Biochemistry 153A

Introduction to Structure, Enzymes and Metabolism

Spring Quarter 2015

M, T, R, F 10:00 - 10:50 am, Young Hall CS50

Pre-requisites: Chemistry 14D or 30B

Recommended: Life Sciences 2, 3, 23L

U1A RNA splicing protein bound to

a short stem-loop of U1 snRNA
 Biochemistry 153A
Introduction to Structure, Enzymes and Metabolism
Instructor: Dr. Jeanne Blain Hokulani Morin-Leisk
Office: Young Hall 3086
Telephone: 310.794.4355
email: leisk@chem.ucla.edu
Office hours: M, T, R, F; 12:00-1:30pm

Teaching Assistants:

Jung-Reem Woo
email: jwoo@chem.ucla.edu
Office hours: TBA

Andrew Guttentag
email: aguttent@chem.ucla.edu
Office hours: TBA

Eric Raftery
email: raftery@chem.ucla.edu
Office hours: M 8:00 9:00 Young Hall 6096

John Abendroth
email: abend@chem.ucla.edu
Office hours: F 11:00am1:00pm Young Hall 1343
 Biochemistry 153A
Introduction to Structure, Enzymes and Metabolism

Course Description:
The course provides an introduction to the molecules, macromolecules, and processes found in
living systems. The structures of amino acids, nucleotides, lipids, and sugars and their
corresponding higher-order structures, i.e. proteins, nucleic acids, membranes, and
polysaccharides, are presented with an emphasis on their biological functions in the central
metabolic pathways. The kinetics and mechanisms of enzymes and the energetics of biological
systems are examined with a quantitative approach.

Syllabus and course schedule:

The detailed syllabus and exam schedule is found on the course website.
The lecture schedule will likely be updated during the semester but exam and quiz
dates are set.

Mbius protein fold?

Human apolipoprotein A-1
 Biochemistry 153A
Introduction to Structure, Enzymes and Metabolism

Textbook and links to essential online material:

Text: Lehninger Principles of Biochemistry (6th Edition) by David L.
Nelson and Michael M. Cox, ISBN: 0-7167-7108-X. OR
Fundamentals of Biochemistry (4th Edition) by Voet, Voet and Pratt

Webpage: https://ccle.ucla.edu/course/view/15S-CHEM153A-1
Announcements, reminders, updates, problem set and
exam questions, answers and grades, important links, slides,
handouts and much more. Check it often!

Textbook Webpages:
Lehninger: http://bcs.whfreeman.com/lehninger6e/
Voet: http://bcs.wiley.com/he-bcs/Books?action=index&
itemId=0470547847&bcsId=6982
Contains some very useful information and tutoring materials

Other important links:

PyMOL Webpage: http://pymol.org/educational/
Link to PyMOL software download page and instructions manual

RCSB Protein Data Bank (PDB): http://www.rcsb.org/pdb/home/home.do

Link to PDB site and PDB file downloads
 Biochemistry 153A
Introduction to Structure, Enzymes and Metabolism

Lecture materials online:

The day before each lecture, a skeleton of the lecture notes will be posted
on the website. The skeleton notes will contain drawings/graphs. I plan to
print these out for your own note-taking. I will use the document cam or a
tablet PC to write down important points and fill in the notes during the
lecture.

I do not plan to post the filled in notes on the website.

Problem sets online:

I will post problem sets online every week and a half. These problems are
designed to prepare you for exam questions. I will include an approximate
amount of time required to work through all the problems. If you find youre
spending more time than what is suggested, get help from me or the TAs.
 Biochemistry 153A
Introduction to Structure, Enzymes and Metabolism

Assessment and Grading:

Summary of the final grade components:
[45%] Two in-class, 1-hour exams
[35%] Final Exam
[16%] Quizzes in class and online
[ 4%] Clicker responses
---------------------------
[100%] Final Grade

Please do not abbreviate answers unless specifically stated on exam or quiz instructions.

Clicker responses receive full credit even for incorrect answers. However, for grades on the
borderline number of clicker responses and correctness may be taken into account.

