test 1 // general microbiology

intro to history 1 & 2, microscopy, microbes & the tree of life, central metabolism

what is microbiology?

the study of microorganisms

what are the main three microorganisms?

1. prokaryotes (bacteria & archaea)

2. small eukaryotes (fungi & yeast)

3. viruses

are prokaryotes unicellular or multicellular?

unicellular

are small eukaryotes unicellular or multicellular?

can be either

which of the two main microorganisms are considered “alive”?

what does it mean for them to be alive?

prokaryotes and small eukaryotes

they can self-propagate/reproduce

which of the three main microorganisms are not considered alive?

what does it mean for them to not be alive?

viruses

they cannot self-propagate/reproduce; they need a host in order to be able to do so

why is microbiology considered important?

because microorganisms cause human, animal, & plant diseases

• if we can identify the cause of a disease, we can prevent and/or treat it

how long ago was the origin of the earth?

4.5 bya

how long ago did bacteria & archaea (microbes) appear?

4 bya

how long ago did phototrophic bacteria appear?

• at this time, there was a dominance of microbes that can ___ but don’t use ___

3.5 bya

• photosynthesize, O2

how long ago did the transition to an oxygenated environment happen?

which microorganisms were responsible for this and how long ago did they appear

2-3 bya

cyanobacteria; ~2.25 byaw

how long ago did eukarya appear?

2 bya

how long ago did humans, vascular plants, mammals, and animals appear?

0.5 bya

describe the central dogma

include all of the processes that go from one component to the other

main: dna → rna → protein

• dna making more dna: dna replication

• dna to rna: transcription

• rna making more rna: rna replication

• rna to dna: reverse transcription

• rna to protein: translation

90% of biomass in oceans is ___ (~___ cells)

microbial

10²⁹

____ ____ contribute to 1% of global biomass & 50% of CO2 fixation

marine phytoplankton

describe the volta experiment

methane produced by microbes found in sediment can be lit on fire

describe fermentation tanks

microbes generating ethanol from sugars found in corn

microbes contain majority of ___ ___

earth’s biomass

~___ microbial cells on earth

10³⁰

microbes can be found kilometers ___ ___ ___ and kilometers ___ ___ ___

up in atmosphere

below earth’s surface

more ____ cells are associated with the human body than human cells

• ____ has the highest density (amount: ___ ___)

microbial

• gut, (10¹³ bacteria)

most snowflakes form around ___

bacteria

what are some human uses of microbes?

1. yeast (alcohol, baking)

2. bacteria (yogurt, cheese)

robert hooke (time period: ___ ___)

• probably the first person to observe ___

  • achieved ___ magnification

    • could only see ___ ___ (e.g., plants, fungi, algae)

• coined the term “___”

  • saw series of boxes/”tiny rooms” in ___ ___

• wrote first book on ___ observations titled “___”

late 1600s

• microorganisms

  • 30x

    • larger microbes

• cell

  • sliced pork

• microscope; micrographia

antoni van leeuwenhoek (time period: ___ ___)

• had a hobby of ___ ___

• built his own ___ ___ ___

• ____ ____ ____ ____ published his letters

• achieved ___ magnification

  • allowed him to see ____

late 1600s

• lens grinding

• single lens microscope

• royal society of london

• 300x

  • bacteria

what is spontaneous generation?

give an example

• ____ was against spontaneous generation

• early experiments showed that when food was ___ and ____ ____ ____, rot didn’t happen

  • shows that ___ were killed and didn’t come back/grow

    • counter: ___ ___ is needed

what were the two competing theories at this time?

the idea that living organisms formed spontaneously from natural elements (life from non-living elements)

• pasteur

• heated; sealed from air

  • microbes

    • fresh air

competing theory #1 (spontaneous gen.):

• air carries a “vital force”

  • fresh air allows life from nonliving

competing theory #2 (germ theory):

• air carries “seeds” or “germs”

  • fresh air carries microbes

louis pasteur (time period: ___ ___)

• pasteur experiment; used ___-___ ___

  • allowed ___ ___ to reach sterile medium, but trapped ___ in neck

    • no growth

  • then allowed medium to come into contact w/ trapped ___

    • growth

what did this show?

mid 1800s

• swan-necked flask

  • fresh air; microbes

  • microbes

this disproved spontaneous generation by showing that airborne microorganisms cause growth, not a “vital force” in the air

• if spontaneous gen. were true, there would’ve been growth under the first condition

germ theory of disease:

edward jenner (time period: ___ ___)

• vaccination for ___ ___ from cow pox

  • trains ___ ___ ___ to recognize and kill ___

louis pasteur (time period: ___ ___)

• vaccines for ___, ___ ___, and ___

joseph lister (time period: ___ ___)

• concept of ___ of wounds & surgical rooms

  • killing bacteria prevents ___

late 1700s

• small pox

  • adaptive immune system; pathogens

late 1800s

• anthrax, foul cholerae, and rabies

mid 1800s

• disinfection

  • infections

pure culture techniques:

robert koch

• first used ___ ___, ___, or ___ under a bell jar

• can grow microbes, but ___

julius petri

• invented ____ ____!

