Study Notes on The Chemical Level of Organization
THE CHEMICAL LEVEL OF ORGANIZATION
Chapter 2
Elements & Atoms
Matter: The substance of the universe.
Element: A pure substance made of subatomic particles; cannot be created or broken down by ordinary chemical means.
Compound: Two or more elements joined by chemical bonds.
Atoms
Two Models of Atomic Structure
The Planetary Model: Suggests electrons orbit the nucleus in distinct paths like planets around the sun.
The Electron Cloud Model: Suggests electrons exist in regions of probability rather than fixed orbits.
The Periodic Table of the Elements
Common Elements in the Human Body
Most Common Elements:
Oxygen (O): 65%
Carbon (C): 18.5%
Hydrogen (H): 10%
Nitrogen (N): 3%
Calcium (Ca): 1.5%
Phosphorus (P): 1%
Potassium (K): 0.4%
Sulfur (S): 0.3%
Sodium (Na): 0.2%
Chlorine (Cl): 0.2%
Magnesium (Mg): 0.1%
Trace Elements: Include boron (B), chromium (Cr), cobalt (Co), copper (Cu), fluorine (F), iodine (I), iron (Fe), manganese (Mn), molybdenum (Mo), selenium (Se), silicon (Si), tin (Sn), vanadium (V), and zinc (Zn); each constituting less than 1.0% of the body.
Chemical Bonds
Bond: A weak or strong electrical attraction holding two or more atoms in proximity.
Molecule: Two or more atoms held by a chemical bond, often of the same element (e.g., H2).
Compound: Two or more atoms of different elements (e.g., H2O).
Ion: An atom with a (+) or (-) electrical charge.
Cation: A positively charged ion (lost electrons).
Anion: A negatively charged ion (gained electrons).
Isotope: Different forms of an element due to differing numbers of neutrons; heavy isotopes may be unstable (radioactive).
Electron Shells
Types of Chemical Bonds
Ionic Bonds: Created through the transfer of electrons between ions of opposite charges.
Covalent Bonds: Electrons are shared in a mutually stabilizing relationship; can be classified as polar or non-polar.
Hydrogen Bonds: Weaker bonds that occur between polar molecules, represented by dotted lines.
Characteristics of Chemical Reactions
Types of Fundamental Chemical Reactions
Synthesis Reaction: Two components bind to form a larger molecule.
Decomposition Reaction: Bonds between components of a larger molecule are broken, resulting in smaller products.
Exchange Reaction: Bonds are both formed and broken, rearranging components of the reactants.
Electrolytes
Salt: A compound that provides ions other than hydrogen and hydroxide.
Electrolyte: A salt that ionizes in water, allowing electrical conduction; example: sodium chloride (NaCl), essential for human life.
Acids, Bases & Salts
Acids: Source of H+ ions, also called proton donors (e.g., lemon juice).
Bases: Accept H+, release OH-, known as proton acceptors (e.g., baking soda).
pH Scale: Measures the strength of acids and bases based on H+ concentration; the scale ranges from 0 to 14.
Neutral: pH of 7
Acidic: pH < 7
Basic: pH > 7
Buffer Systems
Buffers: Convert strong acids or bases into weak ones, regulating pH through chemical buffers (e.g., HCO3, phosphate, protein).
Physiological Buffers: Role of respiration and urination in pH control.
Intracellular Fluid (ICF): Neutral pH of 7.
Extracellular Fluid (ECF): Neutral pH range of 7.35-7.45.
Acidosis: Occurs if pH falls below neutral; Alkalosis: If pH rises above neutral.
Properties of Water
Comprises 50-70% of the adult body and about 75% in infants.
Functions in:
Transportation as blood plasma.
Absorbing and dissipating body heat (e.g., sweating).
Lubrication (e.g., between visceral and parietal layers).
Acting as the universal solvent in cellular processes (hydrophilic vs. hydrophobic).
Hydrolysis: Water can break down compounds, while dehydration synthesis uses water to link compounds.
