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AP Bio- Energy 3: Cellular Energetic Practice

3 of 5 of my Energy Domain. Image Credits: Biology (Campbell) 9th edition, copyright Pearson 2011, & The Internet Provided under the terms of a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. By David Knuffke.
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David Knuffke

on 14 October 2014

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Transcript of AP Bio- Energy 3: Cellular Energetic Practice

Cellular Energetics
Enzymes!
Organization:
Biological catalysts.

Proteins and some RNA molecules (examples?)
How do they do it?
Enzymes interact with reactants ("
substrate
")

Cause breaking/formation of particular atomic bonds to be more energetically favorable.

This work is localized to an area of the enzyme called the "
active site
".
Induced Fit
The shape of the active site of an enzyme is shape-specific for a particular substrate.

The binding of a substrate to the active site induces the necessary conformational change of the enzyme to catalyze the reaction.
Reactants
Enzyme-Substrate
Complex
Enzyme
Products
Examples:
The active site is localized to a small area of the enzyme
Topoisomerase:
Involved in minimizing mechanical stress on DNA during replication.

Makes a temporary cut in the helix.
Blue
: 2 polypeptide chains.
Orange
: DNA Double-Helix
Purple
: Active site.
Evolutionary Considerations:
Rubisco!
Attaches carbon dioxide to sugar precursor molecules in photosynthesis.

50% of all protein found in a
chloroplast.
Co-factors
Most enzymes require accessory compounds many of which you are familiar with as ("
vitamins
") or metal ions (aka "
minerals
") in order to be functional.
Magnesium ion (
green
) associated with rubisco's active site.
A manganese ion (
dark green
) is visible in the topoisomerase active site.
Evolution plays a central role in enzyme structure and function.

Various studies have been conducted to investigate the effect of evolution on enzymes.

These include:
analysis of enzyme genes (sequence comparison).
Artificial selection of enzyme activity in laboratory settings.
Ethnographic/Demographic studies of enzyme genotypes and enzymatically determined phenotypes.
Variation + Natural Selection = Adaptation
Regulation:
Enzymatic function can be stimulated or inhibited by factors in the cell.
Competitive Interactions
Non-Competitive Interactions
vs.
A molecule other than the substrate binds to the active site.
Regulation is accomplished without occupying the active site.
Allosteric Interactions
"Other-site"
Stimulate or inhibit enzyme activity by causing a conformational change in the enzyme.
Activation:
Inhibition:
Binding of an activator molecule can stabilize the enzyme in an active conformation.
Binding of an inhibitor molecule can stabilize the enzyme in an inactive conformation.
Constant Oscillation
Active
Inactive
Activator
Inhibitor
Binding of a substrate molecule to on active subunit of an enzyme can also trigger stabilization of the active conformation in all subunits ("
cooperativity
")
Important enzymes for cell death (apoptosis and necrosis).

Data from an experiment to determine if caspase enzymes can have an allosteric site.

The active and inactive forms of caspase 1 were already known.

Hypothesis: Allosteric inhibition of caspase 1 will lock the enzyme in an inactive conformation.
"-ase"
A common nomenclature suffix for enzymes.
prefix: usually refers to enzyme's substrate
Ex. Caspase
Compartmentalization
Localization of specific enzymes (and the reactions they mediate) within compartments of the cell allow for more control over when and where particular metabolic reactions occur in eukaryotes.
Environmental Influence:
Like all proteins, enzyme structure (and therefore function) can be effected by the conditions of the enzyme's environment.

There are three major environmental conditions that effect enzyme structure and function
1. Temperature
2. pH
3. Concentration (enzyme, substrate, cofactors)
Feedback:
Many metabolites have regulatory effects on enzymes that catalyze the metabolic pathways that result in the production of those metabolites.
Big Questions:
Make Sure You Can:
How do living systems control their metabolism?

How do living systems carry out a wide variety of specific chemical reactions?
Explain how enzymes function as catalysts.

Explain the induced fit model of enzyme function.

Provide examples of enzyme-catalyzed reactions in biological systems.

Explain the relationship between enzyme structure and function.

Explain the major modes of regulation of enzyme activity.
Practice
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