BIO 112 Exam 1

Prion

  • A misfolded infectious protein. 

  • Formidable pathogen against animals and plants. 

  • Appears to cause degenerative brain diseases in animals (scrapie in sheep, mad cow disease, Creutzfeldt-Jakob). 

  • Can be transmitted in food, act slowly, and are virtually indestructible.

  •  Work by converting normal proteins into misfolded ones and aggregating into a complex to convert more

 


Pandemic

  • A global outbreak of disease (covid). 

  • An epidemic is a general outbreak (ebola).


Viral Envelope

  • Surround the capsids of the viruses found in animals. 

  • Derived from membranes of the host cell’s plasma membrane as the viral capsids exit. Contain a combo of viral and host cell molecules.

  •  Used as one of key variables to classify a virus as an animal virus (both the membrane and if they have an RNA genome). Viral glycoproteins on the envelope bind to the specific receptor molecules on the surface of the host cell. 

  • Some viruses form membranes from the host’s nuclear envelope and are replaced by an envelope made from golgi apparatus (herpesvirus).

 



Lytic Cycle

  • Bacteriophage replicative cycle that results in death of the host cell. 

  • A phage that only reproduces by the lytic cycle is a virulent phage.

 


Virus

  • An infectious particles that consists of genes and a protein coat

  • Much simpler structure than prokaryotes

  • Can cause a wide variety of diseases

  • We consider them “borrowed life”



Reverse transcriptase

  • Retroviruses use reverse transcriptase to copy the host’s RNA genome into their DNA 

  • HIV is a retrovirus that uses reverse transcriptase and causes aids

  • Enzyme carried by retroviruses


Emerging virus

  • Suddenly become apparent

  • HIV, AIDS, and COVID all suddenly just happened and caught everyone off guard

  • One cause of emerging viruses is mutation of existing viruses that make new viruses that spread more and are highly contagious

  • Another cause is the spread of a viral disease from a small and isolated population

  • Another cause is the spread of existing viruses from animals to humans

    • 3 quarters of emerging viruses are caused by this

    • The swine flu




Lysogenic 

  • The lysogenic cycle replicates the phage genome without destroying the host

  • The viral DNA molecule is incorporated into the host cell’s chromosome

  • Some prophages often express “lysogenic conversion” genes that give the host cell some advantage, and in response to environmental signals many prophages can undergo “induction” to enter the lytic cycle to produce progeny and kill the host cell.​



Host specific

  • Every virus has a host range: a limited number of host species it can infect

  • There must be a fit between the virus proteins and specific receptors on the cell


Paralogous

  • Result from gene duplication

  • A mutation duplicates and causes a exponential growth of mutations 

  • Can diverge within a species because they are present in more than one copy

Homology

  • Genetic similarities due to shared ancestry

  • Ideal phylogeny

  • Allows us to assume that organisms with similar morphologies are likely to be more closely related than organisms with different sequences

Basal Taxon

  • Diverges early on the history of a group and originates near the common ancestor of the group

  • Oldest organism (evolutionarily speaking)

Molecular Clock

  • A gene which mutates at a constant rate

  • Rate allows inferences to how long ago a mutation occurred

  • Extends phylogenies beyond the fossil record

  • Is not always accurate because

    • Some genes evolve irregularly

    • Rate of evolution deviates from average periodically, even in reliable clocklike genes

    • Same gene may evolve at different rates in different taxa

Sister Taxa

  • Groups that share an immediate ancestor that is not shared by any other group

    • Does NOT infer that one came from another 

Analogy

  • Genetic similarities due to convergent evolution

  • Not ideal - usually accidental 

  • Formed due to evolution honing in on a characteristic based on the environment

  • Convergent Evolution

    • Similar features in independent evolutionary lineages


Phylogeny

  • Evolutionary history of a species or group of species

  • Assumes the history is linear

  • Hypothesis - Not fact

Clade

  • Groups of organisms

  • Ex: Birds, frogs, etc

Monophyletic

  • Consists of the ancestor and all of its descendants

  • Only true clade

Paraphyletic 

  • Consists of an ancestral species and some, but not all, of the descendants

Polyphyletic

  • Distantly related species but none of their common ancestors

Derived 

  • A shared character found in all members of a clade but was not found in the common ancestor

Binomial Nomenclature

  • Method of naming species through taxonomy based on resemblance

  • Uses two names to identify species - Genus species

  • Species are more specific than the genus

  • Includes classifications like domain, kingdom, phylum, class, order, family, genus and species 

    • Dear King Phillip Came Over For Great Spaghetti

  • Domain

  • Broadest classification of binomial nomenclature

Horizontal Gene Transfer

  • Gene transfer from one species to another through prokaryotes

  • Transfer of genetic information between organisms that are not ancestors

  • Created gray areas between domains

Maximum Parsimony

  • The least amount of assumptions for an observation that are consistent with the facts.

