microbio fall 2025

kutztown university applied environmental microbiology Dr. Aruscavage

what is the definition of micobiology?

study of organisms: acellular/ unicellular entities that require a microscope to see

what are the domains and are they eukaryotic or prokaryotic?

Eukarya: eukaryotic

Bacteria:prokaryotic

Archaea: prokaryotic

What is the benefits/ purpose of rRNA?

-DNA is harder to make than RNA

-it can be replicated

-high mutation rate

-can form bends and form a “double stranded” shape

-act as enzymes

endosymbiosis theory

prokaryotes combine to make eukaryotes

Ex: mitochondria and chloroplasts

what is the purpose of the mitochondria

ATP synthesis

what is the purpose of choroplasts

sugar is made in photosynthetic organisms to use as energy

what are features of the eukaryotic cell membrane?

-double layer

—phospholipid bilayer

—-made of glycerol, phosphates, fatty acids

what is the purpose of proteins in the phospholipid bilayer?

structure and transport

what is the purpose of sterol compounds in the phospholipid bilayer?

structure

are fungi unicellular or multicellular?

both. unicellular can ferment sugar to alcohol (yeast) and has true nucleus and organelles

how does fungi get its source of energy?

cannot make its own food, absorbs it

what type of reproduction does fungi have?

its spore bearing, sexual or asexual reproduction

what is budding?

a form of asexual reproduction commonly found in fungi where a new cell pinches off from an old cell where organelles are replicating. DNA synthesis coincides with budding and once there is a bud scar, it can no longer replicate at that site. SEXUAL reproduction starts when stress occurs

is yeast unicellular or multicellular? What is a well known thing that it does to convert once substance to another?

unicellular. It converts sugar to alcohol

what type of stressors can cause sexual reproduction in yeast?

• heat

• dehydration

• nutrient availability

• alkalinity/acidic envi

• UV light

• etc…

how does sexual reproduction work in yeast?

1. change shape to oblong (shmoo)

2. no longer can bud

3. release pheromones into the environment (shmoo is in response to pheromones)

4. that are either + or -

5. the opposite accepts and infuses

6. form zygote (can bud sometimes)

7. diploid (2n- 2 copies of genes)

8. meiosis to form 4 haploid (n) cells in a cluster with a protective coating (cyst)

what is mold?

microscopic, multicellular fungi

the mycelium, or mass of mold cells, is visible to the eye but not the individual cells

what is the reproductive structure of molds?

spores

-used in identification

-sexual or asexual

-hyphae

-sporulates in times of low nutrients, UV light, or other stressors

-has internal time clock

what is hyphae?

its filament that searches for food in fungi, its visible

what are some attributes/layers of hypae?

apical growth rate:

-growing zone is furthest out. It expands by adding vesicles & endoplasmic reticulum

absorption zone: releases enzymes to breakdown compounds for energy

-ATP synthesis

-no growth w/o this layer

Storage zone:

-nuclear division, wall formation, and active for transcription/ translation

Senescene zone:

-inactive region, stores building blocks for cell growth

wha is mycorrhizae?

symbiotic relationship bt/wn mold & plants

connects to root hairs

constant nutrient source

mineral/water uptake

endo- and ectomycorrhizae

what is dimorphic fungi?

yeast like or mold like, based on temp

what are protists like?

-most aquatic

-engulf bacteria

-saprophitic

-predatory

what are amoebioas like? some types?

-amoeba, phusarum, entomeba

-binary fission replication

-pseudopodia used to move

-chemotaxis- pushing toward chemical signals

-captures organisms by engulfing/ trapping

what are ciliates? some characteristics?

• predatory protozoans

• paramecium for ex.

