Key Terms - Roots Prefixes Mono– = Single Di- = two Poly- = many Iso- = equal – i.e. same but different Suffixes -ase = enzymes -ose = sugars -ine = nucleotides – Adenine, Thymine, Cytosine and Guanine -ine = amino acids – -an – -ic acid 1 Hydrocarbons counting: Meth = 1 Eth = 2 Prop = 3 But = 4 Pent = 5 Hex = 6

Chemical Bonds Ionic Between Atoms – Electron donation – Forming ions Between macromolecules – +/-, not involving hydrogen Covalent Electron sharing Strongest bonds Only between Atoms 2 Hydrogen Bonds Only between molecules Caused by polar charges – Uneven distribution of hydrogen around another molecule

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Laboratory Synthesis of Organics Miller 1953 – Able to synthesize organic molecules from inorganic (abiotic) compounds – Give us insight into the possible origins of life. Vitalism – belief that a biological force outside of the laws of physics and chemistry created organic molecules Mechanism – chemical and physical laws govern all natural phenomenon 4

The Miller Experiments Stanley Miller 1953 – Series of experiments to determine if rudimentary organic molecules could form under the conditions of early earth – Heat – Electric current 5

Atomic Structure 6

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Table

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Ionic Bonds Donated electron – Creates differently charged atoms that are attracted to each other 13

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Chemistry of Life Atom = basic unit of all matter – Subunits: Proton = Positive Charge Neutron =Neutral Charge Electron = Negative Charge Atoms are “balanced” when equal number of protons (+) and electrons (-) Elements = matter consisting of only 1 type of atoms – E.g. Gold Compounds = matter consisting of 2 or more types of atoms – E.g. Table Salt = Sodium (Na) and Chlorine (Cl) 15

Hydrogen Bonding Created by the unequal positioning of hydrogen atoms in organic molecule 16

Hydrogen Bonding The unequal distribution of hydrogen atoms creates a positive and negative pole to the molecule. This allows for attractive forces, and affinities 17

Hydrogen Bonding - Water 18

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Important Properties of Water Solid form less dense than liquid (ice floats) Surface tension (cohesion) Universal Solvent Non-conductive Absorbs heat – Temp. Moderation 20

Dehydration & hydrolysis Synthesis and breakdown of molecules Synthesis results in creation of water Reactants Products 21 Fig 5.2

Glycolysis - Sugars 22

Complex Sugars 23

Fatty Acids 24

Lipids Long fatty acid chains Glycerol head Strong covalently bonded structures Hard to break down 25

Trans Fats 26

Amino Acids Base composed of: – Amino Group - NH 2 – Carboxyl Group - CO 2 H – CH R side Chain Amino & Carboxyl the same across amino acids Side groups give molecule unique characteristics 27 Side chain (R group) Amino group Carboxyl group  carbon

20 Amino acids Side chains are non- polar/hydroph obic 28

Poly-Peptides Long chains of amino acids from through dehydration Animo (N-terminus Carboxyl (C- terminus) 29

Structural Hierarchy of Proteins Primary – Peptide Chains – Animo Acid (peptides) Poly peptides Secondary - Folding – α-Helix – β-Pleated Sheet Tertiary – Subunit – Interaction of secondary structures Quaternary – Aggregate Macromolecule – Interaction of subunits 30

Peptide chains Long sequence of amino acid molecules Connected by dehydration reactions Translated from DNA code Sequence is critical – Primary structure of Protein 31

Folding Interaction between non-adjoining amino acids give secondary structure α-Helix β-Pleated Sheet H-bonds 32

Subunit H-bonds & Ionic Bonds Hydrophobic/Vand er Waals interactions 33

Macromolecule Interactions between subunits to create large structures with highly specified tasks 34

Enzymes Break-down/synthesize complex molecules – Speed up natural process – i.e. sugar breakdown 35

Transcription & Translation DNA copied to RNA (Transcription) RNA leaves the nucleus – Protein regulated channel RNA is “Read” by ribosome and Translated into the protein sequence 36

Nucleotides 37

DNA – Nucleotide Pairing 38

DNA – Nucleotide Pairing Adenine (A) to Thymine (T) – 2 hydrogen bonds Cytosine (C) to Guanine (G) – 3 hydrogen bonds 39

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41 Figure 1.24 Observations Question Hypothesis #1: Dead batteries Hypothesis #2: Burnt-out bulb Prediction: Replacing bulb will fix problem Test of prediction Test falsifies hypothesis Test does not falsify hypothesis Prediction: Replacing batteries will fix problem