phosphofructokinase
CHEM 6101/8101
BIOCHEMISTRY
Dr. J. K. Krueger
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phosphofructokinase |
CHEM 6101/8101
BIOCHEMISTRY
Dr. J. K. Krueger |
Final exam is scheduled for Burson room 118 on Wednesday Dec. 12 from 8 am - 10:45 am. Take home portion of this exam is due by 9 am.
A classmate of yours had a very important question concerning your take home exam. Please email me if you also have ANY questions. I may share them with the rest of the class if I feel it may be a common question, but I will keep the person who sends the question anonymous. Keep an eye on your email. Okay, so here is the first question and my response:
I had a question about the last section of the take-home. Question #3 asks for the illustration of the chemical steps. Should we be considering the complete reaction here or just the one that this discussed in the article. IE Glutamine, ATP, Bicarbonate --> Carbamoyl phosphate OR Glutamine --> Glutamic Acid and Ammonia. I ask because the article doesn't discuss the entire reaction, only the hydrolysis of Glutamine, and yet at the top of the page on the exam it has the whole summarized reaction. My initial impression is to just "stick with whats in the article" but I just wanted to make sure.
Your initial impression was incorrect. In questions 3 – 5, you will need to review the background information on this enzyme and describe all of the reactions that are catalyzed by this enzyme, not just the one on the small subunit. You are correct to point out that my choice of wording “Review the attached article to answer the following 9 questions” may have been misleading. The attached article (and scheme I by the way) describes the mechanism only for reaction 1- the release of ammonia from glutamine hydrolysis and not any of the other three reactions that occur on the large subunit. The exam asks you to examine all four reactions catalyzed by this enzyme (the one on subunit A described in this paper, as well as the next three that occur on the large subunit). The purpose is primarily so that you can put this first reaction in context of what comes next, after the NH3+ is released. Another structure paper on this enzyme put out by the same group may help with this if you have difficulty with the brevity of the M&B textbook on this enzyme or any of the other biochemistry textbooks. It’s a really cool enzyme because it has three active sites within a single folded polypeptide chain and the three high energy intermediates generated at each site (including the ammonia produced at the active site of the small subunit) need to travel from one site to another without diffusing away in order to ultimately generate the stable product, carbamoyl phosphate.
I have a question about part f on the phosphoglycerate mutase question. The notation on the mutation is says H8A. Does that mean alanine is in the active site as well in place of a general base or is alanine functioning with histidine in another function?
Yes. X#Y is short-hand notation that molecular biologists use for site-directed mutants where the X residue at position # is replaced by Y residue. In this case, H8A means the histidine at position 8 is replaced with an alanine via site-directed mutagenesis. The histidine is no longer there, it has been replaced with an alanine. The question is asking what will be the implications of this? In other words, what is the role of the histidine in the enzyme activity scheme and what would happen to the enzyme if it’s functionality were replaced with the functionality of an alanine side-chain? Hope that helps.
