Final - Part 4 Flashcards
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Phylogenetic trees & taxa
Define
Phylogenetic trees: diagrams that depict the hypothesized evolutionary relationships between taxa
Taxon: Groups of organisms
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Phylogenetic trees can be based on:
3 changes
- Morphological changes (physical/appearance)
- Developmental changes (works best on multicellular organisms)
- Molecular changes (DNA, Protein sequences)
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Taxon, Branch, Root, Node
Define them and how they’re used (draw the tree as an example)
- Taxon: Branch tip (sometimes extinct taxa included)
- Brnach: A taxon over time from ancestor to descendant
- Node: Represents speciation event (creation of new species)
Ancestral taxon that split 2 or more descendant taxa.
WARNING! Evolutionary change happens continually along branches, not instantaneously at nodes.
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- Monophyletic group
- Paraphyletic group
- Polyphyletic group
Describe them
Monophyletic group (Clauder)
* ancestral taxon + ALL its descendants
* Use snip test to determine! (only 1 cut allowed)
Paraphyletic group
* Last common ancestor + most of its descnedants
Polyphyletic group
* Organisms that arise from multiple common ancestors + excludes most descendants
* Used to identify species that have undergone Convergent evolution
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Parallel Evolution vs Convergent Evolution
Define thm with examples
Parallel Evolution: Trait results from shared ancestry: homologous trait
Convergent Evolution: Trait results fom shared lifestyle: Analogous trait
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3 Misconceptions of phylogeny
1.Living species at the tip of phylogenetic trees are more evolved than the extinct species closer to the root.
- It’s NOT about being more successful/complex.
2.Taxa appearing at branch tips are NOT equivalent to the ancestral taxa!
- The branch tips represent the extinct common ancestor between the spliting taxa
3.Phylogenetic trees are hypotheses
- Hard to test empirically.
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Biodiversity
Define
Diversity of living things that exist NOW in a given environment.
- Abundance (population per species)
- Species richness (how many different kinds species)
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How to assess biodiversity
Also define metabarcoding
- Extensive sequencing of DNA fragments taken directly from the environment.
- Metabarcoding: Relies on assessments of a short genetic sequence (RNA) that exists in all life.
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- How do we know which DNA fragment come from what species?
- How do we figure out how many of each species exist?
- Do the bio project 2 thing
- If you have the sequences out, just see how many times that sequences appear.
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2 Ways to see abundance
- Relative abundance: depicts the proportions each taxon/species exists within the total population.
- Absolute abundance: the *actual # *of individuals of each taxon/species
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At a minimum, viruses have:
2
- Proteins
- Nucleic acids
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- What do viruses impact?
- How big are viruses?
- Where/how viruses originated?
Just say vaguely. It’s ok
- Basically all living things
- Extremely small (20nm ~ 250nm)
- We don’t know lmao
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How to classify viruses
2 ways
Whether or not they contain a lipid membrane
1. Naked Virus: Does not have a lipid membrane. The virion usually consists of just capsid (a protein protecting the genome)
2. Enveloped virus: contain a small envelope of lipid membrane derived from the host. 1 more layer of protection!
How their genome is arranged
1. Genome made of DNA or RNA?
2. Genome is single- or double-stranded?
3. Genome is directly readable by a ribosome?
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Functions of viruses
3 main functions
Viruses modify the central dogma!
- DNA –> RNA –> Protein
- Viruses do reverse transcription: reverse transcribe RNA into DNA
Viruses exploit their host cell’s normal functions to generate more copies of themselves.
- Use cell’s DNA replication machinery
- Cell entry/exit mechanism
- Protein synthesis
- nom nom nutrients
Viruses cause disease
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How do viruses infect?
5 steps (it’s just summary)
- Attach to the host
- Enter the host
- Make virus parts
- Assemble new virions
- Leave the host cell
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Classify SARS-CoV-2
- Has an envelope
- Has a single-stranded RNA genome
- Genome is (+) = directy readable by a ribosome
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How does analyzing viral genome sequences help
2
- Helps us find out where that viruses come from
- Building phylogenetic trees with viral genome sequences he us determine relationships between viruses circulating in a given area on different parts of the world.
