MIDTERM Gen Microbiology Dr. R SummerCourse 2026

Microbe

microscopic agent that interacts with its environment

(alive or not)

- includes viruses

microorganisms

a microscopic organism

- ALIVE

- ubiquitous

- cellular: bacteria, archaea

Acellular

no cellular structure

- viruses

- viroids

- prions

Prokaryotes

- Prokaryotic cells are smaller than eukaryotic cells

- lacking membrane bound organelles

- include bacteria and archaea.

- Smaller ribosomes 30S, 50s

Eukaryotes

- organisms made up of one or more cells that have a nucleus and membrane-bound organelles

- small part of domain classification

- ex: Protists, Yeast

3 Domains

Bacteria, Archaea, Eukarya

Bacteria

- 16 S rRNA

- in cell wall, PEPTIDOGLYCAN

- single celled

- most dont have membrane bound nucelons

- prokaryote

Archaea

- 235 rRNA

- Prokaryote

- single cell

- no peptidoglycan; Have PSEUDOMUREIN cell walls

- extremophile

- unique membrane lipids

extremophile

organism that grows under extreme or harsh conditions

(specially archaea)

Protists

single-celled or simple multicellular eukaryotic organisms that generally do not fit in any other kingdom

Acellular microorganisms

Viruses

Viriods

Satellites

Prions

Viruses

Acellular

- not alive b/c require host cell to replicate

- lack ribosomal RNA

- ex: bacteriophages

Viroids

Acellular

infectious agents composed of RNA

Satellites

Acellular

coinfect with viruses

Prions

Acellular

infectious proteins -> denatured

ViruS veruss Virion

VIRUS - intracellular form (already in cell)

ViRION - extracellular form

- not live long

Structure Gram + bacteria

in CELL WALL:

- 10% techoic acids (imbeded in cell wall)

- 90% peptidoglycan

CYTOPLASMIC MEMBRANE (w/thin it = proteins)

No outer membrane

thick peptidoglycan layer in cell wall retains crystal violet stain. in Gram staining -> purple

Gram + and Gram - value in medical diagnostic and treatment

many antibiotics target bacterial cell wall

(animal and human not have cell wall)

target gram-negative = Polymyxins

- disrupt lipid membranes in outer membrane

- many infectious caused by this bacteria more diffucult to treat

target gram-positive = PENICILLINS

- interfeer with contruction of cell wall. Prevent peptidoglycan from being assembled and repaired

Gram -

CELL WALL:

- outer membrane

(w/thin - phospholipids, LPS (lipopoly-saccharide layer) + lipid A

- periplasmic space

(w/thin- thin PEPTIDOGLYCAN layer)

CYTOPLASMIC MEMBRANE

Gram staining, appear pink

3 structures ALL CELLS have in common

- DNA

- Ribosomes

- Cell membrane

Archaeal CELL WALL

PSEUDOMUREIN - NAG but NO NAM

- maybe S-layers on top

NO peptidoglycan

process ALL cells do (Requirements for LIFE)

- METABOLISM:

build and breakdown compounds to take anergy and trasform into waste

- GROW:

increase the # cells

- EVOLVE:

genetic change

Differentiation

process some cells do

modification of cellular components to form new structures

helps with enduring extreme environmental changes

result of it in Bacteria = ENDOSPORES

What are Endospores? What is their purpose?

differentiation reults in endospore

nongrowing, heat-resistant and light-refractive dormant structure formed inside of some bacteria that can withstand adverse conditions

only produced by gram-positive bacteria and its production is usally triggered when a nutrient becomes limiting

Structure of endospores

multilayered

(some have) EXOSPORIUM

outer protenaceous layer

ENDOSPORE COAT

layer of spore specific proteins

OUTER SPORE MEMBRANE

CORTEX

composed of peptidoglycan

INNER MEMBRANE

developes from cytoplasmic membrane od vegetative cell

CORE

contain DNA and ribosomes

develops from the cytoplasm of the vegetative cell

dehydrated

Mycobacteria

acid-fast bacteria

has murein (peptidoglycan) & cytoplastic membrane (like GRAM - BACTERIA)

mycoplasma

group of pahtogenic bacteria related to gram + bacteria. they lack cell wall

Thermoplasma

Archaea with NO cell wall

grows at pH

Sporulation Cycle

1. asymmetric cell division

2. engulfment of forespore by mother cell -> outer membrane surrounds developing endospore

3. late sporulation: cortex and spore coat are formed

4. dehydration of spore -> using Ca2+ uptake, dipicolonic acid and SASPs (small acid-soluble spore proteins)

5. germination spore develope into a vegetative cell

Cell membrane (ALL CELLS)

semipermeable barrier

separates the inside of cell (cytoplasm) from external enviro

role - transport substances inand out cell

cell membrane structure Archaeal

can be bilayer or monolayer

glycerophosphate head + hydrophobic tails of repeating ISOPRENE LIPDS

- isoprene = 5-carbon hydrocarbon; NOT FATTY ACIDS

have an ETHER linkage that connects hydrophobic tails and glycerophasphate head groups.

