Fundamental Chemistry of Life

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, fundamental to the composition of matter.
• Atoms are the smallest units of elements, bonding in specific ratios to form molecules and compounds, essential for biological functions.

Organic Compounds in Living Organisms

• Organic compounds primarily consist of carbon (C), hydrogen (H), oxygen (O), and sometimes nitrogen (N); these four elements account for approximately 96% of living organisms' mass.
• The remaining 4% includes other essential elements like calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), and magnesium (Mg), crucial for biological functions.

Understanding Polar Molecules

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

Polar & Nonpolar Molecules

• Polar molecules attract other polar molecules, which increases their solubility in polar solvents like water. This is crucial for biological reactions.

Chemical Reactions in Biological Processes

• Four crucial types of chemical reactions in biological processes include dehydration, hydrolysis, neutralization, and redox reactions.
• Dehydration reactions remove water to form larger molecules, essential for macromolecule synthesis.
• Hydrolysis reactions use water to break down larger molecules into smaller subunits, crucial for digestion and metabolism.
• Neutralization reactions involve the reaction between acids and bases, producing salt and water, which is critical for maintaining pH balance in biological systems.

Dehydration and Hydrolysis Reactions

• Methyl acetate forms from methanol and acetic acid through a dehydration reaction, which removes water to form a bond.
• Hydrolysis reverses this process, splitting methyl acetate back into methanol and acetic acid using water.
• These reactions are fundamental in metabolism and biomolecule synthesis.

Neutralization Reactions

• Neutralization involves an acid and a base reacting to create salt and water (e.g., HCl + NaOH → H2O + NaCl).
• They are essential for maintaining pH balance in biological systems, crucial for enzyme activity and metabolic processes; hence vital for biochemistry and medicine.

Redox Reactions

• Redox reactions involve electron transfer during oxidation (electron loss) and reduction (electron gain).
• These reactions are coupled, meaning one cannot happen without the other, crucial for energy transfer in metabolic pathways, like cellular respiration, where glucose oxidation produces ATP.

Properties and Importance of Water in Biology

• Water makes up approximately 70% of the human brain, playing a vital role in cognitive functions and neural processes.
• It constitutes around 90% of lung tissue, essential for gas exchange and respiratory health.
• Bone tissue contains about 22% water, contributing to its structural integrity and flexibility.
• Water is a universal solvent, dissolving a wide range of substances, crucial for many biological reactions and cellular processes.
• Hydration shells surround ions and molecules, preventing re-association and facilitating transport.
• Water's polarity allows it to interact with 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 organic molecules, crucial for life due to their unique bonding properties.
• Carbon's ability to form four covalent bonds allows for diverse molecular structures and chemical behavior, including chains, rings, and branches.

Isotopes of Carbon

• Carbon-12, carbon-13, and carbon-14 are isotopes of carbon, differing in the number of neutrons they have.

Carbon Structures in Biochemistry

• Hydrocarbons consist solely of carbon and hydrogen atoms.
• Carbon skeletons (chains, branches, and rings) form the backbones of biochemical molecules, influencing their properties and functions.

Carbon Structures and Bonding

• Carbon skeletons can be linear, branched, or ring-shaped.
• Ring structures, like glucose and fructose, are crucial in energy metabolism.
• Carbon's ability to form chains and rings is fundamental to organic chemistry and biochemistry.

Bonding Properties of Carbon

• Carbon can form single, double, and triple bonds.
• Single bonds allow for free rotation; double and triple bonds create rigidity.
• The type of bond affects the physical properties of molecules (e.g., boiling and melting points).

Major Classes of Biological Molecules

• Living organisms use complex molecules containing carbon, hydrogen, and other elements.
• Major classes include carbohydrates, lipids, proteins, and nucleic acids.
• Carbohydrates are energy sources and structural components.
• Lipids form membranes and store energy.
• Proteins have diverse functions including catalysis, transport, and structural support.
• Nucleic acids (DNA and RNA) store and transmit genetic information.

Functional Groups in Organic Chemistry

• Functional groups are small reactive groups of atoms influencing the properties and reactivity of molecules.
• Examples include hydroxyl (-OH), carboxyl (-COOH), and amino (-NH2) groups.
• These groups are crucial in biological reactions.

