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Basic Enzymology

Basic Enzymology. Characteristics and capabilities of a bacterium Genotype: Coded for in the DNA including plasmids Genes code for proteins Proteins are or are responsible for the traits of the cell Examples: Sugars present on O-antigen of LPS Whether the bacterium has a flagellum

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Basic Enzymology

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  1. Basic Enzymology • Characteristics and capabilities of a bacterium • Genotype: Coded for in the DNA including plasmids • Genes code for proteins • Proteins are or are responsible for the traits of the cell • Examples: • Sugars present on O-antigen of LPS • Whether the bacterium has a flagellum • Being able to use the sugar sucrose as a nutrient • Mostly these proteins are enzymes • All enzymes are proteins (except for some RNAs)

  2. Enzymes • Have a distinct 3D shape essential for activity • Are biological catalysts • Speed up the rate of a chemical reaction • Lower activation energy by holding molecule in a favorable place • Not consumed or permanently changed • Highly specific • Will react some with similar molecules especially if their concentration is high.

  3. Enzyme function depends on shape Product Substrates Enzyme brings substrates together in active site, increasing the rate at which they react. http://www.columbia.edu/cu/biology/courses/c2005/images/substratesarelig.6.gif

  4. Decrease in activation energy http://upload.wikimedia.org/wikipedia/commons/thumb/e/e3/Activation2_updated.svg/300px-Activation2_updated.svg.png

  5. Basic enzyme kinetics Lineweaver-Burk http://dept.physics.upenn.edu/courses/gladney/mathphys/images/michaelis-menton.gif http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/L/Lineweaver_Burk.gif

  6. Inhibition • Enzymes can be inhibited by disrupting their 3D shape • Adding high concentration of salt • Large changes in pH • Increasing temperature • Disrupts ionic attractions, H-bonds, etc. • Chemicals can bind permanently to enzyme • Changing shape • Binding to active site, preventing chemistry or substrate access • Competitive inhibition • Inhibitor resembles substrate, competes for active site

  7. Competitive inhibition http://www.elmhurst.edu/~chm/vchembook/images/573compinhibit.gif

  8. Allosteric sites In allosteric site, inhibitor is not reacted, but causes a shape change in the protein. The substrate no longer fits in the active site, so it is not chemically changed either. ghs.gresham.k12.or.us/.../ noncompetitive.htm

  9. More about Enzymes • Sometimes an enzyme needs help • Protein alone = apoenzyme • Helper molecule: cofactor • Could be inorganic like a metal ion (Fe+2) • Could be organic coenzyme (like CoA, NAD) • Apoenzyme + cofactor = holoenzyme. • Cofactors have an effect on nutrition • Bacteria have certain mineral requirements. • Vitamins are cofactors that are needed in the “diet”.

  10. Metal cofactors Mg+2 ATP http://www.bmsc.washington.edu/WimHol/grafx%20research%20sum%20part%201/dengjmbfig4a.jpg

  11. Organic cofactors Acetyl CoA http://www.biochem.arizona.edu/classes/bioc462/462b/graphics/LDH-Lehn4un1417-p538.jpg http://biominer.bime.ntu.edu.tw/magiicpro/Examples/P10933/MaxSup_3.1qfy_S.png http://www.steve.gb.com/images/molecules/cofactors/acetyl_coenzyme_A.png

  12. Metabolic reactions require enzymes • Reactions operate in pathways: A B C D Where A-D are different molecules Each step is catalyzed by a different enzyme. Many, many catabolic and anabolic reactions can take place in a cell; each reaction requires a different enzyme. Thus, there are many different enzymes present in a cell and a great many genes in the DNA coding for them all.

  13. Which way? Depends on which direction gives a decrease in the free energy of the products cf. the reactants: a negative ∆G. There is a standard free energy change (both reactants and products at 1.0 M) that indicates which direction the reaction would go. http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/images/pep.gif

  14. Concentration important! In the example, if another reaction removed lactate, the concentration would be kept low, driving the reaction left to right.This also lowers ∆G, meaning reaction goes left to right.

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