CHEM 141: The Chemical Principles of Life I

Winter Quarter 2017 Syllabus

Course Description
This is the first course in a two-quarter sequence (141/143), which will examine biological science
through the lens of chemistry. In this sequence students will gain a qualitative and quantitative
understanding of the molecular logic of cellular processes, which include expression and transmission
of the genetic code, enzyme kinetics, biosynthesis, energy storage and consumption, membrane
transport, and signal transduction. Connections to foundational principles of chemistry will be made
through structure-function analyses of biological molecules. Integrated lessons in structural,
mechanistic, and physical chemistry will underscore how molecular science and molecular innovation
have impacted biology and medicine. Prerequisite: CHEM 35 & Basic Calculus

During this quarter, we will cover seven broad topics. Under each topic below, you will find a list of
core chemical concepts and learning goals. You have been introduced to these core concepts in
previous CHEM courses; in this course we will briefly remind you of these concepts, and then build on
them. The learning goals listed below represent some of the most important biochemical principles that
you will learn from this course.

Instructors for 141

Chaitan Khosla Justin Du Bois Charlie Cox
khosla@stanford.edu jdubois@stanford.edu ctcox@stanford.edu
Shriram #269 Lokey #237 STLC Room # 205
650.723-6538 650.724.4557 650.485.1041

Head Teaching Assistant

Anna Elleman
aelleman@stanford.edu

Course Meeting Times

Lecture Section 01: 10:30 11:20 pm MWF STLC 114
Lecture Section 02: 12:30 1:20 pm MWF STLC 114

Students must attend the lecture section in which they are enrolled. To encourage participation and
application of material, all students must have an iClicker to participate (both version 1 or 2 is fine).
Clicker questions will be assigned, and points will only be awarded if students participate in the lecture
section for which they are enrolled. Clicker questions will be graded in part for participation and in
part for correctness.

Thursday Tutorials

Students must attend tutorial section on Thursday (numbered section 03-07). Sections will include
(depending upon week) review of more challenging course material & problems, introduction to some
biochemical techniques & tools, case studies and applications. Sections will be held in STLC Room
115.

The Thursday section will include a brief group quiz.

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 Section Time Lead TA Facilitator TA 1 Facilitator TA 2
9:00 10:20 am Melissa Gray Payton Weidenbacher Sabrina Weby
10:30 11:50 am Payton Weidenbacher Melissa Gray Zhenqin Wu
12:00 1:20 pm Sabrina Weby Zhenqin Wu Joshua Visser
3:00 4:20 pm Zhenqin Wu Sabrina Weby Joshua Visser
4:30 5:50 pm Joshua Visser Payton Weidenbacher Melissa Gray

Grading:
Best 6 of 7 Homework Assignments 20%
Clicker Questions (0.1% per question) 5%
Thursday Section Assignments 5%
Mid-Term Exam #1 20% (W 6:00 7:20 pm, Feb 8)
Mid-Term Exam #2 20% (W 6:00 7:20 pm, Mar 1)
Final Exam 30% (W, 7:00 10:00pm, Mar 22)

Homework is due on the Monday after the Problem Set is released at 5 pm in the bin located outside
of Dr. Coxs office STLC #205. Because of the number of students in the course, late homework will
not be accepted.

Missing an exam: If you will miss a midterm for any reason, (illness, family emergency, etc.), you
must communicate this to the Head TA, (Anna Elleman), or an instructor as soon as possible before the
exam. If you take an exam, it will be graded and counted toward your final grade. If you miss a
midterm WITHOUT a valid reason, your grade on that midterm will be zero.

Students requiring special arrangements, such as alternative venues, for taking exams must inform the
Head TA at least one week in advance.

Regrades

Requests for regrades must be made in writing no later than 1 week after the exam has been returned.
Do not hesitate to ask for a regrade if you note an error in the grading of the exam. The issue being
raised for regrade must be clearly stated in a brief note and accompanied by the entire exam. Write
nothing on the exam itself. The entire exam is subject to regrade and this can result in either an
increase or decrease in your grade. The head TA will send more detailed information once the exams
are returned.

Office hours
Office hours are available to further clarify lecture concepts or assist students in developing an approach
towards tackling chemistry problems. Students are highly encouraged to rework misunderstood problems
from returned exams and psets and discuss them during OHs.

