Cycles 1-5

How are viruses simular to cellular life?

• Viruses contain genetic material (DNA or RNA)

• They can reproduce, but only inside a host cell

• They experience mutations and evolve through natural selection

How are viruses different from cellular life?

• Viruses are not considered alive

• They do not have a plasma membrane enclosing cytoplasm

• Have a protein shell containing genetic information

• They are obligate parasites

What does it mean that viruses are obligate parasites?

They must infect host cells to reproduce and make proteins because they cannot reproduce independently

Why is treatment of viruses difficult?

• Viruses use the host cell to reproduce

• Drugs must target processes the virus needs but the host cell does not

• Difficult to not harm host cells and have serious side effects

• Viruses can evolve resistance to drugs

Where did HIV originate?

• HIV originated from SIV (simian immunodeficiency virus), which has a long history of affecting non-human primates.

• HIV first infected humans in sub-Saharan Africa.

What is a zoonotic disease, and what is spillover?

• Zoonotic disease: infectious disease that jumps from animals to humans

• Spillover: transer of a pathogen from one species to another

Why is spillover more likely beteen closely related species?

Closely related species habe more similar biological characteristics, making it easier for a pathogen to infect a new host.

Why can zoonotic diseases be more harmful in a new host?

The new host's immune system has no prior evolutionary experience or built-up defence against the pathogen, leading to an uncontrolled or overreacting immune response.

How many times did SIV spill over into humans, and which HIV form is most common?

• At least 5 seperate spillover events

• HIV-1 group M is the most common and aggressive form

What type of virus is HIV, and what cells does it infect?

HIV is a retrovirus with an RNA genome that infects immune cells.

What are the main steps of the HIV lifecycle?

1. HIV fuses with the host immune cell.

2. Reverse transcriptase converts viral RNA into double-stranded DNA.

3. Integrase inserts viral DNA into the host's DNA.

4. Viral DNA is transcribed and translated to produce new viruses.

What is the function of reverse transcriptase in HIV?

Converts viral RNA into double-stranded DNA.

What is the function of integrase in HIV?

Inserts viral DNA into the host cell's DNA.

What is AZT, and how does it prevent HIV replication?

• AZT is an antiviral nucleotide analog similar to thymidine.

• Reverse transcriptase may incorporate AZT into the growing DNA strand.

• Once AZT is added, DNA synthesis stops.

• This prevents successful HIV replication.

How do AZT-resistant HIV variants arise?

• Random mutations occur in the reverse transcriptase gene.

• Some mutations make HIV resistant to AZT.

• These mutations occur spontaneously, even when AZT is absent.

How does HIV evolve resistance to AZT over time?

• HIV's high mutation rate creates genetic variation.

• Some variants are AZT-resistant.

• When AZT is present, resistant variants are more likely to reproduce.

• Susceptible variants are less likely to reproduce.

• Resistance mutations are passed to offspring.

• Over time, resistant variants become more common.

Does AZT cause HIV to develop resistance mutations?

No. Resistance mutations occur randomly, regardless of whether AZT is present. AZT selects for resistant variants that already exist or arise randomly.

What are the three main principles of evolution by natural selection?

1. Heritable variation

2. Non-random survival or reproduction

3. Change in the genetic makeup of a population over generations

What is heritable variation?

• Individuals in a population have genetic differences.

• Mutations create new genetic variants.

• These differences can be passed from parents to offspring.

How does HIV demonstrate heritable variation?

• Some HIV variants are AZT-resistant, while others are susceptible.

• Resistance results from genetic mutations.

• Resistant variants pass these mutations to offspring.

What is non-random survival or reproduction?

• Not all individuals survive or reproduce equally.

• The environment determines which variants have an advantage.

• Individuals with advantageous traits are more likely to reproduce.

How does AZT demonstrate non-random reproduction?

When AZT is present, resistant HIV variants are more likely to reproduce, while susceptible variants are less likely to reproduce.

How does natural selection change the genotype of an HIV population?

• Resistant variants produce more offspring.

• Resistance mutations become more common over generations.

