Biochemistry I
Lecture 1
Lecture 1: Introduction to Biochemistry
August 23, 2015
Gordon Rule - rule@andrew.cmu.edu
Learning goals:
 Infer orbital hybridization from geometry.
 Identify functional groups.
Web Resources: OLI course page can be found at: http://oli.web.cmu.edu or via
Blackboard. OLI access code = BC-F2015, instruction page can be found on Bb.
Please spend some time this week to become familiar with the following areas of OLI:
 Syllabus
 Goals and Expectations
 Problem Sets & Exams
Course Grading Scheme:
Problem sets (11 to 12)
15%
Lowest three dropped.
Lowest 5 of 15 dropped. Open Thursday, close 11:59PM
OLI quizzes (15)
10%
on following Sunday.
Open Thursday before, close 12:01AM day of lecture.
bonus quiz (40)
4%
In-class exams (3)
45%
Half of lowest one dropped (2 x18%, 9%)
Comprehensive final exam
30%
Tentative letter grades: <50 R, 50-60 D, 60-80 C, >80 B, >90 A
Best Advice:
1. Time spent learning structures and concepts in the first 4 weeks of class will be very well spent.
2. Do the OLI web pages, self-assessment exercises, and bonus quizzes. The latter help me assess
the progress of the class on a day-by-day basis – which is good for you.
Your Weekly Schedule:
 Bonus OLI quiz before each lecture.
 Review notes after lecture.
 Weekly OLI quiz on weekend.
 Problem set on weekend.
1
Biochemistry I
Lecture 1
August 23, 2015
Course Overview:
Chemistry Review:
Atomic Orbitals: All orbitals hold at most 2
electrons. The s orbital is spherically
symmetric. The three p orbitals (px, py, pz)
are bi-lobed and hold a total of 6
electrons (2x3).
Order of filling: 1s, 2s, 2p, 3s, 3p. When
orbitals of equal energy are filled (e.g. 2p)
the electrons fill the orbitals with one electron first.
Hybrid Orbitals: Carbon, nitrogen, and oxygen, usually form hybrid orbitals,
which show a mixture of s and p character.
sp2: The s and two of the p-orbitals combine, giving three (3) sp2 orbitals.
Note, one of the p orbitals is still present.
3
sp : The s and all three of the p-orbitals combine, giving four (4) sp3
orbitals.
2
Biochemistry I
Lecture 1
August 23, 2015
Geometric Properties of Hybrid Orbitals:
Covalent bonds indicate the sharing of electrons between atoms. Usually two half-filled orbitals
combine to form the bond. Hence hydrogen forms one bond while carbon forms four.
H: 1s1
1 bond
2
2
2
C: 1s 2s 2p
4 bonds
3×sp2 + pz or 4× sp3
N: 1s2 2s2 2p3
3 or 4* bonds
3×sp2 +pz or 4× sp3
O: 1s2 2s2 2p4
2 or 3* bonds
3×sp2 +pz or 4× sp3
2
4
S:
... 3s 3p
2 bonds
P:
...3s2 3p3
5 bonds
*When protonated.
Hybrid orbitals in bond formation: e.g. CH4 (methane)
Double bonds occur when two atoms share two pairs of
electrons, e.g. C=O, the bond directly between the
atoms is called a sigma (σ) bond, the bond formed by the
pz orbitals is called a pi (π) bond.
Aromatic Compounds
 Ring formation - can contain nitrogen.
 Atoms in ring are sp2 hybridized - planer
 Form single bonds with each other
 Remaining pz orbitals form a delocalized
ring of electrons, giving rise to a “partial”
double bond between adjacent atoms.
 Absorb UV/visible light
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Biochemistry I
Lecture 1
August 23, 2015
Organic molecules and Functional Groups: A functional group is a subset of atoms within a larger
molecule, e.g. methyl group, ethyl group. Functional groups have unique properties.
Non-Polar (carbon and hydrogen only):
Alkanes
Aromatic
Alkene
Methane
(methyl)
Propane
(propyl)
Pentane
Butane
ethene
Hexane
Ethane
(ethyl)
Polar Functional groups (contain an electronegative atom):
Carbonyl group
Alcohols
H
H
H
H
O
H
Methanol
O
O
S
H
H
Thiol
(sulfhydral)
H
H
H
H
O
H
Ethanol
Ketone
Aldehyde
O
O
H
H
O
H
carboxylate
N
N
H
H
Amine (ethyl amine)
Amide (acetamide)
Examples – identify the functional groups on these amino acids:
4
O
O
Ester
Benzene