Biochemistry II

Biochemistry II, Spring 2017

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Syllabus for Spring 2017

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

Here are materials for you to study:

Exam #

Chapter Problems Other Materials
1 8 Chapter 8 problems

*Chapter 8

1 9 Chapter 9 problems

*Chapter 9
Be sure to read about CRISPR. Why is it a hot topic? What problems need to be solved for it to work on humans?
Summary of Cloning and Stem Cells

2 10 Chapter 10 problems:2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 22

Chapter 10

  1. Dietary Cholesterol Supplementation Improves Growth and Behavioral Response of Pigs Selected for Genetically High and Low Serum Cholesterol
  2. Pigs Fed Cholesterol Neonatally Have Increased Cerebrum Cholesterol as Young Adults1

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

Exam 1 resources

Exam 1, 2010
Exam 1, 2012
Exam 1, 2013
Exam 1 2015

Exam 2 resources:

Example of an essay exam from 2007.
Exam 2, 2011
Exam 2, 2012
Exam 2, 2013
Nice overview of many different transport mechanisms

Exam 3 resources

Exam 3, 2011
Exam 3, 2014
Exam 3, 2015
Exam 4, 2015
Exam 3, 2011
Exam 3, 2014
Practice Glycolysis and more!
Exam 4 take home 2016

TCA Cycle!

Practice the Kreb's Cycle

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

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

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

  1. Dietary Cholesterol Supplementation Improves Growth and Behavioral Response of Pigs Selected for Genetically High and Low Serum Cholesterol
  2. Pigs Fed Cholesterol Neonatally Have Increased Cerebrum Cholesterol as Young Adults1

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.

Biochemistry II Writing Assignments
Stanislaus Journal of Biochemical Reviews

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

Signalling Presentations:

Apoptosis by TM and Eliza
Steroid hormones by Steve and Jose
Vision by Esther and Carrie
Olfactory Signalling by Alexander and Christopher
Taste by Jing and Julie
Vasopressin by Adam and Jose
Adrenergic Signaling by Chris and Ryan

Old web site for CHEM 4420

Old Web site for CHEM 4420

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