Ch. 21 Genomes/Evolution and Ch. 22 Darwinian Evolution

Genomics

The study of the entire set of genes and their interactions within an organism

Bioinformatics

The application of computational tools to manage, analyze, and understand biological data

Metagenomics

The study of genetic material recovered directly from environmental samples

Human Genome Project

Mapped and sequenced all the genes in the human genome, providing insights into genetic functions and disorders

Percentage of human genome transcribed

75%

Percentage of human genome encoding protein vs bacteria

1.5% of human genome encodes proteins vs 85-90% of bacterial genome encodes proteins

Do humans have identical genomes/expression?

Human genome is 99.9% identical, but gene expression is very different

Junk DNA

non-protein encoding dna

Alu/L1 Sites

• Alu elements are short, repetitive DNA sequences found abundantly in the human genome

• L1 sites refer to LINE-1 elements (Long Interspersed Nuclear Elements), a type of transposable element found in the human genome which can replicate and insert themselves into new locations in the genome using an RNA intermediate

Human genome vs others

The human genome differs from the genomes of other species in terms of size, gene count, and complexity of gene usage.

• Size: 3.2 billion base pairs

• Gene Count: 20,000-21,000 protein-coding genes

Alternative Splicing

a process by which a single gene can produce multiple different messenger RNA (mRNA) transcripts, leading to the production of diverse proteins from the same gene

Explain how CRISPR-CAS would be used once a potential gene has been identified

Once a potential gene of interest has been identified, CRISPR-Cas9 can be used to precisely edit or manipulate that gene in the genome. This is done through a targeted process that involves creating a guide RNA that directs the Cas9 enzyme to the specific location in the genome, where it makes a cut. The gene can then be modified, disrupted, or repaired to study its function or treat diseases.

Proteomics

the large-scale study of proteins, which are the primary functional molecules in cells. It aims to identify, quantify, and understand the structure, function, interactions, and modifications of proteins within a biological system

What can be learned from microarrays

Microarrays are powerful tools in molecular biology that allow researchers to analyze the expression of thousands of genes simultaneously, as well as to detect genetic variations.

How many exons present in a gene?

simple genes have 1-2, complex can have several dozen.

How many ways is a genome spliced?

Transposable Elements

DNA sequences that can change their position within the genome, potentially causing mutations or altering gene expression

Three ways transposons move

• Cut and Paste: the transposon is excised from one location in the genome and inserted into another.

• Replicative Mechanism: the transposon is copied, and the new copy is inserted at a different location, while the original remains in place

• Retrotransposition: This method involves an RNA intermediate. The transposon is transcribed into RNA, then reverse-transcribed back into DNA before being inserted into a new location

Transposons in evolution

influence genetic diversity, mutations, and evolutionary change by creating new genetic variations or altering the regulation of genes

Deletion/Duplication from Transposons

Transposons can cause deletions and duplications in the genome by inserting themselves into specific locations in the DNA. Their movement can disrupt existing genetic sequences, leading to structural changes like gene deletions or duplications, which can impact gene function and contribute to evolution.

DNA sequence “blocks”

distinct regions or segments of DNA within a genome that have specific patterns or functions

Human vs Chimpanzee Chromosomes

human chromosome 2 is the result of an end-to-end fusion of two chromosomes that are separate in chimpanzees (12 and 13)

Gene families

groups of related genes that share a common evolutionary origin and often have similar sequences and functions

3 steps to form gene families

• Gene Duplication: A key process where an extra copy of a gene is created, allowing one copy to evolve while the other retains its original function. Can occur through unequal crossing over, retrotransposition, or whole-genome duplication.

• Divergence: Duplicated genes acquire mutations

• Selective Pressure: Maintains beneficial mutations and leads to the specialization of gene family members

example of different functions in gene families

IgG, IgA, IgM, IgE: These different classes of immunoglobulins (antibodies) come from the same gene family but perform different functions in the immune system, such as targeting pathogens for destruction or neutralizing toxins.

Related proteins in globin gene family

• Hemoglobin: Involved in oxygen transport in the blood.

