BLOCK 1 BIO4

Question 1

How do viruses require extensions of the central dogma of molecular biology?

Answer 1

Viruses extend the central dogma of molecular biology. For example, retroviruses(HIV) use reverse transcriptase to convert their RNA genome back to DNA, creating an RNA → DNA → RNA → protein flow.

Additionally, some viruses bypass the DNA stage altogether, going directly from RNA to protein, RNA viruses(SARS, flu) RNA → protein or RNA → RNA

Some viruses such as ncRNA bypass the protein stage and goes direct to cells

Question 2

What is the difference between the lytic and lysogenic cycles of viruses?

Answer 2

The lytic cycle involves the virus taking over the host cell, replicating, and causing the cell to burst or lyse make a bigger army and overtake. (Impatient)
The lysogenic cycle involves the virus integrating its DNA into the host’s DNA and lying dormant, wating to attack.
(Hitch a ride/patient)

Question 3

What characterizes a retrovirus?

Answer 3

Retroviruses are characterized by their RNA genome and they use reverse transcriptase to transcribe RNA into DNA. This allows the viral genetic material to integrate into the host’s DNA.

Retroviruses are associated with certain cancers and diseases in humans, such as HIV/AIDS.

Question 4

What is gain-of-function research?

Answer 4

Gain-of-function research is medical research that genetically alters an organism in a way that may enhance the biological functions of gene products.

In virology gain-of-function research is usually employed with the intention of better understanding current and future pandemics.Vaccine development, in the hope of gaining a head start on a virus and being able to develop a vaccine.

Question 5

How can sequence (protein, RNA) alignments be used to construct phylogenetic trees?

Answer 5

Sequence alignments of proteins or RNA can be used to construct phylogenetic trees by identifying similarities that indicate evolutionary relationships.
The mutations accumulated over time are compared, and statistical methods are applied to determine the tree topology that best describes the relationships.

Question 6

What is the evidence that all life on earth descends from a common ancestor, Last universal common ancestor (LUCA)?

Answer 6

LUCA, as evidenced by genetic similarities across species, fossil. Indicating common lineages, anatomical similarities among different species, biochemical similarities in metabolic processes, and the identification of genes common to almost all cells today. Suggest an LUCA cells

Question 7

What are the conditions for evolution in biology?

Answer 7

The conditions for evolution are
Natural variation
Genetic variation in a population, traits that are differ hereby phenotypic differences.
Inheritance
Traits are heritable, i.e passed on to offspring
Selection
Variabillity in traits gives rise to differences in performance
Competition “Survival of the fittest”

Question 8

What is an allele? What is the gene pool?

Answer 8

An allele are different variants of a gene, which exist in the chromosomes and two sets of chromosomes are diploid cells.
They can occur in pairs or multiple alleles can affect a trait’s expression.
Alleles can be recessive or dominant is can have an effect on the phenotype of the organism
If paired alleles are identical, it’s homozygous; if different, it’s heterozygous.

A gene pool refers to the combination of all the genes (including alleles) present in a reproducing population or species.
A large, diverse gene pool increases biological variabillity and adaptability vs small where it gene pool are inbreeding

Question 9

How can genetic diversity in a population of organisms be increased?

Answer 9

Genetic diversity can be increased through:

Mutation and Gene Duplication: These create new alleles and genes.

Mating and Fertilization: These lead to new gene combinations.

Natural Selection: This changes allele frequencies over time, favoring beneficial traits.

Question 10

Be able to perform simple calculation on numbers of ancestors as a function of time

Answer 10

How many generations must you go back in your ancestry before you have
just over 1 billion (1x10^9) ancestors?
Assuming the average generation time is about 25 years, how long ago do you estimate that you had these 1 billion ancestors?

2^x > 1 × 10^9
𝑥 > log2 (10^9)
𝑥 > 29.9 = 30
30 * 25 =750 year ago

Question 11

What is natural selection? What types of effects can natural selection have on a given trait/property?

