Exam 2 Flashcards
Bacteria
No nucleus
Archaea
Cells do not contain a nucleus; they have a different cell wall from bacteria
Eukarya
cells do contain a nucleus.
Branch Point
indicates where two lines diverges
Basal Taxon
A lineage that evolved early and remains unbranched
sister taxa
when two lineages stem fro the same branch point
Clade
a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor (also monophyletic group)
Monophyletic
consists of an ancestral species and all of its descendants
Paraphyletic
consists of an ancestral species and some, but not all, of its descendants
Polyphyletic group
includes distantly related species but does not include their most recent common ancestor
limitations of phylogenetics trees
-closely related taxa may look similar, but not always.
-if evolved under different circumstances (selection pressure) taxa may look every different
Taxonomy
grouping of classifying species together based on similarities & differences.
Taxa
hierarchy of groupings
Linnaean classification system
Domain, Kingdom, phylum, class, order, family, genus, species
Dear king philip came over for good soup
Advantages of phylogenetic classification
-tells evolutionary history
- does not “rank” organisms and does not suggest that 2 identically ranked groups are comparable.
Cladistics
method of hypothesizing relationships among organisms; divergence of taxa as a result of evolution
Characters
anatomical or physiological or behavioral or genetic sequences
Shared Ancestoral character
Characteristic found in the ancestor of a group.
Shared derived character
Characteristic only found in some of the organisms in a group. This is because this characteristic derived at some point, but does not include all of the ancestors in the tree.
Maximum parsimony
least amount of DNA base changes.
Principle of maximum parsimony
-fewest evolutionary events
-events occurred in the simplest, most obvious way
Horizontal Gene transfer
Transfer of genetic material from one species to another species.
More prevalent in prokaryotes
Mutations and HGT are important sources of genetic variation
Three primary models of HGT
Transformation
Transduction
Conjugation
Transformation
naked DNA uptaken by bacteria
transduction
Genes transferred from one cell to another by a bacteriophage
Conjugation
genes transferred between two bacterial via the pilus (direct contact)
Transposons
Jumping genes; mobile section of DNA that can move between genomes
endosymbiont
When a cell lives inside another cell with mutual benefit.
Endosymbiotic Theory
Eukaryotic cells are believed to have evolved from early prokaryotes that were swallowed.
ex: mitochondria and chloroplasts are both organelles suggested to have arisen via endosymbiosis.
Classic Tree model
Originated with Charles Darwin; does not account for HGT
Web and Network Models
Eukaryotes evolved not from a single prokaryotic ancestor but from a pool of many species sharing genes by HGT.
Ring of Life Model
Proposed that all three domains evolved from a pool of prokaryotes swapping genes via HGT.
Discover of Viruses
Electron microscope allowed the first views of viruses.
First seen / discovered virus
Tabacco mosaic Virus (TMV)
Three hypotheses aroun the evolution of Viruses
Regressive, Progressive or Escapist, Self replicating
Regressive Hypothesis
Viruses evolved from free-living cells or from intracellular prokaryotic parasites
Progressive or Escapist Hypothesis
Viruses originated from pieces of DNA that escaped from a host cell and gained the ability to to move between cells
Self-replicating hypothesis
Viruses may have originated from self-replicating entities similar to trasposons (jumping genes) or other mobile genetic elements
Viral morphology
- single virus particle, sized around 20-250 nm (super small)
- noncellular; lacks almost all cell components
- made up of nucleic acid core, capsid and SOMETIMES outer envelope.
Virus shapes
Helical, icosahedral, enveloped, complex
Helical
long and cyndrical
-> ex: TMV
Icosahedral
roughly spherical shaped (non enveloped)
-> ex: Adenovirus
Enveloped
have membranes surrounding the capsids
-> ex: Influenza virus
Complex/Head and tail
infect bateria and gave a head that is similar to icosahedral viruses and a tail shaped like helical viruses
-> ex: Bacteriophage
Genome
total genetic content of a virus; only codes for proteins that the virus can get w/o the host
Viruses that encode their own enzymes use?
RNA Dependant RNA Polymerase (RDRP)
Why are there more errors in the enzymes RNA viruses use?
RNA doesn’t have a self checker like DNA does, so mistakes go unchecked.
DNA Viruses
- Often double stranded but can be single stranded.
- Replication in nucleus
- Some may have DNA polymerase and so they’ll do replication in the host cell’s cytoplasam
-> ex: small pox virus
RNA Viruses
- Usually single stranded but can be double stranded
- Replication happens in cytoplasam
- Mutations happen very often bc RNA polymerase does not have a proofreader
-> Ex: Influenza viruses, coronaviruses.
Baltimore classification system
Groups viruses based on how the mRNA is produced during the replication cycle of the virus.
