Final Exam Study Guide

Some microbial activity results in the production of oxygen

Bioremediation

Gut health and vitamin production

Production of food products: cheese, yogurt, alcoholic drinks, and fermented vegetables like kimchi

Play a role in nutrient cycling and nitrogen fixation; makes important nutrients available to plants

Found in root nodules of legumes

Used to produce products such as antibiotics

How are microbes beneficial?

Pathogenic microorganisms can cause disease

Can form biofilms on surfaces like pipes, damaging infrastructure

Biofilm can form on implants, posing a health risk to patients

Involved in food spoilage

How are microbes harmful?

Bright-field microscopy

Differential Interference Contrast (DIC) Microscopy

Confocal Scanning Laser Microscopy

Phase-Constract Microscopy

Dark-Field Microscopy

Fluorescence microscopy

Transmission Electron Microscopy (TEM)

Scanning Electron Microscopy (SEM)

What are the major types of microscopy?

Bright Field Microscopy

What type of microscopy is shown?

Differentail Interference Constrast (DIC) Microscopy

What type of microscopy is shown?

Confocal Scanning Laser Microscopy

What type of microscopy is shown?

Phase-Contrast Microscopy

What type of microscopy is shown?

Dark-Field Microscopy

What type of microscopy is shown?

Fluorescence Microscopy

What type of microscopy is shown?

Transmission Electron Microscopy (TEM)

What type of microscopy is shown?

Scanning Electron Microscopy (SEM)

What type of microscopy is shown?

The most common type of light microscope often requires dyes to improve contrast.

What is Bright-Field Microscopy?

Creates a relatively 3-D image of internal cell structures, helping one to view them without stains, by using a polarizer within the microscope condenser.

What is Differential Interference Contrast (DIC) Microscopy?

Uses a laser and a fluorescence microscope to create computer-generated, high-contrast images.

What is Confocal Scanning Laser Microscopy?

A phase ring is used to create increased contrast in the specimen against a dark background.

What is Phase-Contrast Microscopy?

A stop is used to block light from hitting the specimen directly, creating a dark background and allowing living specimens to be viewed with greater contrast.

What is Dark-Field Microscopy?

Used to view natural fluorescence or with fluorescent dyes such as DAPI.

What is Fluorescence Microscopy?

Blue Fluorescent dye that complexes with cell DNA

What is DAPI?

Allows internal cell structures to be viewed at very high magnifications (to the molecular level).

What is Transmission Electron Microscopy (TEM)?

Very effective for viewing 3-D external surface structures at high magnifications.

What is Scanning Electron Microscopy (SEM)?

Coccus

Coccobacillus

Bacillus

Vibrio

Spirillium

Spirochete

Pleomorphic

What are the major bacterial morphologies?

Diplococci

Streptococci

Tetrads

Sarcinae

Staphylococci

What are the major bacterial arrangements?

Coccus

What is the morphology of the bacteria shown?

Coccobacillus

What is the morphology of the bacteria shown?

Bacillus

What is the morphology of the bacteria shown?

Vibrio

What is the morphology of the bacteria shown?

Spirillium

What is the morphology of the bacteria shown?

Spirochete

What is the morphology of the bacteria shown?

Pleomorphic

What is the morphology of the bacteria shown?

Diplococci

What is the arrangement of the bacteria shown?

Streptococci

What is the arrangement of the bacteria shown?

Tetrads

What is the arrangement of the bacteria shown?

Sarcinae

What is the arrangement of the bacteria shown?

Staphylococci

What is the arrangement of the bacteria shown?

No membrane-bound organelles (no mitochondria or nucleus)

Unicellular

Circular DNA

Asexual Reproduction

Has a capsule

Has ribosomes

Has a cell membrane

Contains Cytoplasm

What is a prokaryotic microbe made up of?

Membrane-bound organelles

Both asexual and sexual reproduction

Can be unicellular or multicellular

Linear DNA

Has ribosomes

Has a cell membrane

Contains Cytoplasm

Has a nucleus

Has a Golgi Complex

Has a mitochondria

Has a rough endoplasmic reticulum

What is a eukaryotic microbe made up of?

Has ribosomes

Has a cell membrane

Contains Cytoplasm

Have a Flagellum

Have a plasma membrane

What are the similarities between eukaryotic and prokaryotic microbes?

