Chemistry and Chemical Level of Organization Online Notes

Water Molecule Polarity

  • Hydrogen atoms have a slight positive charge.
  • Oxygen atom has a slight negative charge.

Hydrogen Bonds

  • Form between water molecules.
  • Occur between the positive charge of hydrogen and the negative charge of oxygen.
  • Individually weak but collectively contribute to water's properties.
  • Constantly forming and breaking in liquid water.
  • Lock in place when frozen, causing expansion.
  • Break entirely in the vapor state, slowing evaporation and contributing to surface tension.
  • Hydrogen bond: attraction of the positive charge on the hydrogen atom to the negative charge on the oxygen

Chemical Reactions

  • Defined by the formation or breaking of chemical bonds between atoms.
  • Reactants are rearranged to form products.
  • Metabolism: all reactions occurring in the human body at a given time.
  • Allow us to do work.

Work and Energy

  • Work: movement of an object or change in physical structure.
  • Energy: the capacity to do work.
  • Kinetic energy: energy in motion.
    • Examples: muscle contraction, flowing water, electricity in a wire.
  • Potential energy: stored energy (latent energy), potential to do work.
    • Examples: food, gasoline.
  • Energy conversion is not 100% efficient; heat is always a byproduct.
  • Energy cannot be created or destroyed, only transformed.

Types of Chemical Reactions

  • Synthesis (combination) reactions: smaller particles bond to form larger molecules; anabolic.
    • A+B→ABA + B \rightarrow AB
  • Decomposition reactions: bonds in a larger molecule are broken down; catabolic.
  • Exchange (displacement) reactions: bonds are made and broken.

Factors Influencing Reaction Rate

  • Most reactions require an enzyme (protein) to lower activation energy.
  • Factors:
    • Temperature
    • Particle size
    • Reactant concentration
    • Presence of enzymes
  • The reaction may still occur without the enzyme, but it would take a long time for that to happen.

Exergonic and Endergonic Reactions

  • Exergonic reaction: releases energy; catabolic.
  • Endergonic reaction: products contain more potential energy than reactants; anabolic.
  • Enzymatic reactions are necessary for processing metabolites.
    • Metabolites: molecules synthesized or broken down in the body.

Organic vs. Inorganic Nutrients

  • Organic nutrients: contain carbon and hydrogen, generally formed through covalent bonds.
    • Examples: carbohydrates, fats, proteins, nucleic acids.
  • Inorganic nutrients: do not contain carbon, generally formed via ionic bonding.

Water as a Universal Solvent

  • Water dissolves substances due to its polar charges, which disrupt ionic bonds.
  • Polar substances are hydrophilic (water-loving), nonpolar substances are hydrophobic (water-fearing).

Electrolytes

  • Body fluids contain electrolytes with important functions.
    • Examples: sodium chloride (membrane potential), potassium, calcium (organ systems).

pH Regulation

  • Water dissociates into hydrogen ions (H+H^+) and hydroxide ions (OH−OH^-).
  • Maintaining pH is crucial for chemical reaction efficiency.
  • pH scale: 0-14 (0-7 acidic, 7 neutral, 7-14 basic).
  • Acids: release hydrogen ions in solution (proton donors), pH < 7.
  • Bases: release hydroxide ions in solution (proton acceptors).
  • Salt: electrolyte that dissociates to form ions, not reflected on the pH scale.

Buffers

  • Resist changes in pH by releasing or absorbing hydrogen ions.
  • Often a weak acid with a salt of that acid.
  • Body fluids contain buffers (e.g., carbonic acid, sodium bicarbonate).

Organic Compounds

  • Contain carbon, unique to living systems.
  • Many are polymers of similar units (monomers), synthesized by dehydration synthesis and broken down by hydrolysis.
  • Four major groups: carbohydrates, proteins, lipids, nucleic acids.

Carbohydrates

  • Contain carbon, hydrogen, and oxygen in a 1:2:1 ratio.
  • Classes: monosaccharides, disaccharides, polysaccharides.
  • Function: primary fuel source, structural molecules.
    • C<em>6H</em>12O6C<em>6H</em>{12}O_6

Monosaccharides

  • Simple sugars with 3-7 carbon atoms.
  • Can be straight chains or rings.
  • Examples: triose (3C), pentose (5C), hexose (6C - glucose, fructose, galactose).
  • Isomers: same molecular formula, different structure (e.g., glucose and fructose - C<em>6H</em>12O6C<em>6H</em>{12}O_6).

Disaccharides

  • Two monosaccharides combined by dehydration synthesis.
  • Too large to pass through cell membranes.
  • Broken down by hydrolysis.
    • Example: sucrose (glucose + fructose).
    • Dehydration synthesis: creates sucrose from glucose and fructose.
    • Hydrolysis reaction: we can do that by adding water, and we get glucose and fructose.