Reactions Involving Functional Groups

• Dehydration reactions involve removing water to form larger molecules, like joining sugar molecules to form starches.
• Hydrolysis reactions add water to break down large polymers into smaller molecules, essential for digestion and metabolism.
• Understanding these reactions is crucial for metabolic pathways and energy transfer.

Comparison of Ethane and Ethanol

• Ethane (C2H6) is nonpolar and cannot dissolve in a cytosol, making it not usable as energy.
• Ethanol (C2H5OH) is polar, dissolving in cytosol and usable as an energy molecule.

Proteins and Nucleic Acids

• Proteins are large molecules consisting of amino acid monomers linked by peptide bonds.
• Amino acids have carboxyl, amino, and an 'R-group', giving them various properties.
• 9 amino acids are essential, needing to be obtained through the diet.
• Nucleic acids (DNA and RNA) store and transmit genetic information; DNA stores long-term information, RNA is crucial in protein synthesis.
• Nucleic acids are polymers of nucleotides containing sugar, phosphate, and nitrogenous bases.

Mechanisms of Enzyme Action

• Enzymes lower activation energy by bringing substrates together, changing substrate shape, or altering charge environments.

Role of Activation Energy

• Activation energy is the minimum energy necessary for a chemical reaction to start.
• Enzymes accelerate reactions by lowering this barrier.

Enzymes in Biological Systems

• Enzymes are biological catalysts accelerating chemical reactions by lowering activation energy without being consumed.
• Enzyme activity is influenced by factors like temperature and concentration; changing any of these can significantly alter the efficiency of an enzyme.

Cell Structures and Organelles (Overview)

• Organelles are specialized structures within a cell with distinct functions necessary to its operation.
• The plasma membrane acts as a barrier, regulating substance entry and exit.
• The nucleus houses the cell's DNA and is enclosed by a nuclear envelope continuous with the endoplasmic reticulum (ER).
• Cell structure plays a significant role in homeostasis.

The Nucleolus

• The nucleolus is a dense region in the nucleus responsible for rRNA synthesis and ribosome subunit assembly.

The Endomembrane System

• The ER (rough and smooth), Golgi apparatus, vesicles, and plasma membrane work together to synthesize, modify, package, and transport proteins and lipids.
• This system is crucial for cellular communication and waste disposal.

Lysosomes, Peroxisomes, and Vacuoles

• Lysosomes contain enzymes to break down waste and debris.
• Peroxisomes break down fatty acids and amino acids (involved in detoxification).
• Vacuoles are storage compartments, particularly in plant cells (responsible for turgor pressure).

Mitochondria and Energy Production

• Mitochondria are considered the "powerhouses" of eukaryotic cells.
• They produce ATP through aerobic respiration (cellular energy).
• The inner mitochondrial membrane is highly folded into cristae, increasing the surface area for ATP production and electron transport chain activity.

Cytoskeleton

• The cytoskeleton is a network of filaments (microtubules, microfilaments, and intermediate filaments).
• It provides structural support, movement (cellular), and cell division, among other functions.
• The extracellular matrix (ECM) plays a significant role in supporting and anchoring cells.

Plasma Membrane

• The plasma membrane separates the cell's internal environment from the external surroundings, regulating substance movement.
• It maintains homeostasis by regulating nutrient intake and waste expulsion.

The Fluid Mosaic Model

• The fluid mosaic model describes the plasma membrane.
• It consists of a phospholipid bilayer with embedded proteins and cholesterol, and glycolipids and glycoproteins (for recognition).
• This structure allows for flexibility and fluid movement within the membrane.

Protein Location and Interaction

• Integral proteins span the entire membrane; they're important for transport, receptors, and maintaining homeostasis.
• Peripheral proteins are on the membrane surfaces; they're involved in signaling, structure, and cell shape.

Cell Recognition and Immune Response

• Membrane proteins are critical for cell-to-cell recognition, a key part of immune response.
• Surface proteins (e.g., MHC) present antigens to T-cells, initiating immune responses.

Transport Mechanisms Across Cell Membranes

• Membrane transport is vital for cell function, facilitated by passive and active mechanisms.
• Passive transport (e.g., diffusion and facilitated diffusion) doesn't require energy; it depends on concentration gradients.
• Active transport moves substances against concentration gradients, using energy (usually ATP).

This quiz covers essential concepts in the chemistry of life, focusing on matter, elements, and the molecular foundations of biological functions. Explore the role of organic compounds and their key components in living organisms. Test your understanding of polar molecules and electronegativity.