Comprehensive Study Notes on Biological Chemistry and Organic Compounds

Ionic Bonding and Atomic Interactions

• The Mechanism of Ionic Bonds: In an ionic bond, electrons are not shared but are transferred from one atom to another, often described as “stealing.”

• Example: Sodium Chloride ($NaCl$):

  • Sodium ($Na$): Donates one electron to chlorine and becomes positively charged ($Na^+$).

  • Chlorine ($Cl$): Accepts one electron from sodium, adding “negativity” to its charge, and becomes negatively charged ($Cl^-$).

pH and Chemical Solutions

• Definition of pH: pH measures the level of acid in a substance based on the concentration of hydrogen ions.

• Acidic Solutions:

  • Definition: Acids are defined as proton donors. They release or donate hydrogen ions ($H^+$) into their environment.

  • Scale: Acidity ranges from a pH of $1$ to just below $7$.

• Neutrality: A pH of exactly $7$ is considered neutral (e.g., pure water).

• Basic (Alkaline) Solutions:

  • Definition: Bases are defined as proton receivers (or proton acceptors). They accept hydrogen ions from the solution.

  • Scale: Basicity ranges from above $7$ up to $14$.

• Toxicity and Spectrum: High or low pH values at the ends of the spectrum can be equally toxic to the body.

  • Ammonia: Highly basic with a pH of approximately $12$.

  • Battery Acid: Highly acidic with a pH of approximately $2$.

• Educational Reference: Cited as slide number $41$; emphasizes that acids are proton donors and bases are proton acceptors.

Properties and Mixtures of Water

• The Universal Solvent: Water is capable of dissolving almost any substance ($universal solvent$).

• Composition of the Human Body: The body is composed of approximately $75\%$ water, meaning most internal interactions occur within water mixtures.

• Adhesion and Cohesion:

  • Adhesion: The ability of water molecules to stick to other surfaces or different molecules (e.g., water sticking to the skin or nose).

  • Cohesion: The ability of water molecules to stick to each other (e.g., two drops of water merging into one).

• Interaction with Substances:

  • Hydrophilic: "Water-loving" substances that mix and dissolve well in water (e.g., sugar, salt).

  • Hydrophobic: "Water-fearing" substances that repel water and do not mix (e.g., fats and oils).

    • If oil and water are shaken together, they may appear mixed momentarily but will quickly separate; the heavier component sinks and the lighter fat sits at the top.

• Ionization of Water: Water ($H_2O$) can break apart (dissociate) into:

  • Hydrogen ions ($H^+$), which are the "protons."

  • Hydroxide ions ($OH^-$).

  • The body can dissociate water as needed to donate hydrogen ions to the environment depending on the physiological requirement.

Chemical Processes Involving Water

• Hydrolysis: Derived from "hydro" (water) and "lysis" (breaking apart). This is the process where a water molecule is added to a substance to break it apart.

  • Analogy: Adding water to a pot with burnt rice at the bottom to soften and separate the molecules from the surface.

  • Biological Example: Breaking down a sugar cube by placing it in water.

• Dehydration Synthesis: The opposite of hydrolysis. It involves removing water molecules to join substances together or to harden a substance.

  • Analogy: The crispy, hardened rice at the bottom of a pot occurs because it has been dehydrated.

  • Biological Example: Creating a solid salt or sugar cube requires the removal of water.

• Thermal Stability: Water has a high heat capacity, allowing it to carry and retain heat well. This is vital for maintaining blood temperature as it flows through vessels.

Classification of Mixtures: Solutions, Colloids, and Suspensions

• Solutions:

  • Particle Size: Less than $1\,nm$.

  • Appearance: Transparent; particles are too tiny to scatter light.

  • Behavior: Will pass through membranes and will not separate when standing.

• Colloids:

  • Particle Size: Between $1\,nm$ and $100\,nm$.

  • Appearance: Cloudy/thick; particles are large enough to scatter light.

  • Behavior: Particles are too large to pass through membranes but stay mixed permanently (e.g., blood flowing within the body).

• Suspensions:

  • Particle Size: Greater than $100\,nm$.

  • Appearance: Cloudy and opaque; scatters light.

  • Behavior: Particles are large and do not pass through membranes. Crucially, a suspension will separate into its individual components if left to stand (e.g., blood taken out of the body into a test tube separates into plasma and red blood cells).

• Emulsions: A mixture of one liquid inside another liquid. A primary example is breast milk, which is an emulsion of water, milk, and fat.

Chemical Reactions and Metabolism

• Chemical Reaction Basics: Reactions involve reactants that undergo a process to produce a final product. Some reactions are reversible.

• Reaction Types:

  • Decomposition Reaction: Breaking a complex reactant into simpler components ($ABC \rightarrow A + B + C$).

  • Synthesis Reaction: Taking simple components and joining them to form a complex molecule ($A + B + C \rightarrow ABC$).

  • Exchange Reaction: Molecules exchange components to form new products ($AB + CD \rightarrow AC + BD$).

