and cells pink

What are the steps for performing a gram stain?

1. Crystal violet: stains all cells purple

2. Iodine: locks in purple stain

3. Alcohol: removes purple stain from gram negative cells

4. Safranin: stains gram negatives pink, gram positives stay purple

CIAS

What are the basics of the different kinds of microscopy?

• Phase contrast

  • dark cells on light background

  • doesn’t kill cells

  • best contrast

• Dark-field

  • light cells on dark background

  • light comes in from the sides and scatters

  • good for observing motility

What is immunofluorescence?

Attaching a fluorescent sphere to antibodies so you can identify what pathogen they attach to

Why was the bubonic plague so deadly to Europeans in the middle ages?

Many were already susceptible to disease due to widespread poverty, famine, and unhygienic living conditions weakening immune systems

How is the plague transmitted? Where and why are most cases in the US today?

It is transmitted from animal to human via infected fleas, or from human to human by coughing or sneezing. Most cases in the US are in the southwest because prairie dogs often carry it

What is FISH and how does it work?

It is a DNA probe attached to fluorescent dye. It is used to identify and count cells from a sample

What are the differences between light microscopy and electron microscopy?

Electron can magnify further and has better resolution than light. Electron uses electron beams, while light uses light rays.

What is the difference between SEM, TEM, and probe electron microscopy?

Probe

• resolution down to atomic level

• can see live organisms

• functions by dragging a 1-atom thick probe across specimens

SEM

• specimen is coated w thin film of heavy metal

• uses electron beams to scan specimen

• range of 15x-100000x

TEM

• high magnification and resolution(0.2nm)

• specimen must be very thin and stained

What is DAPI and how is it used?

It’s used in microbial ecology for enumerating bacteria in natural samples. Makes cells glow blue-violet

How do you calculate for total magnification?

Ocular lens x objective lens

What is the basic structure of a lipid?

hydrocarbons. triglycerides are made of glycerol and 3 fatty acids

What is the basic structure of carbohydrates?

Carbon, hydrogen, and oxygen in a 1:2:1 ratio

What is the basic structure of proteins?

amino acids(hydrogen, carboxyl, amino, and R groups)

What is the basic structure of a nucleic acid?

phosphate group, sugar, nitrogenous base

What is the difference between a saturated and an unsaturated fatty acid?

saturated: max number of hydrogens, straight, no double bonds

unsaturated: crooked, double bonds

What are the levels of protein organization?

primary: single chain of amino acids

secondary: simples twists and folds due to h-bonding

tertiary: folding due to side chains

quaternary: multiple tertiary chains folding together

What is chirality? Which does life on earth use?

chirality = having 4 different groups attached

amino acids are left-handed

What occurs during redox chemistry?

LEO GER

reducing agent: loses electrons, is oxidized

oxidizing agent: gains electrons, is reduced

What is Marshall famous for?

finding out that H. pylori caused ulcers and that antibiotics could typically cure it

What is variolation? Give one example.

variolation is the practice of inoculating someone with smallpox matter to instill immunity. Catherine the Great(leader of Russia) popularized variolation in Russia in the 1700s by getting it done herself and having her children get inoculated.

What is the history of the smallpox vaccine?

came to fruition in 1796 by Edward Jenner who injected cowpox into an 8yo boy, then later exposed him to smallpox and he did not contract it. it took a while to gain support, but eventually became mandatory in many countries.

How deadly was smallpox? What were its symptoms?

smallpox had a mortality rate of 30%, and it was even higher in young children. symptoms started as fever, chills, vomiting, headache, then after 1-3 days skin lesions would appear

How did the Belhaouari paper use SEM to illuminate the reproductive mechanism of SARS-COV-2?

the use of SEM allowed researchers to see the entire life cycle of the virus due to its high magnification and resolution, as well as its rapid-imaging ability

What the difference between paraphyletic, monophyletic, and polyphyletic?

Mono - group of a common ancestor and all its descendants

Para - common ancestor and some but not all descendants(ex: bacteria and archaea)

Poly - different ancestors without most recent common ancestor(ex: gram + bacteria)

What are the basic shapes of bacteria?

Cocci

• diplococci(pair)

• streptococci(chain)

• staphylococci(cluster)

• tetrads(4 cocci in a square)

• sarcinae(8 in a cube)

Rods/bacilli

Vibrios

Spirilla

Spirochetes

Haloquadratum

What is the relationship between surface area and volume?

Volume increases faster than surface area. Higher surface area is preferred because it allows for more efficient exchange with the environment

What sets the upper limit on cell size? Lower limit?

