1 Hydrogen Bonding in DNA O O N N N N N O P O O O O P O O O O N N O H O CH 3 H H 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. Connectivity versus conformation b. The nature of atoms c. Covalent bonding and formal charges d. Ionic bonding e. Electronegativity and hydrogen bonds f. The bonding continuum and bond polarity 3. Organic 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 HIV
Transcript
1
Hydrogen Bonding in DNA
O
O
N
N
N
N
N
O
P
OO
O O
PO
O
O
O
NN
O
H
O
CH3H
H
Lectures 2 & 3: An introduction to the molecules of life1. The molecules of life comprise macromolecules and small molecules2. Understanding the molecules of life: chemical structures and bonding
a. Connectivity versus conformationb. The nature of atomsc. Covalent bonding and formal chargesd. Ionic bondinge. Electronegativity and hydrogen bondsf. The bonding continuum and bond polarity
3. Organic molecules and how to draw thema. The molecules of life are organic moleculesb. The geometries of organic moleculesc. Drawing organic moleculesd. Understanding “arrow-pushing” notation
4. Stereochemistry and the molecules of lifea. Stereoisomers and enantiomersb. Drawing stereoisomersc. The tragedy of thalidomided. Geometric isomerse. The role of geometric isomers in vision
5. The molecular components of HIV
2
O
OHHO
HO OH
Ribose
C5O5H10
=C C
C
O
C
CO
H
O H
O
H H
H
O
H
H
H
H H
C
CCC
CO
O
H
H
OH O
H
O
H
H
H
H
H H
O
CO C
CCCH
O H
H
H O
H
OH
H
H
H
H
CCC
O
CC
O O
H
H H
H
HH
O H H O
H H
The Richness of Organic Structures
One bondingscheme out of> 200 isomersof C5O5H10
Three other examples of isomers of C5O5H10:
• The number, geometries, and stability of bonds made to carbon atoms impartenormous structural diversity into organic molecules
Geometries of Organic Molecules
Methane
Ethylene
Acetylene
Tetrahedral
Trigonal (planar)
Linear
• A carbon atom adopts a geometry determined by its number of bonding partners(4 = tetrahedral, 3= trigonal, 2 = linear), as dictated by e–/e– repulsion
• The geometries of non-carbon atoms can be deduced by treating non-bondedelectron pairs as “bonds” that are subject to e–/e– repulsion
Ribose Depicted Six Ways
C C
C
O
C
CO O
O
H
H
H
O
H
H
H
H
H
H
H
CH CH
CH
O
CH
CH2HO OH
HO OH
OHO OH
HO OH
Computer-created models:
Representations that can be drawn by hand:
• What do these lines mean?
Standard drawing
4
Standard Drawing Convention forOrganic Molecules
• Lines are covalent bonds• Intersections and termini of lines represent carbon atoms• Each carbon atom is bonded to enough implied hydrogen atoms to
satisfy the octet rule (four bonds total to each neutral carbon atom)• All non-C, non-H atoms must be shown explicitly (P, O, N, Cl, etc.)
HO
OO H
O
NH
CCCCC
C
OC
CCCCC
C
OC
H
H
H
H
H
H H
H
HHHHH
H
C
CCC
CC
NH
C
C
C
C
CC
H
H
H
H
H
H
HH
Common Groups Found in OrganicMolecules
methyl hydroxyl
amino
carboxylic acid
carbonyl
phosphate
amide carboxylate
ammonium
CH3 Me OH
NH2 NH3
O
OH
O
O
O
NH
OPO
O
O
O
5
HN
N
N
N
O
O
S O
ON
N
Representations of 3-D Structures On Paper
HN
CNC
CC
C
N
N
CH3O
CC
HC
HCCCH
OH2C
H2C
SO
ON
CH2CH2
N
H2C
H2C
H3C
CH3
CH2
CH3
Sildenafil (Viagra)
• Multiple perspectives arerequired to fullyappreciate the structuresof three-dimensionalmolecules in two-dimensional depictions(stay tuned for lab)
Understanding “Arrow-Pushing” Notation• Reaction mechanism: a description of the individual steps by which bonds
are broken and made during a reaction• “Arrow pushing” is a formalism for drawing reaction mechanisms
Simple Rules to Understand Arrow Pushing1) One arrow represents the movement of one PAIR of valence electrons2) The arrow begins where the electrons start (electron-rich atoms or bonds),
and ends where they are going (electron-poor atoms or bonds)
3) An arrow that starts at an atom represents moving a lone pair4) An arrow that starts at the center of a bond represents breaking that bond
5) An arrow that ends at an atom represents forming a new covalent bond ora new lone pair
6) An arrow that ends at a bond represents adding a second (or third) bond
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O
CH3C N
O
CH3
H
HOH
H
Arrow-Pushing Examples
Deprotonation of a carboxylic acid by an amine
Hydrolysis of an amide
Note: lone pair electrons not involved in a mechanistic step are oftennot drawn but are shown here for clarity.
