lecture recording on 12 March 2025 at 12.49.32 PM

Natural Selection and Viruses

Viruses undergo natural selection when they infect host cells, which is a significant area of study in virology and evolutionary biology. Upon infecting a host, a virus replicates, utilizing the host's cellular machinery. This replication process can lead to errors due to the high mutation rates characteristic of viral genomes. As a result, mutations may accumulate among the virions produced, giving rise to genetic diversity within the viral population. Some virions may acquire advantageous mutations that enhance their ability to survive, replicate, and evade the host's immune response, leading to their proliferation and dominance in subsequent infections.

Eukaryotes vs. Prokaryotes

Eukaryotes:

• Described as "bags of bags" or membrane-bound compartments that enable compartmentalization of cellular processes.

• Contain various organelles, such as mitochondria for energy production, endoplasmic reticulum for protein synthesis, and a membrane-bound nucleus that houses genetic material.

• Can be unicellular organisms, such as yeast, or multicellular organisms, exemplified by plants and animals, each exhibiting complex structures and functions.

Prokaryotes:

• Single-celled organisms that lack membrane-bound organelles, making them simpler in structure.

• Their genetic material is not compartmentalized; it exists as a nucleoid region where the DNA is free-floating in the cell. This structure is described as being in a "bag."

• Examples include bacteria, which are essential for various ecological processes, and archaea, which often thrive in extreme environments.

• Both eukaryotes and prokaryotes utilize ribosomes for protein synthesis, although their ribosomal structures differ due to their evolutionary divergence.

Types of Chemical Bonds

Ionic Bonds:

• Occur through the transfer of electrons from one atom to another, which typically happens between metals and nonmetals.

• This electron transfer results in the formation of charged ions; one atom becomes positively charged (cation), while the other's charge becomes negative (anion).

• A classic example is Sodium (Na) donating an electron to Chlorine (Cl), resulting in Na+ and Cl- ions that create sodium chloride (table salt).

Covalent Bonds:

• Formed when atoms share electrons to fill their outer electron shells, providing stability.

• If electrons are shared equally between atoms, a nonpolar covalent bond is the result. In contrast, if the sharing is unequal, a polar covalent bond forms, characterized by partial charges.

• An example of a polar covalent molecule is water (H2O), where oxygen atoms exert a stronger pull on shared electrons compared to the hydrogen atoms.

Hydrogen Bonds:

• Weak attractions that occur between hydrogen atoms covalently bonded to electronegative atoms (like oxygen or nitrogen) and other electronegative atoms.

• These bonds are critical for the unique properties of water, such as high surface tension and its role as a solvent in biochemical reactions.

Molecular Properties

Hydrophobic Molecules:

• Nonpolar molecules that do not interact favorably with water; they tend to aggregate in aqueous environments.

• They are primarily composed of carbon and hydrogen bonds, making them water-fearing. A common example is cholesterol, which is insoluble in water yet crucial for cellular membranes.

Hydrophilic Molecules:

• Polar molecules that readily interact and dissolve in water, often characterized by the presence of functional groups that can form hydrogen bonds, such as hydroxyl (-OH) or carbonyl (C=O).

• An illustrative example is sucrose, a disaccharide that dissolves in water due to its polar characteristics, making it effective in biological systems.

Differences between DNA and RNA

DNA:

• Double-stranded helix structure comprising deoxyribose sugar; this structure encodes genetic information with specific sequences of nucleotides.

• Contains thymine (T) as one of its four bases, which pairs with adenine (A) during base pairing.

RNA:

• Typically single-stranded and includes ribose sugar, which differs from deoxyribose by having an additional oxygen atom.

• Instead of thymine, RNA contains uracil (U), which pairs with adenine during transcription.

• RNA plays various roles in cellular processes, notably in protein synthesis, acting as a messenger (mRNA) that carries genetic information from DNA to ribosomes.

Amino Acids and Protein Structure

Components of Amino Acids:

• Composed of four primary components: an amino group (NH2), a carboxyl group (COOH), an alpha carbon that links these groups, and a variable side chain (R-group) that determines the amino acid's properties.

Protein Structure:

• Primary Structure: The linear sequence of amino acids that forms the protein chain, akin to beads on a string.