Date |
Day |
Topics-Most hand-outs passed out in class and the overhead (ppt files) used in lecture are/will be linked below. |
Quiz |
Read Chap. |
Home-work |
Key posted |
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Part I: Structure and Basic Chemical Principles |
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Aug. 20 |
Mon |
Scope of biochemistry; Water and non-covalent forces
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1 – 2 (M&VH) |
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Aug. 22 |
Wed |
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2 (M&VH) |
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Aug. 27 |
Mon |
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2 (M&VH) |
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Aug. 29 |
Wed |
1 |
3 (M&VH) |
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Sept. 3 |
Mon |
HOLIDAY- NO CLASS |
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Sept. 5 |
Wed |
Bioenergetics |
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3 (M&VH) |
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Sept. 7 |
Fri |
Problem Session 9 – 10:30 |
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Sept. 10 |
Mon |
2 |
4 (M&VH) 2.5 (M&B) |
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Sept. 12 |
Wed |
Nucleic Acids |
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4 (M&VH) 2.5 (M&B) |
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Sept. 17 |
Mon |
Proteins: Amino Acids/Primary structure
These links are to documents that will help you with your homework:
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3 |
5 (M&VH) 2.4 (M&B) |
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Sept. 19 |
Wed |
Proteins: Primary Structure of proteins |
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5 (M&VH) 2.4 (M&B) |
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Sept. 24 |
Mon |
Proteins: Secondary and Tertiary Structure
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4 |
6 (M&VH) |
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Sept. 26 |
Wed |
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7(M&VH) |
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Sept. 28 |
Fri |
Problem Session 9 – 10:30 |
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Oct. 1 |
Mon |
Allostery/ Carbohydrates |
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9 (M&VH) 2.3 (M&B) |
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Oct. 3 |
Wed |
Carbohydrates |
5 |
9 (M&VH) 2.3 (M&B) |
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Oct. 8 |
Mon |
Fall Break NO CLASS |
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Oct. 10 |
Wed |
Lipids |
6 |
10 (M&VH) 2.2 (M&B) |
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Oct. 15 |
Mon |
Lipids Enzymes |
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10 (M&VH) 2.2 (M&B) 11 (M&VH) 2.6 (M&B) |
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Oct. 17 |
Wed |
Enzymes |
7 |
11 (M&VH) 2.6 (M&B) |
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OCT 19 |
FRI |
Problem Session 9 – 10:30 |
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Part II: Metabolic Pathways (or Applied Chemistry) |
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Oct. 22 |
Mon |
Enzymes
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4 (M&B) 12 (M&VH) |
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Oct. 24 |
Wed |
Introduction to Metabolism
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4.2 (M&B) 13 (M&VH) |
Take-home Midterm passed out |
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Oct. 29 |
Mon |
Quiz on enzymes at 9:30 am |
8 |
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Oct. 31 |
Wed |
work on take home mid-term Dr. Mottonen will be available for questions in room 118 Burson from 9:30 until 11 am. |
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protein sequence database and
analysis tools
Protein Explorer Molecular Visualization tool Protein Explorer-EXTRAs, HINTS, Etc.
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Nov. 2 |
FRI |
Problem Session 9 – 10:30 in Burson computer lab |
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Nov. 5 |
Mon |
Glycolysis |
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4.2 (M&B) 13 (M&VH) |
Take-home Midterm due |
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Nov. 7 |
Wed |
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4.2 (M&B) 13 (M&VH) |
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NOV 9 |
FRI |
Problem Session 9 – 10:30 |
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Nov. 12 |
Mon |
Glycolysis/ Fate of Pyruvate |
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4.3 (M&B) 14 (M&VH) |
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Nov. 14 |
Wed |
no lecture today.... just the quiz @9:30 |
9 |
4.4 (M&B) 14 (M&VH) |
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Nov. 19 |
Mon |
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4.3 (M&B) 14 (M&VH) 4.4 (M&B) 14 (M&VH) |
Final Paper Topic assigned- 8101 only- due Dec 5 |
RUBRIC for paper | |||||||||||||||||||
Nov. 21 |
Wed |
Thanksgiving Break NO CLASS |
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Nov. 26 |
Mon |
Citric Acid (aka TCA or Krebs) Cycle |
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4.4 (M&B) 14 (M&VH) |
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Nov. 28 |
Wed |
Electron Transport/ Oxidative Phosphorylatn | 15 (M&VH) |