• tried ___ and ___ as mediums

  • why was one good and the other bad?

• potato slices, gelatin, starch

• inconvenient

• petri dishes!

• gelatin, agar

  • gelatin was bad because of low melting point (28 deg C) and bacteria eat it over time

  • agar was good because it’s solid at body temp (37 deg C), doesn’t get eaten by bacteria, and allows for selection by addition of nutrients

describe the two main methods of growing bacteria

include the general procedure and benefits of each

1. spread plate

• procedure: dilute in liquid, then spread on plate

• benefits: ensures uniform distribution & allows for easy counting

2. streak plate

• procedure: use innoculating loop to pick a colony from a dense plate & streak on a new plate

• benefits: allows isolation of a microbe from a mix of them

robert koch (time period: ___ ___)

koch’s postulates: how to determine if a ___ is causing a ___

→ what were the 4 steps of koch’s postulates?

→ what were some limitations?

late 1800s

microbe; disease

1. organism is present in sick animals and not in healthy ones

2. organism can be grown in pure culture away from animal

3. cells from the pure culture cause disease when inoculated into healthy/susceptible animals

→ If it causes the same disease here, go to step 4

4. organism is re-isolated from exposed animals from step 3 and shown to be the same in pure culture

limitations:

• some microbes are unculturable

• different organisms have varying susceptibility to disease

  • some may get sick while others don’t

• some pathogens only infect humans

environmental microbiology

• some bacteria may require ___-___ ___ conditions

  • ____ ____ are used to adhere to these conditions and include placing an environmental sample under ___ ___ conditions for an organism w/ specific ___ ____

martinus beijernick & sergei winogradsky (time period: ___ ___-___ ___)

• created the ___ ___

  • isolates from ___ ___ and ___ ___

    • mix of microbes coexisting in a ___ system

  • demonstrated ____

    • use of ___ compounds (e.g. sulfur, ammonia) to obtain energy

  • demonstrated fixation of CO2 is not always associated with ___

  • demonstrated the ___ of atmospheric ___ into cellular ___

• environmental-specific growth

  • enrichment techniques, optimal growth, metabolic capabilities

late 1800s-early 1900s

• winogradsky column

  • environmental soil; water samples

    • closed

  • chemolithotrophy

    • inorganic

  • photosynthesis

  • fixation; nitrogen; nitrogen

what is magnification?

the extent to which the image of an object is larger than itself

magnification: product of ___ and ___ lens

objective; ocular

what is resolution/resolving power?

what is the equation for resolution?

the degree to which details are retained in a magnified image / the ability to distinguish between two points

resolution = R = 0.5λ / NA

where —

λ: wavelength of light

NA: numerical aperture (the light-gathering ability of the lens) [dimensionless]

what is a standard light microscope’s best resolution at 1000x magnification (answer in nm and microns)

200 nm / 0.2 microns

bright-field microscope

• ____ ____ in gen micro labs

• light is ___ thru the specimen

  • ____ between the background & cells is generated by ___ or ___ of light

    • only cells with ___ ___ are seen easily

  • ____ of the cells is generally required

    • ____ often ___ the cells

    • ____ cells take up ___ more effectively

    • what are the 4 steps of this?

• most common

• transmitted

  • contrast; absorption; scattering

    • natural pigments

  • staining

    • staining; kills

    • dead; stain

→ 1. spread culture in thin film over slide

→ 2. air-dry

→ 3. pass slide thru flame to heat-fix

→ 4. flood slide w/ stain; rinse & dry

simple stains:

• generally used for ___ ___

• stains are generally ___ ___

  • basic dyes (___) are ___ charged

    • examples?

    • bind to ___ charged cell components

      • examples?

  • acidic dyes (___) are ___ charged

    • bind to ___ charged cell components

      • examples?

