BiCh 110 BiCh110 Syllabus – 2019

BI/CH 110: Introduction to Biochemistry Course Syllabus – Fall / 2019

Course Instructor Bil Clemons (He/Him) 157 Broad Center, x1796, clemons@caltech.edu Office Hours TBD Teaching Assistant(s) Chia-Yu Chien (He/Him) - ccchien@caltech.edu Nicholas Higdon (He/Him) nhigdon@caltech.edu Arjuna Subramanian (He/Him) - amsubram@caltech.edu Karen Orta - Head TA - (She/Her) aorta@caltech.edu Office Hours: M 5-6pm/W as needed – Broad Center 156 (note the doors lock at 5pm) Course Description Lectures and recitation introducing the molecular basis of life processes, with emphasis on the structure and function of proteins. Topics will include the derivation of protein structure from the information inherent in a genome, biological catalysis, the intermediary metabolism that provides energy to an organism, and the use of DNA manipulations, cloning, and expression of proteins in foreign hosts to study protein structure and function. Welcome to Biochemistry! This course is in the process of being revamped this year for your benefit. It will be my first-time teaching both this course and a primarily undergraduate course. This course changed my scientific path and my hope is that it will do that for you too. We will be using a mix of lectures, workshops and problem sets to ensure that you are exposed to the basics of biochemistry. We will begin with a brief overview, discuss the macromolecules of life, and then do a deep dive into metabolism. Lectures will be tied to chapters so the expectation is that you will read the chapter prior to when I talk about the content. It will be a fun quarter! Learning Outcomes By the end of this course, students will be able to:

• Describe the chemical players of life, their structures and chemistry and, consequently, their function.

• Recognize how thermodynamics plays a role in living systems. • Identify the central pathways of metabolism. • Understand how pathways are regulated and integrated under different

environmental conditions. • Process and interact with macromolecular structures. • Explain how information is processed within a cell.

Text: “Biochemistry, 4th Edition” Voet & Voet. This text has not been updated since 2011 which means inexpensive copies can be obtained online. The material will be supplemented with new data as appropriate. In general, the basic material has not changed significantly in the interim. Students will be expected to have read the assigned chapter prior to the lecture. Not all material will be covered, students will be given instructions on sections from each chapter that should be read the week before. For the first week, all 4 chapters should be read.

Course meets:T/Th 11-11:55am 147 NoyesW 2-2:55pm 147 Noyes 3-3:55pm 152 Braun

BiCh 110

BiCh110 Syllabus – 2019 Learning Management System Course material will be maintained at the following website: http://chemistry.caltech.edu/courses/ch110/ In addition, we will use Moodle for quizzes and general course progression. Piazza will be used for class discussion. Rather than emailing questions, I encourage you to post your questions on Piazza. Find our class page at: https://piazza.com/caltech/fall2019/bich110/home We will also be using Plickers during class for assessing the uptake of material. We’ll discuss this on the first day. Assessment Rubric 54% on six problem sets (all six problem sets must be completed); 36% on exams (18% midterm, 18% final), 5% on quizzes, and 5% on attendance and active participation in recitation. The final is not cumulative and instead will cover only the subjects not covered on the midterm. Honor Code “No member of the Caltech community shall take unfair advantage of any other member of the Caltech community.” Our goal is to help you learn the material. We assess your ability to learn the material. It is important that you consider your peers and your own potential as you make decisions. Collaboration Policy For this course you are expected to solve problems individually. You are allowed discussion with other students when difficulties arise. Difficult problems can be addressed in Piazza and will be monitored by the TA and professor. The problem sets you hand in must be your own work and not copied from others. You may seek help from other students, but only after you have made a significant individual attempt to solve it (i.e., 15 minutes of serious effort) and even then, the help should be more in the form of a suggestion than in simply copying someone else’s solution.

Problem Sets: Each problem set is due at the beginning of class on the morning of the due date. New problem sets will be available the day that the last set is due (or when the midterm is due). Questions about homework sets will be addressed using Piazza or during the office hour. Late homework will be penalized 10 points per day. The exception will be problem set 4 where the answer key will need to be posted that day, therefore, late problem sets will not be accepted. Credit will be given for each assigned problem provided that all work is shown. Please try to limit the length of answers on your work. In an essay answer, points will be deducted for incorrect statements, even if the correct answer is buried in the response.

Exams: For each exam, the material will primarily cover the sections covered up to that point. The mid-term will include the material from Ch. 1-15 and the final will be Ch. 16-28. Not all material will be covered in class from each chapter and the exams will only cover concepts that are highlighted in class, problem sets or workshops. We will have review sessions prior to each exam. Topics covered will be based on polling.

Quizzes: To ensure preparation, each week a random online quiz will be assigned to be completed before class. Quizzes will be available by noon the day before class when it is due. We will discuss this the first day.

BiCh 110

BiCh110 Syllabus – 2019 Course Schedule

* Midterm available online. The final will be available Dec. 9th.

