Cycle 1 Flashcards
T/F HIV is not severe
False: more deaths then malaria, influenza, Ebola and covid-19
T/F HIV is still happening
T
T/F HIV is distributed evenly in the world
F
T/F HIV vaccines don’t exist
T
HIV is more prevalent in Africa because?
Historically, it spread there first so it is like “ground zero”, chimpanzee range overlaps
_____ diseases spread (spill over) to humans from nonhuman animals
zoonotic
Zoonotic diseases are more likely between ______
closely related species
Zoonotic diseases are often not very harmful in the original host but _____
much more harmful in new host
____ has a long history of infecting nonhuman primates
SIV (simian immunodeficiency virus)
Where do viruses fit in the tree of life?
They cant because they are not considered living, they do have a evolutionary history
Viruses do NOT have
Lipid membranes surrounding cytoplasm
Viruses have ____ shell with _____ genome inside
protein, nucleic acid
The nucleic acid can be ___ or ____
DNA or RNA, single or double stranded
What drugs are harder to design and usually have more serious side effects?
Antiviral drugs
Retroviruses, including HIV,
have an ____ genome
RNA
Usually process is DNA, RNA, Protein, but _______ disobey central dogma
Retroviruses
Reverse transcriptase is very fast at what it does but makes a lot of mistakes expressed as _____
mutations
HIV has its genome in the form of RNA but it then converts to ____
DNA
HIV has a step called ______ that goes from RNA-DNA
Reverse Transcription
Viral ______ splices (pop into human nucleus) viral DNA into host DNA
Integrase
How does HIV become AZT-resistant?
MUTATION (always happening)
T/F Reverse transcription can happen in cellular life?
False: It is specific to retroviruses
Enzyme that carries out reverse transcription _____
Reverse transcriptase
_____ fuses with host immune cell
Virion
What would happen if injected with purified RNA (just RNA, no viral proteins) from HIV?
Probably be fine because RNA alone cannot transcribe to DNA should not be threat to human health
AZT was a wonder drug at first because it successfully blocked
RT, once disease in cell, cant spread
Viral DNA gets _____,______ and forms new virions
Transcribed, translated
Difference btwn Thymidine and AZT-Triphosphate
Thymidine has OH attached while AZT-Triphosphate has N3
We can target what step of Virus
Reverse transcription
The drug AZT is a nucleoside analog shaped almost like ______
Thymidine (T)
____ stalls synthesis of DNA strand
AZT
After months of AZT treatment, HIV becomes _____: Can still synthesize ___ even when AZT present
resistant, DNA
The structure of susceptible vs resistant diffrence
resistant: subtle change in active site, shaped so cannot attach to AZT not fool
RT makes errors in copying HIV genome (mutations). A ____ fraction of mutations improve AZT (not all)
tiny
Unless there’s another mutation, susceptible virions replicate into ____ virions, resistant virions replicate into _____ virions
susceptible, resistant
Soon becomes genetic and _____ variation in the viral population
phenotypic
AZT treatment: susceptible viruses fail to ______
reproduce
Some variants are able to reproduce in the presence of AZT =______ HIV
drug resistant
_____ cause variation in AZT resistance
Mutations
AZT resistance passed from _____ to _____
Parents to offspring
T/F not all virions reproduce
TRUE: some more successful then others
IF and only if AZT is present, some forms (_______) are more likely to reproduce than others (_______)
AZT-Resistant (huge advantage), AZT-susceptible
Viral population _____ over time
changes (more and more resistant)
Variation + Non random survival =
Evolution by natural selection
Mutations in the HIV genome occur when reverse transcriptase makes errors in copying RNA to DNA. What types of mutations are possible?
Any mutation is possible, because mutations occur randomly
New genetic variants (mutations) are ______ occurring, regardless of the environment
constantly
The environment (in this case, presence vs absence of AZT) affects which variants become more ______, not which variants ____
common, occur
A person infected with HIV is treated with the drug AZT. How does the viral population of HIV (virions) evolve drug resistance?
At any time, random mutations that improve drug resistance may occur. If the drug is present, virions with these mutations are better able to replicate, so the viral population becomes more resistant overtime
HIV’s high mutation rate also makes vaccine development _____
challenging
Mutations in other viral genes change the _____ of the virus
outer structure
Enables HIV to evade our ______
immune system
Difficult to generate vaccine to account for all ________
potential variants
There is still ___ universal HIV vaccine
NO vaccine, and perhaps never
T/F Even non-living things can evolve
T: virus
evolution can be very ____
FAST
Species _____ over time
change
Viral evolution involves themes such as:
-Evolutionary history
-Mutation and variation
-Natural Selection
-Humans as an evolutionary force
Why viruses are sometimes considered to be “alive”, and sometimes not.
Viruses as Alive:
Can reproduce, but only inside a host cell.
Contain genetic material (DNA or RNA).
Can evolve over time.
Viruses as Not Alive:
Cannot reproduce on their own.
Lack cellular structure (no organelles).
Do not metabolize or respond to stimuli independently.
They’re seen as existing in a gray area between life and non-life.
