 phosphofructokinase |
CHEM 4166
Dr. J. K. Krueger |
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phosphofructokinase |
CHEM 4166
Dr. J. K. Krueger |
“All men wondered to see
the water turned into wine. Every day the earth’s moisture being drawn into
the root of a vine, is turned by the grape into wine, and no man wonders. Full
of wonder then are all the things, which men never think to wonder at.”
Pope Saint Gregory the Great
Welcome to the
"wonder"-full world of Biochemistry.
Announcements
Dates to keep in mind:
Homework #6 is Due on Thursday April 12 when homework #7 will be passed out.
Guest lecturer on Thursday April 19 will discuss Protein Crystallography- should be very helpful to you as you write up your enzyme reports.
The written report on your enzyme is due on Tuesday April 24th.
Homework # 7 will be due on Tuesday May 1, the same day of your Exam #2.
The final exam will be on May 10 from 8 am - 10:45 am.
The article on your enzyme for which you will be writing a summary must be approved BY Tuesday March 13. Please select the article that you would like to summarize and send a pdf (preferable) or a citation of that work to me by email asap. for direction, I recommend that you search your enzyme on www.pdb.org and use that resource to select an article. There is a narrated tutorial available that will help you to navigate that website, if you have done it yet, DO IT NOW!
Irregular attendance for this class is becoming a major concern. Please recall the following comments as excerpted from your syllabus. “The format for this class functions most effectively with full classroom participation. It is extremely important that you attend and participate in lecture. Weekly homework assignments (and classroom participation) will be a part (20%) of your total grade” (see syllabus). Yes, this part of the grade is mostly subjective. I certainly understand that you may have other obligations and commitments and/or may not see your participation in this course as a priority. That is perfectly fine as long as you are aware of the consequences. I would hate for there to be any ‘surprises’. If you are sick or there are other interferences beyond your control you may wish to inform me so that your participation grade is not affected as dramatically. “Senioritis” does not count as an excused illness.
Next week begins student discussion of the enzymes from the second stage (last five reactions) in the glycolytic pathway. The discussion may be led by your classmate but this does not mean that you are not also expected to participate, and thus be prepared to participate, in the discussion. An updated list of enzymes that were assigned to each student along with a tentative lecture date can be found here.
Due to the snow day, homework #3 will be due on Thursday Feb. 15th.
Answer key for homework problem set 1 and 2 are now posted in the glass bulletin outside of room 205 Burson.
POWERPOINT Illustrations
Homework Assignments Hand-outs
Catalytic Strategies of Enzymes Problem Set 1 Presentation Grading Sheet
Problem Set 2 feedback regulation handout
Problem Set 3 glycolysis overview sheets Citric Acid Cycle Overheads Problem Set 4 Malate Dehydrogenase H.O.s Electron Transport Overheads Problem Set 5 ETC H.O.s Gluconeogenesis Problem Set 6 Gluconeogenesis H.O.s Fatty Acid Metabolism Problem Set 6 Fatty Acid Oxidation H.O.s Amino Acid Metabolism Problem Set 7 Amino Acid Catabolism
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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 plug-in 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 11: Enzymes/Catalytic Strategies
Catalytic Strategy Examples
| Triose Phosphate Isomerase | Chime Script |
| Chymotrypsin | Chime Script |
| Trypsin | Chime Script |
| Subtilisin | Chime Script |
Chapter 12: Introduction to metabolism
Regulation of Enzyme Activity
| Aspartate_Transcarbamoylase (ATCase) | Kinemage |
| Aspartate Transcarbamoylase (ATCase) | Feedback Inhibition (Allosteric) C |
| Glycogen Phosphorylase | Covalent Modification (Activation by Phosphorylation at Ser 14) |
| G protein (a, b & g subunits + bound GDP) | Hormonal Regulation- Transducer |
| Adenylate Cyclase Activator (Gs alpha) | Hormonal Regulation- Activated transducer molecule |
| Adenylate Cyclase + Gs alpha | Hormonal Regulation- Transducer bound to effector (synthesizes second message = cAMP) |
| cAMP-dependent protein kinase (catalytic domain) | Hormonal Regulation- Signal Transducer (activated by second messager) |
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 | |
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F-6-P ® F-1,6-BP | ATP ® ADP + Pi + H+ |
| Aldolase | |
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F-1,6-BP ® DHAP + G3P | |
| Triose Phosphate Isomerase (TIM) | |
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DHAP ® G3P | |
| G3P Dehydrogenase | |
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G3P ® 1,3-BPG |
2 NAD+
®
2 NADH
2Pi ® 2H+ |
| Phosphoglycerate Kinase | |
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1,3-BPG ® 3PG | 2 ADP + 2H+ ® 2 ATP |
| Phosphoglycerate Mutase | |
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3PG ® 2PG | |
| Enolase | |
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2PG ® PEP +H2O | |
| Pyruvate Kinase | |
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PEP ® Pyruvate | 2 ADP + 2H+ ® 2 ATP |
Chapter 14: citric acid cycle
Excellent overview of the citric acid cycle and the enzymes whose structures are known.
Pyruvate Oxidation- A major entry route for carbon into the citric acid cycle
| ENzyme | PDB ? | REACTION | REACTANTS ® PRODUCTS | CO-FACTORS |
Pyruvate Dehydrogenase Complex
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Pyruvate ® Acetyl CoA + CO2 | Nicotinamide Adenine Diphosphate (NAD+) |
Enzymes involved in the citric acid cycle
| Citrate Synthase | |
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Acetyl-CoA + Oxaloacetate ® Citrate | Coenzyme A (CoASH) |
| Aconitase | |
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Citrate
®
cis-Aconitate + H2O
cis-Aconitate + H2O ® Isocitrate |
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| Isocitrate Dehydrogenase | |
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Isocitrate ® a-Ketoglutarate + CO2 | NAD+ ® NADH |
| a-Ketoglutarate Dehydrogenase Complex | |
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a-Ketoglutarate ® Succinyl-CoA + CO2 | NAD+ ® NADH |
| Succinyl-CoA Synthetase | |
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Succinyl-CoA ® Succinate | ADP + H+ ® ATP |
| Succinate Dehydrogenase | |
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Succinate ® Fumarate | E·FAD ® E·FADH2 |
| Fumarase | |
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Fumarate + H2O ® Malate | |
| Malate Dehydrogenase | |
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Malate ® Oxaloacetate | NAD+ ® NADH |
Chapter 15: electron transport and oxidative phosphorylation