Lect Date Topic Chap Assignments L1 Tu 10/1 Introduction. Life & Scale 1 L2 We 10/2 Water & Thermodynamics 2&3 W1 Background & back of the envelope L3 Th 10/3 Amino acids 4 PS1 Out L4 Tu 10/8 Nucleic acids 5 L5 We 10/9 Protein structure 8 W2 Peptides L6 Th 10/10 Protein folding & Dynamics 9 PS1 Due L7 Tu 10/15 Hemoglobin – a model for molecular biology 10 L8 We 10/16 Protein purification and analysis (N. Riera) 6 W3 Working with PYMOL Th 10/17 Nucleic acid methods (N. Riera) 7 PS2 Due L9 Tu 10/22 Sugars and polysaccharides 11 L10 We 10/23 Lipids and membranes 12 W4 Using the PDB to understand structure L11 Th 10/24 Enzymes 13 PS3 Due L12 Tu 10/29 Rates of enzymatic reactions 14 L13 We 10/30 Enzymatic catalysis 15 W5 Exam Review L14 Th 10/31 Welcome to metabolism 16 PS4 Due* L15 Tu 11/5 Glycolysis 17 L16 We 11/6 Glycogen metabolism 18 Midterm Due W6 Protein Modeling with Computer Software L17 Th 11/7 Signal transduction 19 L18 Tu 11/12 Transport through membranes 20 L19 We 11/13 Citric acid cycle 21 W7 Using kinetics to work with pathways L20 Th 11/14 Electron transport – Oxidative Phosphorylation 22 PS5 Due L21 Tu 11/19 Gluconeogenesis & Glycoproteins 23 L22 We 11/20 Photosynthesis 24 W8 Fun with metabolism L23 Th 11/21 Lipid metabolism 25 L24 Tu 11/26 Amino acid metabolism 26 11/27-28 Thanksgiving Break L25 Tu 12/3 Fatty acid metabolism 27 PS6 Due L26 We 12/4 Nucleotide metabolism 28 W9 Exam review L27 Th 12/5 Discussion

Who am I?

Starting Out at U of Utah

Biochemistry Graduate Program - Incoming 1995

Venki Ramakrishnan MRC Laboratory of Molecular Biology

Tom RapoportHarvard Medical School

Membraneproteinbiosynthesis• Tail-anchoredtarge1ng

• Membraneproteinexpression

Clemons lab @ Caltech

Glycochemistryinbiologicalmembranes

• N-linkedGlycosyla1on• Pep1doglycanbiosynthesis

Chapter 1 Life

Copyright © 2011 by John Wiley & Sons, Inc.

Biochemistry Fourth Edition

Donald Voet and Judith G. Voet

32 3 The Processes of Living

Making a sterol from acetate

Campylobacterjejuni• Comensalofavians(i.e.chickens)• Firstbacteriaiden1fiedwithN-andO-

linkedglycosyla1on• Leadingcauseofbacterial

gastroenteri1s– ¼ofallUSci1zensgetfoodpoisoning

everyyear– Campylobacteraccountsfor14%ofcases– Only500bacteriaarenecessaryforan

infec1on!– Painful,bloodydiarrhea(oSenrequires

hospi1liza1on)• Guillain-BarréSyndrome

– Auto-immunedisorderleadingtototalimpairmentofthemotorneurons

– OSentriggeredbyaCjinfec1on

Nuc

OMIMCRRibSG

Flagellum

Müller..Clemons (2014) Microbiology Open

Tomography of C. jejuni

End Lecture 1

Bil CLEMONSBS Biochemistry Virginia Tech

PhD Biochemistry Venki RAMAKRISHNAN

Pod doc HARVARDMed TomRapoport

CALTECH Dec2005 PROF of Biochemistry

Vitamins essential small organics

PLICKERSwhy Biochem

b premed 15PhD I lawlmBA 8 realworld

Nice split

Central dogma The flow of information

DNA RNA Protein FromFRANELSCrick OHL Symposium 4957Modern DNA RNA Protein

what is this

fMost incorrectly guessed DNA ItsRNA

Clues Tertiary structure and shallow minorgroove

The molecule was cobalamin Vitamin1312 Mott gotthis right

offto 0

70

got 104 Vitamin C L ascorbicacid

scurvyco fator of prolylhydroxylase

fit

4 137 of collagen 25 7 ofBodymass

Triple helix Jello

SLIDE9 11

LIFE IS COMPLICATED

Download The Machinery ofLife By DavidGoodsell

slide 11

The process of making one Lanesterol is complicate

5EEn

LANostero1

Iho Acetate 18 molecules

ch

2520more steps

cholesterol

Bacteria Groka zoted Eukaryotesµ lovescaleG

o

Lines are membranesLIPID BILAYERS n 5amSo for a cell the size of the Rose Bowl

The membrane would be 1inch thick

sina.atace

Gram 1 Game

0 00

iE

O 0 more

cocci Rod Sprivulum

Myfavorite bacteria

mm a 4DeinococcusC jejune Pradiodwans Haloquadratun

3000K Radiator Walysbi

3mW El2mm 012

Slide 15 Haloquadratum Walysbi

A Singlecell brightspotsare gas Vesicles BGASVesicle c Sheetofall

ENDOFFECTURERemaining Noles Not Covered

Bacteria reproduce by fissionGrowth s

s otht

oooIttis

a

Escherichia coli discovered by TheodorEscherichFirstdescribed1886 From Breast

FEEDwr INFANTS

Major strains12 1922 fromSTANFORD DYSENTARYPATIENTModern strains from this are DHSL good for DNA

No Recombination

B strain 1918 Felix d Hirelle Amazona FRENCH CANADIAN

Delbruck Luria o Huxley 1940 established as a lab stain

at CALTECH

Modern version IS 13221 DED PROTEIN EXPRESSION

Slide 16Acha Eukarya

Bacteria

µ

A

f LUCALAST Universal CommonAncestor

o

Golgi

Nucleus stores o protects Genome

ER Golgi Secretorypathway MEMBRANE PROTEIN SYNTHESIS

Mitochondria Bacterialderived ENERGY FROM OXIDATIVE Metabolism

Lysosomes degrading enzymes the stomach

Peroxisomes Oxidizing enzymes

Biopolymers

Nucleic acids Adenine Guanine Thymine Cytosine GUANINE

PROTEIN AlanineTyrosine Leucine Serine

Polysaccharide Glucose Galactose L

lots of complexity

The rest of the slides were a genetics primer AND

some thoughts to thecomposition of a cell