Study Notes for BIOL 101 - Chemical Basis of Life

BIOL 101: UNIT 3 - CHEMICAL BASIS OF LIFE/INTRO TO MACROMOLECULES

3A: ATOMS, BONDS AND WATER

ATOMS

  • Definition of Atoms: All matter is composed of atoms, which are tiny particles made up of protons, neutrons, and electrons.
    • Components:
      • Protons:
        • Mass: 1
        • Charge: Positive
      • Neutrons:
        • Mass: 1
        • Charge: No charge
      • Electrons:
        • Mass: Negligible
        • Charge: Negative

ATOMIC STRUCTURE

  • Nucleus: Contains protons and neutrons. Generally, most of an atom's volume is empty space. For example, if an atom's volume was the size of a stadium, the nucleus would only be the size of a pea.
  • Identity of Atoms: The number of protons determines the atom's identity.
    • Example:
      • 1 proton = hydrogen
      • 2 protons = helium
  • Bonding Behavior & Mass:
    • The number of electrons affects how an atom interacts with others.
    • The number of neutrons affects the atom's weight (mass); protons contribute to mass as well.

THE PERIODIC TABLE

  • Natural Elements: A total of 94 naturally occurring types of atoms (or elements) exist, along with 25 that can be synthesized in the lab.
  • Organization: Elements are organized in the periodic table by their number of protons (atomic number) and electrons.

ELEMENTS

  • Definition: An element is a substance composed of only one type of atom.
    • Example:
      • Aluminum is composed of aluminum atoms.
      • Gold is composed of gold atoms.
  • Unique Properties: Each element possesses unique physical and chemical properties due to the different atoms that compose them.

CHNOPS

  • Key Elements in Life: The six elements that constitute 96% of the mass of all living organisms:
    • C: Carbon
    • H: Hydrogen
    • N: Nitrogen
    • O: Oxygen
    • P: Phosphorus
    • S: Sulfur

NEUTRONS AND ISOTOPES

  • Atomic Mass: The atomic mass is derived from the total count of protons and neutrons.
    • Example: 6 protons, 6 neutrons = carbon with a mass of 12.
    • Notation:
      • Mass Number = Number of Protons + Neutrons
      • Atomic Number = Number of Protons
  • Isotopes: Atoms with the same number of protons but different numbers of neutrons are termed isotopes.
    • Example:
      • Carbon typically has 6 protons and 6 neutrons (atomic mass = 12).
      • Carbon with 8 neutrons is termed "carbon-14" (atomic mass = 14).

ELECTRONS

  • Role of Electrons: The number of electrons (e-) governs how atoms bond and interact with other atoms.
  • Location: Electrons exist in regions termed orbitals, surrounding the nucleus.
  • Orbital Characteristics:
    • Shapes: Can vary.
    • Each orbital can accommodate 2 electrons.
    • Large atoms can fill more orbitals compared to smaller atoms.
  • Electron Shells: Orbitals are filled sequentially, starting from the nucleus.
    • First Shell: Contains 1 orbital fitting 2 electrons.
    • Second Shell: Has 4 orbitals fitting 8 electrons.
    • For practical purposes, shells beyond the second can each hold 8 electrons.

VALENCE ELECTRONS AND REACTIVITY

  • Valence Shell: The number of electrons in the outermost shell (valence shell) dictates the atom's reactivity.
  • Reactivity Rule: Atoms desire to have a 'full' valence shell, typically 8 electrons (the octet rule). Atoms interact (react) to achieve 8 valence electrons by gaining, losing, or sharing electrons.

CHEMICAL BONDS

  • Definition: Attractive forces that hold atoms together to form molecules.
    • Types of Molecules:
      • Consist of multiple atoms of the same element (e.g., O2, O3) or different elements (e.g., CO2, H2O), in which case they are termed compounds.
  • Bonds to Achieve Stable Structures: Atoms form bonds in pursuit of a full valence shell.

TYPES OF CHEMICAL BONDS

  • Ionic Bonds: Involve electron "stealing" whereby one atom transfers one or more electrons to another.
  • Covalent Bonds: Involve electron "sharing" where two atoms share a pair of valence electrons.
  • Hydrogen Bonds: A specific type that does not alter the number of valence electrons.