• largest group of protozoans

• freshwater or salt water, sometimes soil

• primitive digestive system/mouth

• plasmodium is an infectious variety

what is algae? features?

photosynthetic protozoans

plant like

oxygenic photosynthesis

splits water to produce o2

freshwater or salt water

in photic zone

unicellular or colonial

chlorophyll a & b

what is phytoplankton?

algae and photosynthetic bacteria

has cell walls

composed of cellulose

osterocis tauri- .8um

how does algae reproduce?

sexual (mating type/ meiosis) or asexual (mitosis)

asexual caused by stress like Nitrogen

± mating types

± fuse to make 2n/diploid zygote

goes through meiosis

forms 4 cells in protective cyst layer

NO budding in algae, unlike yeast

what are lichens?

symbiotic relationship between fungi and algae

cyanobacteria

early warning for pollution- shrinks. especially air pollution and soil

has unique habitats like in sand and on rocks

survives heat, cold, and drought

slow growing

used for antibiotics and pigments

what are prokaryotes and their shapes?

bacteria- no compartmentalization

coccus(sphere)

rod like(aka bacilli)

-MRE- protein that gives rod shape

spirillum/spirochaete- spiral

-which depends on is how tight spiral are

-helps motility

what is the prokaryotic cell wall like/ benefits?

-mycoplasma bacteria has NO cell wall

offers shape

prevent internal pressure and helps with osmotic stress

no effect on nutrient transport

what is the S layer?

protein layer sitting outside cell wall

made of proteins/glycoproteins

only present in natural habitat

protects like cell wall and helps with osmotic pressure regulation

What is peptidoglycan?

only present in bacteria

also called murein

carbohydrate component and amino acid components

layered (3- 40 ish)

part that stains

What is NAM and NAG?

-N-acetyl muranic acid and N-acetyl glucosamine

-They alternate layers (peptide cross bridge) making cross links connecting peptidoglycan layers

What 4 amino acids make up the chains from (inside to outside) that connect to NAM?

• L-Alanine

• D-glutamic acid

• Diaminopimeruc acid (or Llysine)

• D-Alamine

In what positions do the amino acid cross linkages/ chains connect?

3 —> 4 (Diaminopimeruc acid to D-alamine) with a peptide bond

What is a pentoglycine bridge?

add glycine to the end in between the 3-4 connection of the amino acid chain. Connect with 5 glycines. Other option to the just 3-4 connection

How is a new cell wall created when a cell divides?

1. breaks down crosslinks (+NAM) using enzymes- autolysis

2. components of cell wall are made in cytoplasm (NAM, NAG, amino acids) and carried across cell membrane

3. carrier called bactoprenol carries it across and re-crosslinks

4. transglycosylase enzymes add NAM/ NAG to existing stucture, puts carbs in

5. transpeptidases rebuild crosslinks, new peptide bonds forms

   (all happens within minutes)

How is the gram positive cell wall composed? (bacteria)

• thick later of peptidoglycan (30-40 layers)

• teichoic acid- “rebar/support” improves stability, in mult. layers, adheres to surfaces

• lipoteichoic acid- adheres to cell membrane and wall

• Stain has a hard time leaving layer

How is the gram negative cell wall composed? (bacteria)

• thin layer of peptidoglycan (3-4 layers)

• paraplasm- layer of fluid between cell membrane/ wall and cell wall/ outer membrane

  -(nucleic?) transfer proteins

  -enzymes

• can be decolorized easier than gram pos

How is the gram negative outer membrane composed? (bacteria)

• -unique “2d” membrane

  -inner leaflet same as cell membrane

• lipid A innermost component

  -unique phospholipid with 2-3 fatty acid tails, possibly branched, and modified glycerol

• core polysaccharide gives negative charge

• O- antigen

  -chain of sugars that extend away from cell

  -strain specific even within spp. Immunity doesn’t transfer between strains

What is pourin?

transport protein in gram negative cell outer membrane

What is lipid A?

Technically an endotoxin referred to as B4

-released from cell

-immune response triggered

-can be released in response to antibiotics= bad

What is an acid fast cell?

neither +/- bacteria

-has small amount of peptidoglycan

-diff. staining procedure

-mycobacteric (mycolic acid unique to these)

~mycobacterium tuberculosis

~mycobacterium leprae (leprocy)

~very hydrophobic and prevents phagocytosis in white blood cells

-slow growers (days)

What is mycoplasma?

genus of bacteria

sterols in cell membrane

smaller than walled bacteria

some causes pneumonia

lacks cell wall

Does the domain Archaea have muramic or D-aminopimelic acid? Peptidoglycan?

no to all. These are the building blocks of peptidoglycan, so they have neither

What is the cell wall of Archaea like? Is there diversity in the cell wall?

