BIO3124 MIDTERM 1 UOTTAWA

What are the 3 domains of life?

Bacteria, Archaea, Eukarya

Morphology

Size of microorganisms

(3) Types of cell morphology:

Cocci in chains, Filamentous rods, and Spirochetes (spiral/curved)

Glycocalyx functions

-Thick outer covering of the plasma membrane
-Exists as a capsule or/ slime layer
-Helps to protect the cell from foreign particles

Glycocalyx (CAPSULE):

-Tightly attached, tight matrix, visible if treated with India Ink.
-Enable bacteria to adhere and attach different surfaces.
-The capsule helps to protect bacteria from a host immune system because the capsule surrounds the pathogen associated molecular patterns, which organisms will identify as foreign.
-Enables bacteria to avoid phagocytosis, and therefore will rely on the action of antibiotics to effectively destroy capsule coating.

Glycocalyx (SLIME LAYER):

-Irregular and amorphous
-Loosely attached, easily deformed, assists in surface attachment, protects against phagocytosis, prevents dehydration/ desiccation, provides hydration inside the cell.

Gram-positive bacteria

Bacteria that have simple cell walls with thick layers of peptidoglycan.

Gram-negative bacteria

Bacteria that have complex cell walls with thin layers of peptidoglycan but with lipopolysaccharide

Acid fast bacteria

Thick, outer lipid-rich layer composed of the fatty acid "Mycolic Acid", along with thin layers of peptidoglycan.

Function of plasma membrane

-Fluid phospholipid bilayer that encloses the bacterial cytoplasm
-Semipermeable; Regulates what molecules go into and out of the cell
-Gateway for transport of nutrients
-Prevents leakage
-Anchor for proteins that assist in chemotaxis, bioenergetics and transport
-Site of energy generation

Describe the bacterial cytoskeleton

-Implicated in cell division
-Shapes the morphology of the cell (Cell shape)
-Cell polarity
-Necessary for the movement of molecules to the right location within the cell
-Segregates extrachromosomal DNA such as plasmids and divides chromosomes to both poles of the cell to prepare for cell division.
-FtsZ, MreB and Crescentin

Eukaryotic cytoskeleton

-Made up of filamentous proteins
-Provides mechanical support to the cell and its cytoplasmic constituents
-Helps to maintain the shape of the cell by structural support
-Enables cell movement

Nucleoid

-Genetic information storage and gene expression.
-Not enclosed by a membrane.
-Responsible for controlling the bacteria's activity and reproduction.

Ribosomes

-Translation (Site of protein synthesis)
-Made up of RNA and proteins
-Ribosomes bind to mRNa and begin translation even before the transcription of the mRNA strand is complete.
-The ribosome reads the messenger RNA (mRNA) sequence and translates that genetic code into a specified string of amino acids, which grow into long chains that fold to form proteins.
-Decodes the message and the formation of peptide bonds.

Cell Inclusions

-Made up of various polymers
-Inclusions function as energy reserves, carbon reservoirs, and/or have special functions
-Enclosed by thin membrane
-Reduces osmotic stress
-Carbon storage polymers (Glycogen and Poly-β-hydroxybutyric acid (PHB)).

Endospores

-Formed during endosporulation or sporulation
-Resistant to high temperatures, radiation and other harsh conditions
-Survival mechanism to ensure that the cell can survive past the harsh conditions
-Vegetative or dormant part of the bacterial life cycle
-Structures that essentially protect the bacterial genome (DNA) in a dormant state when environmental conditions are unfavorable (High temperature, acidic conditions, lack of nutrients, etc).
-Present in only some Gram-positive bacteria and is not seen in Archaea

Mechanism of sporulation

-Genetic material aligns in the cell
-Forespore septum is created
-Cell splits into 1/3 and 2/3
-New spore becomes engulfed by its mother cell and continues to grow inside the mother cell
-Cortex is formed
-Cell becomes metabolically inactive and dehydrated
-Endospore is released

What is the advantage of sporulation?

They can protect the original genetic material even in the presence of unfavorable conditions, and can be reactivated from a dormant state when conditions change. The bacteria can then continue to grow and thrive

Flagella

-Found in bacteria
-Long thin appendages
-Come in different arrangements (Polar, lophotrichous, amphitrichous, peritrichous)
-Helical in shape
-Reversible rotating machine (CW) or (CCW).
-Increase or decrease rotational speed speed relative to strength of proton motive force7

Fimbriae

-Enable organisms to stick to surfaces or form pellicles
-Thin sheets of cells on a liquid surface

Pili

-Typically longer and fewer found per cell in consideration for fimbriae.
-Conjugative/ sex pili facilitate genetic exchange between cells.
-Type IV pili adhere to host tissues and support twitching mobility
-Motility of the cell
-Gene transfer

What structures are unique to bacteria?

