Becky Deeley’s Blog

As indicated in email and now in this post, you should study factors that affect populations, all organisms and focus on human populations.  Chapters 5 and 24 address general populations and adaptation.  Chapter 12 focuses on human populations.  Anticipate questions that address survivorship.  We have spent at least two class periods working on the essay.  Can you tell what the focus of the essay will be? 

This is a good forum to ask questions because everyone can see the question and the reply. 

ENZYMES:
Get all the energy you want NOW! Safe and easy!Reliable results with LESS WORK!

Doesn’t this sound like a great product?  This is an actual description of what enzymes do.   Most reactions do not occur without investing energy from the environment.  That environment may be abiotic, like H2O2 spontaneously decomposing.   In this case the energy is supplied in the form of light energy.  Since H2O2 is only a chemical and has no organelles, it doesn’t have any way to harvest energy.  The molecules absorb the little bit of energy they are able to pick up and that splits the molecule.  As we demonstrated in our experiment using H2O2 that was allowed to decompose with light compared to H2O2 decomposed with an enzyme, catalase, allowing the reaction to occur without help is not effective.  The enzyme lowers the activation energy needed to for the reaction to cross the threshold and split the molecule. 

Graphic from Mr. Rick’s Science pages.   http://www.galaxynet.com/~corvid/bio/images/bioi_activation_energy.gif

The top of the curve is the threshold.  If we can lower the threshold, then less energy will have to be used to cause the reaction to occur.    The X axis is energy.  Take a look at the top of the black curve.  It requires more energy for the reaction to occur.  Then compare the height of the lower curve to the upper curve.  The reaction catalyzed by the enzyme requires less energy.  It is more likely for the reaction to occur if an enzyme is able to catalyze the reaction.  Here is another example.  The enzyme that is catalyzing this reaction is hexokinase. 

Graphic from C. Mallory at Miami University.  http://fig.cox.miami.edu/~cmallery/255/255enz/

Hexokinase is adding a functional group, phosphate, from adenosine TRIphosphate to glucose, a hexose, 6 carbon sugar.   Glucose is quite happy-a nice stable molecule.  It is not going to suddenly pick up a phosphate group.  To phosphorylate this molecule, an enzyme is required.  HEXOSE is the sugar.  HEXokinASE is the enzyme, a protein, that phosphorylates the sugar.  Notice the threshold with the enzyme compared to an uncatalyzed reaction.  Enzymes are polypeptides in quaternary conformation.  Due to their complex shape and the order of the amino acids in the peptide chains, they are substrate specific.  Only one substrate will fit in the active site.  To fit, they don’t really fit like a key in a lock.  It is more like a hand in a glove; the glove fits snugly but is slightly altered to fit the hand.  When you pull the glove on your  hand, your hand feels a little squished in places.  That is induced fit.  The active site is like a pocket or groove formed by the protein.  The chemical groups that face into the groove are in the optimum location to work with the substrate.  The enzyme may work by

• bending or stressing the bonds
• creating a  microenvironment of the optimum pH
• allowing a side chain of the enzyme to participate in the reaction
• if there are two or more reactants, the active site holds them in proper position for the reaction to occur.

The enzyme does not permanently alter in conformation during the reaction.  It returns to its original conformation after the reaction and so may be used over and over again.  The rate of reaction can be increased by adding more of the enzyme or increasing the amount of substrate so enzymes are more likely to bump into the substrate.  As the concentration of the substrate is reduced, the rate of reaction slows.   

Enzymes are proteins and proteins have optimum conditions in which they function.  Some enzymes have specific pH range in which they work best.  Some have specific temperature range in which they work best.  Rule of thumb, most enzymes work best at the body’s normal temperature and pH.  Some enzymes work best in higher or lower pH and that can be achieved in organelles or other contained environs within the body.  If the pH is lower than the range in which that enzyme functions, it will denature the protein and the enzyme ceases to work.  This is also true of temperature.  If the range is slightly exceeded, the protein may be able to return to original conformation when the environs return to their preferred range.  If it is greatly exceeded, the protein may lose conformation permanently.  There are many ways that enzymes are controlled and regulated, but we’ll save that for another time!

In gen chem you learned many (I hope) carbon prefixes.  Most refer to the number of carbons in the main chain or in the ring.  Some say it is a ring-cyclohexane is a ring of 6 carbons.  Some suffixes refer to bonding between the carbons: ane is single bonds, ene is at least one db bond, and yne is at least one triple bond.  Alkane, alkene, alkyne.

We learned the names of groups that can be added to carbon chains/rings- the “R” structure.  We are “accessorizing” our carbon structure to give it different properties that then contribute to the new function that structure would have.

So we learned the only nonpolar functional group we will be addressing: methyl -CH3

the rest are polar in nature:
-OH hydroxyl  found in sugars/alcohols
-CO (db bond between the C and the O) carbonyl
       with this group, location is everything.  If it is terminal, it is an aldehyde.  If it is within the R structure, it is a ketone.
-COOH (this is a C w db bond to the O and single bond to the OH) carboxyl   This group makes the R structure acidic.  It is easy for it to give an H+ away. 
-NH2  amino  It is easy for this one to gain a H+.
-SH sulfhydryl  (thiols)
-PO4 phosphate  (as in adenosine triPHOSPHATE)

When these groups and others are added to a R structure, they can contribute to a carbon being bound uniquely-unlike any carbon and with what the other carbons may be bonded  in the chain.  This carbon is now assymmetric.  These are called enantiomers and demonstrate “handedness.”  Enantiomers are a type of isomer. 

Does that sort of answer your question? 

We celebrated the end of summer this weekend.  Just because we are well stuck in to the fleeting first quarter does not mean we have to stay indoors.  Field work will stave off cabin fever.  Keep track of the dates and come prepared to work outside in decidedly not neat, clean environments.  Dress code applies before and after field work; dress for class and bring field clothes and shoes with you. 

7 Sep Fri        ENVS D (C, lunch, D)
10 Sep Mon  Mar Bio (lunch, C, 15 min D)
11 Sep Tue    ENVS B (A, lunch, B)
19 Sep Wed   Mar Bio (lunch C, 15 min D)
29-30 Sep Sat & Sun OVERNIGHT MarBio leave 8:30 AM
                                                                                    return ~2:30pm

30 Sep- 1 Oct Sun & Mon OVERNIGHT AP Bio leave 10:30 
                                                                               return ~2:00 pm
10 Oct Wed   Mar Bio Rudee LEAVE 6:30 AM rtn. 11:30
                                                        F, G, and part of A
31 Oct Wed    AP Bio   F, G, A, and possibly B