Eukaryotes have:

- Membrane-bound organelles

- Multicellular

- Asexual and sexual reproduction

- Linear DNA

Prokaryotes have:

- NO membrane-bound organelles

- Unicellular

- Asexula reproduction

- Circular DNA

What are the differences between eukaryotic and prokaryotic microbes?

Gram-positive

Based on the structure of the cell wall, is this a gram-negative or a gram-positive bacterium?

Gram-neagative

Based on the structure of the cell wall, is this a gram-negative or a gram-positive bacterium?

1. Gram-positive cell wall

2. Plasma membrane

3. Cell wall

4. Teichoic acid

5. Peptidoglycan

6. Lipoteichoic acid

Fill out the structure of this bacterium.

1. Gram-negative cell wall

2. LPS

3. O polysaccharide

4. Core polysaccharide

5. Lipid A

6. Cell wall

7. Outer membrane

8. Peptidoglycan

9. Plasma membrane

10. Periplasm

Gram-positive bacteria have a thick layer.

Gram-negative bacteria have a thin layer.

What is the difference between a gram-negative and a gram-positive peptidoglycan?

Gram-positive bacteria have teichoic acids present.

Gram-negative bacteria do not have teichoic acids present.

What is the difference between a gram-negative and a gram-positive teichoic acid?

Gram-positive bacteria do not have an outer membrane.

Gram-negative bacteria do have an outer membrane.

What is the difference between a gram-negative and a gram-positive outer membrane?

Gram-positive bacteria stain purple (retain crystal violet).

Gram-negative bacteria stain pink (safranin counterstain).

What is the difference between a gram-negative and a gram-positive stain color?

Gram-positive bacteria are more sensitive to antibiotics.

Gram-negative bacteria are less sensitive/more resistant due to their outer membrane.

What is the difference between gram-negative and gram-positive antibiotic sensitivity?

1. Flood the heat-fixed smear with crystal violet for 1 minute

2. Add iodine solution for 1 minute

3. Decolorize with alcohol for 20 seconds

4. Counterstain with safranin for 1 - 2 minutes

Describe the technique used to distinguish gram-negative from gram-positive bacteria in the laboratory.

THe gram-positive cells are purple and the gram-negative cells are colorless.

After doing the third step of staining (decolorizer), what will happen to the gram-negative and gram-positive bacteria?

The gram-positive cells are purple and the gram-negative cells are pink to red.

After doing the fourth step of staining (counterstain), what will happen to the gram-negative and gram-positive bacteria?

Has a phospholipid bilayer with embedded proteins. Made up of hydrophobic tails and hydrophilic heads.

Is semi-permeable

Has anchor proteins that play inportant roles in cell functions.

What is the general structure of a cytoplasmic membrane (plasma membrane)?

Prevents passive leakage of solutes in or out of the cell.

Plays a role in energy conservation (proton motive force) for bacteria and archaea.

Waste removal

Communication with environment

What is the general function of a cytoplasmic membrane (plasma membrane)?

Swimming (flagellar) motility

Twitching motility

Gliding motility

What are the types of motility present in prokaryotes?

Swimming (flagellar) motility

What are the types of motility present in eukaryotes?

Driven by rigid, helical flagella made of flagellin protein; rotating motion

Describe the swimming motility of prokaryotes.

Requires type IV pili (retract and pull movement)

Describe the swimming motility of prokaryotes.

No external propulsive structures; instead, an intracellular tract with "gliding motors" driven by the proton motive force.

Describe the gliding motility of prokaryotes.

Cilia

Flagella

What are the types of flagella that Eukaryotes have?

Short flagella that move in Synchrony to move the cell

Describe the cilia of a eukaryote.

Whiplike motion, contains a cytoskeleton (tubulin), and is surrounded by the cell membrane

Describe the flagella of a eukaryote.

Prokaryotic flagellum:

- Made of flagellin protein (filament, hook, basal body)

- Powered by proton motive force

- About ~20 nm

Eukaryotic flagellum:

- Made of microtubules (9+2 arrangement) and dynein motors

- Powered by ATP

- About ~200 nm

How do prokaryotic flagella differ from eukaryotic flagella?

Only some gram-positive bacteria can produce endospores.

Bacteria that produce endospores are dormant cells that can tolerate extreme environmental conditions (heat, chemicals, radiation, and desiccation).

Bacteria can transition, after very long periods of time, into vegetative cells when the conditions are favorable.

What is the significance of endospore formation?