Its composed of Gram- proteins

has Pseudomurein (Methanogens), which stains Gram+

Some do not have cell walls (ex. thermoplasma and ferroplasma)

What is glycocalyx in prokaryotic cell structure?

the outer region of the bacterial cell wall. Not in every cell

What is a capsule in prokaryotic cells?

usually polysaccharides released by cell

remains attached

helps with attachment to surfaces (polysacc. is sticky)

holds water- prevents desication

prevents phagocytosis (degredation)

makes hard for other cells to recognize it

what is Bacillus anthracis?

a bacteria that causes disease: is in anthrax

What is the slime layer in prokaryotic cells?

polysaccharides released from a cell

Does NOT stay attached

holds water and prevents drying

Can a cell have both a capsule and slime layer structure?

no, they only have one or the other

what is Pili? (pilus singular)

short hair-like structures extending from surface that help adhesion

composed of protein pilin

motile by “twitching”

used for genetic exchange

phages use as an attachment cite to infect bactera

what is Fimbriae?

hair or finger-like appendages on bacteria

many appear on cell

helps with attachment. blindly catches

important for pathogenesis

made of protein

what are flagella used for?

used for locomotion

has many unique forms

what is the basal body of flagella?

embedded to cell membrane/ wall

helps move flagella/ keep it connected

what is the hook on flagella?

small piece of protein, connects basal body to filament and aids in movement

what is the filament in flagella?

the long part of the flagella

whip like motion to move

what is chemotaxis?

attraction (or repellence) based on chemical signals

what is the polar/ monotrichous arrangement for flagella?

single flagellum at one pole

what is the lophotrichous arrangement for flagella?

tuft of flagella at one pole

what is the amphitrichous arrangement for flagella?

flagella at both poles

what is the peritrichous arrangement for flagella?

flagella all over

what is the amphilophotrichous arrangement for flagella?

tuft of flagella at both ends

what is spirochete flagella?

the flagella is inside, cell makes a fast drill action that can penetrate flesh

preset in bacteria causing lyme

describe the cell membrane in prokaryotic cells

phospholipid bilayer

hopanoids- sterol like compounds

embedded proteins

what are the functions of the cell membrane in prokaryotes?

1. active/ passive transport

2. ATP production

3. sugar production in photosynthetic bacteria

4. antibiotic resistance- efflux pump brings in/ ejects using ATP

5. energy conservation- proton motive force, use ions across membrane to generate E

compare the cell membrane of eubacteria and archaea

eubacteria

1. deglycerol

2. ester bonds bt/wn D-glycerol and fatty acids

3. fatty acids

Archaea

1. L- glycerol

2. ether bond

3. isoprene tails (not fatty acids)

4. exteme environments

5. can be branched (lipid monolayer)

6. ^interconnect

What is the nucleoid in bacteria?

holds dna of cell/ genome

no envelope (there are exceptions)

circular (also exceptions)

1 circular chromosome (exceptions)

what is supercoiling?

bending of genetic material

bend around DNA proteins

some pieces on end connect to membrane

has breaking points, H bonds not strong

releives stress with enzymes

What are topiosomerases?

cuts in the DNA to receive stress in molecule, enzymes

What kinds of topiosomerases are there?

1. DNA gyrase- allows supercoil to move in different directions

2. Topiosomerase 1- puts cuts in 1 strand, usually at a bend to relieve stress

what are plasmids?

extra chromosomal elements- carries non-essential functions; can be important/ beneficial adaptations

Ex. metabolism of unique compound, virulence to compete with other bacteria, antibiotic resistance

what do ribosomes do?

protein synthesis. Bacteria has 70-S, eukaryotes have 80-S type

what are some qualities of protein synthesis in bacteria compared to eukaryotes?

polyribosomes- chain next to nucleoid that makes multiple proteins from 1 RNA transcript.

mRNa can make > 1 gene

done immediately as they are being transcribed

eukaryotes CANNOT do this

describe transcription in bacteria

as RNA is getting made from the DNA molecule, ribosomes will bind and start making proteins. Its done fast due to the quick reproduction cycle of bacteria

what are inclusion bodies?

storage granules

stores minerals or large molecules

poly-beta- hydroxybutyrate is most common

-lipid polymer (hydrocarbon)

-storage molecule to make ATP

-like adipose tissue/ fat in humans

what is polyphosphate?

inorganic limiting reagent compound used to store phosphate as needed

what is magnetotactic bacteria

bacteria that orients themselves based on magnetic fields

magnetite inclusion bodies (Fe3O4)

adjusts levels to adjust magnatism

What is DNA made of?