Surface Tension: Molecules attract each other (cohesion) due to hydrogen bonding.
Solutions and Concentrations
Molarity (M): 1M is the atomic weight in 1L of the solution.
Colloid: A heavy, opaque solution (e.g., milk).
Suspension: A mixture that will eventually settle.
Solute: The substance to be dissolved.
Solvent: The substance that dissolves the solute.
Solution: Combination of solute and solvent (e.g., glucose in blood).
Nutritional Chemistry
Monomer: A repeating subunit of a polymer (e.g., simple sugar, amino acids).
Polymer: A large molecule formed from linked monomers (e.g., carbohydrates, proteins, DNA/RNA).
Macronutrients: Required for sustaining life and powering cellular processes.
Macromolecules and Functional Groups
Carbohydrates: Overview and Types
Functions of Carbohydrates
Lipids
Triglycerides: Serve as a fuel source, assist in vitamin absorption, and provide cushioning.
Fatty Acids:
Phospholipids: Composed of two fatty acid chains and a phosphorus-containing group, critical for cell membranes.
Steroids: Four interconnected hydrocarbon rings (e.g., cholesterol).
Prostaglandins: Are active lipid-based signaling molecules.
Functions of Lipids
Stored Energy: Found in fat cells beneath the skin.
Chemical Messengers: Serve roles in cellular signaling.
Cell Membrane Structure: Form crucial components of cell membranes.
Insulation: Protect internal organs.
Buoyancy: Contribute to floating.
Proteins
Monomers: Composed of amino acids.
Structure: Contains Nitrogen (N), Carbon (C), Hydrogen (H), Oxygen (O), and sometimes Sulfur (S).
Peptide Bonds: The bond linking amino acids together.
Polypeptides: Chains of fewer than 100 amino acids.
Characteristics of Proteins
20 Different Amino Acids: Possess both acidic and basic properties, acting as excellent buffers.
Protein Structure:
Primary Structure: Linear sequence of amino acids.
Secondary Structure: Either an alpha-helix or pleated sheet.
Tertiary Structure: The three-dimensional shape.
Quaternary Structure: Multiple polypeptide chains combined.
Denaturation: Alteration of a protein's structure due to heat or chemicals, sometimes reversible.
Functions of Proteins
Structure: Collagen and keratin contribute to the physical makeup of cells.
Communication: Hormones and cell receptors.
Protection: Antibodies and clotting proteins.
Movement: Muscle contraction.
Membrane Transport: Involves channels and carriers.
Catalysts: Enzymes facilitate biochemical reactions.
Enzymatic Reaction Steps
Substrates approach active sites on the enzyme.
Substrates bind to active sites forming an enzyme–substrate complex.
Changes occur internally in the enzyme–substrate complex facilitating interactions.
Product is released, returning the enzyme to its original form.
Nucleotides & Nucleic Acids
Nucleotide Structure:
Phosphate Group: One or more present in the structure.
Pentose Sugar: Either deoxyribose or ribose.
Nitrogenous Base: Can be adenine, cytosine, guanine, thymine, or uracil.
Types of Nucleic Acids:
Summary of Chemical Compounds
Polymers vs. Monomers:
Polymers: Larger structures made of repeating units, such as carbohydrates, proteins, lipids, and nucleic acids.
Monomers: Simple unit structures, e.g., monosaccharides, amino acids, fatty acids, nucleotides.
Dietary Sources and Functions:
Carbohydrates:
Sources: Grains, legumes, vegetables, fruits.
Function: Provide energy and fuel.
Proteins:
Sources: Nuts, meat, dairy, soy.
Functions: Structure, communication, catalyst, movement, membrane transport.
Lipids:
Sources: Oils, butter, egg yolk.
Functions: Energy storage, chemical messengers, cell membrane structure.
Nucleic Acids:
Sources: Meat, fish, fruits, vegetables.
Functions: Genetic info, protein synthesis.
Review Questions
What's Next?
