Biochemistry I 2015

Fall 2015 Materials

Service Learning Schedule for 2015

If you came in to practice, you are on this schedule. If you did not practice, then you will have to contact Dr. Stone (ude.natsusc|enotsk#ude.natsusc|enotsk) to explain why you did not practice.
Each experiment can have up to five people helping the leader (total of six names for each experiment.)
You need to read the experiment before you lead a group of students. This will help make the experiment go smoother. You are responsible for helping your small group of students, so please be prepared.
Date, Time, Room number Title of Experiment Leader, helpers
Mon, Nov 2, 1-3pm, H40 Liver and Hydrogen Peroxide Peter, Melanie, Cayenne, Gurinder, Mohammad N.
Mon, Nov 2, 1-3pm, G34 pH and Cabbage Juice Loretta, Stephanie, Paola, Leanna, Esther
Mon, Nov 2, 1-3pm, H43 Making Thermometers Jose, Jason, Carrie, Steve
Thurs, Nov 5, 1-3pm, H39 Yeast with Hydrogen Peroxide (Mega Foam) Jaspal, Shadi, Jimmy, Nari, Sim, Mohammad N.
Thurs, Nov 5, 1-3pm, H41 pH with pH paper Jasdeep, Jason, Love, Mohammad A., Esther, Gurinder
Thurs, Nov 5, 1-3pm, H42 Polarizing Light Miguel, Kevin, Sidna, Guadalupe, Amanda
Mon, Nov 9, 1-3pm, H40 Dancing Raisins Samsun, Melanie, Carrie, Jason, Jose, Steve
Mon, Nov 9, 1-3pm, G34 Stomach Gases Leanna, Stephanie, Sidna, Sim, Loretta
Mon, Nov 9, 1-3pm, H43 Browning Fruit Ketan, Cayenne, Gurinder, Jaspal, Mohammad N., Love
Mon, Nov 16, 1-3pm, H41 Glow Sticks Cesar, Miguel, Ketan, Cayenne, Sim, Samsun
Mon, Nov 16, 1-3pm, H39 Flowers as pH indicators Maria, Stephanie, Steve, Paola, Esther, Melanie
Mon, Nov 16, 1-3pm, H42 Static Electricity Sandra, Sidna, Navdip, Leanna, Mohammad N.
Mon, Nov 30, 12-2pm, G31 Polymer Play Lindsey, Carrie, Gurinder, Esther, Love
Mon, Nov 30, 12-2pm, G35 Tie Dye Milk Navdip, Sidna, Jason, Jose, Cayenne, Sandra
Mon, Nov 30, 12-2pm,? Glue polymers Ryan, Mohammad A., Sim, Steve, Kodie, Brandon
Thurs, Dec 10, 1-3pm, G32 Non Newtonian Liquid Alexander, Amanda, Mohammad N., Esther
Thurs, Dec 10, 1-3pm, G31 Fruits as pH Indicators Jorge, Guadalupe, Kodie, Brandon, Gurinder
Thurs, Dec 10, 1-3pm, G33 Density Nari, Esther, Jasdeep, Ryan, Nari
Thurs, Dec 10, 1-3pm, G35 Fat in Snacks Sabrina, Kevin, Shadi, James, Love, Melanie

Parade of Enzyme Mechanisms, Wednesday November 25, 2015, Third Floor Lobby of Naraghi

8:00 Class Group members Enzyme Reactants Products
Natalie, Nari, Mallory, Michael Carbonic Anhyrase CO2, H2O H2CO3
Navi, Sim, Edgar, TM, Sidna HIV Protease protein peptides
Vanessa, Chris, Jose, Jason, Thomas Alpha Amylase Amylose Maltose
Steve, Melanie, Carrie, Samsun, Mohammad Enolase 2-phosphoglycerate phosphoenol pyruvate + H2O
Jorge, Alexander alcohol dehydrogenase pyruvate + NADH ethanol + NAD
Love, Ricardo, & Peter phosphoglycerate mutase 3-Phosphoglycerate 2-Phosphoglycerate
10:00 Class Group members Enzyme Reactants Products
Sandra, Maria, Paola,Cesar, Cayenne HIV protease protein peptides
Haider Gurinder, Kettan, Jaspal, Jasdeep Phenylalanine hydroxylase phenylalanine tyrosine
Lyndsey, Brooke, Loretta, Leanna ,Jason Lysozyme polysaccharide smaller polysaccharide
Esther, Stephanie, Guadalupe, Amanda, Mohammad, Miguel alcohol dehydrogenase ethanol + NAD pyruvate + NADH
James, Shadi, Kodi, Kevin, Brandon triose phosphate isomerase dihydroxyacetone phosphate glyceraldehyde-3-phosphate
Sabrina, Ashley, Angelina,Eliza topoisomerase super twisted DNA DNA

Group Assignments for Fall 2015

Wednesday, September 9th: Intermolecular Forces and Amino Acids

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

Worksheets and other Resources

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

Exam 1

++++Homework for Exam I from the book:
Chapter 1: 7,8
Chapter 2: all
Chapter 3: 2,3,4

Other homework for Exam I:

Chapter 1 Scavenger Hunt
What kind of Problem is it? What equation do I use?
pH Exercise
How to Determine the pH of a Weak Acid Solution
In pH and Buffer worksheet, be sure to complete this worksheet. Worksheet
From 2014: pH Boot camp. Do these problems, then check your answers. Answers
Practice questions for Chapter 2 This worksheet focuses on intermolecular forces.
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 isone way to think of the one letter codes.
Bicarbonate Blood Buffer group practice problems.

Old Exams to Practice for Exam 1

(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

Homework for Exam 2 from the book:

Chapter 3: 4-14, 17-22
Chapter 4: all
Chapter 5: 1,3-8

Other materials for Exam 2:

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.
Hemoglobin Binding worksheet done in class.

Old Exams to Practice for Exam 2

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

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.

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

Homework for Exam 3 from the book:

Chapter 5: 9
Chapter 6: all
Chapter 7: TBD

Old Exams to practice for Exam 3

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
Exam 3, 8am
8AM Exam 3 Answers

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

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 Chemistry winner of the "Dance your PhD" contest. Mayonnaise
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