(Deoxyribonucleic acid) made of:

phosphates

sugar (deoxyribose)

nitrogenous base- adenine, thymine; cytosine, guanine

what is semi-conservative replication

cells have 1 old piece of DNa and 1 new piece of DNA

What is the first step for bacterial DNA replication?

DnaA protein in cell triggers process

-cell wall increases

-cell membrane increase in volume

DnaA binds to origin of replication

-DnaB and DnaC bind to DnaA

What is the second step in bacterial DNA replication?

DnaB acts as a helicase

-unwind DNA

-break H bonds bt/wn bases

DnaC loads helicase

-single stranded binding proteins ensure it stays open

DNA polymerase 3 starts replication (some notes on slides for this)

What way does the leading and lagging strand do its thang?

in 5’ → 3’ direction

5’ → 3’ is leading

3’ → 5’ is lagging

-adds a small piece of RNA using enzyme primer

-helps DNA polymerase bind

What is the first step in termination of DNA replication?

1. 2 replisomes converse @ halfway mark from origin

What is the second step in termination of DNA replication?

1. Ter sequences on DNA

   1. stop replicase from continuing

   2. Tus protein binds to Ter and blocks helicase

What is the third step in termination of DNA replication?

1. Separate DNA

   1. topoisomerases cause a double strand break in the DNa

2. Dna is connected to mreB

   1. pulled away/ separates DNA

what does recombinase do?

re-attaches DNA molecule, fixes hole

when cell replicates, plasmid doesn’t, does it on its own

What is binary fission?

1 cell → 2 cells

-haploid

-transcription (making RNA) can occur w/ replication

What is the first step of binary fission? ON EXAM

1. cell elongation (rod shape)

   1. build up DnaA

   2. increase cell volume

What is the second step of binary fission? ON EXAM

1. DNA is separated

   1. rod shaped; spiral use mre-B

      1. makes sure new cells have DNA

      2. cocci don’t have mre-B

What is the third step(s) of binary fission? This step is broken up into a few sub-parts, sorry this is a long ass notecard. ON EXAM

1. septation

   1. select site for septum formation

   2. min. proteins

      1. move through cell, accumulate away from center

2. FtsZ protein creates Z-ring

   1. attaches to cell membrane in middle

   2. Z-ring-meshwork of proteins that align across cell

3. rebuild cell

   1. cell wall/ membrane build along Z-ring

What is the final step of binary fission? ON EXAM

1. Constricting Z-ring

   1. pulls cell membrane in

   2. separate 2 new cells

Not sure if this is technically part of septation based on how notes were given, but its the last thing soooo

What are the phases of the bacterial growth curve?

1. lag phase

2. log phase

3. stationary phase

4. death phase

What happens in the lag phase?

-pop. does not replicate

-recognizes envi.

-building energy storage

-metabolically active

-repair cell damage

-making enzymes for replication

What happens in the log phase?

Early log: bacteria are replicating at fastest rate

Late log: still replicating but slower

-some cell lines die; cant replicate anymore

-nutrients dwindle, waste increases

-space limited

Transition in genes:

-genes for stationary phase begin to be transcribed

-not all cells grow at same rate

What happens in the stationary phase?

-# cells replicating= # cells dying; carrying capacity

-nutrients decrease, waste increases

-cell stays metabolically active, but stops replicating; formant state to protect itself

-gets smaller

-produces secondary metabolites in this phase ONLY

→ things not needed but are beneficial like antibiotics or toxins

What happens in the death phase?

Don’t lose all bacteria but:

-more in cells dying compared to replication

What happens to mother and daughter cells in spore forming bacteria?

1 daughter cell is produced, mother disintegrates

Are spore forming bacteria gram + or -?

gram positive