THE CHEMICAL LEVEL OF ORGANIZATION ### Chapter 2 #### Elements & Atoms - Matter: The substance of the universe, combining all physical objects and materials. - Mass: The amount of matter contained in an object, measured in kilograms or grams, crucial for understanding physical properties. - Weight: Mass affected by the pull of gravity; it varies depending on the gravitational field and is measured in newtons. - Element: A pure substance made of subatomic particles; cannot be created or broken down by ordinary chemical means. Elements serve as the building blocks for all matter in the universe. - Compound: Two or more elements joined by chemical bonds, representing a fixed ratio of elements that exhibit unique properties differing from those of the individual elements. #### Atoms - Atoms: The smallest unit of an element, representing the fundamental building blocks of matter. - Protons: Positively charged particles found in the nucleus; their number defines the element. - Neutrons: Neutral or non-charged particles also present in the nucleus, contributing to the atomic mass but not the charge. - Electrons: Negatively charged particles that orbit the nucleus in electron shells; they play a key role in chemical bonding. - Structure of Atoms: - Generally have the same number of protons and electrons, maintaining electrical neutrality. - The number of protons and neutrons gives mass to the atom (Atomic Mass Number). - The number of protons in the nucleus determines the element (Atomic Number). #### Two Models of Atomic Structure - The Planetary Model: Suggests electrons orbit the nucleus in distinct paths like planets around the sun, which was helpful for understanding simple hydrogen atoms. - The Electron Cloud Model: Suggests electrons exist in regions of probability rather than fixed orbits, indicating that the exact position of electrons cannot be precisely determined, reflecting advances in quantum mechanics. #### The Periodic Table of the Elements - Displays atomic properties of elements, including atomic number, symbol, and average atomic mass, which can help predict chemical behavior. For accurate values, visit physics.nist.gov/constants. - Examples of Elements: - Hydrogen (H): Atomic Mass = 1.00794. - Helium (He): Atomic Mass = 4.002602. - Carbon (C): Atomic Mass = 12.0107; crucial for organic chemistry and the fundamental building block of life. #### Common Elements in the Human Body - Most Common Elements: - Oxygen (O): 65%, critical for respiration and water composition. - Carbon (C): 18.5%, the backbone of organic molecules. - Hydrogen (H): 10%, integral to water and organic molecules. - Nitrogen (N): 3%, a key component of amino acids and nucleic acids. - Calcium (Ca): 1.5%, essential for bone structure and muscle function. - Phosphorus (P): 1%, important for energy transfer (ATP) and genetic material. - Potassium (K): 0.4%, vital for cellular function and signaling. - Sulfur (S): 0.3%, found in amino acids and vitamins. - Sodium (Na): 0.2%, crucial for nerve function and fluid balance. - Chlorine (Cl): 0.2%, important for maintaining osmotic balance and pH. - Magnesium (Mg): 0.1%, critical for enzymatic reactions. - Trace Elements: Include boron (B), chromium (Cr), cobalt (Co), copper (Cu), fluorine (F), iodine (I), iron (Fe), manganese (Mn), molybdenum (Mo), selenium (Se), silicon (Si), tin (Sn), vanadium (V), and zinc (Zn), each constituting less than 1.0% of the body; essential in cellular processes and enzyme function. #### Chemical Bonds - Bond: A weak or strong electrical attraction holding two or more atoms in proximity, essential for forming molecules. - Molecule: Two or more atoms held by a chemical bond, often of the same element (e.g., H2), representing the simplest form of a chemical compound. - Compound: Two or more atoms of different elements (e.g., H2O), exhibiting unique physical and chemical properties from their constituent elements. - Ion: An atom with a (+) or (-) electrical charge due to loss or gain of electrons. - Cation: A positively charged ion that has lost electrons, often found in ionic compounds. - Anion: A negatively charged ion that has gained electrons, contributing to various chemical reactions. - Isotope: Different forms of an element due to differing numbers of neutrons; heavy isotopes may be unstable (radioactive) and important for dating and medical