Flagella and Cell wall

Polyextremophiles

Can survive in extreme heat conditions

Choanoflagellates

Beginning of multicellularity

When does dysbiosis occur?

When the gut microflora balance is out of sync between the good, protective bacteria and the harmful, bad bacteria. Equillibrium fails.

Explain Gram-Staining

-stains polymer peptidoglycan
-gram-positive stains purple, more peptidoglycan
-gram-negative stains red/pink, less peptidoglycan
-important for prescribing the right antibiotic

Resistant

-Changed in genetic code used to resist a particular stress.
-There must be something genetically different
-A genetically acquired tool to resist the toxic effects of an antibiotic.
-The organism's genome is changed, and the genetic material can be shared with other microbes

Persistant

Responding to a certain stress

What's a virus?

-A non cellular particle that infects a host cell and directs it to produce more particles
-Contains viral genome (DNA or RNA) and a protein capsid

What are the 2 ways that bacteriophages can replicate?

1- Lytic cycle
2- Lysogenic cycle

Lytic Cycle

Production of more viruses

Lysogenic Cycle

To infect the host cell and lyse it

Virulent

Viruses always lyse and kill host cell after infection

Temperate

Viruses replicate their genomes in tandem with host genome and without killing host

Virulent vs. Temperate

Virulent always kill host after infection, whereas in temperate they develop a relationship and virus does not kill the host cell after they replicate

process of lytic cycle

-Attachment:
Phage attaches by tail fibers to host cell.
-Penetration:
Phage lysozyme opens cell wall, tail sheath contracts to force tail core and DNA into cell.
-Biosynthesis:
Production of phage DNA and proteins.
-Maturation:
Assembly of phage particles.
-Release:
Phage lysozyme breaks cell wall.

Process of Lysogenic Cycle

-Phage infects cell
-Phage DNA is integrated into host cell
-Cell divides and prophage DNA is passed to daughter cell
-Phage DNA replicates and phage proteins are created
-New phage particles are assembled
-Cell lyses, releasing new phages

What are the 3 ways a virus can infect a host cell?

1- Bacterial phages
2- Directly fusing with the host cell membrane
3- Tricking the receptors of the host cell

What do bacterial phages do?

Directly attach themselves to the host cell and inject their viral genome into the host cell genome

How does a viral genome fuse with a host cell membrane?

It tricks the host cells receptors into allowing the insertion of the viral genome into the host cell genome

What is "Lysing"?

The cell bursts and dies. Caused by viral replication. Viral genome takes over the host cell and causes the virus to replicate and over take the host cell.

What is a provirus/prophage?

A virus/ phage that remains dormant until stimulated (lysogenic cycle). The viral DNA combines itself into the host cells DNA (chromosome).

Impatient Cycle=

Lytic Cycle

"Hitch a ride" or "Patient" Cycle=

Lysogenic Cycle

What does a bacterial cell contain?

-Cell membrane
-Chromosomal DNA
-Ribosomes
-Cell wall
-Flagella, Pili, Fimbriae, Capsules

Structural support of a cell

Cell wall or envelope

Cell wall function

Provides protection against osmotic pressure, allowing it to maintain its shape longer. Typically attached to the cell wall. Like a flexible mesh bag composed of peptidoglycan.

Hypertonic solution

A solution in which the concentration of solutes is greater than that of the cell that resides in the solution. Water particles move out of the cell. Cell membrane shrinks and detaches from cell wall. (Plasmolysis)

Hypotonic Solution

A solution in which the concentration of solutes is less than that of the cell that resides in the solution. Water particles move out of the cell. Cell wall counteracts osmotic pressure to prevent lysing and swelling of the cell.

Isotonic Solution

A solution in which the concentration of solutes is essentially equal to that of the cell which resides in the solution. No net movement of water particles. Cell membrane is attached to cell wall.

Peptidoglycan structure

-Polymer of disaccharide.
-NAG: N-acetylglycosamine -NAM: N-acetylmuramic acid. -Linked by Polypeptide Cross Bridge (PBP)
-Unique solely to bacteria.
-Excellent targets for antibiotics; widespread of antibitoics causes evolution of resistant strains (Immunity).

How does peptidoglycan grow?

-Via a synthesis complex that extends the chain of amino acids.
-Direction of extension is organized by a protein complex that includes MreB (Actin).