A theory that proposes that mitochondria and chloroplasts are descendants of respiratory and phototrophic bacterial cells that were engulfed by early eukaryotes; forming a symbiotic relationship with their hosts

Evidence:Both have their own circular DNA and ribosomes,Reproduce by binary fission, & Double membranes.

What is the endosymbiotic theory?

Both have their own circular DNA and ribosomes.

Reproduce by binary fission.

Have double membranes.

Explain the relevance of the endosymbiotic theory and chloroplast/mitochondria?

Both oxidation and reduction reactions occur together.

Oxidation = Loss of electrons OIL = Oxidation Is Loss)

Reduction: Gain of electrons (RIG = Reduction Is Gain)

In redox, how are oxidation and reduction related to electrons?

** in progress**

What are the major metabolic pathways?

Fermentative organisms:

- Reduce the pyruvate produced during glycolysis

- Pyruvate is the final electron acceptor

- NADH is oxidized back into NAD+ by reducing pyruvate

- Low ATP yield

Respiratory Organisms:

- Use external electron acceptors

- O2 is the final electron acceptor

- NADH donates electrons to ETC, regenerating NAD+

- High ATP yield

How is redox balance achieved by fermentative organisms vs. respiratory organisms?

Electrochemical gradient of protons (H⁺) across a membrane, storing potential energy.

What is the proton motive force in prokaryotes and eukaryotes?

It is generated by the electron transport chain (ETC) in both prokaryotes and eukaryotes.

Pumps protons across:

- cytoplasmic membrane for prokaryotes

- inner mitochondrial membrane for eukaryotes

How is proton motive generated by prokaryotes and eukaryotes?

Prokaryotes:

- utilize the proton motive force across the cytoplasmic membrane to generate ATP and power other cellular mechanisms (motility)

Eukaryotes:

- utilize the proton motive force at the site of cellular respiration, the mitochondria, to make ATP and activate transport of molecules

How is proton motive force utilized by prokaryotes and eukaryotes?

Substrate-level phosphorylation

Oxidative phosphorylation

Photophosphorylation

What are the 3 major mechanisms by which ATP is generated?

Substrate-level phosphorylation

Direct transfer of a phosphate group from a high-energy substrate to ADP (ex., Glycolysis, TCA cycle)

Oxidative phosphorylation

Energy from electron transport & PMF drives ATP synthase (ex., ETC in respiration)

Photophosphorylation

Light energy drives electron flow to create PMF and ATP (ex., photosynthesis)

How do the 3 major mechanisms by which ATP is generated differ?

Microscopic Cell Counts

Viable Cell Counts

Turbidmetric Method

What are the techniques used to measure microbial growth?

Quick and easy

Provides accurate counts of live and dead cells

What are the benefits of Microscopic Cell Counts?

Counts Viable cells in Colony-Forming Units (CFUs)

Counts only living cells

What are the benefits of Viable Cell Counts?

Quick, easy, and can be done without destroying samples

Continuous monitoring of growth

Optical density is porportional to cell number

What are the benefits of the turbidimetric method?

Dead cells cannot be distinguished from live cells (without special stains)

Small cells are difficult to see

Dibris may be mistaken for cells

Mobile cells have to be killed

What are the drawbacks of Microscopic Cell Counts?

Highly sensitive

Provides unreliable results from natural samples (soil or water)

Targets only known species, not unknown

Time-consuming

Not all microbes grow on media

What are the drawbacks of Viable Cell Counts?

Relies on a prepared standard curve

Clumping and biofilms can interfere with accurate readings

Measures total biomass (live + dead cells)

Less accurate

What are the drawbacks of the turbidimetric method?

1. Attachment: cell adheres to the surface

2. Colonization/Microcolony Formation: cells multiply, secrete EPS (Extracellular Polymeric Substances)

3. Development/Maturation: 3-D biofilm stucture develops

4. Dispersal: Cells release to colonize new surfaces

What are the major steps in biofilm formation?

Cause infections

Contaminate surfaces

Biofilm formation at implants, human joints, and indwelling devices can be very difficult to treat

Form dental caries

Corrosion and plugging of pipes

Contaminate fuel storage tanks where they form

Dimish the speed of ships by growing in their hulls

Protect microbes from antibiotics & immune defenses (ex, on catheters, teeth plaques, infections)

How do biofilms impact human health?

Formula: N_t = N_0 × 2^n

N_t = cell number at time "t"

N_0 = initial/starting number of cells

n = number of generations

How do you calculate exponential growth?