O
CH3C N
CH3
O H
OH
HH
OC
O
H3CH
HNH
CH3
O H
N
H
H
HO
C
O
CH3
H N
H
H
HO
C
O
CH3
H
• Arrows move in a way that preserves bonding rules (e.g., 4 bonds to neutral C)
Lectures 2 & 3: An introduction to the molecules of life1. The molecules of life comprise macromolecules and small molecules2. Understanding the molecules of life: chemical structures and bonding
a. Connectivity versus conformationb. The nature of atomsc. Covalent bonding and formal chargesd. Ionic bondinge. Electronegativity and hydrogen bondsf. The bonding continuum and bond polarity
3. Organic molecules and how to draw thema. The molecules of life are organic moleculesb. The geometries of organic moleculesc. Drawing organic moleculesd. Understanding “arrow-pushing” notation
4. Stereochemistry and the molecules of lifea. Stereoisomers and enantiomersb. Drawing stereoisomersc. The tragedy of thalidomided. Geometric isomerse. The role of geometric isomers in vision
5. The molecular components of HIV
7
Stereochemistry and Its Depiction
O
HONH2
CH3
O
HONH2
CH3
O
HONH2
CH3
Alanine(a protein building block)
L-Alanine D-Alanine
Enantiomers
belowthe page
abovethe page
• Isomers: non-identical molecules with the same chemical formula (e.g., C5O5H10)• Stereoisomers: isomers with identical atomic connectivities• Enantiomers: two stereoisomers that are mirror images (enantios = opposite)
Rotate 180°(Same molecule)
Enantiomers of Alanine
L-Alanine D-Alanine
Mirror(Enantiomers)
Mirror(Enantiomers)
Rotate 180°(Same molecule)
• Enantiomers cannot be superimposed
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Chiral Centers and Chiral Molecules
Not superimposable
Chiral
Enantiomers
Superimposable
Achiral
Identical structures
chiral center
• An atom attached to four different groups is a chiral center (asymmetric carbon)• A molecule is chiral if it cannot be superimposed on its mirror image• All chiral molecules contain at least one chiral center• A chiral center usually (but not always) indicates that a molecule is chiral
Four different groups
Small Molecule-MacromoleculeInteractions are Sensitive to Chirality
Enantiomers of a drug
Binding site in a protein Binding site in a protein
• Enantiomers have identical basic properties (boiling point, melting point, color)• In the presence of a chiral probe (e.g., a protein), enantiomers behave differently
Thalidomide: one enantiomertreats morning sickness…
…but the other is apotent teratogen
N
S
O
HNH
R
O
OOH
O
HO
Stereoisomers of Modern Drugs
OO OH
IbuprofenBoth enantiomers effective;
one works slightly faster
PenicillinOne stereoisomer is effective;
others are not effective butnon-toxic
KetoprofenOne enantiomer relieves painand inflammation; the other
prevents tooth disease!
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H
H
Geometric Isomers
H
H
H
H
H H
trans-2-pentenecis-2-pentene
Ethylene is planar and double bondscannot easily be twisted
• When groups attached to each double-bonded carbon atom are different,geometric isomers are possible (cis = Latin for “on this side”, trans = “across”)
• Cis and trans isomers cannot interconvert without breaking the C=C double bond
Retinal: Geometric Isomers in Vision
11-cis-retinal 11-trans-retinal
cis trans
Light
Light
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Rhodopsin: A Protein &Small Molecule Team
• The cis-trans isomerization of retinalchanges the conformation andfunction of rhodopsin, initiating thesignaling cascade driving vision
cis-retinal covalentlybound to opsin
Molecular Componentsof HIV
RNA
Protein
Lipid
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Key Points: An Introduction to theMolecules of Life
• The molecules of life are macromolecules and small molecules• Covalent bonds arise from shared valence electrons and define
the connectivity of a molecule• Ionic and hydrogen bonds arise from electrostatics• Organic molecules contain carbon atoms in one of three
geometries, and are drawn in a standard convention using lines• Reaction mechanisms are described by “arrow pushing”• Chiral molecules are not superimposable with their mirror
images (they exist as enantiomers)• Enantiomers have different properties in a chiral setting• Geometric isomers (cis vs. trans C=C) have distinct properties
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