• The genetic makeup of the population changes.

What does “mutation proposes, selection disposes” mean?

• Mutations create new genetic variants randomly with respect to what is needed.

• Natural selection determines which variants become more common.

• The environment selects variants; it does not determine which mutations occur.

What is the difference between mutation and natural selection?

• Mutation: Creates genetic variation randomly with respect to the environment's needs.

• Natural selection: Non-randomly favours variants that survive or reproduce more successfully in a particular environment.

How does population size affect the likelihood of a specific mutation occurring?

• Larger populations have more individuals reproducing.

• This creates more opportunities for mutations.

• A specific mutation is therefore more likely to occur in a larger population.

• Smaller populations have fewer opportunities for that mutation to appear.

Why is HIV especially likely to produce drug-resistant variants?

• HIV reproduces rapidly.

• HIV has a high mutation rate.

• This creates many opportunities for resistance mutations to arise.

• Larger reproducing viral populations increase the chance that a resistant variant will appear.

Why does HIV's high mutation rate make antiviral drugs less effective over time?

• New genetic variants are constantly produced.

• Some mutations provide drug resistance.

• Resistant variants have a reproductive advantage when the drug is present.

• Over time, resistant variants become more common.

• The drug becomes less effective.

How does HIV escape recognition by the immune system?

• Mutations in HIV's genes change proteins on its outer surface.

• These changes make it harder for the immune system to recognize HIV.

• This allows HIV to evade immune recognition.

How does HIV's high mutation rate affect the long-term effectiveness of both drugs and vaccines?

• High mutation rate creates genetic variation.

• Some variants develop resistance to antiviral drugs.

• Other variants change their outer proteins and evade immune recognition.

• Natural selection can increase the frequency of advantageous variants.

• This makes it difficult to develop treatments and vaccines that remain effective long-term.

What is a belief and a belief system?

• Belief: A conviction or acceptance that certain things are true or real. Beliefs are not necessarily intended to be tested or supported by evidence.

• Belief system: A set of principles or beliefs that form the basis of a religion, philosophy, or moral code.

What is a scientific theory?

A coherent set of testable hypotheses that explain facts about the natural world.

What are the main characteristics of a scientific theory?

• Must be testable through observations or experiments.

• Must be falsifiable (possible to disprove with evidence).

• Must be revised or replaced if evidence falsifies it.

What is the theory of evolution?

Descent with modification from a common ancestor.

What does it mean that evolution happens (change through time)?

• Allele frequencies and phenotypes in populations change from one generation to the next.

• Evolution occurs in populations, not individuals.

What is common ancestry?

• All organisms share common ancestors.

• All life is related, either closely or distantly.

• Related organisms do not necessarily descend directly from one another.

What is speciation?

• An evolutionary lineage diverges into separate daughter lineages.

• This can lead to the formation of new species.

Why is evolution variational rather than transformational?

• Individuals do not evolve within their lifetimes.

• Populations evolve as the frequencies of inherited variations change over generations.

• This differs from Lamarck's idea that individuals transform during their lifetimes and pass acquired changes to offspring.

What are gradualism and transitional forms?

• Large evolutionary changes generally occur over many generations.

• Transitional forms may be found in the fossil record.

• These fossils can show characteristics linking ancestral and descendant groups.

What role does natural selection play in evolution?

• Favours inherited traits that improve survival or reproduction in a particular environment.

• These advantageous traits can become more common over generations.

• Natural selection generates adaptations.

• Explains much evolutionary change, but not all.

What is an adaptation?

An inherited trait that improves an organism's survival or reproductive success in a particular environment.

Why is it incorrect to say mutations occur because organisms need them?

• Mutations are not directed toward an organism's needs.

• Mutations generate genetic variation.

• Natural selection can favour beneficial variants that arise.

Why is it incorrect to say humans descended from chimpanzees?

• Humans did not descend from modern chimpanzees.

• Humans and chimpanzees share a common ancestor.

• Related ≠ directly descended from.

Why is it incorrect to say humans are more highly evolved than plants?