Gram Stains

  • Scientists use gram stains to classify bacteria based on their cell wall

  • Gram Positive is purple

  • Gram negative bacteria is pink

  • Gram positive bacteria have a thick cell wall with peptidoglycan

  • Gram negative bacteria have a thin layer of peptidoglycan cell wall sandwiched between the cell membrane and another outer membrane

  • Gram negative bacteria are MORE RESISTANT to antibiotics, because it is harder to access the peptidoglycan cell wall




Peptidoglycan

  • A network of sugar cross linked with polypeptides

  • Archeal cells lack peptidoglycan, which distinguishes them from bacteria


Resistance (r plasmid)

  • Plasmids that carry a resistance gene

  • Antibiotics do not work against r plasmids

  • R plasmids also have genes that code for the pili that is used to transfer DNA between cells, so then the resistance spreads when DNA transfers


Antibiotics

Bacillus

  • Rod shaped cells

Cocci

  • Spherical shaped cells


Spherical

  • Spherical shaped cells


Binary fission

  • Prokaryotes replicate using binary fission every 1-2 min

  • Cells that reproduce from binary fission are genetically identical, and usually differ from mutations

  • When the cell duplicates its chromosomes and then splits in the middle


Slime layer

  • Sticky layer of polysaccharides or proteins surrounding the cell wall

  • NOT WELL OR ORGANIZED


Capsule

  • Slime layer of polysaccharides/proteins that surround the cell wall

  • WELL ORGANIZED


What do both the slime layer and slime capsule do?

  • Prevent cell from dehydration

  • Protect cell from host’s immune system

  • Adheres cells to other substances


Nucleoid

  • Where prokaryotic cells store their DNA

  • No membrane


Activated

Transduction

  • Phages carry prokaryotic genes from a host cell to another 

  • Generally  unintentional during the phage replication cycle


Transformation

  • Prokaryotic cells take foreign DNA from surroundings

    • Dead DNA


Conjugation 

  • When DNA is processed between 2 prokaryotic cells

  • How does CONJUGATION occur in E Coli?

    • A pilus of the donor cell attaches to the recipient

    • The pilus retracts and pulls the two cells together

    • DNA is transferred through a temporary structure called a MATING BRIDGE



Photoautotroph

  • Get energy from light and food CO2

Photoheterotrophs

  • Get energy from light and food from other nutrients

Chemoautotrophs

  • Get energy from chemicals and food CO2

Chemoheterotrophs

  •  Get energy from chemicals and food from organic nutrients/compounds

Hypertonic

Obligate Aerobe 

  • Require oxygen for cellular respiration


Obligate Anaerobes

  • Die from oxygen and require anaerobic respiration or fermentation


Facultative Anaerobes

  • Use o2 if present and anaerobic respiration/fermentation if not


F plasmid

  • Contains the f (fertility) factor is required for the production of pili

  • Cells containing this function as DNA donors

  • If only part of this is transferred the recipient cell will be recombinant


RNA

  • They type of nucleotide sequence lacks proofreading capabilities

  • Most plant viruses have this genome

  • Nearly all of this type of animal virus have an envelope and many DNA animal viruses do too


Antibiotics

  • They kill bacteria but not viruses or eukaryotic cells

  • They do not work on viral infections


Plasmodesmata

  • Channel protein found in plants that is responsible for spreading viral infections

  • Plant viruses spread disease by two major routes

    • Horizontal transmission, entering through damaged cell walls

    • Vertical transmission, inheriting the virus from a parent

Self Assemble

  • How viral particles piece themselves together just prior to release from a host cell

  • Scientists don’t know how it happens exactly


Lambda

  • A temperate phage widely used in biological research 

  • Infects bacteria with the lysogenic cycle


Vaccine

  • Harmless derivative of pathogenic microbes that stimulates the immune system to mount defenses against the harmful pathogen

  • Prevent certain viral illnesses

  • Can help to treat, not cure viral infections by inhibiting synthesis of viral DNA and by interfering with viral assembly


Retrovirus

  • Type of RNA virus that acts as a template for DNA synthesis. ‘Backwards’ virus. 

  • Use reverse transcriptase to copy their RNA genome into DNA (HIV)

 

rRNA

  • The most acceptable tree of life is based on phylogeny of genes coding for this


Lipids

  • What viral envelopes are made of. 


Mutation

  • One of several reasons for the high levels of bacterial genetic diversity. As well as rapid reproduction and genetic recombination. 

  • Mutations are typically low, but mutations accumulate rapidly with short generation times and large populations


Extreme halophiles

  • Live in highly saline environments. 

  • Ex. archaean that lives in Great Salt Lake