Bio 116 final exam EVERYTHING

Methanogens

live in swamps and marshes and produce methane as a waste product

• Methanogens are strict anaerobes and are poisoned by O2

Extreme halophiles

live in Highly saline environment

Extreme thermophiles

can survive in very high temps

Endotoxin

• Part of outer membrane of gram neg bacteria

• General symptoms

• Less toxic

• Hemorrhage shock and tissue necrosis

• Not actively secreted

• Non specific targets

Exotoxin

Produced inside bacterial cell and released out (secreted)

• Specific targets

• Ex Botulinum toxin and tetanus.

Virulence factor #1

Adhesion - glycocalyx, pili, fimbriae, biofilms

Virulence Factor #2

Invasion – Immune Response Evasion

Virulence factor #3

Colonization – Enzymes

Virulence factor #4

Tissue damage; Disease – Toxins, enzymes

Many antibiotics target

peptidoglycan and damage bacterial cell walls

Gram negative are typically ____ to treat because ____

Harder to treat because of a outer membrane 

Gram positive stain

purple

Where do we find bacteria in humans a lot

Skin, mouth, stomach

Symbiosis

two species live in close contact: a larger host and smaller symbiont

mutualism

both symbiotic organisms benefit

commensalism

one organism benefits while neither harming nor helping the other in any significant way

parasitism

an organism called a parasite harms but does not kill its host

pathogens

Parasites that cause disease

Biofilms

attach to surface with other species and creates a slimy/sticky substance….can be very toxic… (use each other’s waste products)

Where are biofilms found

• Freshwater/marine ecosystems – Rocks – Floating mats • Tissues in animals – Intestine, teeth • Man-made surfaces – Plastic tubing – Bottom of your sink

Autoinducers

Allows interspecies communication

Quorum

Allows communication and coordination of behaviors (strength in numbers help get things done that one species by itself could not)

Phases of growth: Lag

– Cells adjusting to new environment

Phases of growth: Logarithmic/Exponential

Cells divide like crazy!

Phases of growth: Stationary

– Nutrients dwindling, growth slows

Phases of growth: Death

Toxins building up

Endospores

prokaryotes metabolically inactive ….remain viable in harsh conditions for centuries

Events of stationary phase 

1. Production of endospores

2. Biofilm production

3. Toxin production (achieved through Quorum Sensing)

Nitrogen Fixation

some prokaryotes convert atmospheric nitrogen (N2 ) to ammonia (NH3 )

-Nitrogen is essential for the production of amino acids and nucleic acids

Obligate aerobes

require O2 for cellular respiration

Obligate anaerobes

re poisoned by O2 and use fermentation or anaerobic respiration

Facultative anaerobes

can survive with or without O2

Photoautotrophy

Needs light and CO2

Chemoautotrophy

Needs chemical energy and CO2

Photoheterotrophy

Needs light and organic nutrients

Chemoheterotrophy

needs chemical energy and organic

Phototrophs

obtain energy from light

Chemotrophs

obtain energy from chemicals

Autotrophs

require CO2 as a carbon source

Heterotrophs

require an organic nutrient to make organic compounds

Step #1 of horizontal Gene transfer (Transformation)

prokaryotic cell incorporates DNA taken up from environment

Step #2 of horizontal Gene transfer (Transduction) 

phage (virus that infects bacteria) carries prokaryotic gene from one host cell to another

Step #3 of horizontal Gene transfer (conjugation)

DNA transferred from one prokaryotic cell to another (bacteria sex)

Prokaryotic cells divide by

Binary fission

3 factors that contribute to prokaryotic genetic variation

– Rapid reproduction

– Mutation

– Genetic recombination

Flagella

Movement in prokaryotes (toward food or away from toxin)

Cell wall of archaea is made of

Isoprenyl ether

Plant cell walls made of

Cellulose

Fungi cell wall made of

Chitin

Fimbriae

allow them to stick to their substrate or other individuals in a colony

3 common shapes of prokaryotes

spheres (cocci), rods (bacilli), and spirals

Prokaryote cell

• No nucleus

• 1 ‘chromosome’ (circular molecule)

• Some also have plasmids (small circular DNA)

3 domains of life

Bacteria, archaea, Eukarya

Inversion

occurs when a chromosomal segment detaches, flips, and reattaches to the chromosome

translocation

occurs when a chromosomal segment detaches and becomes attached to a different chromosome.

Polyploidy

change in the number of each type of chromosome present

Aneuploidy

addition or deletion of a chromosome

missense mutation

point mutation that causes a change in the amino acid sequence of the protein

• often deleterious, meaning they reduce an individual’s fitness

silent mutations

Mutations that do not change the amino acid sequence of the protein

• said to be neutral, as they do not affect an individual’s fitness.

Translation phase #1 (Initiation)

Small ribosomal subunit binds to mRNA 5’-3’, start codon found, initiator tRNA charged with AUG binds p-site, large ribosomal subunit binds

Translation phase #2 (elongation)

• Amino acids are brought to the ribosome by tRNA

• The imitator tRNA is in the p-site. An amino acyl tRNA binds to the Codon in the A site

• Peptide bond formation occurs between amino acids on the tRNA’s in the P and A sites

Translation phase #3 (termination)

• A release factor bonds to the stop codon and hydrolyzes the polypeptide bond and tRNA in the p-site

• The polypeptide is released to go and allowed to do its job within the cell

• End of translation of that mRNA strand 

A site 

acceptor site for an aminoacyl tRNA

P site

where a peptide bond forms that adds an amino acid to the growing polypeptide chain

E site

here tRNAs no longer bound to an amino acid exit the ribosome

role of tRNA

carries a specific amino acid that can be transferred to protein

Why do transcription and translation occur simultaneously in bacteria

Because they lack a nucleus

Splicing

Introns are removed (spliceosomes)

Exons

coding regions of eukaryotic genes that will be part of the final mRNA product

introns

intervening noncoding sequences (not in final mRNA)

basal transcription factors 

Transcription in eukaryotes is initiated by: These factors begin transcription by matching RNA polymerase with the appropriate promoter region in DNA, a function analogous to that of sigma in bacteria