Chemistry of Life and Organic Compounds

Fundamental Chemistry of Life

• Matter is anything that occupies space and has mass, including living organisms.
• Elements are pure substances that cannot be broken down, fundamental to matter.
• Atoms are the smallest units of elements and combine in specific ratios to form molecules and compounds, crucial for biological functions.

Organic Compounds in Living Organisms

• Organic compounds are primarily carbon (C), hydrogen (H), oxygen (O), and sometimes nitrogen (N).
• These four elements make up about 96% of living organism mass, vital for biological processes.
• The remaining 4% includes essential elements like calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), and magnesium (Mg), playing roles in various biological functions.

Understanding Polar Molecules

• Electronegativity is an atom's tendency to attract electrons, influenced by atomic number and distance from the nucleus, affecting bond formation.
• Polar covalent bonds form when atoms with different electronegativities share electrons unequally, resulting in partial charges.
• Ionic bonds occur when electronegativity difference exceeds 1.7, leading to complete electron transfer, while nonpolar covalent bonds have differences less than 0.4, indicating equal sharing.

Properties of Polar Molecules

• Polar molecules attract other polar molecules, increasing solubility in polar solvents like water, crucial for biological reactions.
• They tend to exclude nonpolar molecules, leading to low solubility in polar liquids, affecting cellular interactions.
• Water’s unique properties, as a polar molecule, are essential for temperature regulation and nutrient transport in biological systems.

Chemical Reactions in Biological Processes

• Four major types of reactions are vital in biological processes: dehydration, hydrolysis, neutralization, and redox.
• Dehydration reactions remove water to join subunits, forming larger molecules, essential for macromolecule synthesis.
• Hydrolysis reactions use water to break down larger molecules into subunits, crucial for digestion and metabolism.
• Neutralization involves acid-base reactions producing salt and water (e.g., HCl + NaOH → H2O + NaCl). This is essential to maintain pH balance in biological systems.
• Redox reactions involve electron transfer, where oxidation is electron loss, and reduction is electron gain, vital for energy transfer.

Properties and Importance of Water in Biology

• Water makes up approximately 70% of the human brain, critical for cognitive functions and neural processes.
• Lungs are about 90% water, essential for gas exchange and respiratory health.
• Bone tissue contains around 22% water, contributing to structure and flexibility.
• Water is a universal solvent, dissolving a wide range of substances, crucial for biological reactions and cellular processes.
• Hydration shells prevent re-association of ions and molecules, facilitating transport within cells.
• Water's polarity allows interaction with both hydrophilic (water-loving) and hydrophobic (water-fearing) substances, influencing cellular interactions and membrane dynamics.

The Role of Carbon in Biological Molecules

• Carbon atoms are the foundational building blocks of all organic molecules.
• Carbon can form four covalent bonds, allowing complex molecular structures and diverse chemical behavior.
• Carbon's ability to form single, double, and triple bonds leads to diverse molecular configurations, critical for biological diversity.

Carbon Structures in Biochemistry

• Hydrocarbons consist solely of carbon and hydrogen (e.g., methane).
• Carbon skeletons can be linear, branched, or ring-shaped, forming the backbone of biochemical molecules.
• Ring-shaped skeletons can link to form larger polymers, essential for biological functions.

Carbon Structures and Bonding

• Carbon skeletons can be linear, branched, or ring-shaped, forming the foundation of biochemical molecules, affecting properties and functions.
• Ring-shaped carbon skeletons can combine to create large polymers vital for biological functions.
• Carbon's versatility allows for a vast array of molecular structures, emphasizing the complexity of life.
• Glucose and fructose are examples of ring structures essential in energy metabolism.

The Molecules of Life

• Living organisms use complex molecules containing carbon, hydrogen, and other elements, instead of simple hydrocarbons.
• Major classes of biological molecules are carbohydrates, lipids, proteins, and nucleic acids, each with distinct functions and properties.
• Carbohydrates are energy sources and structural components.
• Lipids are crucial for membrane formation and energy storage.
• Proteins have diverse functions (catalysis, transport, structural support).
• Nucleic acids (DNA, RNA) store and transmit genetic information.

Functional Groups in Organic Chemistry

• Functional groups are small, reactive atoms influencing larger molecule properties and reactivity.
• They can be polar or ionic, allowing nonpolar molecules to participate in chemical reactions.
• Functional groups significantly alter molecule properties.
• Examples include hydroxyl (-OH), carboxyl (-COOH), and amino (-NH2) groups, giving molecules unique characteristics.

