Evolution
These two key ideas explain how traits become more common when they increase reproductive success.
What are natural selection and fitness?
On a phylogenetic tree, this point represents a common ancestor.
What is a node?
This viral life cycle involves integration of viral DNA into the host genome.
What is the lysogenic cycle?
Unlike bacteria, archaea lack this molecule in their cell walls
What is peptidoglycan?
Disruptions to this internal microbial community can impair digestion, weaken protection against invading pathogens, and alter immune signaling.
What is the gut microbiota?
These structures share similar structure due to common ancestry, even if their functions differ.
What are homologous structures?
A group consisting of an ancestor and all of its descendants is called this.
What is a clade?
These infectious particles contain only protein and no nucleic acids.
bonus: give disease example
What are prions?
What is mad cow disease?
This process converts atmospheric nitrogen (N₂) into ammonia (NH₃)
What is nitrogen fixation?
When gut microbes help digest food, protect against pathogens, and regulate the immune system while also benefiting from nutrients provided by the host, this type of symbiotic relationship is occurring.
What is mutualism?
A hurricane randomly reduces a population size, drastically altering allele frequencies. This is an example of this type of genetic drift.
What is the bottleneck effect?
This principle states that evolutionary changes occur in the simplest way possible when constructing trees.
ex) If two species have wings, it is more______ to assume they inherited wings from a common ancestor that had wings
What is maximum parsimony?
(1 change: evolution of wings) rather than assuming wings evolved independently in both species (2 changes: independent evolution)
This hypothesis proposes that viruses evolved from more complex cellular organisms that lost genes over time.
What is the devolution (regressive) hypothesis?
This structured microbial community attaches to the surface of teeth, secrete a sticky extracellular matrix, and form a structured community that protects them from antibiotics and the immune system.
What is a biofilm?
At this developmental stage, dietary complexity increases significantly, leading to the establishment of a more stable, adult-like microbial community in the gut.
What is the toddler stage?
Match each mechanism to its affect on allele frequencies:
Mutation, Gene Flow, Genetic Drift, Natural Selection
(1) random change, (2) increases alleles that improve reproductive success, (3) creates new alleles, (4) moves alleles between populations
What is...
Mutation → (3) creates new alleles
Gene flow → (4) moves alleles between populations
Genetic drift → (1) random change (strong in small populations)
Natural selection → (2) increases alleles that improve reproductive success ?
When building a phylogenetic tree, this reference group is used to determine ancestral versus derived traits.
What is an outgroup?
Name the four major capsid types and briefly describe one defining feature of each.
Helical: Capsid proteins form a rod or spiral around the genome
Icosahedral: Symmetrical, 20-faced geometric structure
Enveloped: Capsid surrounded by a lipid membrane derived from the host
Head-and-tail (complex): Icosahedral head with a tail structure used for attachment and genome injection (common in bacteriophages)
Name the three mechanisms of horizontal gene transfer.
bonus: explain each one
What are transformation (Uptake of free DNA from the environment)), transduction (DNA transfer between bacteria by a bacteriophage (virus)), and conjugation (Direct DNA transfer between bacteria through a pilus (cell-to-cell contact))?
This major host process is influenced when certain gut microbial communities extract more energy from food, potentially contributing to increased fat storage (obesity) even with similar caloric intake.
What is metabolic regulation (or energy extraction from food)?
In a population of 10,000 individuals, 9% display a recessive phenotype for a genetic disorder. Give me recessive allele (q), dominant allele (p), and % of carriers.
What is:
q = 0.3
p = 0.7
2pq = 0.42 (42% carriers)?
Label the parts of this phylogenetic tree. (https://i.postimg.cc/hPmYjBfR/Screenshot-2026-03-03-at-12-06-00-AM.png)
word bank: branch point, polytomy, basal taxon, sister taxa, root
bonus: explain each one!
Root: Single lineage base
Branch point: Point at which a single lineage evolved
Basal taxon: Lineage that branched off early on, and no new branch was created
Sister Taxa: Two lineage that emerge from the same branch. (Does not mean similar organism)
Polytomy: More than two lineage that emerge from thesame branch. (Does not mean similar organism)
A certain virus infects human immune cells and permanently inserts a DNA copy of its genome into the host chromosome before producing viral proteins.
Explain how this virus alters the normal flow of genetic information and identify the type of virus it is.
What is the reversal of central dogma by going from RNA → DNA before following DNA → RNA → protein, and is it a retrovirus (HIV)?
Compare aerobic respiration, anaerobic respiration, and fermentation in terms of oxygen use and energy yield.
Aerobic → uses oxygen, highest ATP yield
Anaerobic → no oxygen, uses alternative electron acceptors
Fermentation → no oxygen, lowest ATP yield, no electron transport chain
A patient with poor diet, chronic sleep disruption, and repeated antibiotic use develops digestive issues and increased susceptibility to infections. Researchers observe reduced microbial diversity and altered immune signaling.
This condition describes a disruption in the normal balance of the gut microbial community known as this.
What is dysbiosis?