Biochemistry II

Biochemistry II, Spring 2024

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How to read a literature paper: here is a video lesson by. Dr. Dave Baltrus, U of Arizona

Interested in a summer research position? Go here: NSF REU to find a site and apply soon!

Syllabus for Spring 2024

Stanislaus Journal of Biochemical Reviews

Here are materials for for Spring 2024

Exam #	Chapter	Challenge Problems (end of chapter)	Other Materials
1	6 (only section 6.3)	Chapter 6 problems: 8,9,10,11,12	Slides for Project management Science of Scientific Writing by Gopen and Swan. Slides for Membranes and how to do the problems on the membrane transport worksheet. Membrane transport worksheet. Reading notes for Membrane Transport (Section 6.3) Membrane Transport slides Nice Overview of Transport mechanisms Rubric for Oral Presentations
1	8	Chapter 8 problems: 1,2,4,5,6,7,8,9,10,11,12,13,14	General Signaling Slides here is the worksheet
1	8	Chapter 8 problems: 1,2,4,5,6,7,8,9,10,11,12,13,14	Lecture Slides GPCR and more Taste and more GPCR slides, the animation link does not work. Go to the Smartworks site to view. Insulin receptor slides. Tumor Necrosis Factor, Steroid hormones, Vitamins Signal Mechanism Practice Neuronal Signallng Signalling Slides from class Apoptosis slides from Wikipedia More Signalling Slides from class Reading Notes Cell Signalling (Chapter 8) Note: The old exams are not relevant. We used a different book and focused on different topics. Here is a set of practice questions for this first test. There are more questions than you can answer in 50 min, but it should help you focus your studying. Practice for Exam 1, 2020 Resource: GPCR as pharmaceutical target
2	Chapter 9	You need to know the reactions of glycolysis, gluconeogenesis and the tricarboxylic acid cycle. How are these pathways regulated?	For this the writing assignment for this week: Find a figure in one of your references, explain how the data was obtained. What was measured, how was it measured? How do the results of show in this figure support the conclusion of the paper? What did you learn from reading this paper?
2	9		Glucokinase Regulatory Proteinon wikipedia. Regulation of Glycolysis and Gluconeogenesis
2	9	Practice for Exam 2	Trehalose is in our food and may be increasing the virulence of C. dificile. Trehalose is marketed and sold as "Treha". It is generally regarded as safe. The mouse studies with C. difficile may change that. 61 names for sugar, Treha is not on the list.
2	10	Chapter 10 problems: 1, 2, 3, 4,10,11,12,13	Moving Electrons can do work. worksheet Focus on the regulation of the TCA cycle. Practice the Kreb's Cycle Papers Related to Citrate 1. A Role for the Krebs Cycle Intermediate Citrate in Metabolic Reprogramming in Innate Immunity and Inflammation. This paper has the awesome figure on page 3: All the places Citrate can go! 2. Citrate is an anticoagulant 3. Citrate Metabolism in Red Blood Cells This is only the abstract.
3	11		Electron Transport, ATP synthesis, Brown Fat and Malignant Hyperthermia Old Electron Transport slides We did not cover the Mass Spec data in the first slides. It does provide evidence for the spatial arrangement for the complexes in the Electron Transport Chain.
3	16	Chapter 16 problems:	Fat Slides News article: Ketogenic diet improves mental health Insig protein and Cholesterol Homeostasis High Fructose Corn Syrup and Sucrose cause Non Alcoholic Fatty Liver Disease NAFLD How does Ethanol affect lipid metabolism? Alcohol and lipid metabolism by Margaret Sozio and David W. Crabb, Am J Physiol Endocrinol Metab. 2008 Jul; 295(1): E10–E16. Published online 2008 Mar 18. doi: 10.1152/ajpendo.00011.2008 Influence of Fat/Carbohydrate level on the Progression of Fatty Liver Disease and on Development of Osteopenia in Male Rats Fed Alcohol via Total Enteral Nutrition (TEN). Martin J. J. Ronis, Kelly Mercer, Larry J. Suva, Jamie Vantrease, Matthew Ferguson, William R. Hogue,d Neha Sharma, Mario A. Cleves, Michael L. Blackburn, and Thomas M. Badgera. Alcohol. 2014 Mar; 48(2): 133–144. Published online 2014 Feb 1. doi: 10.1016/j.alcohol.2013.12.005 All lipids get peroxidized [http://www.case.edu/artsci/chem/faculty/salomon/Mechanisms.htm Lipid peroxidation produces aldehydes. Omega 3 and omega 6 fatty acids in the diet:Omega Ratio and Metabolism Here are two power point presentations from a Food Science and Technology Class at the University of Tennessee, Knoxville. The first is a good overview of Lipids. The other describes lipid oxidation reactions and focuses on the effects that occur during food processing. Cardiolipin is an essential part of eukaryotic mitochondrial membranes. Vitamin D and the Immune System, a Review by Cynthia Arnow. Vitamin D and the Immune Systme Two papers on cholesterol levels and brain development: Dietary Cholesterol Supplementation Improves Growth and Behavioral Response of Pigs Selected for Genetically High and Low Serum Cholesterol Pigs Fed Cholesterol Neonatally Have Increased Cerebrum Cholesterol as Young Adults1 Power point presentation on Coconut Oil

