Biochemistry I

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Syllabus

Here are the Fall 2024 materials for you to study:

Exam #	Chapter	Problems	Other materials
1	1	Review questions: 1-12 Challenge problems: 1-9	Chapter 1 Scavenger Hunt How to read a journal paper Worksheet for reading your journal article. Worksheet for "Reading a Journal Article" and Sample paper for the worksheet Also look at the old exams, listed below this table
1	2	Review questions: 1,2,3,4,5,6,7,8,9,10,11,12 Challenge problems:14-21,23-34	Chapter 2 Reading Notes Practice questions for Chapter 2 Practice IMF questions What kind of pH Problem is it? pH Exercise How to Determine the pH of a Weak Acid Solution pH Worksheet pH Boot Camp Here are the answers to Boot Camp Bicarbonate Blood Buffer group practice problems Titration Acetic Acid with NaOH note: the pH at 0.00 mL should be 2.84 Osmosis, Correction to Osmosis Calculation
2	3	Review Questions:1-3, 5-20 Challenge Problems:21,23,24,27,29,31,32,33,34,35,37	Chapter 3 Practice Practice multiple choice questions The exams do not have any multiple choice questions, but these are good to practice reading comprehension. Exam Practice MORE practice for the test DNA Practice
2	3	See above for Chapter 3 problems	PCR practice DNA sequencing Worksheet this is an older method where each ddNTP was added to its own reaction mixture, then the fragments were separated by gel electrophoresis. In the newer methods, all reactions are done at once with different fluorescent labels on each type of ddNTP. See the text, page 139. Dideoxy sequencing on YouTube DNA-->RNA-->peptide worksheet done in class.
2	4	Review questions: 1-20 challenge problems: 21-31	Titration of histidine the quadratic equation is needed to solve for pH at 0.00 mL added, Titration of histidine This was done with the $\pi$ tautomer, which was obtained from the old text. This 2011 JACS (Journal of American Chemical Society) paper shows the chemical shifts and assignments for the more common (New Book: Meisfeld and McEvoy) $\tau$ structure. Protonation, Tautomerization, and Rotameric Structure of Histidine: A Comprehensive Study by Magic-Angle-Spinning Solid-State NMR Shenhui Li and Mei Hong, 2011. Both the $\pi$ and $\tau$ structures are found in proteins. Quizlet Flash Cards for amino acids at pH 7 Quizlet Flash Cards One letter codes for amino acids For those who are interested in learning how the one letter codes were established, follow this link This is one way to think of the one letter codes.
2	4	Review questions:1,2,3,4,6,7,11,12,13, Challenge questions:1,2,3,4,5,6,7,8,9,10,11,12,13,14	Protein structure Titration of histidine Review this lesson, so you can determine the pI of a peptide. $\alpha$ helix structure Stuff that should work on your smart phone: look for the amino acids molecular models Fibrous Proteins Collagen: model of alpha chain. model of quaternary structure Keratin: structure of hair Silk: structure of fibroin, the building block of silk produced by silk worms. What is the most abundant protein in the human body? The glue that holds us together. Protein databases structure: triple helix of collagen. Link to information about measuring the amount of secondary structures with circular dichroism.
3	5	Chapter 5 review questions: 1-18 challenge problems: 2, 4, 5, 6, 7, 9	Practice Working with Proteins problems. Practicequestions from old exams. No answers are available.
3	6	Chapter 6 review questions: 1-16 challenge questions:1-14	Link to how the RAT works for detecting infection with SARS-CoV2. Be sure to read about Western Blotting, ELISA and Immunoprecipitation in our text. Hemoglobin Resources Hemoglobin T and R state videos by Dr. Janet Iwasa. Oxygen binding to Myoglobin practice exam questions. 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. Do this worksheet: Hemoglobin Binding worksheet, these are practice exam questions. Concerted model for Hemoglobin binding Oxygen Sequential model for Hemoglobin binding Oxygen Relationship between Keq and rate constants Muscle resources: Muscle contraction a Biochemical perspective, with sample exam questions.
3	7	Chapter 7 review questions:1-11 challenge questions: 1-15	Fall 2024: Dec 2 Asynchronous Complete this worksheet after watching the lessons below 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 Fall 2024: Do this worksheet Enzyme kinetics worksheet Chymotrypsin Evidence for the chymotrypsin mechanism Flash cards for chymostrypsin More flash cards for chymotrypsin Quizlet questions for chymotrypsin You tube to the rescue: Chymotryspin Mechanism more You tube: Just in time for the Holidays! Enzyme regulation: Quizlet flash cards

