Microbiology Unit 1

Prokaryotes

No nucleus or membrane bound organelles

• Bacteria, archaea

Eukaryotes

Nucleus and membrane bound organelles

• Algae, protists, fungi

Germ Theory of Disease

Many diseases are caused by germs/bacteria

• Lead to handwashing + cleaning surgical tools

Resolution

Smallest distance at which 2 objects can be separated and still distinguished

Detection

Determine the presence of an object

Refraction

When light enters a substance that changes its speed, making it bend

• Key to microscopy

Scattering

Small fraction of incident light is scattered in all directions

Bright Field

Dark image of light background

How to increase resolution of bright field

1. Decrease wavelength

2. Immersion oil

3. Wide lens close to object

Simple Stain

Adds dark color to all cells

Differential Stain

Adds dark color to specialized cells

• Gram

• Acid Fast

• Spore

Gram Stain

Positive: Bacteria retain stain due to thick wall

Negative: Bacteria don’t retain stain

Acid Fast Stain

Carbolfuchsin stains waxy layer of mycobacteria

Spore Stain

Stains spores

Steps of a Gram Stain

1. Methanol to fix

2. Crystal violet

3. Iodine to bind +

4. Ethanol wash

5. Safranin

Fluorescent Microscopy

Object absorbs light of defined wavelength (excitation), admitting lower E light and fluorescing (emission)

Fluorophore

Fluorescent chemical compound

Dark Field

Uses light scattering; light object on black background

Electron Microscopy

Uses e- instead of light

TEM

e- go through specimen, showing the inside (requires slicing)

SEM

e- on the surface show outside

Cryo-EM

No coating, shows both surface and interior using flash freeze

Hapanoids

Strengthen membrane; only in bacteria

Peptidoglycan

Part of the bacterial cell wall; attaches protein complexes between membranes to make net

• Gram +: Outside of only membrane

• Gram -: Between inner and outer membrane

Capsule

Sugar-coating bacteria use for attachment and protection from phagocytosis

Gram + Advantages

• Thick = resistant to drying out

• Surface proteins secrete right to surface

Gram + Disadvantages

• Susceptible to penicillin

• Less nuance to protein location

Lipopolysaccharide (LPS)

On gram (-) outer membrane; can be changed to hide from host

Gram - Advantages

• 2 membranes

• Periplasm is similar to organelles

• More antibiotic resistance

Gram - Disadvantages

• Less rigidity

• More susceptible in hostile env

Thylakoids

Capture light and generate ATP; engrained in cyanobacteria cell membrane

Carboxysomes

Use ATP to convert CO2 → sugar

Pilli

Appendage used for

• Movement

• Attachment

• Protein secretion

• DNA uptake

Rotary Flagella

Large, complex appendage for movement

• C-Clockwise = Movement

• Clockwise = Change of direction

Chemotaxis

Attractants and repellents signal sensor —> flagella, telling them which way to spin

2-Component Regulatory System (TCS)

How bacteria sense env and respond genetically

Periplasmic Space

Space between peptidoglycan and wall/membranes

Teichoic Acid

Cell shape, splits peptidoglycan during cell division

Biofilm

Bacteria acts as a multicellular unit

Quorum Sensing

At critical mass, signal released and bacteria change behavior

Catabolism

Breakdown molecules for E

Anabolism

Use energy to build molecules

Fermentation

Catabolism without electron transport chain

• Not very efficient, so bacteria consume a lot

• C is e- acceptor

• No citric acid cycle = less genes

Obligate Aerobes

Organisms that need O2 as e- acceptor

Anaerobic Respiration

Use other things to accept e- when oxygen is scarce

• Often can’t even handle oxygen

Other e- acceptors (Reduced)

• Nitrogen

• Sulfur

• Iron

• Carbon

Other e- Donors (Oxidized)

