BIO 4 - Evolution and Ecology

Question 1

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

Answer 1

Virus can also do:
Reverse Transcriptase: Some viruses use reverse transcriptase to convert their RNA into DNA, altering the usual flow of genetic information.

Replication: Viruses rely on host cell machinery to replicate their genetic material, often encoding their own replication machinery.

So:
A pathway from RNA to DNA
RNA replication

Question 2

What characterizes a retrovirus?

Answer 2

Retroviruses incorporate their genome after reverse transcription from RNA into DNA, into the host DNA. Our genome contains many retroviruses (of the order of 8%).

Question 3

What is gain-of-function research?

Answer 3

Gain of function research on viruses aims to generate viruses that are more transmissible or pathogenic than the naturally occurring variants.

Question 4

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

Answer 4

Sequence alignments, whether of proteins or RNA, can be used to construct phylogenetic trees by comparing the similarities and differences between sequences. This comparison allows researchers to infer evolutionary relationships among organisms. By identifying shared sequence motifs or mutations, they can determine the degree of relatedness between different species or taxa and use this information to construct phylogenetic trees that depict the evolutionary history of those organisms.

Ribosomes, the molecular machines that synthesize proteins, are highly conserved among all life forms and represent a very good basis for the phylogenetic reconstruction of the relationships between all of life. The final tree structure is based on many more genes.

Question 5

*What is the evidence that all life on earth descends from a common ancestor, LUCA?

Answer 5

LUCA – the last universal common ancestor

• The universal genetic code found in all organisms.
• Similarities in molecular structures and biochemical pathways across different species.
  -Phylogenetic analysis showing a branching pattern of descent.
  -Fossil record displaying a progression of life forms.
  -Comparative genomic studies identifying shared genes and genetic elements among diverse organisms.

Question 6

*What are the conditions for evolution in biology?

Answer 6

1. Natural variation
2. Inheritance (Arv)
3. Selection

Question 7

*What is an allele? What is the gene pool?

Answer 7

An allele is a variant form of a gene, which arises by mutation and is found at a specific location on a chromosome. Alleles can result in different observable traits, such as hair color or blood type, and individuals inherit two alleles for each gene, one from each parent.

The gene pool refers to all the alleles of all the genes in a population at any given time. It represents the total genetic diversity within the population and includes the different alleles present for each gene. Changes in the gene pool, such as through mutations, genetic drift, or natural selection, can lead to evolutionary changes within a population over time.

Question 8

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

Answer 8

Sexual reproduction leads to increased genetic diversity, because the genetic material of the parents is mixed and re-combined in a huge number of new ways during the generation of the gametes.

Question 9

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

Answer 9

Process through which populations of living organisms adapt and change
Natural selection can effect changes in phenotype. And over time the selection can result in populations that specialize for particular ecological niches. Finally it can result in evolution of new species.

Question 10

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

Answer 10

Sexual selection:

Natural selection process focusing on traits that enhance an individual’s mating success.
Often involves competition between individuals for mates or mate choice based on specific traits.
Traits selected through sexual selection may not necessarily improve survival but enhance reproductive success.
Examples include elaborate plumage in birds, antlers in deer, or courtship displays in various species.
Artificial selection/breeding:

Human-controlled selection of organisms with desirable traits for breeding purposes.
Involves intentional mating of individuals with specific traits to produce offspring with those traits.
Used in agriculture, animal husbandry, and horticulture to develop crops, livestock, and pets with desired characteristics.
Results in significant changes in traits over successive generations, leading to domesticated varieties tailored to human needs and preferences.

Question 11

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

Answer 11

Depending on where in an open reading frame a single nucleotide change occurs, the effects can be dramatically different. The redundancy of the genetic code leads to many single nucleotide changes to be “silent”, i.e. to not have any immediate effect.
Single point mutations are mostly neutral or deleterious in the context of folded proteins, such as enzymes. However, in the context of promoter regions or other regulatory gene sequences, or in transcription factors, they can lead to a change in gene regulation patterns, which is a powerful lever for phenotypic variation. It has recently been proposed that a single point mutation in the protein Transketolase-like 1 (TKTL1) could be responsible for the cognitive jump between Neanderthals and humans, by stimulating a type of neuron, basal radial glia.

Question 12

*What are examples of mutagens?

Answer 12

A mutagen is a chemical or physical agent capable of inducing changes in DNA called mutations.

Mutagens are chemical agents.
Mutagens are agents or substances that can induce mutations in DNA. Examples of mutagens include:

Reactive oxygen species(ROS)
-superoxide,hydroxyl radicalsandhydrogen peroxide
- often generated by normal cellular processes.

Deaminatingagents, e.g. nitrous acid, can cause transition C -> T mutations

Polycyclic aromatic hydrocarbon(PAH), activated diol-epoxides form DNA adducts
Nitrosamines formed from nitrites added as preservatives to food, formed in smoked foods, tobacco smoke

Alkylating agentsincludemustard gasandvinyl chloride

Alkaloids from plants, such as those fromVincaspecies, can be converted by cellular metabolism into mutagen or carcinogen.

