Chemistry of Life

Topics Covered (Chemistry and Organic Chemistry)

• Structure of Water and Hydrogen Bonding
• Elements of Life
• Introduction to Biological Macromolecules
• Properties of Biological Macromolecules
• Structure and Function of Biological Macromolecules
• Nucleic Acids

Chemistry Unit

Elements: Pure substances that cannot be broken down chemically into simpler kinds of matter

• Human Body: CHNOPS and trace elements (Iron, Iodine)

Atoms: building blocks of all matter. Consist of subatomic particles

• Protons: positive charge, determine element
• Neutron: can be different for an element, producing isotopes
  • All isotopes are chemically identical because they have the same number of electrons in the same configuration, thus, they interact with other atoms similarly
  • Radioisotopes: isotopes with unstable nucleus that stabilizes itself by breaking down (emitting energy and subatomic particles)
    • Spontaneous decay known as radioactivity
    • Ex: carbon 14 decays at a known rate called the half-life. Its half life is 5,730 years
      • Half Life: time required for half of the nucleus of a radioactive sample to decay to its products
    • Used in fossil dating, tracers (incorporate radioisotope into molecule to trace path in a metabolic pathway), and even treat and diagnose certain diseases (ex: radioactive iodine in thyroid gland)
• Electrons: negatively charged, outside the nucleus
  • Equal to number of protons if element is in the elemental state
  • If all electrons in an atom are in the lowest available energy levels, the atom is in its ground state
  • When the atom absorbs energy, its electrons move to a higher energy level, thus, the atom is in the excited state

Bonding: Two atomic nuclei attract the same electron(s). Involves atom’s valence electrons.

• Energy is released when bonds form and supplied when bonds break.
• Ionic Bond: result from transfer of electrons. Forms ions (charged atom due to gain/loss of electron)
  • Lose electron: cation, gain electron: anion
  • Ionic compounds dissociate in water as a sphere of hydration forms around 2 charged ions
• Covalent Bond: Atoms share electrons. Resulting structure is called a molecule.
  • Nonpolar Covalent Bond: electrons are evenly shared by spending equal time around each nuclei
    • Hydrophobic: non polar substance that do not mix/ dissolve in water
      • This is because water is more attracted to another water molecule that has a charge instead of something without a charge
  • Polar Covalent Bond: unequal sharing of electrons because one atom is more electronegative than the other. Results in a hydrophilic molecule
    • Hydrophilic: polar substances that mix with water
    • Electronegativity: Ability of an atom to draw electrons close to itself
      • More electronegative atoms pull on shared electrons more strongly
      • Diatomic molecules (like O2) are always nonpolar covalent because they have equal electronegativities
• Hydrogen Bond: Negative bart of one polar molecule is attracted to the positive part of another. May also form between 2 different parts of a larger molecule
  • Water: oxygen atom exerts greater pull on shared electrons than hydrogen atoms, making the molecule asymmetrical and highly polar. Positive hydrogen on one molecule is attracted to negative oxygen of an adjacent molecule. Thus, water has/is
    • Ability to Moderate Temperatures:
      • High Specific Heat: takes a lot of heat for water to change temperature. Since much of the heat is used to disrupt hydrogen bonds, it takes a long time before the molecules begin moving faster
      • Specific Heat: amount of heat a substance must absorb to increase 1 gram of the substance by 1 C.
      • High Heat of Vaporization: Evaporating water requires absorption of a lot of heat. As water evaporates, the surface of the water cools (most energetic molecules leave and slow one are left behind)
    • Expansion Upon Freezing: ice floats, solid form is bigger
    • Universal Solvent: Water is highly polar, so it dissolves all polar and ionic substances
      • Solvent: liquid that does dissolving
      • Solute: thing getting dissolved
      • Solution: mixture after solvent dissolves solute
        • Aqueous solution: water is the solvent
    • Cohesive and Adhesive behaviour: water molecules attract each other and other molecules. This results in surface tension

Isomers: organic compound with the same molecular formula but different structures. Different structures=different properties

3 types: structural isomers, cis-trans isomers, and enantiomers Structural: differ in covalent arrangement of their atoms Cis-trans/ geometric: differ in spatial arrangement around double bonds Cis: 2 Xs (atom/ group of atoms) are on the same side Trans: Xs on different sides Enantiomers: molecules that are mirror images of each other. Mirror images are called L-(left handed) o D- (right handed) All amino acids in cells are left-handed Receptors only accept certain isomers

Organic Chemistry: study of carbon compounds

Carbon:

• Organic compound: chemical compounds that contain carbon
• Can create 4 bonds resulting in diverse compounds
• Organic chemistry originally dependent on Vitalism (belief in a life force outside jurisdiction of physical and chemical laws). However, researchers later observe organic chemistry is not some intangible life force, but the unique chemical versatility of carbon.