• Evolution does not have a goal or final stage.

• All living organisms have evolved from their ancestors.

• Humans are not evolutionarily superior to plants.

Why are evolution and natural selection not the same thing?

• Evolution = changes in allele frequencies in populations over generations.

• Natural selection = one mechanism that causes evolutionary change.

• Evolution can occur without natural selection.

Why doesn't natural selection produce perfectly adapted organisms?

• Natural selection favours traits that increase reproductive success.

• It does not produce perfect organisms.

• Adaptations depend on existing genetic variation and environmental conditions.

What is the main feature used to recognize evolutionary change through time?

Changes in allele frequencies or phenotypes in a population across generations.

What is the main feature used to recognize common ancestry?

Organisms sharing characteristics because they descended from a common ancestor.

What is the main feature used to recognize speciation?

One evolutionary lineage diverging into separate daughter lineages, potentially forming new species.

What is the main feature used to recognize variational evolution?

Changes in the frequency of inherited variations across generations, rather than individuals transforming during their lifetimes.

What is the main feature used to recognize gradualism and transitional forms?

Large evolutionary changes accumulating over many generations, with possible intermediate forms preserved in fossils.

What is the main feature used to recognize natural selection?

Individuals with advantageous inherited traits survive or reproduce more successfully, causing those traits to become more common.

How can evolutionary change occur without natural selection?

Allele frequencies can change through other mechanisms, such as genetic drift, where changes occur by chance.

What is NASA’s definition of life?

A self-sustaining chemical system capable of Darwinian evolution.

Which features of NASA's definition of life do viruses have?

• Contain genetic material (DNA or RNA).

• Experience mutations and heritable variation.

• Can evolve through natural selection (Darwinian evolution).

Which features of NASA's definition of life do viruses lack?

• Are not self-sustaining.

• Cannot reproduce independently.

• Depend on host cells for protein synthesis and replication.

Why are bacterial and fungal infections often easier to target with drugs?

• Bacteria and fungi are cellular organisms.

• They have cellular structures or processes that differ from human cells.

• Drugs can target these differences, such as bacterial cell walls or fungal cell membranes.

What is the Scale of Nature (Scala Naturae)?

The historical idea that organisms can be arranged in a fixed hierarchy from simple or inferior forms to complex or superior forms.

Why is Scale of Nature thinking incompatible with modern evolutionary theory?

• Evolution does not follow a ladder of progress.

• Organisms are not ranked as more or less evolved.

• Evolution produces branching lineages, not a hierarchy.

• All living species have been evolving since their common ancestors.

How did Lamarck explain evolution?

• Individuals change during their lifetimes through use or disuse of traits.

• These acquired characteristics are passed to offspring.

• Evolution occurs through transformation of individuals.

How did Darwin explain evolution?

• Individuals within populations have inherited variation.

• Some variations improve survival or reproduction.

• Natural selection favours advantageous inherited traits.

• Populations change across generations.

What are homologous traits?

Traits shared by different species because they were inherited from a common ancestor, even if their functions differ.

What are analogous traits?

Similar functions or appearances that evolved independently, rather than being inherited from a common ancestor with that trait.

What is convergent evolution?

When different evolutionary lineages independently evolve similar traits due to similar environmental pressures.

What is a chromosome?

A DNA molecule packed with proteins. Before DNA replication, each chromosome consists of 1 chromatid

What is a chromatid?

One DNA molecule within a chromosome. After DNA replication, each chromosome contains 2 sister chromatids.

What are sister chromatids?

• Identical copies of a chromosome formed during S phase

• Connected at the centromere

• Considered one replicated chromosome while attached

What is the centromere?

The region of a chromosome where sister chromatids remain connected and where the kinetechore forms for spindle attachment.

What are homologous chromosomes?

• Chromosomes of the same type

• Contain the same genes at corresponding locations

• May carry different versions (alleles) of those genes

What is the difference between homologous chromosomes and sister chromatids?

• Homologous chromosomes: Same genes but may have different alleles

• Sister chromatids: Identical copies produced by DNA replication

What is a genome?