Benzene industrial solvent used in production of drugs, plastics,synthetic rubberand dyes.

Question 13

*How can mutations lead to changes in gene expression?

Answer 13

Mutations can lead to changes in gene expression by altering (changing) the sequence of DNA. This can affect regulatory regions, such as promoters or enhancers, impacting the binding of transcription factors or RNA polymerase. Additionally, mutations can directly affect coding regions, changing the amino acid sequence of a protein, potentially altering its function or stability, which in turn affects gene expression.

Question 14

Why can gene duplication be useful for evolution?

Answer 14

Gene duplication can provide new genetic material for mutation, drift and selection to act upon, the result of which is specialized or new gene functions. Without gene duplication the plasticity of a genome or species in adapting to changing environments would be severely limited.

Question 15

What is a pseudogene?

Answer 15

A pseudogene:
Segment of DNA that structurally looks like a gene but is not capable of coding for a protein
Most often derived from genes that have lost their protein-coding ability due to accumulated mutations that have occured over the course of evolution

A DNA sequence that resembles a gene but has been mutated into an inactive form over the course of evolution.

Question 16

*What is horizontal gene transfer?

Answer 16

Horizontal gene transfer (HGT) is the movement of genetic information between organisms,
- DNA can be taken up in a cell and integrated into the cell’s DNA
Viruses are especially good at transferring DNA between individuals
There are even special pieces of DNA, “transposons“, that are designed to jump around on the chromosome.

Transformation: Bacteria take up DNA from their environment
Conjugation: Bacteria directly transfer genes to another cell
Transduction: Bacteriophages (bacterial viruses) move genes from one cell to another

Question 17

*What is a genome-wide association study?

Answer 17

GWAS:
-research approach used to identify genomic variants that are statistically associated with ta risk for a disease or a particular trait.

-Involves surveying the genomes of many people, looking for genomic variants that occur more frequently in those with a specific disease or trait compared to those without the disease or trait.

-Once such genomic variants are identified, they are typically used to search for nearby variants that contribute directly to the disease or trait

Question 18

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

Answer 18

ALE stands for Adaptive Laboratory Evolution.

It is a method used in the laboratory to drive the evolution of microorganisms to adapt to specific environmental conditions or to improve desired phenotypes.

ALE can be performed through sequential serial passages in shake flasks or chemostat cultures.

In shake flasks, nutrients are not limited, and growth parameters can fluctuate.

Chemostat cultures involve limiting one nutritional component and maintaining constant cell density and environmental conditions.

ALE aims to increase fitness over time by selecting for improved phenotypes.

Fitness increases rapidly in the initial stages but slows down over prolonged selection, with the number of mutations steadily increasing.

Mutations identified in ALE studies include single nucleotide polymorphisms (SNPs), smaller insertions and deletions (indels), and larger deletions and insertions, contributing to genetic and gene regulatory changes and fitness improvements.

Question 19

What is convergent evolution?

Answer 19

What is convergent evolution? Convergent evolution occurs when organisms that aren’t closely related evolve similar features or behaviours, often as solutions to the same problems.

Convergent evolution is the type of evolution in which organisms belonging to different origins (distantly related or organism with different phylogeny) evolve independently to have similar kinds of traits:
Body structures that are anatomically different.
Different embryological origins
The traits will have similar functions.

Question 20

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

Answer 20

A significant fraction of all humans who ever lived are alive today (of the order of 7%, according to estimates).
Human activity has changed the composition of the biosphere considerably, but that change mostly manifests in the populations of large animals.
Humans and domesticated mammals far outweigh all wild mammals, but not other animals.
Plants are by far the dominant contributor of biomass on earth.
200 000 wolves vs. 900 000 000 dogs
20 000 wild cats vs. 400 000 000 domesticated cats
1.2 billion cows, 25 billion chickens,…

Question 21

What are examples for green-green dilemmas?

Answer 21

Green-green dilemmas/conflicts are scenarios whereby two worthwhile goals, e.g. species protection and decarbonisation of energy are (or appear to be) in direct conflict.

Wind turbines: green energy source
Bu tcan pose a threat to bird popilations (like red kites)

Question 22

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

Answer 22

STIKORD:
For at fremme et gen kan man benytte CRISPR til at cutte gen ud og lave kopi af det gen man gerne vil fremme. Så når begge myg exempelvis har dette gen vil det med 100% sandsynlighed være i den næste generation. På den måde kan man fjerne det gen i Malariamyg som er skadelig

Ved at indføre et gen, der gør myggen resistent over for malaria-parasitten, kan man potentielt reducere forekomsten af sygdommen ved at forhindre myggene i at overføre parasitten til mennesker. Dette er et eksempel på, hvordan gene drive-teknologi kan anvendes til at bekæmpe sygdomme ved at målrette og manipulere gener i populationsniveauet.