Bactericidal

Kills bacteria

Bacteriostatic

Inhibits bacterial growth

Antibiotics

Drugs that block the growth and reproduction of bacteria

Antimicrobials

Destroy bacteria, fungi, and parasites, depending on the particular drug, generally by interfering with the functions of their cell membrane or their reproductive cycle

Nosocomial infection

Hospital acquired infection

How is antibiotic resistance acquired?

To resist the toxic effects of an antibiotic. Genome changes. Antibiotic kills both bad and good bacteria. Drug resistant bacteria takes over and continues to grow.

What are glycocalyces?

Sticky external sheaths of cells that are loosely attached slime layers or firmly attached capsules. Formed of polysaccharide layers which confer significant strength.

S-layer

-An outermost cell surface layer composed of protein or glycoprotein
-Most common cell wall type
-Resist osmotic pressure
-Present on some Bacteria and Archaea (Gram positive and Gram-Negative)
-May contribute to cell shape and help protect the cell

How is DNA attached?

Attached to the envelope at the origin of replication on the cell's equator.

Stationary Cell Generation

Sessile

Mobile Cell Generation

Swarmer

Cell vesicle function

-Phage decoys
-Vehicles for DNA transfer
-Attractors of partner heterotrophs

Nanotubes

Allow bacteria to directly share proteins and mRNA useful under hostile conditions, such as when exposed to antibiotics

Carboxysyomes

Polyhedral bodies packed with the enzyme Rubsico for C02 fixation

Thylakoids

A flattened membrane sac inside the chloroplast, used to convert light energy to chemical energy for photosynthetic bacteria.

Gas vesicles in bacteria

Help move cells to optimal nutrient levels, provide buoyancy

Magnetosomes

Allows bacteria to orient themselves across a magnetic gradient.

Stalks

Membrane-embedded extensions of the cytoplasm

Monotrichous flagella

Single flagellum

Amphitrichous flagella

Flagella at both ends

Lophotrichous Flagella

A tuft of multiple flagella coming from one pole

Peritrichous flagella

Having flagella located in many places around the surface of the cell

Describe chemotaxis

-Is the movement of an organism in response to a chemical stimulus and direct their movements according to certain chemicals in their environment.

Random Walk

The cellular flagella interchange between running and tumbling

Run (flagella)

Random and biased, high sensory system drives movement toward favoured attractants, push cell forward, flagella bundle together (counter clockwise)

Tumble (flagella)

-Flagellum reverses direction, causing the cell to stop and change course
-Repellants cause numerous tumbles
-Rotate away, bundle falls apart, briefly stops and changes direction (clockwise), goes towards higher concentration of attractants ("Biased Random walk")

Attractrant concentraion increases and prolongs run=

More likely to run towards chemoattractant

Chemotaxis

Response to chemicals changes

Phototaxis

Response to changes in light

Osmotaxis

Response to ionic strength

Hydrotaxis

Response to water

Aerotaxis

Response to oxygen

Strain:

Subtype of species that differs GENETICALLY

Serotype

Strain of bacterium that carries a set of similar antigens on its cell surface, often many in a bacterial species

Where do archaea live?

Extreme environments and conditions

What do Archaea lack?

Peptidoglycan and have no nucleus.

What do bacteria and archaea have in common?

-Lack a membrane bound nucleus
-Possess singular, circular chromosomes
-Similar shapes

Can Archaea form endospores?

No, they cannot

What are Archaea immune to?

Lysozyme's and Penicillin

Pseudomurein (Pseudopeptidoglycan)

-Found in Archaea cell walls
-Polysaccharide similar to peptidoglycan
-Immune to lysozyme's and penicillin
-Composed of NAT and NAG

Hami

Fimbriae-like structures that radiate out from archaea, like barbed wire, function to securely attach archaea to biological and inanimate surfaces. Uses ATP and rotates. Acts like a grappling hook.

Structure of Archaella

-Simpler then bacterial or archaeal flagella
-Uses ATP rather then proton motive force
-Rotating flagella (Eukaryotes have whip-like flagella)

Some archaea can use light to power ATP without:

Photosynthesis; they use bacteriorhodopsin (Light gathering pigment found in vertebrate eyes.

Explain the genetics of Archaea

-Histones for tetrameres
-Nucleosome structure allows for the stacking of units
-Histone tails allow for epigenetic modifications (Controls transcription)

Gene structure of Archaea...

-Promoters;
a) TATA box
b) BRE (B-recognition element)
c) Formation of a pre-initiation complex =TBP, TFB

Outside of the nucleoid, prokaryotic cells may contain extrachromosomal DNA in ______.

Plasmids

Prokaryotic cells lack...

Membrane bound organelles

Large molecules must be actively transported through...

Membrane structures using cellular energy