Biological Molecules and Chemistry Basics

Fundamental Chemistry of Life and Biological Molecules

• Matter is defined as anything that occupies space and has mass, including living organisms.
• Elements are pure substances that cannot be broken down into simpler substances. They are fundamental to the composition of matter.
• Atoms, the smallest units of elements, bond in specific ratios to form molecules and compounds. Molecules and compounds are essential for biological functions.

Organic Compounds in Living Organisms

• Organic compounds are primarily composed of carbon (C), hydrogen (H), oxygen (O), and sometimes nitrogen (N).
• These four elements account for approximately 96% of the mass of living organisms.
• Other essential elements include calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), and magnesium (Mg), playing vital biological roles.

Understanding Polar Molecules

• Electronegativity is an atom's tendency to attract electrons, influenced by atomic number and distance from the nucleus. It affects bond formation.
• Polar covalent bonds form when atoms with differing electronegativities share electrons unequally, creating partial charges within the molecule.
• Ionic bonds form when the electronegativity difference exceeds 1.7, leading to complete electron transfer.
• Non-polar covalent bonds occur with differences less than 0.4, indicating equal sharing.

Polar & Nonpolar Molecules

• Polar molecules attract other polar molecules, increasing solubility in polar solvents like water, crucial for biological reactions.
• Nonpolar molecules tend to exclude nonpolar molecules, resulting in low solubility in polar liquids, affecting cellular interactions.

Chemical Reactions in Biological Processes

• Four crucial reaction types in biological processes are dehydration, hydrolysis, neutralization, and redox reactions.
• Dehydration reactions remove water to join subunits, forming larger molecules (essential in macromolecule synthesis).
• Hydrolysis reactions use water to break down larger molecules into smaller subunits (crucial in digestion and metabolism).
• Neutralization reactions involve the reaction of an acid and a base to produce salt and water, essential for maintaining pH balance.
• Redox reactions involve electron transfers (oxidation and reduction), essential for energy transfer.

Properties and Importance of Water in Biology

• Water constitutes approximately 70% of the human brain, highlighting its critical role in cognitive functions and neural processes.
• The lungs are composed of about 90% water, essential for gas exchange and maintaining respiratory health.
• Bone tissue contains about 22% water, contributing to structural integrity and flexibility.
• Water is a universal solvent, capable of dissolving a wide range of substances crucial for biological reactions.
• Hydration shells form around ions and molecules, preventing re-association and facilitating transport.
• Water's polarity facilitates interactions with both hydrophilic and hydrophobic substances.

Carbon Structures in Biochemistry

• Carbon atoms are the foundation of all organic molecules, crucial for life due to unique bonding properties.
• Carbon forms four covalent bonds, allowing for complex molecular structures.
• Carbon skeletons can be linear, branched, or ring-shaped, affecting properties and functions.
• Ring-shaped carbon skeletons create large polymers, vital for biological functions.

Bonding Properties of Carbon

• Carbon forms single, double, and triple bonds, influencing reactivity and molecular structure.
• Single bonds allow for rotation, while double and triple bonds create rigidity.
• The presence of multiple bonds limits bonding with other atoms, affecting molecular diversity.
• Different bond types affect physical properties like boiling/melting points.

Major Classes of Biological Molecules

• Living organisms use complex molecules with carbon, hydrogen, and other elements.
• Key classes include carbohydrates (energy sources & structural components), lipids (membrane formation & energy storage), proteins (catalysis, transport, & structural support), and nucleic acids (genetic info storage/transmission).

Functional Groups in Organic Chemistry

• Functional groups are small reactive groups that significantly influence molecule properties and reactivity.
• Examples include hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), etc.

Reactions Involving Functional Groups

• Dehydration reactions involve removing water to form larger molecules.
• Hydrolysis reactions add water to break down larger molecules.
• These reactions are crucial in macromolecule synthesis and breakdown.

Proteins and Nucleic Acids

• Proteins are large molecules composed of amino acid subunits linked by peptide bonds, forming specific 3D shapes for functions.
• Essential amino acids (nine) must be obtained through diet.
• Nucleic acids (DNA & RNA) store and transmit genetic information.
• DNA is double-stranded, while RNA is typically single-stranded.
• Both DNA and RNA are formed from nucleotides, which consist of a sugar, a phosphate group, and a nitrogenous base.

Enzymes and Activation Energy

• Enzymes are biological catalysts that accelerate chemical reactions by lowering activation energy.
• They bind to reactant molecules (substrates) temporarily and facilitate the transition to products without being consumed in the process.
• The induced-fit model describes how enzymes change shape when substrate binds, weakening chemical bonds and lowering activation energy.

Cell Structures and Organelles Overview

• Organelles are specialized internal structures within cells with specific functions.
• Eukaryotic cells contain a nucleus that houses DNA.
• The nucleus is surrounded by a double membrane (nuclear envelope).
• The nucleolus is responsible for rRNA synthesis and ribosome subunit assembly.
• Ribosomes are essential for protein synthesis.

The Endomembrane System

• The endomembrane system includes the nuclear envelope, endoplasmic reticulum (smooth/rough), vesicles (transport materials), and Golgi apparatus (modifies/sorts/packages proteins and lipids).
• These organelles work together to synthesize, transport, and modify proteins and lipids within the cell.

Mitochondria and Energy Production

• Mitochondria are known as the powerhouse of the cell. ATP is produced through aerobic respiration in mitochondria.
• Mitochondria have their own DNA and ribosomes which supports the endosymbiotic theory.
• Mitochondrial number varies significantly due to energy demands of different cell types.
• Mitochondria are involved in various metabolic pathways like the citric acid cycle and oxidative phosphorylation which are important for ATP production.

Cell Surface Structures

• The cytoskeleton (microtubules, microfilaments, intermediate filaments) provides structural support, movement, and cell division.

Cell Membrane

• The plasma membrane serves as a physical barrier and regulates substance movement.
• It is a fluid mosaic structure composed of phospholipid bilayer, embedded proteins, and cholesterol.
• Proteins embedded in the bilayer have varied functions, including transport, signaling, and enzymatic activities.

Transport Mechanisms Across Cell Membranes

• Passive transport (diffusion): Substances move from high to low concentration without energy.
• Active transport: Substances move against concentration gradient requiring energy, usually from ATP.

Bulk Transport: Exocytosis and Endocytosis

• Exocytosis is the process of exporting materials from the cell (e.g., secretory proteins).
• Endocytosis is the process of importing extracellular materials into the cell (e.g., phagocytosis, receptor-mediated and bulk-phase).

Cell Recognition and Immune Response

• Membrane proteins are essential for cell-to-cell recognition, including immune responses.
• Surface proteins such as MHC molecules present antigens to T-cells triggering immune responses.

Explore the fundamental chemistry of life with this quiz covering the key concepts of matter, elements, and molecules. Understand the role of organic compounds and essential elements in living organisms, as well as the significance of polar molecules. Test your knowledge and deepen your understanding of biological chemistry.