Gene drives are genetic elements that get transmitted with a higher than purely statistical (50%) probability.
Can be used to combatting (bekæmpelse af) invasive species, eradicating (udryddelse af) disease vectors and eliminating resistances of pests (skadedyr)

Question 23

What features render the future of ecosystems difficult to predict?

Answer 23

New research shows that ecological systems can behave chaotically, making exact long term predictions extremely challenging.

The future of ecosystems is difficult to predict due to factors such as climate change uncertainty, human activities altering landscapes, complex species interactions, feedback mechanisms, emergent properties, globalization, technological changes, and the recognition of chaotic behavior within ecological systems.

Question 24

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

Answer 24

apex-rovdyr hjalp med at kontrollere spredningen af ​​sygdomme i hele dyreriget, og den understøttede også stabilisering af økosystemer.

Question 25

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

Answer 25

Problem:
The primary challenge in recreating an extinct animal solely based on its DNA lies in the degradation and fragmentation of DNA over time. DNA breaks down through processes like hydrolysis and oxidation, resulting in missing or damaged sequences.

DNA Repair: Develop techniques to repair damaged DNA sequences.
Comparative Genomics: Use genomes of related species to fill in missing DNA sequences.
Cloning: Combine intact DNA fragments with cloning techniques to recreate the extinct animal.
Gene Editing: Modify genomes of closely related species to match the extinct animal’s genetic makeup.
Synthetic Biology: Synthesize DNA sequences to reconstruct the extinct animal’s genome.

Question 26

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

Answer 26

Problem:
One problem resulting from excessive nitrogen introduced into the biosphere through human industrial fertilizer production is eutrophication.

Eutrophication occurs when excess nitrogen and other nutrients from fertilizers runoff into water bodies, leading to rapid algal growth. As algae bloom and die, microbial decomposition consumes oxygen, creating “dead zones” where aquatic life cannot survive due to oxygen depletion. This disrupts aquatic ecosystems, causing declines in fish populations and biodiversity, and can harm human health by contaminating drinking water sources

Another provlem:
N2O (greenhouse gas) production

Question 27

• What is the problem resulting from methane production in agriculture?

Answer 27

Problem:
One problem resulting from methane production in agriculture is its contribution to climate change.

Question 28

What is the difference between genetic engineering and breeding

Answer 28

Conventional breeding relies primarily on selection, using natural processes of sexual and asexual reproduction.

Genetic engineering utilizes a process of insertion of genetic material, via a gene gun or other direct gene introduction methods, or by a specially designed bacterial truck, which does not occur in nature.

Genetic engineering and breeding are both methods used to manipulate the genetic makeup of organisms, but they differ in their approaches and outcomes.

Genetic Engineering:

Definition: Involves direct manipulation of an organism’s DNA using techniques like gene splicing and recombinant DNA technology.
Precision: Allows for precise modification of specific genes, including insertion, deletion, or alteration of DNA sequences.
Scope: Can introduce genes from unrelated species, creating organisms with novel traits not found in nature.
Speed: Achieves rapid changes in genetic makeup compared to traditional breeding methods.
Applications: Widely used in agriculture, medicine, and industry to produce genetically modified organisms (GMOs), develop novel therapies, and create industrial enzymes and proteins.
Breeding:

Definition: Involves selecting and mating organisms with desirable traits to produce offspring with improved characteristics.
Natural Variation: Relies on the existing genetic diversity within a species and works by reshuffling existing genes through sexual reproduction.
Scope: Limited to the genetic variation present within a species or closely related species.
Time: Typically a slower process requiring multiple generations of selection and crossing to achieve desired traits.
Applications: Practiced for thousands of years in agriculture to improve crop yields, enhance livestock traits, and develop new varieties of plants and animals.
In summary, genetic engineering offers precise control over genetic modifications and can introduce novel traits from unrelated organisms, while breeding relies on natural genetic variation within a species and involves selecting for desired traits through traditional mating methods.

Question 29

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

Answer 29

The lytic cycle leads to the death of the host, whereas the lysogenic cycle leads to integration of phage into the host genome

Question 30

*What characterizes a retrovirus?

Answer 30

Retroviruses incorporate their genome after reverse transcription from RNA into DNA, into the host DNA. Our genome contains many retroviruses (of the order of 8%).

A retrovirus is a virus that uses RNA as its genomic material. Upon infection with a retrovirus, a cell converts the retroviral RNA into DNA, which in turn is inserted into the DNA of the host cell. The cell then produces more retroviruses, which infect other cells.

There are many technical differences between viruses and retroviruses. But generally, the main difference between the two is how they replicate within a host cell.

Question 31

*What is gain-of-function research?

Answer 31

Gain of function research on viruses aims to generate viruses that are more transmissible or pathogenic than the naturally occurring variants.
Examples: Examples of gain-of-function research include studies that aim to enhance the transmissibility of influenza viruses to better understand how they evolve and spread, as well as experiments that investigate the factors influencing the ability of viruses to cross species barriers.