• bacterial cell surface is usually ___, so this method is commonly used

• all bacteria

• charged molecules

  • (cationic); positively

  • ex. methylene blue, crystal violet, safranin

  • negatively

    • ex. carboxylates, phosphates, polysaccharides, nucleic acids, phospholipids

  • (anionic); negatively

    • positively

      • ex. amino groups, proteins

• negative

what is the purpose of differential stains?

what are three examples and their unique 2 groups?

divides a mixture of bacteria into two groups based on an unique property

1. gram stain (gram + vs -)

• most common

2. acid fast stain (mycobacteria vs. others)

• stains unique cell wall of mycobacteria

3. endospore stain (spore within mother cell)

• stain can be forced into spores; rest is washed out

gram staining

what is the difference between g+ & g- bacteria?

describe the steps of gram staining

explain why it works

g+: thick peptidoglycan layer in cell wall

g-: thin peptidoglycan layer in cell wall

1. flood heat-fixed smear w/ crystal violet for 1 min

• everything takes on stain; all cells are purple

2. add iodine for 1 min

• iodine complexes w/ CV form aggregates; all cells remain purple

3. decolorize w/ alcohol (~20s)

• CV-iodine complex is trapped in g+ cells; g+ cells are purple & g- cells are colorless

4. counterstain w/ safranin for 1-2 mins

• stains both g+ & g- cells, but only visible in g- cells; g+ cells are purple & g- cells are pinkish-red

why it works:

• CV enters cells & is precipitated w/ iodine

• ethanol disrupts cell mem. of all cells

• stain complex is only washed out of g- cells and is retained in g+ cells

dark-field microscope

• light is only on the ___

  • only ___ light reaches eyes

  • cells are ___ against a ___ background

    • no need to ___

  • can’t see ___/___

  • provides better ___ than bright-field

    • can see ___ cells/structures

• edges

  • scattered

  • bright; dark

    • stain

  • color/stains

  • resolution

    • smaller

phase contrast microscope

• special ___ ___

  • puts source light into the same ___

• ____ light = out of phase, which gives ___

• no ___ required

• allows cell visualization while they’re ___

• light condenser

  • phase

• diffracted; contrast

• stain

• alive

fluorescence microscope:

• light source at a ___ that causes the specimen to fluoresce at a ___ ___

• some cells exhibit ___

• fluorescent ___ are used to ___ specific cell structures

• ___-___ proteins can be specifically localized in cells

• wavelength; different wavelength

• autofluorescence

• dyes; stain

• fluorescently-tagged

transmission electron microscope (TEM)

• the electrons that ___ ___ the sample are collected to make image

• ___, ___ sections of fixed samples

• uses ___-___ stains

• pass through

• 2D, thin

• heavy-metal

scanning electron microscope (SEM)

• the electrons that are ___ ___ the sample are collected to make image

• ____ (2D or 3D?)

• cells are coated with ___ ___

• scattered off

• 3D

• heavy metal

e- microscopy has magnification up to ___

100,000x

atomic force microscope (AFM)

• tiny ___ is scanned across & just above sample ___

• scans the ___

• weak ___ ___ between atoms of the ___ and the sample cause ___ to deflect ___ and ___

• provides extremely fine ___

• can be challenging with ___/___/___ samples

• stylus; surface

• surface

• repulsive forces; stylus; stylus; up; down

• detail

• live/sticky/flexible

is size a good way to categorize microorganisms?

NO, because exceptions exist

what are three cellular components all cells have and the functions of them?

1. cytoplasmic membrane

• prevents loss of cytoplasm & controls what goes in + what goes out

2. cytoplasm

• contains ribosomes & metabolic enzymes

3. dna

• genetic material

  • located within nucleoid for prokaryotes and within nucleus for eukaryotes

which cells have cell walls?

what does this help them resist?

bacteria, fungi, and plants

osmotic lysis

animal cells have a ___

• results in cell shape that can ___

cytoskeleton

• change

prok. vs. euk: organelles

p: no organelles

e: internal mem.-bound organelles

prok. vs. euk: nucleus

p: no nucleus

e: nucleus

prok. vs. euk: dna

p: dna condensed into nucleoid

e: dna within mem.-bound nucleus

nearly all eukaryotes have ___ while only plant cells have ___

mitochondria; chloroplasts

prok. vs. euk: chromosome structure

p: 1 circular chromosome + some small circular extra-chromosomal dna (plasmids)

e: multiple linear chromosomes

prok. vs. euk: diploid/haploid

p: haploid

e: diploid

prok. vs. euk: sexual reproduction

p: no sexual reproduction

e: can sexually reproduce

viruses

• can be ___ or ___

• no ___, ___, or ___ activity

• composed of ___ ___ (___ or ___), ___ ___, and ___ (sometimes)

• must infect a ___ or ___ in order to ___

• prokaryotic; eukaryotic

• cytoplasm, ribosomes, metabolic

• nucleic acid (dna or rna), protein capsid, membrane

• prokaryote; eukaryote; reproduce

what is a virus with a membrane present called?

what is a virus with a membrane absent called?

enveloped virus

naked virus

early classification attempts

• linnaeus (year?)

