Life Sciences 1a. An Integrated Introduction to the Life Sciences

Transcription

1 Life Sciences 1a An Integrated Introduction to the Life Sciences Lecture Slides Set 2 Fall rof. David R. Liu In my hunt for the secret of life, I started research in histology. Unsatisfied by the information that cellular morphology could give me about life, I turned to physiology. Finding physiology too complex I took up pharmacology. Still finding the situation too complicated I turned to bacteriology. But bacteria were even too complex, so I descended to the molecular level, studying chemistry and physical chemistry. After twenty years work, I was led to conclude that to understand life we have to descend to the electronic level, and to the world of wave mechanics. But are just, and have no life at all. Evidently, on the way I lost life; it had run out between my fingers. Albert Szent-Gyorgyi, ersonal Reminisces (1937 obel Laureate in hysiology) 1

2 Lectures 2 & 3: The molecules of life and their chemical foundations 1. The molecules of life comprise macromolecules and small molecules 2. Understanding the molecules of life: chemical structures and bonding a. onnectivity versus conformation b. The nature of atoms c. ovalent bonding and formal charges d. Ionic bonding e. Electronegativity and hydrogen bonds f. The bonding continuum and bond polarity 3. rganic molecules and how to draw them a. The molecules of life are organic molecules b. The geometries of organic molecules c. Drawing organic molecules d. Understanding arrow-pushing notation 4. Stereochemistry and the molecules of life a. Stereoisomers and enantiomers b. Drawing stereoisomers c. The tragedy of thalidomide d. Geometric isomers e. The role of geometric isomers in vision 5. The molecular components of IV Lecture Readings Required: IIB lecture notes; McMurry h. 1 (review), h. 3, h. 5, p , p ; Alberts pp , 66, Biological olymers monomers polymer 2 nucleotide monomer 3 3 nucleic acid polymer 2 amino acid monomer protein polymer 2

3 Biological Small Molecules Glucose (Sugar) yridoxine (Vitamin B 6 ) holesterol (Steroid) 2 S 2 2 Serotonin (eurotransmitter) Methionine (Amino Acid) Adenosine Triphosphate (ucleotide) Small Molecules on a Macromolecular Scale DA rotein (DA Ligase) 2 Small molecule (Adenosine monophosphate) 3

4 Small onnectivity Differences an Dramatically Alter the roperties of Molecules Structure = connectivity conformation Even modest changes in connectivity can have profound effects on function 2 2 RA monomer DA monomer water 1 day water 1 day no change! RA degraded RA DA ne onnectivity, Two onformations hange in salt concentration (only for certain DA sequences) B-form DA Z-form DA Similarly, changes in conformation can also dramatically affect function 4

5 The eriodic Table of the Elements,,,,, S (aka S) = 99% of living matter Basic Structure of Atoms A nitrogen atom (nucleus greatly enlarged for clarity) usually 7 neutrons Lewis dot structure 7 protons 7 total 5 valence (in the outer shell ) Electron clouds ( orbitals ) 5

6 The Excerpted eriodic Table period group Electron shell being filled shell 1 shell 2 shell 3 umber of valence : (8) carbon Atomic number (number of protons) Atomic mass (weighted average of 98.9% carbon % carbon-13) ovalent Bonding Basics Water = = = arbon dioxide = Acetylene = = = Typical covalent bond length: ~1 Å (10-10 m) Single covalent bond = two shared valence Double bond = four shared valence Triple bond = six shared valence 6

7 The ctet Rule Many period 2 & 3 atoms tend to form bonds until they have 8 total valence ydrogen (period 1) arbon 4 valence itrogen 5 valence xygen 6 valence et result: eutral makes 4 bonds eutral makes 3 bonds eutral makes 2 bonds eutral makes 1 bond 8 valence Methane 8 valence Ammonia 8 valence Water Formal harges on Atoms To satisfy these bonding principles, atoms of the same element that make different numbers of covalent bonds have different charged states harge = group number # of covalent bonds # of non-bonded l l (hydrochloric acid, In your stomach) Group 6 1 covalent bond 6 non-bonded = 1 net charge Group 5 4 covalent bonds 0 non-bonded = 1 net charge (an important form of the peptide bond) ote how each non-hydrogen atom above still satisfies the octet rule! Group 6 2 covalent bonds 4 non-bonded = 0 net charge (the first step in the reaction catalyzed by IV protease) 7

8 nly Single Bonds an Rotate Freely Single bond Double bond 2nd bond 1st bond Single bonds (but not double or triple bonds) can rotate without disrupting electron overlap, leading to different conformations Bonding Rules Apply to All Structures (Large and Small) 2 = ydrogens are often omitted for clarity... DA = ctet Expansion: hosphorous = 3 or 5 bonds Sulfur = 2, 4, or 6 bonds 8

9 Lectures 2 & 3: An introduction to the molecules of life 1. The molecules of life comprise macromolecules and small molecules 2. Understanding the molecules of life: chemical structures and bonding a. onnectivity versus conformation b. The nature of atoms c. ovalent bonding and formal charges d. Ionic bonding e. Electronegativity and hydrogen bonds f. The bonding continuum and bond polarity 3. rganic molecules and how to draw them a. The molecules of life are organic molecules b. The geometries of organic molecules c. Drawing organic molecules d. Understanding arrow-pushing notation 4. Stereochemistry and the molecules of life a. Stereoisomers and enantiomers b. Drawing stereoisomers c. The tragedy of thalidomide d. Geometric isomers e. The role of geometric isomers in vision 5. The molecular components of IV Ionic Bonding attraction - repulsion - - A molecule that has lost an electron bonds to a molecule that has gained one. These charged molecules are called ions. a l a l - (both ions satisfy the octet rule) 9

10 Ionic Bonds in rotein-da omplexes rotein DA - Base Base Ionic Bond Ionic bonds between oppositely charged groups among the molecules of life mediate many interactions between molecules in living systems Electronegativity & olarity Electronegativity describes the tendency of an atom to pull towards itself... Small difference in electronegativity = nonpolar bond Large difference in electronegativity = polar bond F Differences in electronegativity impart partial positive and negative charges on bonded atoms δ δ 10

11 partial negative charge! - ydrogen Bonding!! partial positive charge donor acceptor hydrogen bond ydrogen bonding arises from the electrostatic attraction between partial positive and partial negative charges created by bonding to electronegative atoms ydrogen Bonding in DA 3 11