Writing Resources

Power point slides on Writing: Better Writing

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
Searching the Literature: use this power point to search ACS Publications, SciFinder and PubMed. You need five primary sources for your writing assignment. Primary sources have experiments and data and have been peer reviewed. Do not use web pages, reviews, book chapters, magazines or news articles.

Corona Virus and COVID-19 information

SARS-Cov2 variants

List of NIH clinical studies related to COVID-19

Class presentations explaining/describing the Clinical trials related to COVID-19

ACE inhibitors and Ace receptor Binding inhibitors may be detrimental by Shivam Gandhi
Darunivar by Miranda Marshall

In this video, UC Berkeley professor and IGI Investigator Britt Glaunsinger, PhD, explains the evolution, genetics, and virulence of coronaviruses. https://youtu.be/8_bOhZd6ieM

Ninja Nerd Science video is also a good synopsis, lots of good explanations of how the disease causes the symptoms. https://www.youtube.com/watch?v=PWzbArPgo-o&feature=youtu.be

New indicator for serious disease: Lactate Dehydrogenase. LDH is released into the blood during pyroptosis: https://www.medrxiv.org/content/10.1101/2020.03.24.20040162v1.full.pdf
Here is a link to a thread that explains pyroptosis of macrophages: https://threadreaderapp.com/thread/1246778158290014214.html

Note: Not sure the mechanism of entry is membrane fusion, there is some evidence that it is via endocytosis. Here is a 2014 paper that looks at the role of ACE2 and some other membrane bound proteases: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3911672/. There are some other graphics showing the interaction of ACE2 and the Corona Virus S protein: Corona Virus information

Why you need to STAY HOME and Break the Chain of Transmission, a must read for anyone considering travel, etc during this outbreak. Why You Must Act Now

ACS has published Corona Virus information and it is available to EVERYONE, no charge.https://pubs.acs.org/page/vi/chemistry_coronavirus_research

NIH researchers publish data on the half life of SARS-CoV2: Aerosol and surface stability of HCoV-19 (SARS-CoV-2) compared to SARS-CoV-1
Median half-lives of SARS-CoV-2
2.7 hrs in aerosols
3.4 hrs on copper
8.5 hrs on cardboard
13 hrs on steel
16 hrs on plastic

How China’s “Bat Woman” Hunted Down Viruses from SARS to the New Coronavirus

Hot off the press: X-ray crystallography of SARS-CoV19 binding to ACE2.Renhong Yan, et al, in Science
Link to Coronavirus 2019-nCoV Global Cases by Johns Hopkins CSSE
BBC article has death rates for men and women. Is smoking a risk factor?BBC: Coronavirus: Are women and children less affected?
Link to 2019-n Cov sequences
Link to CDC Outbreak information
Link to ACE2 paper. ACE2 is in the lungs and inhibition of ACE2 leads to ARDS (acute respiratory distress syndrome)ACE2 information
This site has both RNA and protein distribution for proteins: ACE2 tissue distribution ACE2 is a marker for predicting positive outcomes for renal and liver cancer. (Positive prognosis marker.)
Its not the infectious agent that kills (directly) its the errant immune cells that release TNF and many more cytokines. Here is a link to a review: The meteorology of cytokine storms, and the clinical usefulness of this knowledge