Reactions Involving Functional Groups

• Dehydration reactions remove water to form larger molecules from smaller units (e.g., forming glycosidic bonds).
• Hydrolysis reactions add water to break down polymers into smaller molecules (essential for digestion and metabolism).
• These reactions are critical in macromolecule synthesis and breakdown.

Comparison of Ethane and Ethanol

• Ethane (C₂H₆) lacks functional groups, is nonpolar, and does not dissolve in cytosol, thus not usable as an energy source.
• Ethanol (C₂H₅OH) contains a hydroxyl group, is polar, soluble in cytosol, and can be an energy source.

Proteins and Nucleic Acids

• Proteins are large molecules composed of amino acid subunits linked by peptide bonds, forming specific 3D shapes essential for function.
• Proteins originate from the Greek word "proteois," meaning "first place," highlighting their fundamental biological role.
• Amino acids are the monomer units of proteins.
• Each amino acid has a carboxyl group (-COOH), amino group (-NH₂), hydrogen atom, central carbon atom, and a variable "R" group.
• There are 20 different amino acids each with unique side chains (R-groups) determining their properties.
• Nucleic acids are macromolecules storing and transmitting genetic information. The two main types are DNA and RNA.
• DNA stores long-term information.
• RNA plays a role in protein synthesis
• Nucleic acid structure consists of nucleotide monomers, containing a sugar, phosphate group, and nitrogenous base.

Structure of DNA and RNA

• DNA is a double helix with deoxyribose sugar, phosphate groups, and four nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T).
• RNA is typically single-stranded with ribose sugar, phosphate groups, and nitrogenous bases: adenine (A), guanine (G), cytosine (C), and uracil (U).
• Nucleotides consist of a sugar, nitrogenous base, and one to three phosphate groups.

Nucleotide Polymers and Bonding

• DNA and RNA are formed from chains of nucleotides linked by phosphodiester bonds, connecting the 5' carbon of one sugar to the 3' carbon of the next.
• DNA stability relies on hydrogen bonds between complementary base pairs (A-T and C-G).
• DNA strands have antiparallel orientation (5' to 3' and 3' to 5').

Importance of Nucleic Acids

• Nucleic acids are crucial for storing and expressing genetic information; they guide protein synthesis (transcription and translation).
• Mutations can alter protein structure and function, potentially leading to genetic diseases.

Enzymes and Activation Energy

• Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy.
• They bind reactant molecules, facilitating product formation without being consumed.
• Enzyme names typically end in "-ase" (e.g., sucrase breaks down sucrose).
• Activation energy (Ea) is the minimum energy needed to start a reaction.
• Enzymes lower activation energy in three ways: bringing substrates together, altering charge environments, and changing substrate shape.
• The induced-fit model describes enzyme-substrate interactions where the enzyme adapts to the substrate.
• Reaction rates are proportional to reactant molecules overcoming the activation barrier.
• Enzymes increase reaction rates without altering free energy (ΔG).
• Thermal energy often provides activation energy, but excessive heat can denature proteins
• Maud Menten was a pioneering scientist who contributed to enzyme kinetics.

Cell Structures and Organelles Overview

• Organelles are specialized internal structures performing distinct functions.
• The plasma membrane regulates substance entry and exit.
• Eukaryotic cells have a nucleus housing DNA, protected from cytosolic activities.

The Nucleus: Structure and Function

• The nucleus is surrounded by a nuclear envelope (two lipid bilayers).
• Embedded proteins regulate nuclear material transport.

The Nucleolus and Ribosomal Subunit Assembly

• The nucleolus synthesizes rRNA and assembles ribosomal subunits for protein synthesis.
• It is not membrane-bound and large in protein-synthesis-heavy cells.

The Endomembrane System

• Includes nuclear envelope, ER, vesicles, Golgi apparatus, and plasma membrane.
• These work together to synthesize and transport proteins and lipids.

Functions of Key Organelles

• Lysosomes contain enzymes that break down waste.
• Peroxisomes contain enzymes metabolizing fatty acids and amino acids.
• Vacuoles store water, nutrients, and waste products, which is particularly important in plant cells.

Mitochondria and Energy Production

• Mitochondria produce ATP through aerobic respiration, are the powerhouse of the cell.
• They have their own DNA and ribosomes (supporting endosymbiotic theory).
• Mitochondria numbers reflect cell energy demands.
• Mitochondria are involved in metabolic pathways (e.g., citric acid cycle, oxidative phosphorylation).