applications. #### Electron Shells - Electron Shells: Exist at distinct energy levels around the atomic nucleus, determining the distribution of electrons. - Shell #1 can hold 2 electrons; Shells #2-5 can each hold 8 electrons based on the formula 2n², where n is the shell level. - The number of electrons determines the number of shells and overall atomic structure. - Valence Shell: The outermost electron shell that participates in chemical bonding. - Full Valence Shell: Indicates a stable atom, which does not readily react with others. - Not Full: Indicates a reactive atom, seeking to attain stability. - Most atoms reach stability with exactly 8 electrons in their valence shell (Octet Rule), a key principle in understanding chemical reactivity. #### Types of Chemical Bonds - Ionic Bonds: Created through the transfer of electrons between ions of opposite charges, leading to the formation of stable compounds such as sodium chloride (NaCl). - Covalent Bonds: Electrons are shared in a mutually stabilizing relationship, can be classified as polar (unequal sharing) or non-polar (equal sharing), affecting the molecule's behavior. - Hydrogen Bonds: Weaker bonds that occur between polar molecules, represented by dotted lines, crucial for the unique properties of water and biological macromolecules. #### Characteristics of Chemical Reactions - Chemical Reactions: Energy is required to break and create new bonds; reactions are governed by the conservation of mass and energy. - Types of Energy: - Kinetic Energy: Energy of motion; crucial for molecular interactions. - Potential Energy: Stored energy within bonds, released during reactions; influences reaction spontaneity. - Chemical Energy: Energy stored in bonds, necessary for metabolic processes. - Others: Mechanical, Radiant, Electrical, each serving unique roles in biochemical processes. - Components: - Reactants: Substances entering the reaction that undergo transformation. - Products: Substances produced by the reaction, representing the end result. #### Types of Fundamental Chemical Reactions - Synthesis Reaction: Two components bind to form a larger molecule, creating complexity; Energy is required and stored in the bond as shown by: -
extNOTE+extBOOK</h4><p>ightarrowextNOTEBOOK - Decomposition Reaction: Bonds between components of a larger molecule are broken, resulting in smaller products; vital for metabolic processes. - Example: -
extBOOKWORM<br>ightarrowextBOOK+extWORM - Exchange Reaction: Bonds are both formed and broken, rearranging components of the reactants, showcasing versatility in chemical interactions. - Example: -
extNOTEBOOK+extWORM<br>ightarrowextNOTE+extBOOKWORM #### Electrolytes - Salt: A compound that provides ions other than hydrogen and hydroxide, crucial for maintaining physiological functions and fluid balance. - Electrolyte: A salt that ionizes in water, allowing electrical conduction; example: sodium chloride (NaCl), essential for human life, nerve transmission, and muscle contraction. #### Acids, Bases & Salts - Acids: Source of H+ ions, also called proton donors (e.g., lemon juice); they can increase the H+ concentration in solutions. - Bases: Accept H+, release OH-, known as proton acceptors (e.g., baking soda), often moderating pH levels. - pH Scale: Measures the strength of acids and bases based on H+ concentration; the scale ranges from 0 to 14, essential for biological systems. - Neutral: pH of 7, indicating neither acidic nor basic conditions. - Acidic: pH < 7, indicative of increased H+ ions. - Basic (Alkaline): pH > 7, characterized by decreased H+ ions and higher OH- concentrations. #### Buffer Systems - Buffers: Convert strong acids or bases into weak ones, regulating pH through chemical buffers (e.g., HCO3, phosphate, protein), essential for maintaining homeostasis. - Physiological Buffers: Involve the role of respiration and urination in pH control, impacting overall metabolic function. - Intracellular Fluid (ICF): Neutral pH of 7, maintaining optimal conditions for cellular processes. - Extracellular Fluid (ECF): Neutral pH range of 7.35-7.45, necessary for proper organ function. - Acidosis: Occurs if pH falls below neutral, leading to potential cellular dysfunction. - Alkalosis: If pH rises above neutral, it can disrupt normal physiological activities. #### Properties of Water - Comprises 50-70% of the adult body and about 