Group 1
- Double stranded DNA (dsDNA)
a. dsDNA -> mRNA
ex: Herpes Simplex
Group 2
- Single stranded DNA (ssDNA)
a. ssDNA -> dsDNA (intermediate) -> mRNA
-> Ex: Canine parvovirus
Group 3
- dsRNA
a. dsRNA -> ssRNA -> mRNA
-> Ex: Childhood gastroenteritis (rotavirus)
Group 4
- ssRNA (+)
a.) ssRNA (+) -> serves as mRNA -> directly translated in the host
-> Ex: Common Cold (picornavirus)
Group 5
- ssRNA (-)
a.) ssRNA (-) (complementary to mRNA) -> mRNA
-> Ex: Rabies (rhabdovirus)
Group 6
- ssRNA w/ reverse transcriptase
a.) ssRNA -> (reverse transcriptase) -> inserted into host genome -> mRNA
-> Ex: Human Immunodeficiency Virus (HIV)
Group 7
- dsDNA viruses w/ reverse transcriptase
a.) dsDNA -> ssRNA intermediate -> dsDNA (genome replication); geneome is dsDNA but is replicated through RNA intermediated, the intermediate may then serve directly as mRNA or as a template to make mRNA.
-> Ex: Hepatitis B virus
Reverse Transcriptase
An enzyme that can make copies of DNA from RNA and is found in retroviruses like HIV.
Steps of a Viral Infection
- Attachment
- Entry
- Replication and Assembly
- Egress (release)
Attachment
Receptors on the surfaced of the host cell bind to the virus capsid protein or virus envelope glycoproteins.
-> Viruses are really specific to the cell in which they attach themselves to.
Entry
Viruses may enter through two processes endocytosis (only way if they don’t have an envelope) or through fusion if they are enveloped
Replication and Assembly (DNA Viruses)
Use host cell proteins and enzymes (RNA & DNA polymerase) to replicate the virus’ DNA and transcribe virus’ RNA
Replication and Assembly (RNA Viruses)
RNA core as template for synthesis of virus’ genomic RNA and mRNA
the virus’ mRNA directs the host cell to synthesize the viral enzymes and capsid proteins to make new virons
Replication and Assembly (RNA Retroviruses)
Have RNA genome that must be reverse transcribed into DNA and then is incorperated into the host cell genome DNA
Egress (release)
May involve lysis and death of the host cell
OR
May involve budding, which does not directly kill the host cell (viruses leave the cell individually)
-> sometimes when a virus cell leaves, it takes some of the host cell’s membrane with it which allows them to have an envelope.
Horizontal Transmission
Transfer of a virus from one plant to another through damaged tissue.
Vertical Transmission
Virus is transmitted to the offspring of a plant from the parent.
Symptoms of Plant Viruses
-Tumors called galls
-abnormal cell proliferation (more cells due to increased cell growth & division)
-hypoplasia (decreased growth and virgor)
-Necrosis
Plant Viruses
-Most are ssRNA (i.e TMV)
-Because of their cell wall virus needs plants damage in order for entry
-Can cause devastating crop loss.
Animal viruses enter the host cell easily because?
Animal cells don’t have a cell wall and therefore are easier to penetrate.
Acute Disease
disease that causes a lot of symptoms for a short period and the goes away
ex: influenza and the common cold
Chronic infection
long term viral infections that don’t produce a lot of symptoms.
ex: virus that causes hepatitis C (it lives in in ur liver and causes damage)
Oncogenic Viruses
have the ability to cause cancer
ex: Hepatitis C virus (liver cancer), HPV (cervical cancer)
intermittent symptoms
Hide in the nervous tissue for lifetime and causes symptoms very rarely because they don’t produce proteins
ex: herpes simplex virus (cold sores)
Asymptomatic infection
When infection of a cell by a virus results in the production of new virons without causing symptoms in the host.
ex: human herpesviruses 6 and 7
Vaccines are prepared by using?
Live viruses, killed viruses, or molecular subunits of the virus
How are vaccines made?
they are made by attenuating (weakening) the disease causing virus.
Primary method of controlling viral diseases is through?
vaccination
Antiviral Drugs
Used to treat diseases cause by viruses; inhibits the virus by blocking the actions of one or more of its proteins
ex: Tamiflu
Prions
Contain no nucleic acids and cause fatal neurodegenerative diseases
ex: Mad Cow disease (cows), Creutzfeldt-Jakob Disease (bumans), Kuru, Scrapie, Chronic wasting disease
How do prions infect someone?
PrPc (normal) protein normally present in the brain, interacts with a PrPsc (misfolded version of the protein) and results in holes in the brain.
Viroids
Small circles of RNA only known to infect plants and can reproduce with any host cell. They do not manufacture their own proteins.