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Dec. 3 |
Mon |
Electron Transport/ Oxidative Phosphorylatn |
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15 (M&VH) |
10 |
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Dec. 5 |
Wed |
Fatty Acid Metabolism |
10 |
18 M&V; 3 M&B | take home portion of final exam will be passed out |
paper is due |
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Dec. 12 |
WED |
8 – 10:50 am FINAL COMPREHENSIVE EXAM |
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USEFUL LINKS
| Link To PowerPoint Lectures | You must have PowerPoint or the PowerPoint Viewer | ||||
| Link To Homework and Answerkeys | |||||
| ENZYME KINETICS OVERHEADS AND NOTES | |||||
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| There are many programs that you can use to view a molecule- even large biological macromoleules!, provided its structure is known. In order to use any of these viewing programs though, you will need to get the file that contains the structural information on your protein of interest. The Research Collaboratory for Structural Bioinformatics (RCSB) hosts a web site where data files for ALL known macmromolecular structures are stored in what is called the Protein Data Bank (or PDB for short). | |||||
| THE PROTEIN DATA BANK | The world's repository for protein and other macromolecular structures determined by x-ray crystallography or NMR. | ||||
| PDB Tutorials | Tutorials on how to search and download files from the protein data bank. | ||||
| HIC-UP | Where you can find PDB Files of Cofactors, Prosthetic Groups, and Other "Small" Molecules | ||||
| For this class, we will be using a browser pluggin called CHIME and the molecular viewing software, "PROTEIN EXPLORER". To use the CHIME plug-in, you will need Internet Explorer or version 4.X of Netscape (or older) | |||||
| CHIME Molecular Viewer Plug-in | Chime is distributed by MDL software | ||||
| Protein Explorer | Tutorials, Instructions and other information about using the Protein Explorer | ||||
| RCSB graphics help page | Information from RCSB on numerous available graphics packages for visualizing macromolecules | ||||
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| After you have Chime and Protein Explorer installed and have completed the 1-hr tour to initiate yourself in how Protein Explorer works, the following tutorials will serve as a resource for studying concepts and lessons from the corresponding chapter in your Matthews and VanHolde textbook. | |||||
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| Chapter 5,6 | |||||
| Amino Acid Quiz | |||||
| Secondary Structures Tutorial | |||||
| Protein Architecture/ProteinG Tutorial | |||||
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| Chapter 7 | |||||
| Myoglobin | |||||
| Hemoglobin | |||||
| Hemoglobin Tutorial | |||||
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| Chapter 9- Carbohydrates | CHO Terminology List | ||||
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A chime-script resource for the biochemistry course taught at Arizona | ||||
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carbohydrate mobility within a glycoprotein
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" " | ||||
| disaccharides | " " | ||||
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| Chapter 10- Lipids | |||||
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Diffusion within the lipid bilayer thermodynamically unfavorable flip-flop within the lipid bilayer
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Chime-script and animation resources for the biochemistry course taught at Arizona | ||||
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Transmembrane Protein
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| Valinomycin- an ion transport protein | " " | ||||
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| Chapter 11- Enzymes | |||||
| Enzyme Kinetics Tutorial | The University of
Arizona has an on-line interactive resource called the "Biology Project"
which includes links to problem sets and tutorials in various aspects of
biochemistry.
For a basic understanding of the major issues in Enzyme Kinetics I recommend this particular Tutorial and problem set- to try it out yourself just follow the link to the right. |
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Dr. Stephen Curry at
the Imperial College in London has set up a web page for his Molecular
Biophysics course that includes some chime scripts for common enzymes
including the evolutionarily related proteases to the right. I particularly
liked the discussion in these chime scripts and recommend you visit these
sites to gain further insights into how these enzymes work..
As with all chime scripts, they work best in older versions of netscape, 4.7 or older, (which is available in the chemistry department's computer lab). |
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| Chapter 12 | |||||
| Metabolism Tutorial | Here is the link to the University of Arizona's Biology Project Tutorial on Metabolism. | ||||
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Chapter 13: Glycolysis
| ENzyme | PDB ? | REACTION | REACTANTS ® PRODUCTS | CO-FACTORS |
| Hexokinase |
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Glucose ® G-6-P |
ATP ® ADP + Pi + H+ |
| Phosphoglucoisomerase |
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G-6-P ® F-6-P | |
| Phosphofructokinase |