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Disease & Pathogen
define them
Disease: a condition that imparis normal cellular or tissue function ; may cause death.
Pathogens: An entity that causes disease in a host.
- Virus is pathogen
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Attach to the host
What is the normal function of the receptors?
Viruses attach to their specific host cell through some sort of receptor the host has.
- The normal function of the receptors are NOT for letting the pathogen in. (The virus exploits the function)
- The normal functions: regulates blood pressure & fluid/electrolyte balance.
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Make Virus Parts
Also, SARS-COV-2 case? HIV case?
Once inside, the virus makes use of all the cell’s normal function/systems to prduce parts for new viruses.
- Reverse transcription happens here
SARS-COV-2 case:
- The genome of SARS-CoV-2 is single-stranded RNA, has a 4’ cap and poly-A tail. The host cell will think “Hey, it looks like normal mRNA, let’s translate it”
- It’s not a retrovirus so instead of doing reverse transcription, they will make new copies of itself.
- To make new copies, this single-stranded RNA is the template to make complementary RNA, which is NOT READABLE by ribosomes to make it function as normal proteins. The only thing they can do with this complementary RNA is to keep making copies of the virus RNA……..
HIV Case:
- MERGE their genetic material with the host genome.
- These viruses remain with us for life.
- They can reaectivate: not once in life. anytime the genome is transcribed/translated the viruses activate too.
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Enter the host
Don’t forget the key words! Also, do all viruses enter this way?
Once there is an interaction, the virus enters the host using endocytosis (the host’s normal cellular systerm)
- Some viruses don’t do this! They just inject their genetic material into the cell.
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Assemble New Virions
New virions (virus particles) are assembled.
- Proteins come together to form a capside around viral genomes.
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Leave the host
Don’t forget the keyword! Also what do some other cells do?
Assembled virl particles now must leave the cell by using: Exocytosis
Some viruses just EXPLODE the host cell!
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Ecology of Viruses
1. Are viruses alive?
2. Does / how concepts of evolution apply to viruses?
3. If viruses disappeared today, what might happen?(2)
4. Which part of the virus is most likely to be selected (evolution sense)
- NO, but they’re definitely biological.
- Concepts of evolution apply to viruses too: variations… some variants are successful… the population changes over time with respect to the variants…
- Evolution slows down, we will be overrun with bacteria
- Spike protein is part that’s most likely to be selected. (very 1st step)
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Do plants have immune systems?
Yes
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2 kinds of immune system
describe them and compare them
Innate Immunity:fast, first line defence, recognizes general signs of pathogens (not specific), always present
Adaptive immunity:slow (takes some time to build up), triggered by infections (한 번도 infected 되지 않았으면 없음), generates immunological memory(if this infection happens again, our body is ready, specific
Adaptive immunity example: antibodies
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Antibody
Describe what it is
Proteins that bind to antigens (virus, bacteria) that triggers an immune response to fight off the antigen.
- Very specific - they can only interact with antigens that have matching shape
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How do antibodies help fight off viruses?
2 ways
1. Neutralization: Antibodies bond to the spike proteins, so the pathogens can’t interact with cells.
2. Opsonization: White bllod cells triggered to NOM NOM the pathogen
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What do our bodies do if antigens come into our body?
in terms of # of antibodies
Encounters with antigens result in a sudden increase in the matching antibodies being made.
These antibodies remain in our blood = immunological memory
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Cross-reactive
Define / describe what it is. When does it work?
If 2 antigens are similar enough, antibodies generated for 1 antigen may be cross-reactive.
-> The antibody works for both antigens.
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Variolation
Just describe the general idea and connection to cow pox
Old technique that used scabs from an infected individual to hopefully induce a milder form of small pox and result in future immunity.
John Fewster in the early 1800s realized that cowpox antibodies are cross-reactive against smallpox! (cowpox is a milder form)
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3 types of vaccines
1. Attenuated vaccines: uses weakened pathogens. (But what if the pathogens go back to normal?)
2. Inactivated vaccines: Uses killed or no longer disease-causing pathogens (not a strong vaccine :/ )
3. Subunit vaccines: Only part of the pathogen is used.
- The part that attacches to the host (surface proteins)
