Study Notes on Biochemical Foundations
Overview of Lipids
Definition: Lipids are a diverse group of hydrocarbons, primarily lacking oxygen.
Nature: Mostly nonpolar and hydrophobic (water-fearing).
Mix of compounds made of hydrocarbons; mostly carbon and hydrogen, less oxygen.
In water, lipids don't form a true solution (e.g., oil and water don't mix).
Example: Do not mix with water (polar); relates to the phrase "like dissolves like".
Polar vs. Nonpolar Molecules
Polar Molecules: Have a charge or a partial charge due to the presence of oxygen (e.g., water).
Nonpolar Molecules: Lack charge; do not mix well with polar substances like water.
Example: Lipids are mostly nonpolar, which is fundamental to their function.
Terms to Know:
Hydrophilic: Water-loving, usually polar/charged.
Hydrophobic: Water-fearing, usually nonpolar.
Lipophilic: Fat-loving.
Lipophobic: Fat-fearing.
Relationship: Hydrophilic substances are often lipophobic and vice versa.
Triglycerides
Definition: One of the most common dietary lipid groups and main form of stored fat in the body.
Structure: Composed of glycerol and three fatty acid chains; fatty acid chains are nonpolar and hydrophobic.
Function: Provide energy during periods of rest; serve as the primary dietary fat. At rest, a majority of energy used to keep the body alive is taken from triglycerides stored in fat.
Types of Fats:
Saturated Fats: Single bonds between carbon atoms; linked to high cholesterol levels (considered bad fats), increase the risk of heart disease. Common sources: meat, dairy, coconut, palm oil.
Unsaturated Fats: One or more double bonds; found in healthy sources like fish oil (considered good fats), thought to reduce heart disease risk (e.g., Omega-3 fatty acids in salmon).
Trans Fats: Trans configuration of double bonds; generally unhealthy (linked to processed foods).
Phospholipids
Definition: Essential component of cell membranes containing hydrophobic and hydrophilic parts. Amphiphilic molecules with both a polar (water-loving) and nonpolar (fat-loving) region.
Structure:
Hydrophilic Head: Contains a phosphate group; interacts with water.
Hydrophobic Tails: Composed of fatty acid chains; repel water.
Importance: Create a bilayer that serves as the foundation for cell membranes, allowing selective permeability. They orient themselves to interface with water both inside (intracellular fluid) and outside (extracellular fluid) the cells, with hydrophobic tails forming the core of the bilayer.
Steroids and Hormones
Definition: Another category of lipids that includes hormones such as thyroid hormone and prostaglandins.
Function: Serve as signaling molecules within the body.
General Characteristics of Lipids
Nonpolar Nature: Generally lack the presence of oxygen, leading to primarily nonpolar characteristics.
Composition: Rich in carbon and hydrogen bonds (hydrocarbons) with no charge.
Key Takeaway: Important for dietary sources and cellular structure.
Proteins
Definition: Made of amino acid monomers; foundational biological macromolecules. A protein is an organic molecule made of amino acids linked by peptide bonds, which are covalent bonds. A peptide is a very short chain of amino acids.
Key Structure Components:
Monomers: Amino acids (20 different types); each made up of a nitrogen group, a carbon group, and a varying "R" group.
Polymers: Amino acids linked by peptide bonds to form peptide chains, which fold into proteins.
Function: Structure and function are related to the folding and complexity of the protein structure. A protein's shape dictates its function.
Protein Structure Levels:
Primary Structure: Linear chain of amino acids.
Secondary Structure: Initial folding (alpha-helices, beta-sheets).
Tertiary Structure: Further folding to form a 3D structure.
Quaternary Structure: Multiple polypeptide chains assembling together (e.g., hemoglobin).
Types of Proteins:
Structural proteins: Collagen, Keratin, actin, myosin.
Enzymatic proteins: Lactase, ATP synthase, Na/K-ATPase.
Other functions: Movement, storage proteins, antibodies, hormone proteins. Hemoglobin, for example, is a protein in red blood cells that transports oxygen.
Enzymes and Protein Function
Definition: Proteins functioning as catalysts in biological reactions.
Significance: Specific shape is crucial for binding substrates at the active site, enabling the enzyme's function (like puzzle pieces fitting together). Chemical reactions are catalyzed by enzymes: "substrate" + enzyme -> product + enzyme. Example: Amylase breaks down disaccharides.
Denaturation: Process where proteins lose their structure and, consequently, their function due to environmental factors like pH or temperature. Denaturation is a change in structure, such as unraveling or misfolding, which leads to proteins losing their functional shape and ability to work. This can occur in extreme heat, acids, bases, or chemical stress. For example, blood pH set point is , and the usual range is ; outside this range, proteins denature.
Nucleotides
Definition: Building blocks of nucleic acids (DNA and RNA). ATP is a nucleotide.
Components:
Phosphate Group: Essential for the nucleotide structure.
Sugar: Deoxyribose in DNA, ribose in RNA.
Nitrogenous Base: Purines (adenine, guanine) and pyrimidines (cytosine, thymine for DNA; uracil for RNA).
DNA vs. RNA: Differ in sugar and base composition (DNA contains thymine; RNA contains uracil). A chain of nucleotides forms single-stranded DNA and RNA. Deoxyribonucleic acid (DNA) is a nucleotide that stores genetic information.
Structure of DNA
Double Helix: DNA is formed by two strands held together by hydrogen bonds between complementary base pairs.
Base Pairing Rules:
Adenine pairs with Thymine (A-T).