Office Hour Times: Teaching Assistants Instructors

Sunday 6 8 pm, STLC 115 Dr. Cox M 4 5 pm, F 9 10 am
Tuesday 4 6 pm, STLC 115 Prof. Khosla W 11.30 am 12.30 pm
Wednesday 2:30 4:30 pm, STLC 114 Prof. Du Bois M 11.30 am 12.30 pm
Friday 2:30 4:30 pm, STLC 114

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Accommodations
Students who may need an academic accommodation based on the impact of a disability must initiate the
request with the Office of Accessible Education (OAE). Professional staff will evaluate the request with
required documentation, recommend reasonable accommodations, and prepare an Accommodation Letter for
faculty dated in the current quarter in which the request is being made. Students should contact OAE
(http://studentaffairs.stanford.edu/oae) as soon as possible since timely notice is needed to coordinate
accommodations. In addition, please inform the Head TA as soon as possible, at least one week in advance
of the first exam.

The topics covered in the course are outlined below:

I] Elements of Protein Structure

Core concepts:
Covalent bonds; functional groups
Stereochemistry
Acid-base equilibrium
Nucleophiles and electrophiles
Enthalpy, Entropy, and Gibbs free energy
Equilibrium constant and Gibbs free energy
Reduction and oxidation reactions; Nernst equation
Conformational analysis

Learning goals:
Structures of proteinogenic amino acids
Isoelectric point
Reactivity of amino acids
Structure and reactivity of the peptide bond
Structure and reactivity of the disulfide bond
Secondary, tertiary and quaternary structures of proteins
Non-covalent bonding in protein secondary, tertiary and quaternary structure

II] Ligand Binding and Catalysis by Proteins

Core concepts:
Dissociation constants
Reaction coordinates and transition state theory
Arrow-pushing reaction mechanisms
Reaction kinetics; steady state kinetics

Learning goals:
Non-covalent interactions governing molecular recognition
Lock-and-key versus induced-fit models for molecular recognition
Solvation; role of entropy in ligand binding
Specificity
Multivalency
Qualitative and quantitative descriptions of enzyme-catalyzed reactions
Qualitative mechanisms of peptide bond hydrolysis
Michaelis-Menten kinetics

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 Relationship of Michaelis-Menten kinetic parameters to transition state theory parameters
Quantitative mechanisms of irreversible enzyme inhibition

III] ATP: Structure, Function, Biosynthesis

Core concepts:
Reactivity and energetics of anhydride and phosphoanhydride bonds
G0 and G
Common reaction types in organic chemistry
Energetic coupling between unfavorable and favorable reactions

Learning goals:
ATP structure; role of counterions
Functional classification of enzymes
ATP biosynthesis through glycolysis
Monosubstrate versus bisubstrate enzyme kinetics

IV] NAD(P)H: Structure, Function, Biosynthesis

Core concepts:
Hydrogenation and dehydrogenation reactions
Mitochondria

Learning goals:
Structure and reactivity of NAD+ and NADH
Differences between NADH and NADPH
Cofactors: Flavin nucleotides, Coenzyme A, thiamine, lipoic acid
NADH synthesis via pyruvate oxidation
Citric acid cycle as a route for NADH biosynthesis

V] Carbohydrate and Lipid Metabolism and its Regulation

Core concepts:
Estimating parameter values from fitting experimental data to multi-parametric models
Carbohydrate structure and reactivity
Properties of glycosidic bonds
Fatty acid structure and reactivity
Hormones

Learning goals:
Mechanisms for reversible enzyme inhibition
Allostery
Mechanisms for allosteric enzyme activation
Cooperativity
Post-translational modifications
Monosaccharides, disaccharides, polysaccharides
Activated forms of sugars
Mechanisms of glycosidases and glycosyltransferases
Channeling non-glucose carbohydrates into glycolysis
Glucose biosynthesis via gluconeogenesis
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 Glucose storage in the form of glycogen
Regulation of glucose consumption, storage, and supply in the human body
Enzymology and regulation of fatty acid breakdown, biosynthesis, and storage

VI] Structure and Function of Biological Membranes

Core concepts:
Phase equilibrium
Amphipathic molecules
Structures of biological lipids and membranes

Learning goals:
Structure and properties of phospholipids, glycolipids, cholesterol
Structure and properties of lipid bilayers
Membrane electrochemical potential
Membrane proteins
Mechanisms of membrane transport: simple diffusion, facilitated transport, active transport
Multi-step, coupled electron and proton transport in NADH oxidation by O2
Coupling the energetics of a transmembrane proton gradient to ATP synthesis from ADP