Introduction to Life, DNA, and Gene Expression

Characteristics and Classification of Living Organisms

• Life is not defined by a single action; rather, it is identified through a combination of shared characteristics.

• Main groups of living things include:

  • Bacteria

  • Archaea

  • Protists

  • Fungi

  • Plants

  • Animals

• Biologists characterize life through specific general stages and properties:

  • Presence of Macromolecules: Living things contain nucleic acids, proteins, carbohydrates, and lipids.

  • DNA (Deoxyribonucleic acid): This nucleic acid is essential because its molecules can be replicated, which allows organisms to reproduce themselves.

  • Cellular Composition: All living things are composed of cells, which are the smallest units of life.

  • Organism Types: Organisms can be unicellular (composed of a single cell) or multicellular (composed of trillions of cells, such as humans).

  • Reproduction: Living things generate new individuals that carry genetic material from the parents.

Biological Order, Energy, and Homeostasis

• Reproductive Methods:

  • Bacteria reproduce by making virtually exact copies of themselves.

  • Complex organisms use different ways to generate offspring with parental genetic material.

• Energy and Metabolism:

  • Living things utilize energy and raw materials.

  • Metabolic activities allow organisms to extract energy from nutrients and transform it into work for growth and maintenance.

• Environmental Response:

  • Organisms respond to stimuli.

  • Example: A snail detects the pressure of touch and responds by retracting into its shell.

• Homeostasis:

  • Homeostasis refers to a relatively constant and self-correcting internal environment.

  • Behavioral Homeostasis: A snake finds shade to remain cool.

  • Physiological Homeostasis: Humans produce sweat to regulate body temperature.

• Evolution and Adaptation:

  • Populations evolve through natural selection.

  • Individuals with beneficial genetic traits survive and reproduce more effectively than those without them.

  • Giraffe Neck Example: A long neck is viewed as an adaptive trait for reaching high leaves or for winning fights between males.

Genetic Material and the Hierarchy of Life

• Hierarchical Structure: Biological organization can be viewed on a scale from $10$ (molecules) down to $1$ (complex systems).

• Cell Theory: States that all living organisms are made from cells.

• Chromosomes and Genetic Material:

  • Chromosomes contain genetic material in the form of DNA ($deoxyribonucleic acid$).

  • Before cell division, DNA is copied to ensure each new cell receives the same genetic information.

  • Hereditary diseases are transmitted to next generations or new cells through this copying process.

Molecular Composition of DNA and Proteins

• Nucleotides: The specific building blocks of DNA arranged in a particular order.

  • $A$: Adenosine

  • $T$: Thymine

  • $G$: Guanine

  • $C$: Cytosine

• Complementary Base Pairing:

  • $A$ always pairs with $T$.

  • $G$ always pairs with $C$.

• The Biological Message: The sequence of these bases functions like an alphabet. Any error or change in this arrangement results in a mutation or disease.

• The Central Dogma: The flow of information follows the path of Replication $\rightarrow$ Transcription $\rightarrow$ Translation.

  • Replication: Copying the DNA.

  • Transcription: Copying a DNA strand into mRNA.

  • Translation: Converting mRNA sequence into a sequence of amino acids to form a protein.

• Phenotype and Function: The resulting protein performs specific biological functions and determines the phenotype of the organism.

Gene Expression and Specialization

• Principles of Gene Expression:

  • Every cell in the human body contains the exact same set of genes (the full genome).

  • Not all genes are expressed in every cell; cells express unique subsets of genes to perform specialized functions.

  • Skin Cells: Express genes for a tough protective protein.

  • Hair Follicle Cells: Express genes for the proteins that make up hair.

• The Crystalline Gene Case Study:

  • Eye lens cells express crystalline, a specific protein that helps focus light.

  • DNA Structure: A double helix made of two long nucleotide strands.

  • Sequence comparison: The insulin gene sequence (e.g., $CCT, GTG, CGG, CTC$) differs from the crystalline sequence even though they use the same four nucleotides ($A, T, C, G$).

• Process of Expressing Crystalline:

  • Transcription: DNA is copied into Messenger RNA (mRNA).

  • RNA Composition: Single-stranded and uses Uracil ($U$) instead of Thymine ($T$). The bases are $A, U, C, G$.

  • Nucleotide-to-Amino-Acid Translation: The mRNA sequence dictates the link of amino acids (building blocks of proteins).

  • Protein Folding: The amino acid chain folds into a three-dimensional shape, often depicted as a ribbon model.

  • Regulation: While skin cells contain the crystalline gene, they do not express it because gene expression is regulated based on the cell's needs.

Genomics, Bioinformatics, and Ecosystems

• The Genomic Approach:

  • High-throughput technology is used to sequence DNA and study all gene functions simultaneously.

  • Bioinformatics: Computational tools process large volumes of data collected from databases over the last $50$ years.

  • Data analysis involves comparing sequences to a reference to identify mutations.

• Energy Flow in Ecosystems:

  • Energy enters the ecosystem as light.

  • Energy is lost to the surroundings as heat.

  • Energy flows in a one-way direction through the system.

• Feedback Regulation:

  • Positive Feedback: A regulation form where the end product speeds up its own production.

  • Example: After a meal, insulin rise is triggered to facilitate the entry of glucose into cells, reaching a maximum within the first hour.