Biochemistry at CSU, Stanislaus

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Classrooms and Experiments for all of the Experiments at Crowell Elementary
Discussion Board for Biochemistry I, aka how do I communicate with my group members?

Biochemistry I, Fall 2014

Just in time for the holidays: Cookie Chemistry

8:00 Class Group members Enzyme Reactants Products
Daniel, Forrest, Romel and Javier PvdJ the growing peptide, lysine, and ATP Pyoverdine siderophore
Berta, Daljit, Timothy and Brett Lysozyme polysaccharide part of peptidoglycan cleaves (B1->4) linkage between N-acetyl muramic acid and N-acetyl glucsoamine
Monica, Haider, Ravi, Khoja, Jessica, Forrest Phenylalanine hydroxylase phenylalanine + O2 tyrosine + H2O
Gerardo, Chris, Derrick HIV protease peptides with F and P cleaves peptide bond between F-P, C side of F, N side of P
Carla, Tamara, Cheyanne, Broneil, Bobby, and Jag Glyceraldehyde-3-phosphate dehydrogenase glyceraldehyde-3-P + NAD + Pi 1,3 bis phosphoglycerate + NADH, H+
10:00 Class Group members Enzyme Reactants Products
Vanessa, Paige, Sandeep, Anthony, and Janeice Alpha amylase amylose maltose
Lupe, Priya, Samantha, Katelyn, and Felicia Alcohol dehydrogenase ethanol + NAD acetaldehyde + NADH
Joseph, Laura, Hung and Ratha HIV Protease peptides with F and P cleaves peptide bond between F-P, C side of F, N side of P
Erik, Jordan, Nguyen, Ashley, Darryl Acetylcholinesterase acetylcholine acetic acid and choline
Jared, Harinder, Michael, and Luis Lysozyme polysaccharide part of peptidoglycan cleaves (B1—>4) linkage between N-acetyl muramic acid and N-acetyl glucsoamine

To get inspired for your performance, view the 2014 Chemsistry winner of the "Dance your PhD" contest. Mayonnaise

Syllabus for Fall 2014
Calendar for CHEM 4400, Biochemistry Fall 2014
Lehninger Web site

Protein structure and function

You will want to explore the structure of your protein using these resources. Your paper that is due this Friday should describe the structure and function of the normal protein. What are the key structural elements that contribute to its function? What amino acids are essential for the normal function?
Go to the Protein Data Bank and download a file.
PDB Exercise
Down load the pdb viewer to your computer
Download Pymol, another viewer for pdb files

Notes from class

Add acid to a buffer
pOH
Titration

Assignments

Monday, September 8: Group Presentations. Assignment for Monday, Sept. 8th
In Class worksheet, work with your group to complete this worksheet. Sept 3 Worksheet
pH Boot camp is due September 3rd, in class.Answers
Sign up for your Paper topic: List of Defective Protein Diseases
Know your amino acids for Friday, September 12th. You need to know the names, structures, one letter codes, three letter abbreviations and the pKR values for the seven ionizable side chains. Use the Quizlet links below, or make your own flashcards.
On Wednesday, September 24th, we will have group presentations: Titration of a Peptide and Determine the pI for your Peptide.
Hemoglobin Binding Exercise: October 20thHemoglobin Binding
More info aboutHemoglobin and myoglobin binding

Worksheets and Exercises

Chapter 1 Scavenger Hunt
pH Exercise
How to Determine the pH of a Weak Acid Solution
What kind of Problem is it? What equation do I use?
Practice questions for Chapter 2
Bicarbonate Blood Buffer group practice problems.
Quizlet Flash Cards for amino acids at pH 7.
Quizlet Flash Cards One letter codes for amino acids
Enzyme kinetics worksheet
Hemoglobin binding worksheet

Resources

Hemoglobin T and R state videos by Dr. Janet Iwasa.
Resource for Altitude Sickness, be sure to check out the calculators. Also, read about high altitude pulmonary edema (HAPE) the cause is not understood, but it is very serious.
Sample Experiment for 5th grade students. Make sure your experiment does not include anything toxic (ask for advice), open flames or a huge mess (no Mentos and Coke.) If you have seen it on Tosh.O it is not a good idea.

Whiteboard lessons

Titration of histidine
Relationship between Keq and rate constants

Enzyme whiteboard lessons

Use this worksheet for the Questions that are answered in these lessons:
Question 1
Question 2
Question 3
Question 4
Question 5
Question 6
Questions 7 and 8
Fun with pKa and enzymes
Allosteric vs Michaelis- Menton
Positive and negative effectors

The first exam for Fall 2014 will have material from the old Exams 1 and 2.

Exam 1

Exam 1 from 2011
Exam 1 from 2012
Exam 1 from 2013
Exam 1 from 2014

Exam 2

Exam 2 from 2013
Exam 2 from 2012
Exam 2 from 2011
Exam 2 from 2005
Exam 2 from 2006

Exam 3

Exam 3 from 2013
Exam 3 from 2012
Exam 3 from 2011
Exam 3 from 2010

**

Biochemistry II, Spring 2014

Syllabus for Spring 2014
Calendar for CHEM 4420

New Information about the Oral Presentations (40 points):
May 14 and 16: There will be 4 presentations on each day. Teams of 3 students will work together to make a 10 min power point slide presentation. Time will be strictly enforced. Submit your Powerpoint to Dr. Stone by 6 pm on May 13th. Any biochemistry topic in chapter 14-20 is allowed. Grades will be based on peer reviews and this rubric. Sign up with your topic and group members on this Presentation Sign up Page.

Old Exams

Exam 1:

Exam 1, 2010
Exam 1, 2012
Exam 1, 2013

Exam 2:

Exam 2, 2011
Exam 2, 2012
Exam 2, 2013
Nice overview of many different transport mechanisms

Exam 3:

Exam 3, 2011

Writing Resources

Writing Course at Duke University
The Science of Scientific Writing by Gopen and Swan
Chemistry Search at CSUS Library
This will help you understand passive vs active voice

Science Olympiad Information

Reading notes

Chapter 8, Procainamide paper, Decoding the Procainamide Paper

Chapter 9
Chapter 10
Chapter 11
Chapter 12 and here are the powerpoint slides for chapter 12
Chapter 13, part I
Chapter 13, part II
Review of kinetics vs thermodynamics

Old web site for CHEM 4420

Old Web site for CHEM 4420

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