• Secondary Structure: Refers to local folded structures that arise from hydrogen bonding between backbone atoms, resulting in alpha helices or beta sheets.

• Tertiary Structure: The overall three-dimensional shape of a protein, shaped by various interactions among R-groups, including hydrophobic interactions, disulfide bonds, and hydrogen bonds.

• Quaternary Structure: Formed by the association of multiple polypeptide chains into a single functional complex, as seen in hemoglobin.

Membrane Transport Mechanisms

Passive Transport:

• Involves movement of substances across the cell membrane along their concentration gradient without the expenditure of energy. Mechanisms include:

  • Simple Diffusion: Movement of small or nonpolar molecules directly through the lipid bilayer (e.g., oxygen and carbon dioxide).

  • Facilitated Diffusion: Involves specific transport proteins aiding in the movement of larger or polar molecules (e.g., glucose).

Active Transport:

• This process requires energy, as it involves transporting molecules against their concentration gradient. An example is the sodium-potassium pump, which maintains cellular ion balance.

Endocytosis:

• A cellular mechanism that engulfs large particles or other cells into vesicles, enabling the uptake of larger substances that cannot traverse the membrane via passive transport.

Metabolism Overview

• Catabolism: The metabolic process of breaking down larger, complex molecules to release energy that can be utilized in cellular activities.

• Anabolism: The building up of smaller units into larger, complex molecules. This process requires energy input and is critical for growth and repair.

Gibbs Free Energy (ΔG)

• Exergonic Reactions: These reactions release energy, represented by a negative ΔG value, and occur spontaneously.

• Endergonic Reactions: Require energy input to proceed, characterized by a positive ΔG value, making them non-spontaneous.

• Enzymatic Function: Enzymes serve to lower the activation energy needed for chemical reactions, thus facilitating metabolic processes more efficiently without altering the energy of reactants or products.

Cellular Processes: Photosynthesis vs. Cellular Respiration

Photosynthesis:

• Occurs in chloroplasts and consists of two main stages:

  • Light-dependent Reactions: Capture light energy, resulting in ATP and NADPH production.

  • Light-independent Reactions (Calvin Cycle): Utilize ATP and NADPH to synthesize glucose from carbon dioxide and water, demonstrating energy transformation.

Cellular Respiration:

• The metabolic process through which glucose is converted into ATP, involving key pathways:

  • Glycolysis: Anaerobic breakdown of glucose into pyruvate, producing a small amount of ATP.

  • Citric Acid Cycle: Occurs in mitochondria and processes acetyl-CoA to generate electron carriers.

  • Oxidative Phosphorylation: The final stage that produces a majority of ATP using electron transport and chemiosmosis, requiring oxygen in aerobic respiration.

Cell Signaling

• Involves receptors located on the cell membrane that bind specific ligands, triggering intricate signal transduction pathways. These pathways ultimately lead to various cellular responses such as gene expression, cell growth, or apoptosis.

• Receptor Tyrosine Kinases: A specialized class of receptors that, upon ligand binding, undergo a phosphorylation process that activates downstream signaling pathways crucial for various physiological responses.

DNA Replication and Transcription

DNA Replication:

• A critical cellular process where DNA polymerase synthesizes two identical DNA strands from a single template strand, ensuring genetic fidelity during cell division.

Transcription:

• The process involving the synthesis of RNA from a DNA template, occurring in all cells. This action leads to protein synthesis or the production of RNA molecules that carry functional roles beyond merely encoding proteins.

Mitosis vs. Meiosis

Mitosis:

• Produces two genetically identical diploid daughter cells, essential for growth, repair, and asexual reproduction.

Meiosis:

• A specialized form of cell division that reduces the chromosome number by half, yielding four genetically varied haploid gametes. This process includes crucial events such as crossing over and independent assortment that contribute to genetic diversity within populations.

Genetic Variation and Alleles

Alleles:

• Alternate versions of a gene that arise from mutations. They can be classified as homozygous (having two identical alleles) or heterozygous (having two different alleles), influencing an organism's phenotype.

Inheritance Patterns:

• Dominant alleles express their associated phenotypes when present, while recessive alleles require two copies to manifest in the phenotype.