Answer 11

Natural Selection: It’s a process where populations of organisms adapt and change. Individuals with better-suited traits for the environment are more likely to survive and reproduce, passing these traits to their offspring.

Effects of Natural Selection on a Given Trait: It can cause microevolution with beneficial alleles becoming common. Result in disruptive selection.

Question 12

What is sexual selection? What is artificial selection/breeding?

Answer 12

Sexual Selection: It’s a special case of natural selection acting on an organism’s ability to obtain or successfully copulate with a mate.
It involves intersexual selection, choice of mates and competition for mates
Disadvantages for survival but lead to higher chance of reproductive success.

Artificial Selection/Breeding: It’s the human-driven process of choosing desirable traits in plants and animals to enhance and perpetuate those traits in future generations.
It’s similar to natural selection but driven by human decisions.

Question 13

What different kind of effects on protein synthesis can single point mutations in DNA
have?

Answer 13

Single point mutations in DNA can:
- Be silent and have no effect.
- Change protein synthesis altogether.
- Cause the gene to become more active or silent.
- Change the amino acid sequence of the resulting protein.
- Insert or delete extra letters of the genetic code.
- Duplicate an entire gene or region of a genome.

Question 14

What are examples of mutagens?

Answer 14

Examples of mutagens include:
1- Physical Agents: Such as ultraviolet radiation and X-rays.

2- Chemical Agents: Like tobacco products and various chemicals.

3- Biological Agents: Transposons and Insertion sequences (IS).

Question 15

How can mutations lead to changes in gene expression?

Answer 15

Mutations can lead to changes in gene expression through:
1- Point Mutations: Random changes to one or a few DNA bases.

2- Substitution Mutations: Replacement of one nucleotide for another.

3- Deletion and Insertion Mutations: Removal or addition of one or more nucleotides.

4- Environmental Factors: Chemicals, radiation, and ultraviolet light can cause mutations.

5- Transcription Factors: Proteins that bind to specific sequences of DNA and control gene expression.

Question 16

Why can gene duplication be useful for evolution?

Answer 16

Gene duplication can be useful for evolution as it:

1. Creates New Genes: It provides an opportunity for the duplicated gene to evolve new functions, creating new genes with novel functions.
2. Provides Opportunity for Natural Selection: A duplicated gene provides a less-constrained chance for natural selection to shape a novel function.
3. Facilitates Evolution of Species: It’s important for the evolution of species as it facilitates the creation of new genes.

Question 17

What is a pseudogene?

Answer 17

A pseudogene is a DNA segment that resembles a gene but cannot code for a protein. They are often derived from genes that lost their protein-coding ability due to mutations over time. They look like genes but do not encode proteins and are typically mutated copies of genes. Studying them helps understand an organism’s genome’s evolutionary history.

Question 18

What is horizontal gene transfer?

Answer 18

1. Horizontal Gene Transfer: It’s the movement of genetic material between organisms other than by vertical transmission from parent to offspring. It occurs between different species and between different organelles within eukaryotes.
2. Significance of HGT: It influences our understanding of evolution, especially bacterial evolution. It’s a primary mechanism for spreading antibiotic resistance in bacteria and plays a key role in bacterial evolution.

Question 19

What is a genome-wide association study?

Answer 19

A Genome-wide association study (GWAS) is a research approach that:
- Observes a genome-wide set of genetic variants in different individuals.

• Identifies any variant associated with a trait.
  Focuses on associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases.
• Classifies participants first by their clinical manifestation(s), known as phenotype-first.
• Uses SNP arrays to read millions of genetic variants from each person’s DNA sample.
• Associates variants that are more frequent in people with the disease.
• Considers the associated SNPs to mark a region of the human genome that may influence the risk of disease.

Question 20

What is adaptive laboratory evolution and what is it useful for?

Answer 20

Adaptive Laboratory Evolution (ALE) is a research approach that:
- Is frequently used in biological studies.