• Myoglobin: Found in muscle tissue, where it helps with oxygen storage.

• Both belong to the globin gene family, but their functions are adapted for different tissues and needs.

exon shuffling

a process by which exons, the coding regions of genes, are rearranged or recombined between different genes

tissue plasminogen activator

Exon shuffling likely played a role in the evolution of tPA by combining different exons coding for these domains, possibly from a common ancestral gene. Over time, this combination allowed the protein to acquire a more specialized role in clot breakdown.

horizontal gene transfer

the process by which an organism transfers genetic material to another organism that is not its offspring

• Kissing bugs and transposons: Kissing bugs can acquire new genes through HGT from the bacteria in their gut or from external sources like other insects or environments.

• Viruses and transposons: viruses acquire or exchange genetic material with other organisms, including other viruses, bacteria, or even the host cells they infect

vertical gene transfer

genes are passed from parent to offspring

syncytin gene vs virus

Syncytin is a gene that plays a critical role in the formation of the placenta in mammals; derived from retrovirus.

Gag, Arc, Rec

homeobox genes

• a large family of regulatory genes that play a critical role in the development and organization of body plans in animals, plants, and fungi

• encode transcription factors that regulate the expression of other genes, influencing processes like cell differentiation, body patterning, and organ formation.

when did humans and chimpanzees diverge?

6-7 million years ago

Human vs Chimpanzee Genome

The human genome and the chimpanzee genome are very similar, with about 98-99% of their DNA sequence being identical.

Importance of:

• Genes involved in regulating brain size

• Tuberculosis defense

• Malaria defense

• FOX2P

• crucial for cognitive function, brain development, and the evolution of humans and other species

• helps improve our understanding of immune responses and potential therapeutic targets

• key to improving malaria control and prevention strategies

• a gene that plays a critical role in the development of language and speech in humans. It is associated with the motor control required for speech production, including the coordination of mouth and tongue muscles

descent with modification

the concept that species evolve over time, with new generations inheriting traits from their ancestors but with slight variations or modifications; can lead to new species over time

natural selection

a process where individuals with traits that provide a survival or reproductive advantage are more likely to pass on their genes to the next generation

extinction

the permanent disappearance of a species from Earth

fossils

the preserved remains or traces of organisms from the past

artificial selection

the intentional breeding of organisms by humans to emphasize or enhance desired traits, such as size, color, or yield. Unlike natural selection, where environmental pressures determine which traits are advantageous, artificial selection is guided by human preferences.

Theory of Natural Selection

1. Variation: Individuals within a population exhibit variations in their traits (e.g., size, color, behavior)

2. Overproduction: Organisms produce more offspring than can survive to adulthood.

Finch Beak Shape

On the Galápagos Islands, Darwin observed finches with different beak shapes and sizes, each adapted to specific food sources, showing how natural selection leads to diversity.

Homologous vs Analogous Structures

• Homologous: Structures that are similar in anatomy due to a shared evolutionary ancestry, even if they serve different functions in modern species.

• Analogous: Structures that are similar in function but not in anatomical origin, arising independently in unrelated species.

Vertebrate Embryos

Vertebrate embryos share several common characteristics during early development, reflecting their shared evolutionary ancestry. These features include structures like the notochord, pharyngeal arches, dorsal hollow nerve cord, and postanal tail, which are characteristic of the phylum Chordata.

Pharyngeal Arches

structures that form in the embryonic development of vertebrates. They are paired bulges that develop on either side of the head and neck region, contributing to the formation of important structures in the face, neck, and throat.

Postanal Tail

an extension of the body that runs past the anus and is a key characteristic of all chordates at some stage in their development

ungulates

a diverse group of large mammals that are primarily characterized by their hooves

biogeography

the study of the distribution of organisms, species, and ecosystems across geographic space and through geological time

staphylococcus aureus

Gram-positive, spherical bacterium that is commonly found as part of the normal flora on human skin and mucous membranes; can become pathogenic

molecular evolution

the process of genetic change at the molecular level, including changes in DNA, RNA, and protein sequences over time