Guanine pairs with Cytosine (G-C).
Importance of Hydrogen Bonds: Provide enough strength for stability while being easily separable for replication.
Cell Diversity and Development
Cells have diverse shapes, amounts of organelles, and functions, all originating from stem cells.
Stem cell: When sperm meets egg, a zygote forms and bundles into different cells. Stem cells can differentiate into various cell types (e.g., bone cell, muscle cell, simple squamous cell).
Progenitor cells: Somewhere in between; these cells can change along the way, turning from one cell type to another.
Cell Membrane Structure and Function
Phospholipid Bilayer: Main structure of cell membranes; creates a barrier between intracellular (inside cell) and extracellular (outside cell) environments. Nearly all lipids are nonpolar, except for the phospholipid bilayer.
Fluid Mosaic Model: Describes the dynamic nature of membrane components (lipids and proteins can move laterally within the bilayer). The membrane is not rigid or stiff; it's always flowing. Cholesterol contributes to this fluidity.
Proteins Embedded: Perform various functions, including transport across the membrane, signaling, structural roles, communication between cells, and recognition.
Types of Membrane Proteins:
Integral Proteins: Span the membrane; may form channels for substance passage or communicate outside and inside the cell in different ways.
Peripheral Proteins: Associate loosely with the membrane; typically involved in signaling and structural support.
Glycoproteins: Used for cell signaling.
Receptors: Must have a certain shape to bind to specific signaling molecules (ligands like hormones or sugars), initiating a cellular response. This "puzzle piece" fit ensures proper communication and function, and disruptions can lead to diseases.
Membrane Transport Mechanisms
Membrane is selectively permeable: It picks and chooses what can pass through.
Permeability:
Small, nonpolar, fat-soluble molecules (lipids, oxygen gas, carbon dioxide gas) can move freely across the membrane.
Water-soluble molecules (glucose, amino acids) cannot cross the plasma membrane easily as they are repelled by the hydrophobic tails of the phospholipid layer; they need integral channels to pass through.
Passive Transport: No energy required; substances move from high to low concentration. This is built around the principle that things go from high to low concentration naturally, driven by kinetic energy. An example is the spread of perfume in a room.
Simple Diffusion: Movement of small nonpolar molecules directly across the membrane. Stops once equilibrium (chemical gradient) is reached.
Electrical Gradient: Depends on the charge of the substance; charges move down the electrical gradient towards the opposite charge (e.g., outside cell is often more negative than inside).
Facilitated Diffusion: Requires specific protein channels or carriers for larger or polar molecules to cross the membrane without energy. It's still passive because it moves down the concentration gradient, utilizing the kinetic energy inherent in molecules.
Types of Channels: Some require a receptor to open (ligand-gated), others open due to physical change from pressure (mechanically-gated, e.g., pressure receptors), and voltage-gated channels respond to changes in electrical potential. The membrane is good at carrying electrical signals; current is often initiated by sodium.
Osmosis: Diffusion of water molecules across a semi-permeable membrane, moving down its concentration gradient. In small amounts, water can move directly through the membrane, but channels (aquaporins) make it more efficient. The amount of solute in water affects its concentration.
Tonicity: Refers to the concentration of solutes outside the cell relative to the inside, significantly affecting cellular osmosis. Maintaining balance is crucial, especially in blood (e.g., IV solutions have specific water to salt concentrations). When there is a high concentration of solute outside the cell, water will follow it.
Active Transport: Requires energy (e.g., ATP) to move substances against their concentration gradient (from low to high concentration), often likened to pushing many people into a small space.
Sodium-Potassium Pump (Na+/K+-ATPase): Uses ATP to pump sodium () ions out of the cell and potassium () ions into the cell, against their concentration gradients. This is crucial for maintaining proper ion balance and cell viability.
ions from the intracellular fluid bind to the pump.
ATP hydrolysis provides energy, causing a conformational change (change in shape) in the pump; a phosphate ion stays attached.
The pump opens to the extracellular side, releasing ions.
ions from outside the cell bind to the pump.
The phosphate detaches, causing another conformational change, and the pump opens to the intracellular side, releasing ions.
This pump ensures a large amount of out of the cell and a large amount of inside the cell.
Secondary Active Transport: Uses the electrochemical gradient of one substance (often ) to move another substance against its concentration gradient. It requires a partner (symporter or antiporter).
Symporters: Move two substances in the same direction (e.g., sodium and glucose entering the cell together). The sodium gradient created by the Na+/K+ pump helps glucose diffuse into the cell. This process is crucial for cells to obtain glucose for energy production; it cannot happen if sodium is in low quantity.
Antiporters: Move two substances in opposite directions.
Vesicle-Mediated Transport:
Endocytosis: Process where cells engulf substances into the cell by enclosing them in a vesicle formed from the plasma membrane. Fluidity of the membrane allows for endocytosis.
Phagocytosis: "Cell eating" – process where cells engulf things of interest (e.g., particles and nutrients).
Pinocytosis: "Cell drinking" – cell takes in fluid and dissolved substances.
Receptor-Mediated Endocytosis: Requires specific receptors on the surface; particles of interest bind to these receptors, triggering vesicle formation.
Exocytosis: Process where substances are released from the cell. Vesicles containing substances fuse with the plasma membrane and release their contents to the extracellular environment (e.g., pancreatic acinar cells excreting digestive enzymes).
Conclusion
Summary: Understanding types of lipids, proteins, nucleotides, and membrane structures, along with transport mechanisms, is essential