IONIC BONDS

  • Formation: Occur between a metal and a nonmetal where outermost electron(s) are 'stolen' leading both to achieve 8 electrons in their valance shell.
  • Charges Resulting: Both atoms acquire a charge, yielding one positive (donor) and one negative (recipient). These charged species are termed ions.
    • Properties: Ionic bonds are strong in their solid state but tend to dissolve in water.

COVALENT BONDS

  • Nonmetals Interaction: Form between two nonmetals where electrons are shared.
    • Bond Characteristics: Atoms believe the shared pair is theirs, leading both to achieve 8 valence electrons (or 2 for Hydrogen). These bonds are very strong and difficult to break.

POLAR COVALENT BONDS

  • Definition: When two distinct atoms share electrons and one pulls them more strongly than the other due to electronegativity.
    • Electronegativity: Measures an atom's ability to attract electrons.
    • Charge Distribution: The stronger atom (higher EN) carries a slight negative charge, while the other atom carries a slight positive charge, resulting in polarity: a positively and negatively charged pole.

ELECTRONEGATIVITY (EN)

  • Trends in the Periodic Table: EN is highest in the top right corner and lowest in the bottom left corner.
    • Nonpolar and Polar Bonds:
      • If two atoms have similar EN, their bond is considered nonpolar (e.g., H-C bonds).
      • If there’s a significant difference in EN, the bond will be very polar (e.g., H with O or N).

HYDROGEN BONDS

  • Nature of Bonds: Attraction between two polar molecules, specifically between an H that is part of a polar covalent bond and F, O, or N in another molecule.
    • Properties of Water: Many of water's unique properties derive from extensive H-bonding between molecules. They are individually weak but collectively form strong interactions.

POLARITY IN MOLECULES

  • Polar Molecules: Have partial positive and negative charges due to polar covalent bonds within the molecule and typically include F, O, or N atoms.
  • Nonpolar Molecules: Generally neutral and consist mostly of C and H.
  • Dissolution Properties: Polarity influences whether a molecule can dissolve in water.

LIKE DISSOLVES LIKE

  • Dissolution Principle: Polar substances dissolve well in polar solvents such as water (polar molecules are hydrophilic). Nonpolar substances dissolve in nonpolar solvents like oils but are not soluble in water (nonpolar molecules are hydrophobic).

UNIQUE PROPERTIES OF WATER

  • Hydrogen Bonding: Extensive hydrogen bonding in water leads to unique properties such as:
    • Ice floats
    • High specific heat & heat of vaporization
    • Cohesion and surface tension
    • Excellent solvent for polar molecules and ions

ICE FLOATS

  • Density and Structure: In ice, water molecules form a rigid lattice-like structure due to hydrogen bonds, leading to a lower density than liquid water, causing ice to float. This insulation protects aquatic life beneath.

HIGH SPECIFIC HEAT

  • Definition: The energy required to raise 1g of a substance by 1 degree Celsius.
  • Impact on Water: Water requires considerable energy to change its temperature due to H-bonds needing to be broken before molecular movement increases, stabilizing environmental temperatures.

HIGH HEAT OF VAPORIZATION

  • Energy for State Change: A large amount of energy is required for water to transition from liquid to gas, resulting in a cooling effect in the environment (e.g., sweating in humans).

COHESION, ADHESION, SURFACE TENSION

  • Cohesion: Water molecules stick together, promoting surface tension, allowing some insects to walk on water.
  • Adhesion: Water molecules can also stick to solid surfaces, aiding in water transport in plants.

WATER AS A SOLVENT

  • Biological Reactions: Polar biological molecules are soluble in water, and many significant biochemical reactions occur in aqueous environments.

DISSOLUTION OF IONIC COMPOUNDS IN WATER

  • Sodium Chloride (NaCl): When dissolved, Na+ ions attract the negative pole of water (O) while Cl- ions attract the positive pole (H). This interaction facilitates the dissociation of ionic bonds.

UNIT 3: INTRO TO MACROMOLECULES

CARBON AND ORGANIC MOLECULES

  • Importance of Carbon: Carbon forms four covalent bonds due to having four electrons in its valence shell (seeking four more).
    • Ability to form single, double, or triple bonds increases its versatility in building large, stable molecules.