All the genetic information contained in one complete set of an organism’s chromosomes

What does the n-value represent?

The number of different chromosome types in one complete chromosome set.

What does the coefficient of n represent?

The number of complete chromosome sets in a cell, also known as ploidy

What does 1n, 2n, 3n, and 4n mean?

1. Haploid (1 set)

2. Dipoid (2 sets)

3. Triploid

4. Tetraploid

What is the C-value

The amount of DNA in one complete, unreplicated haploid genome, measured in base paids (bp) or DNA mass (pg)

What does the coefficient of C represent?

The total amount of DNA in a cell expressed as multiples of one unreplicated haploid genome

What is the difference between n and C?

n = number of chromosome sets

C = amount of DNA

What are n and C during G1 in a diploid cell?

2n, 2C.

• The cell has 2 chromosome sets, and DNA has not yet been replicated

What happens to n and C during S phase?

• DNA replication doubles C

• n remains unchanged

• Diploid cell: 2n, 2C —> 2n, 4C

What are n and C during G2 in a diploid cell?

2n, 2C.

• DNA replication is complete, and each chromosome contains 2 sister chromatids

What happens to n and C after mitosis and cytokinesis?

Each diploid daughter cell has 2n, 2C

Why doesn’t DNA replication change ploidy?

DNA replication produces sister chromatids, not additional sets of homologous chromosomes

Why can C change without n changing?

DNA replication doubles the amount of DNA but doens not increase the number of chromosome sets

What is the C-value paradox

Genome size does not necessarily correspond to organismal complexity. Less complex organisms can have larger genomes than more complex organisms.

What 5 things cause differences in genome size?

• Whole genome duplication

• Transposable elements

• Repetitive and noncoding DNA

• Pseudogenes

• Long introns and intergenic regions

What is whole-genome duplication?

Duplication of an entire set of chromosomes, increasing the number of genome copies

Whst are transposable elements?

DNA sequences that can mpve pr copy themselves into different locations within the genome

How do you determine ploidy from a karyotype?

Count how many homologous chromosomes are present in one chromosome group.

• That is the coefficient of n

How do you determine the total chromosome number?

Multiply the n-value by the ploidy coefficient

Total chromosomes = n-value x number of chromosome sets

How do you determine the coefficient of C from a karyotype?

Count the chromatids of one homologous group. Each chromatid represents one copy of that chromosome type’s DNA

How can you tell whether chromosomes have replicated in a karyotype?

Unreplicated chromosome: one chromatid

Replicated chromosome: 2 sister chromatids connected at the centromere

What are n and C throughout meiosis in a normal diploid organism?

• Before S phase: 2n, 2C

• After S phase: 2n, 4C

• After meiosis I: 1n, 2C

• After meiosis II: 1n, 1C

What happens during meiosis I?

Homologous chromosomes seperate, reducing the number of chromosome sets from diploid to haploid

What happens during meiosis II?

Sister chromatids seperate, reducing DNA content from 2C to 1C in each haploid cell

Why is meiosis difficult in triploid organisms (3n)?

• Each chromosome type has three homologs.

• Three homologs cannot usually separate evenly.

• This often produces gametes with unbalanced chromosome numbers.

• Triploids frequently have reduced fertility.

How does ploidy affect gamete production?

• Diploid (2n): Usually produces balanced haploid (1n) gametes.

• Triploid (3n): Often produces unbalanced gametes.

• Tetraploid (4n): Can produce balanced diploid (2n) gametes.

What is the structure of DNA?

• 2 strands forming a double helix

• Each strand contains nucleotides

• Strands are antiparallel

• Strands are held together by hydrogen bonds between complementary bases

What are the 3 components pof a DNA nucleotide?

• Deoxyribose (5-carbon sugar)

• Phosphate group

• Nitrogenous base (A, T, C, or G)

What are the complementary base pairings?

• Adenine (A) with thymine (T)

• Cytosine (C) and guanine (G)

• A-T has 2 hydrogen bonds

• C-G has 3 hydrogen bonds