• Iron

• Nitrogen

• Sulfur

Nitrogen Fixation

N2 → NH3

Nitrification

(NH3, NO2, NH4) → NO3

Denitrifying

NO3 → N2

Assimilation

Using N to make DNA, RNA, AA etc

Dissimilatory Metal Reduction

Uses metal for ETC, and doesn’t assimilate them

• Sulfur

Aromatic Carbon Pollutants

Created from burning fuels

TCA Cycle

e’s taken from C-rings

Autotrophs

Pull CO2 and use it to make organic molecules

Heterotrophs

Use pre-formed organic molecules

Lithotrophs

Build with C, but don’t use C based molecules for E

Oxygenic Phototrophs

Generate O2, use sunlight to fix C

Unique aspects of archaea

• Ether linked membranes

• Histone homologs and reverse DNA gyrase

• Many RNA polymerases

• Pseudopeptidoglycan

Methanogens

Produce methane by breaking down products from other organisms

Sulfolobales

Live near volcanoes in 80-90°C and low pH, oxidize sulfur

Permeases

Substrate specific carrier proteins

Siderophores

Secreted by bacteria to bind to Fe and bring it to the cell

Endospores

Dormant, resistive structures that protect bacteria’s DNA

• Created when starved

• Gram +

Induced Differentiation

Isn’t necessary for life but is caused by environmental conditions

Obligate Differentiation

At some point in an organism’s life it has to differentiate to live

PVC

Lack peptidoglycan and has similar membrane bound structures to eukaryotes

CPR

Can’t culture, no ETC, cant make AA or nucleotides

• Obligate symbiotes

Volatile Fatty Acids (VFA)

Short-chain acids that are produced by fermentation flora and broken down by methanogens

Methanofuran

First enzyme in a chain that transfers H and reduces C in methanogens fermentation

Firmicutes

Low GC gram +

• Bacillus

• Staphylococcus

• Strepococcus

• Lactobacilluis

Bacillus

Spore-forming firmicutes

• B.Thuringiensis

B.Thuringiensis

Bacillus; Biocontrol agent, spores produce mosquito insecticide

Staphylococcus

Firmicutes; cocci in clusters and found on skin

Strepococcus

Firmicutes; cocci in chains found in mucus membranes

Lactobacillus

Firmicutes; Metabolizer used for probiotics

Actinobacteria

High GC gram +

• Harsh conditions

• Fuzzy structures

• Scavenge nutrients in soil

• Symbionts with ants and sponges

• Strepotomyces and C.diphtheria

Streptomyces

Actinobacteria; major antibiotic

C.diphtheria

Actinobacerial; only in pharynx and makes toxin that targets protein synth

Proteobacteria

Diverse metabolism and gram -

• Alpha-Epsilon

Alpha

Proteobacteria; Work with host

• Rhizobium

• Rickettsias

Rhizobium

N fixer

• Alpha

Rickettsias

Intracellular pathogen (Rocky Mt Fever)

• Alpha

Beta

Proteobacteria; Oxidizers and pathogens

• Nitrosomes

• Neisseria

Nitrosomonas

Used in wastewater treatment to oxidize ammonia to nitrite

• Beta

Neisseria

Causes meningitis and gonorrhea

• Beta

Gamma

Proteobacteria; metabolically diverse, gut micrboes and S lithotrophs

• Beggiatoa

• Thioplaca

• E.coli

• Proteus

Baggiatoa

Oxidize H2S → S

• Gamma

Thioplaca

Oxidize S in marine sediment

• Gamma

E.coli

Some can cause illness

• Gamma

Proteus

UTI + kidney infections; lots of flagella to swarm

• Gamma

Delta

Proteobacteria; S reducing and fruiting bodies

• Randos

• Bdellovibrio Bacteriovorus

Bdellovibrio Bacteriovorus

Infects other bacteria

• Delta

Epsilon

Proteobacteria; hostile conditions (gut, sea vents)

• Campylobacter

• Heliobacter

Campylobacter

Found in high intestinal track

• Epsilon

Heliobacter

Found in stomach lining

• Epsilon

Deep Branching Gram -

Spirochetes and bacteroidetes

Spirochetes

Deep branching gram -; Spiral cells with interal flagella

• T.pallidium

• Borrerlia Burgdorferi

T.pallidium

Syphilis

• Spirochete

Borrelia Burgdorferi

Lyme disease

• Spirochete