75% in infants; its unique properties support life. - Functions in: - Transportation: Acts as a medium in blood plasma for nutrient and gas exchange. - Absorbing and dissipating body heat: e.g., sweating aids thermal regulation. - Lubrication: Reduces friction between visceral and parietal layers in organs. - Acting as the universal solvent: Facilitates biochemical reactions (hydrophilic vs. hydrophobic interactions). - Hydrolysis: Water can break down compounds, essential for digestion and metabolic processes, while dehydration synthesis uses water to link compounds, crucial for macromolecule formation. - Surface Tension: Molecules attract each other (cohesion) due to hydrogen bonding, affecting biological interactions like capillary action. #### Solutions and Concentrations - Molarity (M): 1M is the atomic weight in 1L of the solution, a standard unit of concentration used in chemical reactions. - Colloid: A heavy, opaque solution (e.g., milk) that does not settle; crucial for understanding mixtures. - Suspension: A mixture that will eventually settle; important in pharmacology and food science. - Solute: The substance to be dissolved, impacting solution chemistry. - Solvent: The substance that dissolves the solute, typically water in biological systems. - Solution: Combination of solute and solvent (e.g., glucose in blood), fundamental to cellular processes. #### Nutritional Chemistry - Monomer: A repeating subunit of a polymer (e.g., simple sugar, amino acids); crucial for building larger complex molecules. - Polymer: A large molecule formed from linked monomers (e.g., carbohydrates, proteins, DNA/RNA); useful in various biological functions. - Macronutrients: Required for sustaining life and powering cellular processes; they are the primary sources of energy and essential for growth. #### Macromolecules and Functional Groups - Macromolecules: Carbohydrates, Proteins, Lipids, Nucleic Acids—a diverse group essential for life. - Functional Groups: - Hydroxyl (-O-H): Polar; participates in dehydration synthesis and hydrolysis processes, increasing solubility in water. - Carboxyl (-COOH): Found in fatty acids and amino acids, contributing to acidic properties. - Amino (-N-H2): Component of proteins, containing both an amino and carboxyl group, highlighting its role in biological reactions. - Methyl (-C-H3): Found within amino acids and other compounds; influences molecular interactions and gene expression. - Phosphate (-P-O4^2-): In phospholipids and nucleotides, central to energy transfer (ATP) and structural components of DNA/RNA. #### Carbohydrates: Overview and Types - Basic Structure: Carbon, Hydrogen, Oxygen represented as (CH2O)n; provides energy and structural components. - Forms: - Monosaccharides: - Hexose Sugars: Glucose, fructose, galactose—primary energy sources. - Pentose Sugars: Ribose, deoxyribose—critical in nucleic acid structure. - Disaccharides: Pair of monosaccharides linked by glycosidic bonds (e.g., sucrose, lactose, maltose); hydrolysis splits them into monosaccharides for energy. - Polysaccharides: - Starches: Easily digestible plant-based foods, major energy storage for plants. - Glycogen: Stored in tissues, primarily the liver and muscles, serving as a quick energy source. - Cellulose: Provides fiber, essential for digestive health and supporting plant structures. #### Functions of Carbohydrates - Energy Source: All body cells can utilize glucose; its breakdown produces ATP, fueling cellular activities. - Cell Structure: Carbohydrates bind with proteins and lipids, forming glycoproteins and glycolipids essential for cell signaling and structure. #### Lipids - Triglycerides: Serve as a fuel source, assist in vitamin absorption, and provide cushioning around organs, playing a vital role in health. - Fatty Acids: - Saturated: No double bonds; solid at room temperature, typically found in animal fats. - Unsaturated: Contains double bonds (includes trans fats), liquid at room temperature; often healthier fats from plants and fish. - Phospholipids: Composed of two fatty acid chains and a phosphorus-containing group, critical for cell membranes, creating bilayers. - Steroids: Four interconnected hydrocarbon rings (e.g., cholesterol, hormones), influencing metabolism and cell signaling. - Prostaglandins: Active lipid-based signaling molecules that regulate a variety of physiological