Materials from Spring 2018

Exam #	Chapter	Challenge Problems (end of chapter)	Other Materials
	8	Chapter 8 problems: 1,2,4,5,6,7,8,9,10,11,12,13,14	GPCR slides, the animation link does not work. Go to the Smartworks site to view. Insulin receptor slides. JBC paper"Dual Regulation of Glycogen Synthase Kinase-3β by the α1A-Adrenergic Receptor". The α1A-Adrenergic receptor cascade involves Gq, PLC, IP3, Ca⁺² and diacyl glycerol. Ca⁺² and diacyl glycerol activate PKC and PKC phosphorylates GSK3β (Glycogen Synthase Kinase -3β). The phosphorylated form of GSK3β is inactive and thus can not phosphorylate Glycogen Synthase (GS). This makes Glycogen Synthase more active and promotes glycogen synthesis; this is the opposite of what is in your book. The book gives a general statement that activation of PKC inhibits glycogen synthase. After reading this journal article, the full story becomes clearer. The α1A-Adrenergic receptor has another pathway that does inhibit glycogen synthesis. The α1A-Adrenergic receptor cascade inactivates Akt (aka PKB). Akt is activated by the Insulin cascade: which is shown in the video and in the powerpoint slides. When Akt is inactivated by the α1A-Adrenergic receptor cascade, it does not phosphorylate GSK3β. The unphosphorylated form of GSK3β is active, it phosphorylates Glycogen Synthase to make GS less active. Catecholamines work against insulin by binding to the Gq coupled receptor that results in the inactivation of Akt (mechanism under study). This allows GSK3β to remain active and it phosphorylates and inactivates GS. The net result of catecholamines binding to the α1A-Adrenergic receptor is less glycogen synthesis, as stated (vaguely) in the text. Signal Mechanism Practice Neuronal Signal Mechanism Reading Notes Cell Signalling (Chapter 8)
2	9		Glucokinase Regulatory Proteinon wikipedia. JBC paper"Dual Regulation of Glycogen Synthase Kinase-3β by the α1A-Adrenergic Receptor". Control of Glycogen Synthase
2	10	Chapter 10 problems: go to the Smartworks Reading questions and TCA problems	Mechanisms presented in class: Aldolase Glyceraldehyde-3-Phosphate dehydrogenase Enolase Citrate Synthase Succinyl CoA Synthetase Know your mechanism in detail! Pyruvate Dehydrogenase mechanism Also, review the Nernst Equationworksheet that we did in class.
2	11	Chapter 11 problems: Smartworks reading quiz	Electron Transport powerpoint from class.
Old material from	Spring 2017	The current material will be above	this section
2	10	Chapter 10 problems:2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 22	Chapter 10 All lipids get peroxidized [http://www.case.edu/artsci/chem/faculty/salomon/Mechanisms.htm Lipid peroxidation produces aldehydes. Omega 3 and omega 6 fatty acids in the diet:Omega Ratio and Metabolism Here are two power point presentations from a Food Science and Technology Class at the University of Tennessee, Knoxville. The first is a good overview of Lipids. The other describes lipid oxidation reactions and focuses on the effects that occur during food processing. Cardiolipin is an essential part of eukaryotic mitochondrial membranes. Vitamin D and the Immune System, a Review by Cynthia Arnow. Vitamin D and the Immune Systme Two papers on cholesterol levels and brain development: Dietary Cholesterol Supplementation Improves Growth and Behavioral Response of Pigs Selected for Genetically High and Low Serum Cholesterol Pigs Fed Cholesterol Neonatally Have Increased Cerebrum Cholesterol as Young Adults1 Power point presentation on Coconut Oil Be sure you can recognize (and briefly describe the biological function of) these hormones: testosterone, estradiol, cortisol, aldosterone and vitamin D. They are all made from cholesterol, they all affect the expression of genes by binding to receptors. But what exactly do they do? What tissues do they affect?
2	11	Chapter 11 problems: 4-17, 19, 20, 22	Chapter 11
3	12	Chapter 12 problems: 2,3,14,15,19,22	Chapter 12 A summary of GLUT4 and Insulin and here are the powerpoint slides for chapter 12, go to slide 14 for more GLUT4 mobilization GLUT4 transport
3	13	Chapter 13 problems: 1-15, 17, 19,20,21,22,23-27	Chapter 13 resources: Reading notes: Chapter 13, part I Reading notes: Chapter 13, part II Review of kinetics vs thermodynamics
3	14	Chapter 14 problems:	Chapter 14 resources: Practice Glycolysis and more! Chapter 14: Glycolysis, Gluconeogenesis, Pentose Phosphate Pathway Summary Slide Be sure to go to SmartWorks to practice Glycolysis questions. Practice the problems and get points! Metabolic Regulation (Chapter 15) Summary Slides
Final Exam	Chapter 16	We will do this in class on Monday, May 15th	Practice the Kreb's Cycle