Old Exams to Practice

(no answers will be provided)
Exam1 from 2017
Exam 1 from 2011
Exam 1 from 2012
Exam 1 from 2013
Exam 1 from 2014
Exam 1 from 2015

Exam 2 from Fall 2022
Exam 2 from Spring 2017
Exam 2 from Fall 2016 (has hemoglobin questions)
Exam 2 from Fall 2015 (has hemoglobin binding duration question)
Exam 2 from 2014
Exam 2 from 2013
Exam 2 from 2012
Exam 2 from 2011
Exam 2 from 2005
Exam 2 from 2006

Exam 3 from Spring 2017
Exam 3 from 2015
Exam 3 from 2014
Exam 3 from 2013
Exam 3 from 2012
Exam 3 from 2011
Exam 3 from 2010

Just in time for the holidays: Cookie Chemistry
Read about high fructose corn syrup, HFCS

Biochemistry I, Fall 2014

Fall-2014-Experiments for Service Learning at Crowell Elementary

Protein structure and 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 pK_R 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

Just in time for the holidays: Cookie Chemistry

Sugar worksheet done in class.
Read about high fructose corn syrup, HFCS the problem is not the fructose. The HFCS delivers pure glucose to the blood. This causes spikes in insulin which can increase bad cholesterol and more fat production.

Table summarizing GAG (Glucosaminoglycans):

taken from The Medical Biochemistry Page
Reactions for the formation of A1c, the hemoglobin glycation product that is used to determine blood glucose levels over time.

10:00 Parade

Enzyme	Reactants	Products
Lysozyme	polysaccharide part of peptidoglycan	cleaves (B1->4) linkage between N-acetyl muramic acid and N-acetyl glucsoamine
Acetyl Choline esterase	acetyl choline	acetic acid and choline
Glyceraldehyde-3-phosphate dehydrogenase	glyceraldehyde-3-P + NAD + Pi	1,3 bis phosphoglycerate + NADH, H+
Alpha Amylase	starch (amylose and amylopectin)	cleaves alpha 1—>4 linkage of starch
Alcohol dehydrogenase	Ethanol + NAD+	acetaldehyde, NADH

Noon Parade

Enzyme	Reactants	Products
Glyceraldehyde-3-phosphate dehydrogenase	glyceraldehyde-3-P + NAD + Pi	1,3 bis phosphoglycerate + NADH, H+
Alpha amylase	amylose	maltose
Alcohol dehydrogenase	ethanol + NAD+	acetaldehyde + NADH
HIV Protease	peptides with F and P	cleaves peptide bond between F-P, C side of F, N side of P
Acetylcholinesterase	acetylcholine	acetic acid and choline
Lysozyme	polysaccharide part of peptidoglycan	cleaves (B1—>4) linkage between N-acetyl muramic acid and N-acetyl glucsoamine
Acetyl Choline esterase	acetyl choline	acetic acid and choline	available

To get inspired for your performance, view the 2014 Chemistry winner of the "Dance your PhD" contest. Mayonnaise
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Experiments for Kids This link will take you to the Experiments Designed by Biochemistry I students, Fall 2020.
Each experiment has a worksheet and a video to help guide you through the learning experience.