• Provides insights into the basic mechanisms of molecular evolution.
• Studies adaptive changes in microbial populations during long term selection under specified growth conditions.
• Selects for strains with growth-coupled phenotypes.
• Uncovers genotype-to-phenotype relationships and the molecular mechanisms underlying desired complex phenotypes when coupled with next-generation sequencing and omic technologies.
• Is used by many researchers to create microbial cell factories.

Question 21

What is convergent evolution?

Answer 21

Convergent evolution is a process where:
- Species independently evolve similar features.

• It creates analogous structures with similar form or function.
• These structures were not present in the last common ancestor of those groups.
• A classic example is the recurrent evolution of flight in different species.
• Homologous structures or traits have a common origin but can have dissimilar functions.
• The opposite of convergence is divergent evolution, where related species evolve different traits.

Question 22

How have humans shaped the biomass distribution on earth since their appearance?

Answer 22

Humans have significantly influenced the biomass distribution on Earth by:
- Increasing the mass of human-made materials to exceed that of all biological organisms.

• Enhancing consumption and urban development.
• Producing concrete, metal, plastic, bricks, and asphalt in large quantities.
• Projecting to triple global biomass by 2040 if current trends continue.
• Halving the mass of plants since the first agricultural revolution.

Question 23

What are examples for green-green dilemmas?

Answer 23

• Shower vs Bath: The environmental impact varies based on factors like shower type and duration.
• Wind Energy vs Wildlife Conservation: The production of wind energy can sometimes harm airborne animals, creating a dilemma between renewable energy and wildlife conservation.

Question 24

What is a gene drive and what can it be used for?

Answer 24

A gene drive is a genetic engineering technique that increases the likelihood of a specific gene being passed onto the next generation. This allows the gene to rapidly spread through a population. It can be used for purposes such as exterminating disease-carrying insects, controlling invasive species, or combating herbicide or pesticide resistance.

Question 25

What features render the future of ecosystems difficult to predict?

Answer 25

The future of ecosystems is hard to predict due to factors like changes in biodiversity, environmental changes such as climate change and habitat loss, changes in human activities and policies, and advancements in technology.

Question 26

What is the ecological justification for the de-extinction of the tasmanian tiger?

Answer 26

The de-extinction of the Tasmanian Tiger is justified ecologically as it could restore balance to Tasmania’s forests by controlling overabundant herbivores and sick animals. It could also improve agriculture and vegetation, protect native species, and maintain infrastructure by controlling rabbit overpopulation. Additionally, it could have helped control the spread of diseases like the Tasmanian devil facial tumour disease.

Question 27

Why is it not possible to re-create an extinct animal simply based on its DNA? What
are strategies to overcome these problems?

Answer 27

Recreating an extinct animal from its DNA is challenging because old DNA breaks into tiny pieces that can’t be fully reassembled. Even with a high-quality genome, it’s impossible to recreate many key genes. This means any resurrected animal would differ in some important ways. Also, different environmental pressures would alter their genomes in novel ways. To overcome these challenges, scientists are exploring back-breeding, cloning, and genetic engineering. Advances in biotechnology, bioinformatics, and genetics have made it possible to create simulacra of long-dead species.

Question 28

What is a problem resulting from too much nitrogen being introduced into the
biosphere through human industrial fertilizer production?

Answer 28

Excessive nitrogen from human industrial fertilizer production can cause air pollution, impair breathing, limit visibility, alter plant growth, harm forests, soils and waterways, exacerbate climate change through nitrous oxide emissions, and lead to algal blooms and oceanic “dead zones”.

Question 29

What is the problem resulting from methane production in agriculture?

Answer 29

Methane production in agriculture contributes significantly to climate change. It’s a potent greenhouse gas released primarily through burps from ruminant livestock and rice production. These emissions have been increasing and contribute to global warming. However, with proper management and climate-friendly farming practices, these emissions can be stabilized.

Question 30

What is the difference between genetic engineering and breeding?

Answer 30

Selective breeding uses natural processes to mate organisms with desirable traits over generations without altering their genetic material. In contrast, genetic engineering directly alters an organism’s genome in a lab, introducing changes to its genetic material using methods that do not occur naturally.