The Dynamic Cytoskeleton

• The cytoskeleton provides support, movement, and cell division.
• It has three components: microtubules, microfilaments, and intermediate filaments.

Cell Surface Structures

• Cell walls (plant cells) provide rigidity, composed mainly of cellulose.
• Extracellular matrix (ECM) supports and anchors cells and facilitates communication.
• Cell junctions (e.g., tight, gap, desmosomes) allow interaction between adjacent cells.

Structure and Functions of the Plasma Membrane

• The plasma membrane separates the cell's interior and exterior and maintains homeostasis.
• Movement of substances is regulated to sustain efficient metabolic processes.
• Membrane structure enables compartmentalization crucial for eukaryotic organization.

The Fluid Mosaic Model

• The model describes the membrane as a dynamic phospholipid bilayer with embedded proteins.
• Phospholipid molecules exhibit rapid movement, contributing to membrane fluidity.
• Proteins vary in size and function; these proteins determine different parts of the membrane's mosaic nature.

Components of the Plasma Membrane

• Phospholipids (hydrophobic tails, hydrophilic head): form a bilayer protecting the cell interior and regulating permeability.
• Glycolipids (lipids with carbohydrate chains): play roles in cell recognition and signaling.
• Glycoproteins (proteins with carbohydrate groups): assist in cell recognition and communicate.

Membrane Asymmetry and Fluidity

• The inner and outer bilayer sides have different compositions leading to different functions for proteins affecting cellular interactions and signaling.
• Factors affecting membrane fluidity include lipid composition, temperature, and fatty acid saturation.
• Saturated fatty acids pack tightly; unsaturated fats have kinks, influencing fluidity at lower temperatures.

Role of Sterols and Membrane Proteins

• Sterols (e.g., cholesterol) affect membrane stability by influencing fluidity and permeability.
• Membrane proteins have various functions, including transport and enzymatic activity.

Protein Location and Interaction

• Integral membrane proteins span the lipid bilayer, interact with the hydrophobic core, often as transporters or receptors.
• They are vital for cellular communication and substance movement.
• Examples include ion channels and G-protein-coupled receptors.
• Integral proteins are classified as single-pass or multi-pass.
• Orientation is asymmetric, with extracellular and intracellular domains.

Peripheral Membrane Proteins

• Peripheral proteins are membrane-surface proteins (primarily interacting with cytosol) through non-covalent interactions.
• They have roles in signaling pathways, shape maintenance, and cell integrity.
• Examples include spectrin and ankyrin in red blood cells.

Cell Recognition and Immune Response

• Membrane proteins are essential for cell-to-cell recognition and immune response, and for identifying and reacting to pathogens.
• Surface proteins (e.g., MHC molecules) present antigens to T-cells, initiating immune responses.
• Immune response specificity comes from the diverse membrane protein repertoire.

Transport Mechanisms Across Cell Membranes

• Membrane transport is crucial for cell survival, nutrient intake, waste removal, and environmental communication.
• The plasma membrane has selective permeability to maintain homeostasis.
• There are passive and active transport processes, with passive transport relying on concentration gradients, and active transport requiring energy (ATP).
• The sodium-potassium pump is an example of primary active transport.

Passive Transport Mechanisms

• Passive transport moves substances across a membrane without energy, primarily driven by diffusion from high to low concentration.
• Diffusion seeks dynamic equilibrium, meaning continuous movement with balanced conditions.
• Concentration gradient, molecule size, charge, and membrane permeability affect diffusion rate.

Factors Affecting Diffusion

• Larger concentration gradients equal faster diffusion rates.
• Smaller nonpolar molecules diffuse more easily than larger charged ones.
• Temperature increases molecular movement, enhancing diffusion.
• Membrane permeability is selective, blocking substances based on necessity.

Active Transport Mechanisms

• Active transport moves substances against their concentration gradient, using energy (typically ATP).
• Electrochemical gradients utilize differences in ion concentration and charge across a membrane to exert stored potential energy.
• The sodium-potassium pump is a critical example establishing ion gradients.

Bulk Transport: Exocytosis and Endocytosis

• Exocytosis exports materials (e.g., secretory proteins, waste) from cells.
• Secretory vesicles fuse with the plasma membrane, releasing contents outside.
• Endocytosis imports materials (e.g., proteins, aggregates) into cells (pinocytosis, receptor-mediated, phagocytosis).