  • ____ kingdoms

    • what were they and what did they include?

  • didn’t include ___

  • structure based on ___

  • introduced ___ naming by ___ and ___

• whittaker (year?)

  • ____ kingdoms

    • what were they and what did they include?

  • based on ___, ___, and ___

• 1753

  • two

    • animalia (higher animals & protozoa) & plantae (higher plants, algae, and fungi)

  • prokaryotes

  • microscopy

  • latin; genus; species

• 1969

  • five

    • monera (bacteria), protista (algae & protozoa), plantae (photosynthesizers), fungi (nutrient uptake thru absorption), & animalia (nutrient uptake by ingestion)

  • appearance, structure, and metabolism

molecular-based approach to phylogeny

carl woese (time period?)

• ____ ____ in proks.; ___ ___ in euks.

• ancient molecule that ___ ___ have

  • part of ___; essential for ___

• changed very ___ over evolutionary time

  • why?

• sequenced ___

  • why?

• can create tree based on ___ ___ between species

1970s

• 16S rRNA; 18S rRNA

• all cells

  • ribosomes; translation

• slowly

  • because most mutations would lead to cell death; only certain mutations allowed

• easily

  • because only ~0.03% of the genome is needed for it to be sequenced

• rRNA differences

current tree of life

• ____ domains

  • what are they?

• archaea are more related to ___ than ___

  • discovered by ___

• LUCA =

  • where bacteria diverge from ___ and ____

• what is endosymbiosis?

  • what are two endosymbionts?

    • look like ___, but can’t ___ on their own

• three

  • bacteria, archaea, eukarya

• eukarya; bacteria

  • woese

• last universal common ancestor

  • archaea; eukaryotes

• bacteria that have been engulfed by eukaryotic cells to form organelles

  • mitochondria & chloroplasts

    • bacteria; grow

classification based on energy (method of generating ATP)

label #1-9

1. chemicals

2. chemotrophy

3. organic compounds (contain C-H bond)

4. inorganic compounds (e.g. CO2)

5. chemoorganotrophs

6. chemolithotrophs

7. light

8. prototrophy

9. phototrophs

classification based on carbon source

• ____ vs ____

  • describe each

• heterotrophs vs. autotrophs

  • heterotrophs require organic compounds as carbon source (e.g., sugars, proteins, lipids) & autotrophs use CO2 as carbon source (e.g., thru photosynthesis + chemosynthesis)

chemoheterotrophs / chemoorganoheterotrophs use what for energy and what as carbon source?

what are some examples?

energy: organic compounds

carbon source: organic compounds

examples: humans, many bacteria, fungi

chemolithoautotrophs use what for energy and what as their carbon source?

what are some examples?

energy: inorganic compounds

carbon source: CO2

examples: sediment bacteria, oceans, deep sea vents

photoautotrophs use what for energy and what as their carbon source?

what are some examples?

energy: light

carbon: CO2

examples: plants, algae, photosynthetic bacteria

photoheterotrophs use what for energy and what as their carbon source?

what are some examples?

energy: light

carbon: organic compounds

examples: some bacteria

notable bacteria

• spirochetes

  • pathogens

    • associated diseases?

• chlamydia

  • STD

    • ____ ____ pathogen

• cyanobacteria

  • ____ the atmosphere

  • became ___

• gram + bacteria

  • ____ formers

    • associated disease?

• proteobacteria

  • ancestors led to ___

  • examples?

• syphillis, lyme disease, ulcers

• obligate intracellular

• oxygenated

• chloroplasts

• spore

  • MRSA

• mitochondria

• e. coli, salmonella, pseudomonas

archaea

• prokaryotes that live in ___ environments

• e.g.

  • halophiles (require high ___)

  • methanogens (produce ___, found in ___ & ___ gut, ___ [anaerobe or aerobe?])