responses, including inflammation. #### Functions of Lipids - Stored Energy: Found in fat cells beneath the skin, serving as an energy reserve. - Chemical Messengers: Serve roles in cellular signaling, including hormone actions. - Cell Membrane Structure: Form crucial components of cell membranes, maintaining integrity and function. - Insulation: Protect internal organs and help regulate body temperature. - Buoyancy: Contribute to floating, particularly in aquatic organisms. #### Proteins - Monomers: Composed of amino acids, the building blocks of proteins necessary for various biological functions. - Structure: Contains Nitrogen (N), Carbon (C), Hydrogen (H), Oxygen (O), and sometimes Sulfur (S). - Peptide Bonds: The bond linking amino acids together, essential for protein formation. - Polypeptides: Chains of fewer than 100 amino acids, important for specific biological roles. #### Characteristics of Proteins - 20 Different Amino Acids: Possess both acidic and basic properties, acting as excellent buffers, maintaining pH balance. - Protein Structure: - Primary Structure: Linear sequence of amino acids that dictate protein function. - Secondary Structure: Either an alpha-helix or pleated sheet, formed due to hydrogen bonding. - Tertiary Structure: The three-dimensional shape, critical for functionality. - Quaternary Structure: Multiple polypeptide chains combined to form functional proteins like hemoglobin. - Denaturation: Alteration of a protein's structure due to heat or chemicals, sometimes reversible; impacts function. #### Functions of Proteins - Structure: Collagen and keratin contribute to the physical makeup of cells and tissues. - Communication: Hormones and cell receptors regulate biological processes and cellular responses. - Protection: Antibodies and clotting proteins defend against pathogens and prevent blood loss. - Movement: Muscle contraction driven by protein interactions, essential for locomotion. - Membrane Transport: Involves channels and carriers that facilitate molecular movement across membranes. - Catalysts: Enzymes facilitate biochemical reactions, increasing the reaction rate without being consumed. #### Enzymatic Reaction Steps 1. Substrates approach active sites on the enzyme, initiating interaction. 2. Substrates bind to active sites forming an enzyme–substrate complex, critical for reaction specificity. 3. Changes occur internally in the enzyme–substrate complex facilitating reactions among substrates, stabilizing transition states. 4. Product is released, returning the enzyme to its original form, allowing for subsequent reactions. #### Nucleotides & Nucleic Acids - Nucleotide Structure: - Phosphate Group: One or more present in the structure, crucial for linkage of nucleotides. - Pentose Sugar: Either deoxyribose or ribose, impacting the structure of DNA vs RNA. - Nitrogenous Base: Can be adenine, cytosine, guanine, thymine, or uracil; the sequence encodes genetic information. - Types of Nucleic Acids: - DNA & RNA: Fundamental for genetic coding and protein synthesis, respectively. - DNA forms a double helix stabilized by hydrogen bonds between nitrogenous bases, crucial for replication. #### Summary of Chemical Compounds - Polymers vs. Monomers: - Polymers: Larger structures made of repeating units, such as carbohydrates, proteins, lipids, and nucleic acids. - Monomers: Simple unit structures, e.g., monosaccharides, amino acids, fatty acids, nucleotides, essential for biochemistry. ##### Dietary Sources and Functions: - Carbohydrates: - Sources: Grains, legumes, vegetables, fruits; essential for energy supply. - Function: Provide energy and fuel for cellular processes. - Proteins: - Sources: Nuts, meat, dairy, soy; important for building and repairing tissues. - Functions: Structure, communication, catalyzing biochemical reactions, movement, membrane transport. - Lipids: - Sources: Oils, butter, egg yolk; provide stored energy and insulation. - Functions: Energy storage, signaling molecules, structural components of cell membranes. - Nucleic Acids: - Sources: Meat, fish, frui’ts, vegetables; critical for genetic information. - Functions: Genetic info storage, protein synthesis, cellular regulation. #### Review Questions - Refer to the provided worksheet for questions to solidify understanding of the material. #### What's Next? - PackBack reminder and Topic 2 Quiz details.