Biochemistry Graphics

This is a collection of animated and still graphics which illustrates significant biochemical concepts and processes. It has been taken for the most part from the Integrated Biochemistry Learning Series, a HyperCard-based course in Medical Biochemistry. Our students find that animations of complex processes often aid understanding in a way that one or two still diagrams cannot. If these materials seem useful, they may be used directly on line, or they may be downloaded for projection from a computer during a standard lecture.

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Additional topics and graphics will appear in the future.
Some Technical Notes and Instructions

Bioenergetics
Enzymology
Heme Metabolism
Lipid Metabolism
Membrane Phenomena
Metabolic Interrelationships
Physiological pH Regulation
Structures

Bioenergetics

Proton pumping by the electron transport system and ATP synthesis by the F1Fo ATPase when ATP concentration is high.

This is a boring movie because at high ATP concentration there is no electron transport, no proton pumping and no ATP synthesis. To be appreciated, this sequence must be contrasted to its companion, which is described in the following paragraph. (63K animation)

Proton pumping by the electron transport system and ATP synthesis by the F1Fo ATPase when ATP concentration is low.

In this animation ATP concentration is low, so the proton gradient can drive the F1Fo ATPase in the reverse direction, synthesizing ATP. Dissipation of the proton gradient allows the electron transport system to pump protons out of the mitochondria to replenish the gradient.(346K animation)

The Mechanism of Pyruvate Dehydrogense

An acetyl group is transferred to lipoyllysine of the transacetylase, and then to CoA. The dihydrolipoyl group is then reoxidized by dihydrolipoyl dehydrogenase.(80K animation)

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Enzymology

The Lock and Key Mechanism of Enzyme-Substrate Interaction

A substrate molecule binds to an enzyme site that matches it exactly.(71K animation)

The Induced Fit Mechanism of Enzyme-Substrate Interaction

A substrate molecule binds to an enzyme site that does not match it exactly, and in the process changes the shape of the enzyme so that an exact fit occurs.(72K animation)

Enzymes Lower the Activation Energy of a Reaction

In a plot of free energy vs. progress of a reaction the presence of an enzyme is shown to lower the activation energy.(48K animation)

Mechanism of a Typical FAD-linked Enzyme

FAD is reduced by the first substrate and then reoxidized by a second substrate.(56K animation)

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Heme Metabolism

Difference Between the I and the III Series of Porphyrins

This animation emphasizes the difference between the APAPAPAP sequence of substituents in the I-series of porphyrins and the APAPAPPA sequence in the III-series. A link to this animation is also found in the "Heme and Iron Metabolism" module of NetBiochem. (260K animation with sound)

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Lipid Metabolism

Mammalian Desaturation of a Long Chain Fatty Acid

A double bond is placed at the omega - 9 position of a saturated fatty acid. This animation emphasizes the location of the desaturation, but does not show a mechanism. (216K animation)

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Membrane Phenomena

Cyclic AMP Activation of Protein Kinase A

An effector (agonist) binds to a cell membrane, triggering intracellular synthesis of cAMP and activation of protein kinase A, which phosphorylates intracellular proteins. (80K animation)

The IP3 Pathway

An effector (agonist) binds to a cell membrane, triggering intracellular hydrolysis of phosphatidylinositol-4,5-bisphosphate, activation of a Ca(II)-calmodulin-sensitive protein kinase and activation of protein kinase C by diglyceride. (96K animation)

Protons Bound to an Artificial Fatty Acid Membrane

Bonds holding protons to a half-titrated fatty acid membrane are shown to resonate. (96K animation)

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Metabolic Interrelationships

The Cori Cycle

The cycling of metabolic intermediates through the Cori Cycle is shown. (123K animation)

The Glucose Alanine Cycle

The cycling of metabolic intermediates through the Glucose Alanine Cycle is shown. (94K animation)

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Physiological pH Regulation

The Na+ for H+ Exchange Mechanism

This is the process by which sodium ions are moved from the renal tubule fluid to the tubule cell in exchange for hydrogen ions. (98K animation)

The Reabsorption of HCO3-

Protons in the tubule fluid react with bicarbonate ions in the tubule fluid, producing carbon dioxide. This carbon dioxide is returned to the blood to replace the carbon dioxide which had produced bicarbonate in the previous step. (122K animation)

Formation of Titratable Acidity of the Urine

Protons in the tubule fluid are buffered by phosphate in the tubule fluid, producing titratable acid. (54K animation)

NH4+ Excretion

Protons in the tubule fluid react with ammonia, producing ammonium ions. (54K animation)

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Structures

Equilibrium Between the Open Chain and Ring Forms of Glucose at the Anomeric Carbon

The structure of glucose is shown as being an equilibrium between the open chain form and the alpha and beta anomers of the ring form. (139K animation)

Resonance in the Peptide Bond

The peptide bond is shown resonating between the single- and double-bonded forms, giving rise to its partial double bond character. (200K animation)

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Some Technical Notes and Instructions:

The animations were converted from a HyperCard program (Integrated Biochemistry Learning Series) to QuickTime at the rate of 10 frames per second. This was chosen to produce relatively smooth movies without making files so large that their value would be incommensurate with the transfer time.

There is a controller bar at the bottom of each movie. To start any movie you must click on the forward arrow in this bar. If you want to examine a specific point in the movie (say, because it went by too fast) you can move the slide to that point (by clicking at the desired location in the controller bar) and thereby view the corresponding frame for as long as you want.

To use the animated (.mov) files you must have a QuickTime player installed on your computer.

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jb

Last modified 10/8/97

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