MOLECULES OF LIFE

  • Essential Organic Molecules: The following organic molecules are found in all organisms:
    • Proteins
    • Carbohydrates
    • Lipids
    • Nucleic Acids
  • Polymers: These molecules are polymers consisting of repeating smaller units known as monomers, potentially exceeding a molecular weight of 1000 g/mol, thus referred to as macromolecules.

FUNCTIONAL GROUPS

  • Defining Characteristics: Functional groups within large biological molecules affect their chemical properties, like polarity and charge, thereby influencing their interactions with other molecules and water.

MACROMOLECULE STRUCTURE

  • Structure Equals Function: Structural configurations reflect function; similar molecules across different organisms tend to serve analogous functions, indicative of evolutionary relationships.
  • 3D Shape and Properties: Functions depend significantly on the three-dimensional shape and chemical properties (polarity, charge).

CONDENSATION AND HYDROLYSIS REACTIONS

  • Condensation Reactions: Link monomers via covalent bonds while releasing a water molecule, requiring energy.
  • Hydrolysis Reactions: Break bonds between monomers using water molecules, which releases energy.
    • Hydro = Water, Lysis = Breaking apart.

PROTEINS

  • Roles of Proteins: Proteins perform various functions such as:
    • Hormones
    • Antibodies
    • Membrane receptors
    • Transport molecules
    • Gene regulatory proteins
    • Structural proteins
    • Enzymes

AMINO ACIDS

  • Building Blocks of Proteins: There are 20 different amino acids, and proteins are composed of one or more polypeptide chains.
  • Peptide Bonds: Bond formation between amino acids occurs via condensation reactions, with "poly" signifying many peptide bonds linking amino acids.

TABLE OF AMINO ACIDS

  • Categorization: Amino acids can be divided based on their side chains:
    • Charged Hydrophilic: Includes Arginine, Histidine, Lysine, Aspartic Acid, Glutamic Acid
    • Polar (Uncharged) Hydrophilic: Includes Serine, Threonine, Asparagine, Glutamine
    • Nonpolar Hydrophobic: Includes Alanine, Isoleucine, Leucine, Methionine, Phenylalanine, Tryptophan, Valine.

LEVELS OF PROTEIN STRUCTURE

  • Primary Structure: The specific sequence of amino acids within a polypeptide chain dictates the protein's ultimate shape and function.
  • Tertiary Structure: Three-dimensional folding of the polypeptide chain is influenced by interactions between R-groups, which include:
    • Ionic bonds between charged R-groups
    • Hydrogen bonds between polar R-groups
    • Hydrophobic interactions of nonpolar R-groups
    • Covalent disulfide bridges between cysteine R-groups.

MULTI-UNIT PROTEINS

  • Subunit Composition: Some proteins consist of multiple subunits or polypeptide chains that are essential for function, for example, hemoglobin.

FUNCTIONAL RELEVANCE OF PROTEIN STRUCTURE

  • Determinant Factors: Protein function is contingent upon its final shape (3D structure) and surface polarity of R-groups, which can determine interaction types, including ionic, hydrophobic, and hydrogen bonds.

CONDITIONS AFFECTING PROTEIN STRUCTURE

  • Factors Impacting Structure:
    • Temperature increases lead to rapid molecular movement, disrupting hydrogen bonds and hydrophobic interactions.
    • pH changes can affect R-group ionization, disrupting ionic interactions.
    • Changes in solvent polarity can disrupt hydrogen bonds and hydrophobic interactions.
    • Denaturation occurs when a protein loses its 3D structure.

INCORRECT FOLDING OF PROTEINS

  • Spongiform Encephalopathies: Diseases like BSE/mad cow disease and Creutzfeld-Jacob disease arise from abnormal protein folding (prions) in the brain and can cause progressive neurodegeneration, ultimately fatal.

CARBOHYDRATES

  • Definition: Carbohydrates are macromolecules typically characterized by the formula CmH2nOn composed of carbon chains connected to –H and –OH groups, serving primarily as energy sources and structural materials.
  • Molecular Weight: The molecular weight of carbohydrates ranges from under 100 to over 100,000 daltons.