Regrade requests will be accepted up to 3 working days after the assignment is returned.
Include a type-written explanation of the suspected error.
Return the assignment with the explanation stapled to the front.
Regrade submissions are subject to a full regrade at the discretion of the TA
or instructor.
 Registering your Cliker:
Go to student registration in the iClicker block on
the course website
Things you can do to make this class easier more rewarding:
1) Come to class.

2) Take good notes and review them soon after class ends while material is still fresh.

3) Master the basics - functional groups, weak vs. strong interactions,

amino acid structures & properties etc., this will make future topics a lot easier.

4) Dont forget the big picture - why do we study a specific type of interaction?
why do we care about a specific molecule or reaction mechanism?

5) Keep up with material posted to CCLE.

6) Ask questions! Get help if you feel like

youre struggling.

7) Dont wait until the last minute to do

problem sets or study for exams.

8) Follow-up lectures with textbook reading.

9) Interactive quizzes on ccle.

10) Go to office hours.

Cell Biology
Structural features common to all cells Genetics
Prokaryotes vs. Eukaryotes Sequence defines structure
The bacterial cell vs. the animal cell Central dogma

Physics
Free energy
Kinetics

Chemistry
Carbon and functional groups
Biological macromolecules

Evolution
The first biomolecules
The RNA world
Mutation and
Natural Selection
Phylogeny of the three domains of life
The Universal Features of Cells
Cellular structures are made up of component parts

Focus: - Structure of macromolecules and their component parts

- How these structures dictate function
 Chemical Foundations
The chemistry of carbon and its functional groups....

4 single bonds = tetrahedral

1 double, 2 single bonds = trigonal planar

The chemistry of biological molecules is centered on carbon, but the beauty lies in
the reactivity of functional groups associated with carbon:
Small biomolecules are constituents of macromolecules
Carbon and functional groups combine to make small biomolecules (amino acids, nucleotides),
which combine to make macromolecules (proteins, DNA, RNA)

Amino acid Protein

(polymer chain of
20 different amino
acids)

Nucleotide

Nucleic Acid
(polymer chain
ATP of 4 different
nucleotides)
 Physical Foundations
Work, whether in the form of a cell making DNA, or the muscle contractions of an Olympic
sprinter, requires energy, the conversions of which are bound by the laws of thermodynamics.
Free Energy (G): amount of energy available to do work
G = Gproducts - Greactants
Free energy change (G) in a reaction at a constant temperature (T), is related to the degree of
disorder (entropy, S), and the number of bonds formed or broken (enthalpy, H) through the
Gibbs equation:

G is - = exergonic reaction, spontaneous and releases energy, favorable

G is + = endergonic reaction, requires energy, unfavorable

S is + = more disorder H is - = heat is released

S is - = more order H is + = heat is absorbed

Because most reactions involving macromolecules require energy input, they are
often coupled to an exergonic reaction such that the sum of the reactions is favorable:
amino acids protein (G is +)
ATP ADP + Pi (G is very -)

The sum of the two reactions is -, and therefore exergonic

Physical Foundations: Keq and G
Equilibrium is reached when the rate of
product formation exactly matches the
rate of reactant formation

Keq =
 Direction of the reaction
Free energy changes: Concentrations:
Go = standard Keq = standard
G = in the cell [P]/[R] = in the cell

-Reverse (towards reactants) -Reverse (towards reactants)

-Forward (towards products) -Forward (towards products)

-Equilibrium (i.e. Death) -Equilibrium (i.e. Death)

 Genetic Foundations
A linear polymer of DNA contains all the instructions for forming every cellular component

The structure of the molecule suggests how this information is stored, copied into another DNA
molecule, and translated into a functional protein. I.e. the structure helps to define its function

Hexokinase gene
 Evolutionary Foundations
The first biomolecules arose abiotically from the primordial soup, then evolved chemically

The Miller and Urey experiment, 1953

 Evolutionary Foundations

Replication is only near-

perfect.

Selective pressure allows

organisms to evolve the new
gene to adapt to changes in
their environment