-> first viriod to be discovered was potato spindle tuber viriod (PSTV)
Anoxic
The earth’s atmosphere because there was no molecular oxygen
Which organisms were able to live on earth anoxic surface?
Anaerobic
Phototrophs
organisms that convert solar energy into chemical energy
Cyanobacteria
“blue-green algae,” evolved from phototrophs; the ancestral cyanobacteria began to oxygenate through photosynthesis and the increase O2 allowed the evolution for other life forms
Extremophiles
Bacteria and Archaea that are adapted to grow under extreme conditions (deep see vent, heat, dry, cold, radiation, etc.)
Culture Medium
Contains all the nutrients needed by the target microorganism can be liquid or solid
Pure Culture
a laboratory culture containing a single species of microorganism
Koch Postulates (1)
- Microorganism must be found in abundance in all organisms suffering the disease but should not be found in healthy organisms
Koch Postulates (2)
the microorganism must be isolated from a diseased organism and grown in pure culture
Koch Postulates (3)
the culture microorganism should cause disease when introduced to a healthy organism
Koch Postulates (4)
Microorganism must be re-isolated from the inoculated diseased experimental host and identified as being identical to the original specific causative agent.
Prokaryotes consist of which two domains?
Bacteria and Archaea
Four common structures in prokaryotes
- Plasma Membrane
- The cytoplasm
- A double stranded DNA genome
- Ribosomes
3 main shapes for prokaryotes
- Cocci
- Bacilli
- Spirilli
Prokaryote Structures
No membrane bound organelles and therefore their DNA is found in the nucleoid. Ribosomes are free and there are no microtubules
The features of a typical prokaryotic cell
Flagella, Capsules, pili
(these not found in all)
Gram Negative Bacteria
Proteobacteria, Chlamydias, Spirochetes, Cyanobacteria
Proteobacteria
-Gram Negative
!! - Includes Nitrogen fixing bacteria
-includes common gastrointestinal pathogen
Chlamydias
Gram Negative; all are endoparasites (live w/in animal cells)
-ex: chlamydia in humans causes STDS
Spirochetes
-Spiral shapes
-many free living (not dependent on another organism)
-> ex: syphilis (STD), Lyme disease (Borrelia Burgdorferi)
Cyanobacteria
-Generate O2 during photosynthesis
-Some are also Nitrogen fixers
-Cyanobacteria can make toxic “blooms”
Gram Positive Bacteria
-Gram Positive Bacteria
-Decomposers in the soil.
-include many pathogens
–> Bacillus anthracis (anthrax), Clostridium tetani (tetanus)
–> Staph and MRSA infections, Strep throat
Domain: Archaea
Includes extremophiles and methanogens
Cell wall in prokaryotes
lies outside the plasma membrane and protects and prevent cell lysis.
Bacteria cell walls are made with what?
Peptidoglycan
Archaea cell walls are made with what?
other structural polysaccharides. (do NOT have peptidoglycan)
Structure of prokaryotic plasma membrane?
Selectively permeable and the phospholipid bi-layer has two layers of lipid molecules.
Bacterial Membrane
fatty acids linked to glycerol
Archael Membrane
branched isoprene chains linked to glycerol
Plasmids
Circular DNA that replicates independently from chromosomes in viruses.
Steps in a Gram stain
- Crystal Violet
- Iodine
- Alcohol
- Counter stain (safrin pink)
Gram Stain
Reflects cell wall type; gram+ have a thick cell wall with peptidoglycan which traps the crystal violet and iodine. Gram- bacteria has a thin cell wall so the crystal violet gets washed out and the counterstain remains (pink).
Purpose of capsule and slime layer
Both serve the purpose of allowing the cell to stick to other surfaces, resist attacks from the host’s immune system, and hold in moisture. Slime layer is loosely attached and can be washed off while the capsule is tightly attached to the bacterial cell.
Flagellum
facilitates movement and bacteria can have multiple
Fimbriae
short pili; helps bacteria stick to each other and to other surfaces
Genetic diversity in prokaryotes
high rate of cell division = many mutations
One mutation can change phenotype
Mutations (except lethal ones) are passed on in clones
Selection favors the best clone
Short generation times = rapid evolution
Endospores
Understress, some bacteria pack up all their key resources and structures and go into a dormant/non-reproductive form. They can always turn back to normal later.
Nitrogen cycle
- N2 -> 2. NH3 -> 3. NO2- & NO3- -> N2
- Nitrogen fixation
- Ammonification
- Nitrification
- Assimilation
- Denitrification
Symbiosis
two species living in close relationship
Parasitism
smaller parasite benefit at expense of the host
Commensalism
one species benefits without any impact on the other species
Mutualism
both species benefit from each other.
exotoxins
produced by both gram- and gram+ bacteria
endotoxins
toxic outer membrane of gram- bacteria