MONOSACCHARIDES

  • Monomer of Carbohydrates: Monosaccharides (simple sugars) serve as the building blocks for carbohydrates; the most common is glucose (C6H12O6) and most exist as ring structures under physiological conditions.

DISACCHARIDES

  • Formation: Disaccharides, or "two sugars," are formed when two monosaccharides link via a condensation reaction; an example is sucrose, made of glucose and fructose.

POLYSACCHARIDES

  • Definition: Composed of many (hundreds to thousands) monosaccharides linked together, polysaccharides serve as energy storage and structural materials, such as starch, glycogen, and cellulose, which can be branched or linear.

STARCH

  • Function: Starch serves as energy storage for plants, formed from glucose monomers; it can create aggregates known as starch grains utilized by new seedlings for energy.

CELLULOSE

  • Function: Cellulose is a fundamental component of plant cell walls, being the most abundant macromolecule, non-branched, consisting of glucose monomers, and more chemically stable than starch, providing structural integrity in harsh conditions.

GLYCOGEN

  • Function: Glycogen is the primary energy storage for animals, highly branched for rapid glucose access.

SPECIAL CARBOHYDRATES

  • Chitin: A derivative polymer of glucosamine, which constitutes the exoskeleton in insects and crustaceans and the cell walls of fungi.

LIPIDS

  • Definition: Lipids are hydrocarbons that are nonpolar and not water-soluble, aggregating in aqueous solutions to avoid water.
  • Types: Include triglycerides (fats and oils), phospholipids (cell membranes), pigments, steroids, vitamins, and waxes.

TRIGLYCERIDES

  • Structure: Composed of one glycerol molecule bonded to three fatty acids; primarily serves as energy storage.

PHOSPHOLIPIDS

  • Structure: Similar to triglycerides but with one fatty acid replaced by a phosphate group (PO4), making the "head" polar and the tail nonpolar (amphipathic).

PHOSPHOLIPIDS IN CELL MEMBRANES

  • Arrangement: In water, phospholipids align with heads contacting the water and tails sheltered away, forming a phospholipid bilayer structure of cell membranes.

PIGMENTS AND VITAMINS

  • Carotenoids: Serve as pigments providing yellow/red coloration in vegetables and function in photosynthesis.
  • Vitamin A: Carotenoids can be converted into Vitamin A essential for vision.

STEROIDS

  • Structure: Comprised of multiple carbon rings linked together; cholesterol is a key component of cell membranes and synthesized in the liver.
  • Steroid Hormones: Hormones such as estrogen and testosterone are derived from cholesterol.

WAXES

  • Properties: Hydrophobic and pliable at room temperature; secreted by various glands in birds and mammals for waterproofing and maintaining pliability of feathers and hair.

NUCLEIC ACIDS

  • Definition: Polymers specialized for genetic information storage and transmission.
  • Types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

ROLES OF DNA AND RNA

  • Purpose of DNA: Encodes hereditary information to pass across generations.
  • Role of RNA: Through intermediates, RNA translates DNA information to specify protein amino acid sequences.

NUCLEOTIDES

  • Structure: Monomers that join to form nucleic acids, containing:
    • A sugar (ribose in RNA, deoxyribose in DNA)
    • A phosphate group (PO4)
    • A nitrogen-containing base (adenine, guanine, cytosine, thymine in DNA; uracil in RNA).

BASE PAIRING IN DNA

  • Partner Bonds: Two anti-parallel strands of DNA are linked via hydrogen bonds through complementary base pairing:
    • A pairs with T (thymine)
    • C pairs with G (guanine)

DNA STRUCTURE

  • Configuration: Structured as a twisted ladder with sugar and phosphate forming the sides and paired bases acting as the rungs, twisting into a double helix. The sequence of bases conveys genetic information.

RNA STRUCTURE

  • Characteristics: Typically single-stranded and shorter than DNA, it corresponds to a single gene and can base-pair with itself. Base pairing comprises A-U and C-G pairs.

GENETIC INFORMATION USE

  • DNA Replication: Creates an exact copy of original DNA before cell division to ensure genetic information is accurately passed on to new cells or offspring.
  • Transcription: Converts DNA information into RNA, enabling protein synthesis based on genetic templates.