ether link stronger than ester linkage, make some archaeal extremophiles

Cell membrane structure Bacteria

bilayer

primarily composed of phospholipid bilayer

Phosphoipid - glycerophosphate head + FATTY ACIDS tails connected by ESTER linkage

amphipathic

A molecule that has both a hydrophilic region and a hydrophobic region.

ex: phospholipids in Bacteria and Eukaryotic cell membranes

hydrophilic - glycerophosphate head

hydrophobic - fatty acids

Plamid

extrachromosomal DNA

Nucleoid

region inside the cell that has one closed circular chromosome

NOT nucleous

A non-membrane-enclosed region in a PROKARYOTIC cell where its chromosome is located.

Ribosomes

BACTERIA & ARCHAEA - 70S encoded by 16S RNA

50S

30S

EUKARYOTES 80S encoded by 23S

60S

40S

the ribosome of bacteria are encoded by what gene?

16S rRNA

the ribosome of Eukaryotes is encoded by what gene?

23 S

Storage inclusions

storage of nutrients, metabolic end products, energy, building blocks

Capsules

protective layers surrounding some bacterial cells

composed of polysaccharides

Organized, impermeable

enhance bacterial virulece by protecting agains phagocytosis and aiding in ADHERANCE to surfaces

protect from defication/ drying out

Slime layer

less organized than capsules

facilitates motility

precvents the cell from drying out

phagocytosis

A type of endocytosis in which a cell engulfs large particles or whole cells

polysacchorides

long chains of carbohydrates

monosaccharides - ex: glucose

capsules are made of these,

Peptidoglycan

Made of a sugar polymer and polypeptide- NAG and NAM

Cell wall of prokaryotes, but NOT ARCHAEA.

polypeptide

A polymer (chain) of many amino acids linked together by peptide bonds.

polymer

A long molecule consisting of many similar or identical monomers linked together.

flagella

A long, whip-like filament that helps in cell motility.

pattern of motility = flagellation

Many bacteria are flagellated, and sperm are flagellated.

Types of Flagella

Monotrichous - 1 flagellum

Lophorichous - cluster of flagella in 1 or both ENDS

Peritrichouse - spread over entiere surface

fimbria

A short, hairlike protein appendage of a prokaryotic cell that helps it adhere to the substrate or to other cells.

sweeps DNA

FOR attachment

often a virulence factor

pili

long

multiprotein Appendages that allow bacteria to attach to each other and to transfer DNA

play role in twitching, gliding, motility, biofilm formation and pathogenesis

cell structure bacteria

cell wall (SOMe bacteria have it some not) - peptidoglycan (murein) layer

cell membrane

cytoplasm

Glycocalyx

The external surface of a plasma membrane that is important for cell-to-cell communication

Metabolism

teh sum of all biochemical reactions an organisms needs for life

Catabolism

Metabolic pathways that break down molecules, releasing energy.

anabolism

Metabolic pathways that construct molecules, requiring energy.

ATP

(Adenosine Triphosphate) main energy source that cells use for most of their work

Reducing Power

ability to donate electrons using electron transfer reactions - i.e. redox reactions

What is the classification of humans and why?

We are Chemo-organo-hetero-trophs

because

chemo- energy source from molecules

organo - electron donors are organic cpds

hetero - carbon source is organic compounds

Classification of organisms that use sunlight as their energy source

photo-trophs

classification of organisms whose electron donors are inorganic compounds

litho-trophs

classification of organisms that use carbon dioxide as their carbon source

auto-trophs

classification of organisms that use ORGANIC COMPOUNDS as their carbon source

hetero-trophs

classification of organisms that use organic compounds as their electron donor

organo-trophs

classification of organisms that use preformed molecules as their energy source

chemo-trophs

electron tower

represents a range of reduction potentials for redox couples from the most negative at the top to the most positive at the bottom

greater the difference between the E' of the donor and the E' of the acceptor --> greater reduction potential, the more ATP that is generated

reduction potential

the tendency of a substance to gain electrons

according to the electron tower what are the best pair of molecules for greatest ATP generated

best electron donnor = glucose

best electron acceptor = oxygen

Fermentation

process that follows glycolysis

its purpoe is to recycle NADH into NAD+

metabolic process converts carbohydrates into acid or alcohol

No NET GAIN of ATP

ALWAYS ANAEROBIC process

it is a substrate-level phosphoralation

Under what conditiosn does fermentation happen and why?

