Biochemistry I

2017 Syllabus

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Here are the Fall 2017 materials for you to study:

Exam #

Chapter Problems Other materials
1 1 Review questions: 1-12
Challenge problems: 1-9
Chapter 1 Scavenger Hunt
Also look at the old exams, listed below this table
GroupSept1
1 2

Review questions: 1,2,3,4,5,6,7,8,9,10,11,12
Challenge problems: 2,3,4,5,6,7,8,9,10,11,12*,13,14*

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Chapter 2 Reading Notes
Practice questions for Chapter 2

  1. What kind of pH Problem is it?
  2. pH Exercise
  3. How to Determine the pH of a Weak Acid Solution
  4. pH Worksheet
  5. pH Boot camp Here are the answers to Boot Camp
  6. Practice IMF questions
  7. Bicarbonate Blood Buffer group practice problems
  8. Titration of histidine the quadratic equation is needed to solve for pH at 0.00 mL added,
  9. Titration Acetic Acid with NaOHnote: the pH at 0.00 mL should be 2.84
  10. Osmosis, Correction to Osmosis Calculation
2 3 Review Questions:1-3, 5-19
Challenge Problems: 1,4,5,6,7,9,10
Chapter 3 Practice
Practice multiple choice questions
Exam Practice
MORE Exam Practice
2 3 See above for Chapter 3 problems DNA sequencing Worksheet
Dideoxy sequencing on YouTube
2 4 Review questions: 1-14
challenge problems: 1-14
  1. 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.
  2. Quizlet Flash Cards for amino acids at pH 7
  3. Quizlet Flash Cards One letter codes for amino acids
  4. For those who are interested in learning how the one letter codes were established, follow this link
  5. 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
$\alpha$ helix structure
Stuff that should work on your smart phone: look for the amino acids molecular models
Fibrous Proteins

  1. Collagen: model of alpha chain. model of quaternary structure
  2. Keratin: structure of hair
  3. Silk: structure

What is the most abundant protein in the human body? The glue that holds us together.
Protein databases structure: triple helix of collagen.

Empty

row, end of material for Exam 2
3 5 Chapter 5 review questions: 1-18
challenge problems: 2, 4, 5, 6, 7, 9
Study the in class worksheet. Practice Working with Proteins problems.
3 6 Chapter 6 review questions: 1-16
challenge questions:1-14

Hemoglobin Resources

  1. Hemoglobin T and R state videos by Dr. Janet Iwasa.
  2. Oxygen binding to Myoglobin worksheet done in class.
  3. 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.
  4. Hemoglobin Binding worksheet done in class.
  5. Concerted model for Hemoglobin binding Oxygen
  6. Sequential model for Hemoglobin binding Oxygen

Muscle resources:

  1. Muscle contraction a Biochemical perspective, with sample exam questions.
3 7 Chapter 7 review questions:1-11
challenge questions: 1-15

Use this worksheet for the Questions that are answered in these lessons:

  1. Question 1
  2. Question 2
  3. Question 3
  4. Question 4
  5. Question 5
  6. Question 6
  7. Questions 7 and 8
  8. Fun with pKa and enzymes
  9. Allosteric vs Michaelis- Menton
  10. Positive and negative effectors
  11. Allosteric vs Michaelis- Menton
  12. Positive and negative effectors

Chymotrypsin
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 mechanisms:

Warrior Thanksgiving Parade of Mechanisms.

Each group of 4-5 students will choose an enzyme and present the chemically correct mechanism in a fun and festive way!

Enzyme Reactants Products Group members
Alcohol dehydrogenase ethanol + NAD+ acetaldehyde + NADH Jose, Ricardo, Cali, Yasmin, Hector
Catalase Hydrogen peroxide Water + Oxygen Sergio, Chris, Masha, Maysam, Jaskert
Alpha Amylase starch (amylose and amylopectin) cleaves alpha 1—>4 linkage of starch Nicole, Sunpreet, Margarita,Nathalie,Yvette
HMG CoA Reductase HMG CoA Mevalonate Noveleen, Simranpreet, Rupinder, Navdeep, Sharill
RNAase A RNA cleaves the phophodiester bond between two ribonucleotides in RNA Najiba, Nazo, Isaac, Navneet, Jasan

Enzyme regulation: Quizlet flash cards

End of material for Exam 3

Discussion Board for Biochemistry, aka how do I communicate with my group members?

Old Exams to Practice

(no answers will be provided)

Exam 1 from 2011
Exam 1 from 2012
Exam 1 from 2013
Exam 1 from 2014
Exam 1 from 2015

Exam 2 from 2016
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 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 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

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):

GAGtable

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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