Welcome to LS1A
Section
Week 2
Junaid Malek, M.D.
Contact Info
• [email protected]
• Cell Phone: (781) 354-8846
• Office Hours
• Before or after class/section or by
appointment
Molecules of Life:
The Cell and HIV
• Goal of this course is to understand basic
chemical and biological principles and their
relevance to scientific discovery
• Use HIV and cancer as two specific vignettes
to highlight basics of biology and chemistry
HIV: A Global Crisis
• 40 million infected worldwide
• 1 million infected in U.S. (~1 in 300 people)
• >11,000 individuals infected daily
Discovering HIV
• What are the different classes of potential
disease causes?
•
•
•
•
Causation vs.
Correlation
• What is the difference?
• Any examples?
Origin of HIV
• Relationship to SIV
• Zoonosis
• ? Spread from Pan troglodytes troglodytes
Atomic Structure
• Atomic number of element refers to the
number of protons in the element
• This equals the number of electrons in the
neutral atom
• Outer electrons are called valence electrons
• The Octet Rule
Draw a Lewis Dot
structure for CH2O
O
H
C
H
Formal Charge
• FC = (group #) - (# of non-bonded
electrons) - (# covalent bonds)
Calculate the FC
Start by drawing
electrons
• =O
• FC=
• -O
• FC=
• =C=
• FC=
• -H
• FC=
O
H
C
O
Calculate the FC
•
=N=
•
•
FC=
-H
•
H
H
FC=
N
H
H
Periodic Trends:
Electronegativity
• Q: Why doesn’t an atom just stay neutral?
• A: Having a full octet of electrons is
energetically favorable!
Electronegativity Trends
Which Substance is More
Stable?
H3C
O
or
H3C
NH
Which Substance is More
Stable?
Cl Mg Cl
or
Cl
2+
Mg
Cl
Drawing Molecules
• Lewis Dot
• Kekule
• Standard Line
Draw (NH2)2CO using
Lewis dot, Kekule and
standard line drawings
What are the Molecular
Geometries?
• NH
3
• Cl CO
2
•
NH4+
• HS
•
2
Bonds
• Electron-sharing exists on a spectrum, from
covalent bonds to ionic bonds
• In some covalent bonds, electrons are
shared equally (e.g. H-H bond)
• In some covalent bonds, electrons are
shared unequally (e.g. O-H bond in water)
• In ionic bonds, electrons aren’t shared at all
(e.g. between Na+ and Cl-)
Bonds (cont.)
• Q: How can we predict what type of bond
occurs?
• A:
• Ionic bonds will occur between atoms
with the greatest difference in
electronegativity
• Covalent bonds will occur between atoms
with similar electronegativity
Polar Covalent Bonds
• Occur between atoms with small but
significant differences in electronegativity
• Example: bonds between electronegative
atoms such as F, O, N or Cl and hydrogen
• These polar covalent bonds are essential
to creating hydrogen bonds, which are key
to life!
Polar Covalent Bonds
Hydrogen Bonds:
The Rules
• The hydrogen (“electron donor”) must be
bonded to an electronegative atom (F, O, N
or Cl)
• The electronegative F, O, N or Cl must have
a lone pair of electrons to engage in the
bond. Why?
•
Hydrogen Bonds:
The Rules (cont.)
• A linear geometry (i.e. a 180 degree axis)
must exist between the X-H bond
• Q: Where is the hydrogen atom most
partially-positive?
•
• The X-H bond must be withing 2.5-3.0
Angstroms from eachother
Which of these can form
an H-bond with another
molecule of itself?
H3C-F
H-F
H3C-CH2-CH2-OH
H3C-CH2-CH2-Cl
Adenine-Thymine Base
Pairs of DNA
O
H
H
N
N
N
H
N
N
N
R
O
N
R
Indicate sites that can serve as H-bond donors and
acceptors
If the two base pairs were positioned like this, where would
the H-bonds be?
Isomers
Constitutional isomers
Isomers
Geometric Isomers
Stereoisomers
(not geometric isomers)
Enantiomers
Diastereomers
Isomers: Definitions
• Constitutional isomers differ in connectivity
between atoms
• Stereoisomers do not
• Geometric isomers differ in the relative
positions of atoms connected to the carbon
atoms of a C=C bond (e.g. cis vs. trans)
Chirality
• Tetrahedral carbons bonded to 4 different
groups are said to be chiral centers
• Two categories
• Enantiomers (exact mirror images)
• Diastereomers (non-mirror images)
Enantiomers
Diastereomers:
Tartaric acid
Stereoisomers
• Any chiral molecule can have only one
enantiomer
• Molecules with multiple chiral centers can
have many diastereomers
• Q: If a molecule has n=3 chiral centers, how
many stereoisomers can it have?
• A:
Draw a constitutional
OH
OH
O
Draw a Geometric
OH
OH
OH
OH
Draw a stereoisomer
H
Cl
Cl
H
other dra
possible
Circle the Chiral Centers
Q: How many stereoisomers does cholesterol have?
A: 8 stereocenters, thus 28=256 stereoisomers!