Polysaccharides

  • Polymers of simple sugars (8+ monosaccharides).
  • Formed by dehydration synthesis, broken down by hydrolysis.
  • Examples: starch (sugar storage in plants), glycogen (sugar storage in animals), cellulose (indigestible to humans).
    • Polysaccharide cellulose is indigestible to humans and is found in plant cell walls. We don't have the enzyme to break down cellulose.

Lipids

  • Contain carbon, hydrogen, and oxygen (less oxygen than carbohydrates).
  • Nonpolar, insoluble in water.
  • May contain phosphorus, nitrogen, or sulfur.
  • Examples: fats, oils, waxes.
  • Require special transport in the blood.
  • Functions: cell components, energy reserve (twice as much as carbohydrates), chemical messengers, cellular structure.

Fatty Acids

  • Long chains with attached hydrogen atoms.
  • Head (carboxylic acid group - COOH) is hydrophilic, tail is hydrophobic.
  • Saturated: no double bonds, maximum hydrogen, solid animal fats.
  • Unsaturated: one or more double bonds, liquid plant oils.

Glycerides

  • Triglyceride: glycerol + three fatty acids (formed by dehydration synthesis).
  • Monoglyceride: One glycerol plus one fatty acid.
  • Diglyceride: One glycerol plus two fatty acids.
  • Triglyceride: glycerol plus three fatty acids.
  • Function: energy storage, insulation, protection.

Phospholipids and Glycolipids

  • Modified triglycerides with two fatty acid chains and a phosphorus-containing group.
  • Important in cell membrane structure (hydrophilic head, hydrophobic tail).

Steroids

  • Interlocking four-ring structures.
  • Cholesterol is the basis for all steroids formed in the body.

Leukotrienes and Prostaglandins

  • Derived from arachidonic acid.
  • Leukotrienes: produced by cells in response to injury/disease.
  • Prostaglandins: coordinate cellular activity, powerful in small quantities.

Proteins

  • Contain carbon, oxygen, hydrogen, nitrogen (sometimes sulfur/phosphorus).
  • Polymers of 20 amino acids, joined by peptide bonds (dehydration synthesis).

Amino Acid Structure

  • Amine group + carboxylic acid group + variable side chain.

Peptide Linkage

  • Carbon-nitrogen linkage of amino acid side chains.
  • Dipeptide (2 amino acids), tripeptide (3 amino acids), polypeptide (many amino acids).

Protein Structure

  • Primary: amino acid sequence.
  • Secondary: coiling (helix) or pleating (sheets) with hydrogen bonds.
  • Tertiary: folding to expose/hide amino acids, held by hydrogen bonds.
  • Quaternary: combining multiple polypeptide subunits.
    • The coronary structure of a polypeptide is the combining of four or more proteins to form a more complex structure. This level of structure is not very common.

Fibrous vs. Globular Proteins

  • Fibrous: strand-like, water-insoluble, stable (e.g., collagen).
  • Globular: compact, spherical, water-soluble, specific functional regions (e.g., enzymes).

Denaturation

  • Breaking bonds that hold folds and coils, changing physical/chemical shape.
  • Caused by high heat or changes in pH.
  • Irreversible if structure is damaged beyond repair.

Enzymes

  • Catalysts: speed up reactions by lowering activation energy.
  • Specific to each reaction due to unique structure.
  • Substrates: reactants in enzyme reactions.
  • Active site: region where the enzyme binds the substrate.
  • Saturation limit: the Substrate concentration required to have a maximum rate of reaction.
  • Enzyme substrate complex form when the substrate binding occurs.
  • The denaturation of the enzyme typically prevents the enzyme substrate complex from forming so the chemical reaction would shut down or not occur.

Nucleic Acids

  • DNA, RNA, ATP.
  • Contain carbon, oxygen, hydrogen, nitrogen, and phosphorus.
  • Building blocks: nucleotides (nitrogenous base, pentose sugar, phosphate group).
  • DNA: genes (mostly in the nucleus, some in mitochondria).
  • RNA: intermediate form for decoding DNA into proteins.

Nucleotides

  • Phosphate group, pentose sugar (deoxyribose in DNA, ribose in RNA), nitrogen base.
  • Bases:
    • Purines (double ring): adenine, guanine.
    • Pyrimidines (single ring): cytosine, thymine (DNA), uracil (RNA).

DNA and RNA Structure

  • Nucleotides linked by sugar-phosphate bonds.
  • DNA: double-stranded helix.
  • RNA: single-stranded.
  • Forms of RNA: messenger RNA, transfer RNA, and ribosomal RNA.

ATP

  • Adenine-containing RNA nucleotide with two or three phosphate groups.
  • High-energy phosphate bonds are hydrolyzed to release energy.
  • Energy currency of cells (cells die without it).
  • AMP (one phosphate), ADP (two phosphates), ATP (three phosphates).