Upper: SA to V ratio. Biggest known cells are about 750 microns, but this is very rare

Lower: Cell has to be big enough to have room for organelles. Bigger cells have a better advantage against predators. Smallest cells are about 0.15 microns

What are the main purposes of the cell membrane?

protection and structure

What is the structure of the cell membrane?

Lipid bilayer with floating proteins

How does passive diffusion work?

Passive diffusion: high to low concentration, no energy required, common for O2, CO2, and H2O

How does facilitated diffusion work?

high to low concentration, no energy, proteins help transport larger molecules, smaller concentration gradient required

How does primary active transport work?

ABC transporters move molecules against the gradient

How does secondary active transport work?

uses ion gradients to cotransport substances. Symporters move both molecules in the same direction, while antiporters move them in opposite directions

How does group translocation work?

energy dependent with chemical modification

What are the structures of gram - and gram + cell walls?

Gram -

• multi-layered

• outer membrane with LPS and lipoproteins

• thin peptidoglycan layer

• periplasm is 20-40% volume

• Braun’s lipoprotein connects outer membrane to peptidoglycan layer

Gram +

• thick peptidoglycan layer

• may have teichoic acids

What is the basic structure of peptidoglycan? What is meant by D-amino acids?

it is a mesh-like structure of identical subunits made of cross-linked NAM, NAG, and D-amino acid chains. D-amino acids are right-handed; this is one of the few places where right-handed amino acids exist on earth

What is periplasm?

it is between the plasma membrane and cell wall. it secretes exoenzymes and aids in degradation of large nutrients

What is the difference between lysozyme and penicillin? How do they work?

Lysozyme: breaks bond between NAM and NAG

Penicillin: inhibits peptidoglycan synthesis

They both degrade the peptidoglycan layer, but lysozyme does it by breaking it down whereas penicillin does it by stopping it from being made

What is a capsule? Slime layer? How are they different? What are their purposes?

Capsule: disorganized, firmly attached to the cell

Slime layer: loosely organized, easily washed off

Both are made of polysaccharides and help protect the cell

What are the different cell inclusions?

Carbon storage polymers, sulfur globules, magnetosomes, gas vacuoles

How are prokaryotic and eukaryotic ribosomes different?

prokaryotes are 70s and eukaryotes are 80s

What is a nucleoid? What is a plasmid? What kind of genes are on plasmids vs. chromosomes?

Nucleoid: no membrane, 1 closed circular double-stranded DNA molecule

Plasmid: small closed circular DNA molecules that exist and replicate independent of the chromosome

The plasmid contains few genes that are not essential, while chromosomes carry the essential genes

What are pili/fimbriae?

short, thin, hair-like structures for attachment, motility, and sometimes DNA uptake(sex pili)

What are flagella? How are they constructed?

whip-like structures for movement. made of basal body, hook, and filament

What powers flagellar movement?

they respond to temporal differences. the basal body rotates ccw to run and cw to tumble

What are the patterns of flagella?

monotrichous: one flagella

amphitrichous: one at each end

lophotrichous: cluster at one or both ends

peritrichous: spread over entire surface

How does a microbe approach an attractant?

directed movement towards the attractant; longer runs when closer to the attractant, equal runs and tumbles when not near an attractant

What is an endospore?

a complex dormant structure that is very resistant and formed by some bacteria

What helps protect an endospore from its environment?

calcium dehydrates it, SASPs, spore coat, and exosporium

How does an endospore form?

1. DNA becomes more dense

2. asymmetric cell division

3. endospore septum grows around protoplast

4. forespore formation

5. exosporium synthesis

6. calcium dehydrates, SASPs form, coat layers form

7. maturation

8. lysis of cell and endospore release

How does an endospore reactivate?

1. activation

2. germination

   1. outgrowth/emergence of vegetative cell

What kind of organisms are the earliest branches of the tree of life? What does this imply?

they’re thermophiles, which implies that life started in a hot environment

Can archaea be pathogens? Do they affect us or our health?

No, but they are an important part of our microbiome and can aid in our digestion

How are archaea like bacteria?

• no membrane bound organelles

• one circular chromosome

  • 70s ribosome

How are archaea like eukaryotes?

• no peptidoglycan in cell walls

  • don’t form endospores

How are archaea unique?

• have glycerol diethers and diglycerol tetraethers in the plasma membrane lipids

• flagella are composed of multiple different flagellins

  • ribosome is a mix of bacterial ribosomes and eukaryotic ribosomes

How are eukaryotes like bacteria?

• don’t have hami

• both have cell membrane made of a phospholipid bilayer

How are eukaryotes unique?

• larger

• more complex

• membrane bound organelles

• nucleus

• bigger ribosomes(80s)

• have cholesterol in plasma membrane

• endocytosis