  • hyperthermophiles (require high ___)

  • extremophiles (require extreme ___, ___, or ___)

• extreme

  • salt

  • methane; termite; cow; anaerobe

  • temperature

  • temperature; salt; pH

notable eukarya

• diplonomads

  • pathogen

    • example? (has no ___)

• ____ ____

• giordia (mitochondria

• green algae

life evolution vs. earth history

• LUCA appeared ___ ___

• cyanobacteria appeared between ___ ___

• 3.5-4 bya

• 2-3 bya

what is catabolic metabolism / catabolism?

is it energy-requiring or energy-producing?

breaking down available nutrients to extract energy and provide simple organic building blocks for synthesizing new cell components

energy-producing

what is anabolic metabolism / anabolism?

is it energy-requiring or energy-producing?

using simple organic building blocks to produce more complex cell components aka ‘biosynthesis’

energy-requiring

in catabolic metabolism, is the energy level of the reactants above or below that of the products?

above; since energy is released, the reactants have more energy than the products

in anabolic metabolism, is the energy level of the reactants above or below that of the products?

below; since energy is required for anabolism to happen, the reactants have less energy than the products

enzymes

• biological ___

  • usually ___, sometimes ___

  • reduce ___ ___ for the rxn to progress

• increase the ___ of rxn

• are not ___ within rxns and can go on to ___ other rxns

• do not determine rxn ___

• ____ frequency of substrates reaching the transition state

• catalysts

  • proteins, RNA

  • activation energy

• rate

• consumed; catalyze

• direction

• increases

enzymatic rxns

• substrate binds to ___ ___ of enzyme

  • substrate cleaves off ___ and the ___ substrate leaves as ___ ___

    • can also go in the ___ direction (___ rxn)

      • ____ ___ bind and leave as ___ ___ after cleaving

      • much ___ likely to occur

• active site

  • site; single; two products

    • other (reverse)

      • two substrates; one product

      • less

enzymes

• names usually end in “__”

• have an ___ ___ that substrates bind to

• enzyme & substrate may undergo ___ changes during catalysis

  • enzyme holds substrate in the right ___ for rxn to progress

• may have ___ ___ covalently bonded to enzyme

  • must be ___ to function

  • not normally ___

  • examples?

• may have ___ bound temporarily during rxn

  • ____ between enzymes & are ___

  • examples?

• “-ase”

• active site

• conformational

  • conformational

• prosthetic groups

  • attached

  • released

  • ex. heme, Fe-S cluster

• coenzymes

  • move; recycled

  • ex. NAD+, FAD, coenzyme A

redox

• e- donor = ___ = ___ agent

• e- acceptor = ___ = ___ agent

• e- donors usually release ___ as well as e-s, both of which e- acceptors accept

• all e- donors have ___ ___

• oxidized; reducing

• reduced; oxidizing

• protons

• reduction potentials

redox tower

• half rxns present at the top of the tower want to ___ e-s and “___ ___” the tower

• half rxns present at the bottom want to ___ e-s

• 2 half rxns together: e-s always wanna go “___” the tower

  • if two half rxns make the e-s go ___, the overall rxn is energetically unfavorable

• ____ form gives e'-s to ___ form

• what is the order of the written half rxns on the redox tower?

• donate; go down

• accept

• down

  • up

• reduced; oxidized

• [oxidized form]/[reduced form] (E0’) # of e’ transferred

e- transfer

• in the cell, e- transfers are facilitated by ___ ___ ___

• these are ___ that interact w/ enzymes which catalyze redox rxns, ___ e-s, and can then ___ to another site to ___ e-s to an ___ ___ on the redox tower

• examples?

• intermediate electron carriers

• coenzymes; accept; diffuse; donate; acceptor lower

• NAD+/NADP+, FAD+

high energy bonds

• high energy bonds are used as ___-___ ___ for energy

• high energy bond examples?

• low energy bond examples?

• short-term storage

• ATP→ADP, ADP→AMP, PEP, acetyl phosphate, acetyl-coA

• AMP→adenosine, glucose 6-phosphate

substrate-level phosphorylation

• a way to form ___

  • ____ ____ donated from ___ ___ to ___ to form ___

    • example of a donator?

• ATP

  • phosphate group; organic compounds; ADP; ATP

    • PEP

oxidate phosphorylation

• a way to form ___

• ____ membrane forms ___ to become less ___

  • powered by ___ ___ ___ (___)

    • H+ moves down a ___ (___ to ___ concentration) across a membrane

      • ____ to ____ of cell

• ATP

• energized; ATP; energized

  • proton motive force (PMF)

    • gradient (high; low)

      • outside; inside