Study Notes on Homology and Central Dogma

Basic concept relates to evidence of the interconnectedness of all life forms.
Homology refers to common structures inherited from a common ancestor.
Understanding the central dogma is fundamental to appreciating biological relationships.

The central dogma describes the flow of genetic information:
- DNA -> RNA -> Protein
- DNA (Deoxyribonucleic Acid) stores genetic information.
- RNA (Ribonucleic Acid) acts as a messenger and intermediary.
- Proteins are synthesized based on instructions encoded in DNA, which ultimately dictates cellular function and structure.
Universality of the central dogma among all organisms supports the idea of a shared evolutionary history.

Genetic code refers to the sequences of nucleotides in DNA that determine the sequences of amino acids in proteins.
Example: triplet code, where specific codons like UCU correspond to specific amino acids, such as serine.
Though there are minor exceptions across different organisms, the core principles remain constant:
- E.g., some fungi have modified codons.

Several key indicators provide support for the idea of a last universal common ancestor (LUCA):
- Universal use of genetic code
- Cellular membranes composed of lipids
- All living organisms use lipid bilayers to maintain internal environments.
- Metabolic pathways
- Many metabolic pathways, such as glycolysis, are conserved across diverse organisms, supporting evolutionary links.
LUCA is believed to exist around 3.5 billion years ago, but multiple life forms may have emerged before it without leaving evidence in the fossil record.

The question arises: which came first; DNA, RNA, or proteins?
Hypothesis around RNA world:
- Polyfunctional roles of RNA, including storage of genetic information, catalysis, and protein synthesis.
- RNA's ability to act as a catalyst (ribozymes), demonstrated in studies from the 1980s.
- Ribosomes, complex molecules composed of both RNA and proteins, utilize rRNA for catalysis during protein synthesis.
RNA World Hypothesis posits RNA as the key molecule for early life, suggesting it might precede DNA and proteins.

The emergence of cellular life required a transition from communal replication to individual cellular organisms.
Wrapped in lipid bilayer membranes, early self-replicating RNA molecules likely transitioned into cellular life, marking the Darwinian threshold.
Once cellular structures formed, organisms began adopting vertical gene transfer, where genetic information is passed from parent to offspring.

Membrane formation is critical for the development of cellular life.
Phospholipids naturally form lipid bilayers when mixed with water, demonstrating self-organization.
Hypotheses suggest that early life originated around deep-sea hydrothermal vents, where these early cells could thrive amid abundant nutrients.

Earth is about 4.5 billion years old, with the earliest evidence of life dating back to 3.5 billion years ago.
Transition from single-celled to multi-cellular organisms marked by significant evolutionary milestones recorded in the fossil record.
Major geological events, like meteor impacts and volcanic eruptions, have influenced biological diversity and extinctions throughout Earth's history.

Refers to episodes when Earth was extensively covered in ice, drastically changing life.
Likely resulted from significant climate changes tied to atmospheric composition, specifically greenhouse gases:
- Oxygen levels influence global temperatures significantly.

Bacteria and archaea are fundamental life forms characterized by simpler cellular structures than eukaryotes but distinguished by metabolic diversity.
Prokaryotes differ: lack organelles and defined nuclei, smaller size and simpler reproduction through binary fission.
Horizontal gene transfer allows prokaryotes to share genetic information, increasing genetic diversity.

Average size: 10 to 100 times smaller than eukaryotic cells.
The cellular structure includes:
- Cell wall
- Plasma membrane
- Cytoplasm
- Nucleoid (not membrane-bound)
Some bacteria have flagella and pili aiding in movement and adhesion.

Prokaryotes show exceptional metabolic diversity; they can be classified as:
- Phototrophs: obtain energy from sunlight.
- Chemotrophs: obtain energy from chemical compounds.
Classification of carbon needs:
- Autotrophs: can fix their own carbon (e.g., photosynthetic organisms).
- Heterotrophs: must obtain carbon from the environment.

Aerobic processes: Use oxygen as an electron acceptor; higher energy yield (e.g., glucose oxidized to carbon dioxide and water).
Anaerobic processes: Use alternative electron acceptors (e.g., nitrate, sulfide) and products vary greatly (e.g., methane).
Redox reactions play critical roles in energy conversion across all living organisms, especially in prokaryotic metabolism.

Prokaryotes exist in various extreme environments (extremophiles) and can adapt to conditions that eukaryotes cannot.
Their metabolic capabilities have profound implications on ecological systems and biogeochemical cycles.
Research indicates vast undetected microbial diversity, possibly numbering trillions of species, indicating a rich area for further exploration.

Microbial populations are vital for maintaining ecosystem functions; they interact with eukaryotes and play roles in nutrient cycling, disease resistance, and health.
Concepts like the human microbiome illustrate the importance of microbial communities in health and disease.

The study of prokaryotes enriches our understanding of early life, evolution, and biochemical processes.
While eukaryotes are often the focus, prokaryotes remain an essential aspect of life on Earth, contributing to ecological balance and diversity.