Occurs in ANAEROBIC environment because in presence of oxygen cell prioritizes pathways that yield the most amount of energy- Aerobic respitartion

Lactic Acid Fermentation

break down glucose into 2 pyrubate and lactic acid (in this process NADH -> NAD+

then pyrubate is metabolized by enzyme lactate into lactate

Ethanol Fermentation

glucose -> pyrubate -> acetaldehyde (toxic) and CO2 (turn NADH -> NAD+) -> ethanol

Glycolisys

Occurs in the cytoplasm

glucose, 2 ATP, NAD+ -> pyruvate

results in formation 4ATP and NADH

primery pathway for cellular respiration AND fermentation

Can microbes only do glycolysis? Why?

NO b/c has limiting factor of NAD+ - the electron carrier

Aerobic respiration

occur in plasma membrane

Glycolysis -> pyrubate -> Krebs cycle -> respiration (electron trnasport chain)

electron transfer from reduced electron donnor to external electron acceptor (OXYGEN) .

> turns NADH -> NAD+ and produces A LOT OF ATP

Oxidative phosphoralation

Anaerobic respiration

ONLY in PROKARYOTES

electron transfer from reduced electron donnor to external electron acceptor (NOT Oxygen).

> turns NADH -> NAD+ and produces A LOT OF ATP

All EUKARYOTES respire OXYGEN because...

have a mitochondria and it does not allow to use any other electron acceptor other than oxygen

also b/c multicellular organisms need more energy, The reduction potential between oxygen and glucose is really big, which gives for the best production of ATP. This is why aerobic respiration produces more ATP than anerobic respiration.

oxidative phosphorylation

steps:

1. uses energy from redox reactions in Electron transport chain to phosphorylate ADP

builds H+ concentration gradient -used to-> create a lot ATP

2. Chemiosmosis - diffusion of ions across a membrane down their concentration gradient

where does oxidative phosphorilation happen?

in plasma membrane & Electron Transport Chain

where does susbtrate-level phosphorylation occur?

in cytoplasm

substrate-level phosphorylation

uses enzyme and susbtrate to DIRECTly catalizing the transfer of a phsophate group into APT -> ATP

creates small amount of ATP during Glycolysis and Krebs Cycle

Types of Phosphorylation

Substrate-level Phosphorylation

Oxidative Phosphorilation

Main differences between fermentation and Anerobic respiration

Fermentation is a substrate-level phosphorylation meaning it directly phosphoralates ADP into ATP by breaking the chemical bonds of organic compounds

the compound is oxydized and the redox reaction with NADH -> NAD+ and a fermentation product for excretion

there is NO NET GAIN of ATP

ANAEROBIC RESPIRATION = oxidative phosphoralation -> the phosphoralation of ADP into ATP is by electron transport chain. it is not a direct process.

you also have an electron transfer from a reduced electron donor to an electron acceptor to produce a LOTof ATP

Krebs Cylce (citric acid cycle)

process during cellular respiration that breaks down a carbon molecule to produce molecules that are used in the electron transport chain

process acetyl-CoA to produce energy trhough oxydation of organic compounds -> CO2, ATP, and electron carriers (NADH and FADH2)

Minimum temperature

temperature bellow which growth is not possible

optimum temperature

temp at which growth is MOST RAPID

maximum temp

temp above which growth is not possible

Psychrophiles

microbes with low temperature optima

(cold-loving)

optimun temp 4C (fridge temp)

NOT pathogens

Psychotrophs

Organisms that grow between 0-30 degrees celsius and are responsible for most food spoilage while in the refrigerator

temperature range in which can function = in body temperature -> fridge temp

Chaperones

proteins that assist other proteins in folding/ refolding

help proteins achive corect 3D shapes

Mesophile

midrange temp optima

HUMAN PATHOGENS

can function btw 10 -45C

Thermophile

high temp optima

NO human pathogen

optimal temp 45-65C

Hyperthermophile

VERY high temp optima

65- 140C

What do Microbes need to survive? Growth factors NEED to keep in mind when cultivating colonies

- Temperature

- pH

- Water activity (salt concentration)

- micro and macronutrients

- Oxygen or lack of it

Neutrophile

grow optimally at CIRCUMNEUTRAL pH range (-> pH 5.5 - 7.9)

Acidophile

grows optimally at a enviro with pH below 5.5

acid-tolerant AND need high concentrations of protons for cytoplasmic membrane stability

** cytoplasmic pH values ALWAYS need to be near neutrality

Alkaliphile

pH optima of 8 or higher in environment

** intracellular pH ALWAYS remain near neutral pH

in media, buffers are needed to

keep the enzyme solution at optimal pH

ensures enzyme remain catalitically active and unaffected by protons or hydroxyl ions generated in enzymatic reaction

water activity

measure of water availability

depends on concentration of solutes

more solutes -> bind to water -> less water available

aw - ration of vapor pressure of air in equilibrium with a substance or solution to the vapor pressure of pure water

0 - no free water

1 - pure water

positive water balance

(normal state of cell)

cytoplasm of cell has higher solute concentration than the enviro -> tendency water to diffuse into the cell

Halophiles

require at least some NaCl to grow