• Metabolism: Definitions include all chemical processes in the body, such as breaking down nutrients or building tissue.

  • Anabolism: Energy-consuming process of building complex molecules (similar to synthesis). Example: Building proteins for breast milk.

  • Catabolism: Energy-releasing process of breaking down molecules (similar to decomposition). Example: Breaking down glucose to release energy.

• Oxidation and Reduction:

  • Oxidation: A molecule gives up an electron and releases energy. Oxygen is a common electron acceptor (oxidizing agent).

  • Reduction: A molecule gains an electron. (Memory aid: You are "reduced" when you gain an electron).

Organic Compounds: Carbohydrates

• Composition: Long chains of carbon, hydrogen, and oxygen.

• General Formula: $CH_2O$. For instance, two carbons would equal $C_2H_4O_2$.

• Glucose: The most important carbohydrate in the body ($C_6H_{12}O_6$).

• Sugar Nomenclature: Sugars usually end in "-ose" (e.g., glucose, sucrose, fructose) and can start with the root "sacchar-".

• Levels of Complexity:

  • Monosaccharides (Monomers): Single sugar molecules. The three main ones in the body are Glucose, Galactose, and Fructose.

  • Disaccharides: Two monomers joined together.

    • Maltose: Glucose + Glucose.

    • Sucrose (Table Sugar): Glucose + Fructose.

    • Lactose (Milk): Glucose + Galactose.

  • Oligosaccharides: Short chains of $3$ to $10$ monosaccharides.

  • Polysaccharides (Polymers): Long chains, often $50$ or more monosaccharides.

    • Glycogen: The form in which sugar is stored in the liver and muscle cells.

    • Starch: A plant-based polymer (e.g., in potatoes) containing about $3,000$ glucose molecules; used as an energy source.

    • Cellulose: A plant-based polymer that humans cannot digest; provides fiber to prevent constipation.

Organic Compounds: Lipids

• Types of Lipids:

  1. Fatty Acids: Chains of $4$ to $24$ carbons. Saturated (full of hydrogen) vs. Unsaturated (contains double bonds between carbons).

  2. Triglycerides: Three fatty acids bonded to one glycerol. Neutral fats. They are liquid (oil) at room temperature but turn solid when cold.

  3. Phospholipids: Found in cell membranes. They are amphipathic (or antipathic), meaning they have a hydrophilic head and a hydrophobic tail.

  4. Eicosanoids: Derived from arachidonic acid. They act like hormones. Prostaglandins are a common type responsible for signaling inflammation and pain.

  5. Steroids: Carbon chains that form rings. Cholesterol is the parent steroid from which others are made.

• Cholesterol Facts:

  • $85\%$ is made internally by the body; $15\%$ comes from diet.

  • Necessary for nervous system development in children and for making hormones and bile acids.

  • HDL (High-Density Lipoprotein): "Good" cholesterol.

  • LDL (Low-Density Lipoprotein): "Bad" cholesterol; responsible for clogged arteries, strokes, and heart attacks.

  • Increasing HDL naturally helps decrease LDL.

• Trans Fatty Acids: Contain covalent bonds in an opposite angle. They are difficult for the body to break down and contribute heavy risk for heart disease.

Organic Compounds: Proteins and Enzymes

• Protein Composition: Polymers made of $20$ different amino acids. They consist of an amino group, a carboxyl group, and a variable R group (radical group) that gives each amino acid its identity.

• Peptide Terminology:

  • Dipeptide: $2$ amino acids.

  • Tripeptide: $3$ amino acids.

  • Oligopeptide: Small chain (< 15 amino acids).

  • Polypeptide: More than $15$ amino acids.

  • Protein: More than $50$ amino acids.

• Structure Levels:

  • Primary: Simple chain of amino acids.

  • Secondary: Coiling or folding of the chain.

  • Tertiary: Complex bending/folding into globular or fibrous shapes.

  • Quaternary: Multiple polypeptide chains joined together (e.g., Hemoglobin, which has four structures and an iron center that binds oxygen).

• Denaturation: The destruction of a protein's shape and function due to extreme heat or pH changes. Examples include cooking an egg (it cannot be reversed) or burning hair keratin with a flat iron.

• Enzymes:

  • Biological catalysts that speed up reactions (turning hours of work into seconds) by lowering activation energy.

  • Names usually end in "-ase".

  • Amylase: Found in saliva (pH $7$). Breaks down starch in the mouth but denatures in the acidic stomach (pH $2$).

  • Pepsin: Built to work in the stomach at pH $2$ to break down meat proteins but denatures in the duodenum (pH $8$).

Nucleotides and ATP

• Nucleotide Components: Consist of a nitrogenous base, a sugar, and a phosphate group.

• Adenosine Triphosphate (ATP):

  • Structure: Adenine (base), Ribose (sugar), and three phosphate groups.

  • Function: The primary energy transfer molecule in the body.

• Genetic Material:

  • DNA (Deoxyribonucleic acid): Stores genetic information.

  • RNA (Ribonucleic acid): Involved in protein synthesis and genetic signaling.