Functional Group: Give organic molecules distinctive properties. These are the components of organic molecules most commonly involved in chemical reactions

• 7 most important: hydroxyl, carbonyl, carboxyl, animo, sulfhydryl, methyl, phosphate
  • 1st 6= polar, increasing the solubility of organic compounds in water. Methyl is not reactive but serves as a recognizable tag on biological molecules
    • Arrangement of methyl groups in male and female hormones affects their shape and function

Stanley Miller Experiment:

• Concluded complex organic molecules could arise abiotically under conditions that to have existed on the early Earth

Macromolecules: Polymers built from monomers

• Polymer: long molecule consisting of many similar building blocks
  • Made by Dehydration Synthesis: combine 2 monomers and remove a water molecule
    • Take hydrogen (H) from one monomer, and hydroxyl (OH) group from another
  • Broken down by Hydrolysis: separate monomers by “adding water” (add H+ to one monomer and OH- to another)
    • Ex: process of digestion: organic material in food enters as polymers that are too large to enter our cells, so within the digestive tract, various enzymes attack polymers and speed up hydrolysis. The released monomers are released back into our bloodstream for distribution to body cells. Those cells then use dehydration reactions to assemble the monomers into new polymers that perform specific functions within the cell.
  • Shape and arrangement determine function

Carbohydrates: Sugars, and polymers of sugar

• Monosaccharide: serves as energy, the first thing a cell will use. If there is not enough sugar, body will start breaking down fat for energy
  • Generally 1:2:1 ratio
  • Spatial arrangement of parts around asymmetric carbon (carbon attached to 4 different atoms, or 4 different groups of atoms) creates diversity.
  • Glucose: Carbonyl group with multiple hydroxyl groups (placement of these groups makes difference). Glucose is a hexose, meaning it is six carbons long
• Disaccharide: 2 monosaccharides joined by a glycosidic linkage
• Polysaccharide: structure and function determined by sugar monomers and positions of glycosidic linkages

Lipids: hydrophobic. Serve as energy storage, structure, and hormones. No true polymers, and not big enough to be considered a macromolecule.

• Fatty Acid: hydrocarbon chain with carboxyl group at one end
  • Hydrocarbon: molecules with only hydrogen and carbon. Can undergo reactions that release a relatively large amount of energy
• 1) Triglyceride/Fats: 1 glycerol, 3 fatty acids. Serve as energy storage and insulation.
  • Fatty acids vary in lengths (# of carbons) and double bond (location and #)

• • 2) Phospholipids: 2 fatty acids, 1 phosphate group and 1 glycerol
    • Tails are hydrophobic (fats) and hydrophilic head (phosphate group and glycerol)
    • Cell Membrane: phospholipid bilayer. Formed through self assembly of phospholipids in an aqueous solution.
  • 3) Steroids: carbon skeleton consisting of 4 fused rings. Chemical groups attached determine function
    • Cholesterol: stabilize cell membranes
      • Serves as buffer: preventing lower temperatures from inhibiting fluidity and preventing higher temperatures from increasing fluidity too much
      • Too much cholesterol-> cardiovascular disease
    • Estrogen and Testosterone: sex hormones
  • 4) Wax: prevent water loss

Proteins: Have diverse structures which result in diverse functions including: storage, transport, regulatory, receptor, movement, structure, enzymatic, and immune

	Amino Acid: monomer. 20 amino acids Polypeptide: polymer. Consists of amino acids joined by peptide bonds which were formed by dehydration synthesis Protein: consists of 1 or more polypeptides, each folded and coiled into a specific shape

• Protein Structure is determined by:
  • Amino acid sequence
  • Physical and chemical conditions: Altered Ph, Salt concentration, Temperature results in denaturation, making it biologically inactive
  • Folding:
    • Chaperonins (chaperone proteins) assist folding
      • 
      • Misfolding-> Prions: misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein

Nucleic Acid: 2 types of Nucleic Acids: DNA and RNA which encode all hereditary information. DNA instructs its own replication

• Monomer: nucleotides which consist of a phosphate, 5 carbon sugar (deoxyribose or ribose) and a nitrogenous base (adenine, cytosine, guanine, and thymine (DNA) or uracil (RNA)
• Polymer: Nucleic Acid: DNA or RNA
  • DNA
    • DNA directs the synthesis of mRNA which controls protein synthesis by specifying the amino acid sequence of all proteins
    • The two strands of DNA are antiparallel. One strand runs from 5’->3’ while the other strand runs from 3’-> 5’
    • Complementary Base Pairing: (A-T) (G-C)
      • A and G are purines while T and C are pyrimidines.
        • Purines pair with pyrimidines to ensure antiparallel structure
      • A-T form 2 hydrogen bonds
      • G-C form 3 hydrogen bonds
  • RNA
    • RNA is typically single stranded