T/F American do not majority agree with the statement above/there is controversy
True
The very basic features of animal viruses and how they infect cells and replicate. You don’t have to understand or memorize in great depth here.
Basic Features of Animal Viruses:
Genetic Material: Either DNA or RNA (not both).
Protein Coat (Capsid): Protects the genetic material.
Envelope: Some have a lipid envelope derived from host cells, aiding in entry.
How They Infect Cells and Replicate:
Attachment: Virus binds to specific receptors on the host cell surface.
Entry: Virus or its genetic material enters the host cell.
Replication: Viral genetic material hijacks the host cell’s machinery to replicate itself.
Assembly: New viral particles are assembled inside the host cell.
Release: New viruses exit the host cell, often destroying it, and go on to infect other cells.
How HIV evolves resistance to drugs we use to treat it, and why the effectiveness of any new anti-viral drugs is likely to decrease over time
How HIV Evolves Drug Resistance:
High Mutation Rate: HIV has an error-prone reverse transcriptase enzyme, leading to frequent mutations in its genetic material during replication.
Selective Pressure: When antiviral drugs are used, they target specific parts of the virus. Mutant strains that survive the treatment can reproduce, while non-resistant strains are suppressed.
Rapid Replication: HIV replicates very quickly, giving it more opportunities to produce resistant strains.
Resistance Accumulation: Over time, HIV accumulates multiple mutations, leading to resistance against several drugs or entire drug classes.
Why Effectiveness of New Antiviral Drugs Decreases Over Time:
Mutation and Adaptation: As new drugs are introduced, HIV adapts through further mutations, leading to resistance.
Cross-resistance: Some mutations may cause resistance to multiple drugs within the same class, reducing the effectiveness of new treatments in that class.
Viral Diversity: HIV exists as a population of diverse strains (quasispecies), making it easier for some variants to develop resistance.
Incomplete Adherence: If patients don’t follow the prescribed treatment fully, it allows partially resistant strains to survive and multiply, hastening resistance development.
Limited Drug Targets: Antiviral drugs often target specific viral enzymes or proteins, so once mutations alter these, new drugs become less effective.
How viruses are similar to cellular life, and how they are different
Similarities Between Viruses and Cellular Life:
Genetic Material: Both contain DNA or RNA.
Evolution: Both can mutate and evolve over time.
Reproduction: Both produce offspring, but viruses require a host cell to do so.
Differences Between Viruses and Cellular Life:
Structure: Viruses lack cellular components like organelles, while cellular life has complex structures (nucleus, mitochondria, etc.).
Metabolism: Viruses don’t carry out metabolic processes; cells do.
Reproduction: Viruses can’t reproduce independently, unlike cells which can reproduce on their own through processes like mitosis or binary fission.
Response to Stimuli: Cellular life can respond to environmental stimuli; viruses cannot do so independently.
Evolutionary origins of HIV and why treating viral diseases is difficult
Evolutionary Origins of HIV:
Zoonotic transmission: HIV originated from primates. HIV-1 likely came from chimpanzees, and HIV-2 from sooty mangabey monkeys.
Cross-species transmission: The virus likely jumped to humans through hunting and consumption of infected primates, evolving into forms that infect human immune cells.
Mutation and adaptation: HIV evolved rapidly, making it highly infectious and able to evade the human immune system.
Why Treating Viral Diseases is Difficult:
High mutation rates: Viruses like HIV mutate quickly, leading to drug resistance.
Intracellular replication: Viruses hide inside host cells, making it hard to target them without damaging healthy cells.
Latency: Some viruses, like HIV, can remain dormant in host cells, evading treatment and reactivating later.
Principles underlying evolution by natural selection: heritable variation, non-random reproduction or survival, change in genotype of a population
Principles Underlying Evolution by Natural Selection:
Heritable Variation:
Individuals within a population have differences (variations) in traits, such as size, color, or behavior.
These variations are often genetic and can be passed from parents to offspring.
Non-Random Reproduction or Survival:
Some individuals have traits that give them an advantage in their environment (e.g., better camouflage or faster speed), allowing them to survive and reproduce more successfully.
Survival and reproduction are not random but depend on these favorable traits.
Change in Genotype of a Population:
Over generations, the frequency of favorable genes (genotypes) increases in the population, while less favorable ones decrease.
This leads to a gradual change in the population’s genetic makeup, driving evolution
How viral mutation rate affects the likelihood of developing a longterm effective vaccine, or developing longterm effective antiviral drugs
Viral Mutation Rate and Vaccine/Drug Challenges:
Vaccines: High mutation rates change viral proteins, making vaccines less effective over time (e.g., flu shots needing updates).
Antiviral Drugs: Mutations in viral enzymes lead to drug resistance, reducing long-term effectiveness.
Long-term Issue: Constant mutations make it hard to create lasting vaccines or antiviral treatments.