+++Resources for Exams

How does Ethanol affect lipid metabolism?
Alcohol and lipid metabolism by Margaret Sozio and David W. Crabb, Am J Physiol Endocrinol Metab. 2008 Jul; 295(1): E10–E16. Published online 2008 Mar 18. doi: 10.1152/ajpendo.00011.2008
Influence of Fat/Carbohydrate level on the Progression of Fatty Liver Disease and on Development of Osteopenia in Male Rats Fed Alcohol via Total Enteral Nutrition (TEN). Martin J. J. Ronis, Kelly Mercer, Larry J. Suva, Jamie Vantrease, Matthew Ferguson, William R. Hogue,d Neha Sharma, Mario A. Cleves, Michael L. Blackburn, and Thomas M. Badgera. Alcohol. 2014 Mar; 48(2): 133–144. Published online 2014 Feb 1. doi: 10.1016/j.alcohol.2013.12.005

From the Lipid Library:
Overview of fatty acid oxidation by Natasha Fillmore, Osama Abo Alrob, Gary D. Lopaschuk

Reading notes and Resources

Chapter 8, Hydroquinone Paper, Decoding the Hydroquinone Paper
Read about the Next Generation of Sequencing in this review of DNA sequencing: DNA Sequencing
Link to IlluminaNext Generation Sequencing
Dideoxy sequencing on youtube.
Chapter 9
Chapter 10

All lipids get peroxidized [http://www.case.edu/artsci/chem/faculty/salomon/Mechanisms.htm Lipid peroxidation produces aldehydes.
Omega 3 and omega 6 fatty acids in the diet:Omega Ratio and Metabolism
Here are two power point presentations from a Food Science and Technology Class at the University of Tennessee, Knoxville. The first is a good overview of Lipids. The other describes lipid oxidation reactions and focuses on the effects that occur during food processing.
Cardiolipin is an essential part of eukaryotic mitochondrial membranes.
Vitamin D and the Immune System, a Review by Cynthia Arnow. Vitamin D and the Immune Systme
Two papers on cholesterol levels and brain development:

Power point presentation on Coconut Oil

Chapter 11
Chapter 12 and here are the powerpoint slides for chapter 12
GLUT4 transport
Chapter 13, part I
Chapter 13, part II
Review of kinetics vs thermodynamics

Chapter 14: Glycolysis, Gluconeogenesis, Pentose Phosphate Pathway Summary Slide
Be sure to practice the multiple choice practice exam questions.Lehninger Practice questions There are multiple choice questions from Chapters 14, 15, 16 and 17.
Fat Metabolism (Chapter 14, 17, 16): Summary Slides
Metabolic Regulation (Chapter 15) Summary Slides
Metabolic Regulation (Chapter 15) Summary Slides

Materials from Spring 2016

Syllabus for Spring 2016

Rubric for Final poster presentation.

Spring 2016 Biochemistry II Writing Assignments
Stanislaus Journal of Biochemical Reviews

EXAM II: Spring 2016, due Thursday, March 17th, submit to Turnitin.com
Exam IIIExam III

Read about the Next Generation of Sequencing in this review of DNA sequencing: DNA Sequencing
Link to Illumina[http://www.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf Next Generation Sequencing
Dideoxy sequencing on youtube.

In the News: BBC article about growing human stem cells in pig embryos. This news story also describes how mouse stem cells were used to grow a mouse pancreas in a rat. The Pig embryos research study was published in Cell. Wu, et al. The mouse pancreas was published in Nature. Yamaguchi et al
Old Slides:
GPCR slides, the animation link does not work. Go to the Smartworks site to view.
Insulin receptor slides.
Tumor Necrosis Factor, Steroid hormones, Vitamins
Corona Virus information

Old web site for CHEM 4420

Old Web site for CHEM 4420

(not supported, may disappear at any moment)

Biochemistry at CSU, Stanislaus

Professor Koni Stone

Biochemistry II, Spring 2024

Here are materials for for Spring 2024

Lecture Slides

Reading Notes Cell Signalling (Chapter 8)

Writing Resources

Corona Virus and COVID-19 information

Class presentations explaining/describing the Clinical trials related to COVID-19

Materials from Spring 2018

Exam 1 resources

Exam 2 resources:

Exam 3 resources

TCA Cycle!

Reading notes and Resources

Materials from Spring 2016

Old web site for CHEM 4420