N_5 hours = (5) x 2^(300 minutes/10)

= 5 x 2^(30)

= 5 x 900

= 5,368,709,120 cells

After eating chicken salad for lunch on a very warm afternoon in South Florida, you place your leftovers in your backpack and forget about them until you get home 5 hours later. As you contemplate whether to finish off those leftovers, you think back to your Microbiology Lecture earlier in the day, where you learned how to calculate bacterial growth. If your chicken salad was contaminated with just 5 cells of a pathogenic bacterium that has a doubling time of 10 minutes, how would you calculate the current number of pathogenic cells?

Temperature

pH

Salinity

Oxygen

What are the environmental effects on growth?

Psychrophiles: Cold-loving (<15°C)

Mesophiles: Moderate temp (20-45°C; includes pathogens)

Thermophiles: Heat-loving (45-70°C).

Hyperthermophiles: Extreme heat (>80°C).

Classify organisms based on their ability to cope with temperature.

Acidophiles: Grow best <5.5; acidic conditions

Neutrophiles: Grow around pH 5.5-8 (most bacteria)

Alkaliphiles: Grow >_ 8; basic conditions

Classify organisms based on their ability to cope with pH.

Halotolerant: Can tolerate salt (e.g., S. aureus).

Halophiles: Require high salt.

Extreme Halophiles: Thrive in saturated salt (e.g., H. salinarum).

Osmophiles: can grow in high-sugar environments

Xenophiles: can grow in very dry envrionments

Classify organisms based on their ability to cope with salinity

Aerobes:

- Obligate aerobes: Require O₂.

- Facultative anaerobes: Grow with or without O₂ (prefer O₂).

- Microaerophilic: need oxygen ut at low levels

Anaerobes:

- Obligate anaerobes: Killed by O₂.

- Aerotolerant anaerobes: Don't use O₂ but tolerate it.

Classify organisms based on their ability to cope with oxygen.

They require a host cell to replicate and need host machinery (ribosomes and enzymes).

Cannot carry out metabolic processes on their own; lack metabolic pathways for ATP and biosynthesis.

Exist as inert virions outside a host.

Why are viruses considered obligate intracellular parasites?

Naked viruses:

- nucleic acid core (DNA or RNA) surrounded by a protein coat called a capsid.

Enveloped viruses have an additional lipid membrane surrounding the capsid.

Enveloped virus:

- nucleic acid core (DNA or RNA) surrounded by a protein coat called a capsid, AND have an additional lipid membrane (envelope; host-derived). surrounding the capsid with viral glycoproteins for host attachment

What is the typical structure of a virion in a naked virus or an enveloped virus?

DNA or RNA (never both)

ss (single-stranded) or ds (double-stranded); linear or circular

Segmented or non-segmented

What do viral genomes consist of (DNA, RNA, ss, ds)?

Plaque assays (counting Plaque Forming Units, PFUs) for bacteriophages

Tissue cultures for animal viruses

How do we measure the amount of virus in a sample?

1. The. ell-phafe mixture is poured onto a solidified nutrient agar plate

2. The mixture is left to solidify

3. Incubation allows for bacterial growth and phage replication

Describe the process of plaque assays.

1. Attachment

2. Penetration

3. Synthesis

4. Assembly

5. Release

What are the 5 steps in the viral replication cycle of T4 phage?

T4 recognizes carbohydrates specifci to the LPS outer membrane of E. coli and attch using tail fibers

What happens a the attachment stage in the viral replication cycle of T4 phage?

Tail pins make contact with cell surface, T4 lyzozyme makes a pore in the cell peptidoglycan layer, and viral genome enter the cytoplasm

What happens a the penetration stage in the viral replication cycle of T4 phage?

T4 genome enters the cell and host-sepcific protein produces ceases, turning into producing viral proteins instead (early, middle, and late proteins)

What happens a the synthesis stage in the viral replication cycle of T4 phage?

T4 virions are assembles, the DNA is packed into a phage head and other steps ensue

What happens a the assembly (maturation) stage in the viral replication cycle of T4 phage?

The phage genome encodes for enzymes that break the plasma membrane and the cell wall of the host

What happens a the release (lysis) stage in the viral replication cycle of T4 phage?

Temperate phages:

- Establish a long-term relationship with their host cells, entering a state called lysogeny

Virulent (lytic) phages:

- Kill their host once infection/replication begins through lysis

How does a virulent (lytic) phage differ from a temperate phage?