T/F humans evolved from earlier species of animals
Probably True
Humans have _____ from other animals
descended
Evolution remains _____ with the general public
controversial
These ideas ____ with some belief systems and creation stories
conflict
a set of
principles or beliefs
which together form
the basis of a religion,
philosophy, or moral
code:
Belief system
Belief/system is ____ intended to be tested or rely on evidence
NOT
conviction or
acceptance that
certain things are true
or real, faith:
- Belief
a coherent set of
testable hypotheses
that try to explain
facts about the
natural world:
Scientific theory
Scientific theory Must be _____ and _____.
testable, falsifiable
Other examples of scientific theory
Gravity, quantum theory, the big bang
Modern-day coelacanths
have barely changed at
all relative to their
ancestors that lived 400
million years ago
Gradualism and transitional forms
Examples of hypothesis/falsifiable statement
“AZT-resistant forms of HIV will increase in
frequency if a patient is taking AZT. These
forms will NOT increase in frequency if the
patient is not taking AZT”
(1) Evolution happens.
_____ frequencies in a population change
from one generation to the next
allele
If falsified,
____ the theory.
change
(2) All life is related through _____
______.
common ancestry
is this a scientific statement: “Positive thinking can cure cancer, if you try
hard enough”
NO, cant prove
Judge ruled
that Intelligent
Design should
____ be taught
in a science
class as an
alternative to
evolution
NOT (not scientific)
Individuals do ____
‘evolve’ within a
lifetime; populations
evolve from one
generation to the
next.
NOT
some possible observation or experimental
finding could prove the theory (or the hypothesis) to be ____
wrong
What is the theory of evolution?
Descent with modification from a common ancestor
Dolphins and sharks have not shared a common
ancestor for ~ 500 million years, but have a very
similar body shape
Speciation variational nature of evolution
Humans are _____ to chimpanzees: this
does not mean we are descended from
chimpanzees
related
(3) Speciation: _____ diverge into
_______ lineages
Lineages, daughter
- To which aspect(s) of evolutionary theory
does it relate? (EXAMPLES IN THE SLIDESHOW): Male birds with bright
feathers attract more
mates and produce
more offspring than
unattractive males
Selection is an important mechanism of evolution
Evolution is not
transformational, but
______.
variational
some transitional forms may be found in the ______
fossil record
takes many
generations to produce large changes
Gradualism and transitional forms
Selection generates _____, and explains
much evolutionary change (but not all).
adaptation
Cave salamanders live
in a dark environment,
but they still have
vestigial eyes and optic
nerves
Common ancestry + gradualism
Mutations are not directed towards the
____ of the organism
needs
Tetrapod vertebrates (non-fish) use their forelimbs
very differently, but generally all have the same
bones arranged in the same order
Common ancestry (homology)
T/F No living species are ‘more highly evolved’
than any other living species
TRUE
Selection results in adaptation, but usually
not in _____
perfection
All life on earth uses
pretty much the same
genetic code
Common ancestry
During embryonic
development, baby
dolphins grow then
resorb hindlimb buds
Common ancestry
What if we discover a
new life form with a
genetic code very
different from ours?
Common ancestry
Life on earth today has evolved ______
gradually
that _____ over time, giving rise to cells,
and continuing to change in different ways
and diverging into new and diverse forms of
life.
changed
originating from _______, perhaps a self-replicating molecule, that existed more than
4 billion years ago
one entity
- Life continues to _____.
evolve
Characteristics of a scientific theory; differences between scientific theories and belief systems; how scientific theories can be tested, potentially falsified, and updated.
Scientific Theory: Evidence-based, explanatory, predictive, testable, falsifiable.
Belief Systems: Based on conviction, not necessarily testable.
Testing: Through experiments and observations.
Falsification: Can be disproven with new evidence.
Updating: Refined with new data.
Major components of modern evolutionary theory: change through time, common ancestry, speciation, variational rather than transformational, gradualism, role of selection.
Change Through Time: Species evolve over time.
Common Ancestry: All life shares a common ancestor.
Speciation: Formation of new species from existing ones.
Variational: Evolution through variations, not transformation of individuals.
Gradualism: Evolution occurs slowly and gradually.
Misconceptions about the theory of evolution, and why they are incorrect.
“Evolution is just a theory”: In science, a theory is a well-supported explanation, not a mere guess.
“Humans evolved from monkeys”: Humans and monkeys share a common ancestor, not a direct lineage.
“Evolution is random”: Natural selection, not random processes, drives adaptation and survival.
“Evolution leads to perfection”: Evolution results in adaptations suited to specific environments, not perfection.
“Individuals evolve during their lifetime”: Evolution occurs over many generations in populations, not in individual organisms.
Both the spines of a cactus and the pitcher of a pitcher plant are actually modified leaves. Based on this evidence, what can be reasonably inferred about spines and pitchers?
The growth of spines, pitchers, and leaves on a plant have several similar steps, that originated from a shared, common ancestor.
How various real or hypothetical observations might support, undermine or revise components of evolutionary theory.
Support: Fossil discoveries showing transitional forms support gradualism and common ancestry.
Undermine: Finding complex structures without intermediates might challenge gradualism but usually leads to revisions or new hypotheses.
Revise: Genetic evidence revealing unexpected similarities or differences can refine our understanding of speciation and common ancestry.
