basic enzymology
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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 - PowerPoint PPT PresentationTRANSCRIPT
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)
1
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.
2
3Enzyme function depends on shape
Substrates
Product
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
Decrease in activation energy 4
http://upload.wikimedia.org/wikipedia/commons/thumb/e/e3/Activation2_updated.svg/300px-Activation2_updated.svg.png
Basic enzyme kinetics 5
http://dept.physics.upenn.edu/courses/gladney/mathphys/images/michaelis-menton.gifhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/L/Lineweaver_Burk.gif
Lineweaver-Burk
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
6
8Allosteric 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
9More 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”.
Metal cofactors 10
Mg+2 ATP
http://www.bmsc.washington.edu/WimHol/grafx%20research%20sum%20part%201/dengjmbfig4a.jpg
Organic cofactors 11
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
Acetyl CoA
http://www.steve.gb.com/images/molecules/cofactors/acetyl_coenzyme_A.png
12Metabolic 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.
Which way? 13
Depends on which direction gives a decrease in the free energy of the products cf. the reactants: a negative ∆G.
http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/images/pep.gif
There is a standard free energy change (both reactants and products at 1.0 M) that indicates which direction the reaction would go.