BYU-I Chem481 Test 2

K_cat= overall rate of the reaction. Most likely approximate to the slow rate determining step.

The Catalyzed reaction will proceed more rapidly, will have lower energy intermediates, will go through a different pathway, but will have the same starting and ending energy states.

It stabilizes the transition state.

False. Coenzyme Cofactors are not prosthetic groups when they easily unbind.

NO! While they do lower the intermediate energies required for certain transition states, they do not effect the beginning or ending energy states.

• K_{eq is related to .} 
• Not The Activation Energy.

Uses Water to shuffle protons.

Uses anything but water.

It will be the step involving the highest energy transition state.

They will be the low energy troughs before the final product.

It would bind so tightly to the substrate that to move to a different conformation would require more energy than the cell could provide. The Activation energy would be increased!

The negative energy interactions between the enzyme and the substrate help to negate the positive energy needed to modify the substrate. This is 1 way.

• Entropy is a measure of the randomness and disorder in a system.
• .S.

Typically Enzymes Decrease Entropy. This is useful In Catalyzing a reaction.

By binding to the substrate. It's binding affinity overcomes the drop in Entropy.

IMF (mult weak interactions).

The leChatlier principle. Free substrate increases the binding to enzymes and pushes the reaction forward. Free product increases the probability of the reverse reaction occurring.

It is the Initial Rate.

• 1. V₀ is what matters.
• 2. the ES complex forms ASAP!

AS FAST AS PHYSICALLY POSSIBLE.

K₁ Will occur the fastest because all free enzyme will quickly bind to the substrate.

[ES] is constant. Initially all free Enzyme will bind to substrate, and then as the substrate is processed into product, the Free enzyme will bind to new substrate so quickly that it will appear that all available substrate is constantly bound.

• K₁ is fastest.
• K_-1 is next.
• K₂ is slowest and the rate determining step.

V/[S]

rectangular hyperbola.

K_m

• 
• V₀=1/2V_max

• 
• V₀=0

• 
• V₀=Vmax

When K₂ is the rds.

• V_max=K_cat[E_tot]
• This helps us to approximate the Vmax. 
• Kcat is the actual turnover number.
• s^-1
•  

• k_cat/K_m
• This is an index of catalytic efficiency.
• Very useful because inside cells enzymes function at very low concentrations.

When the specificity constant approaches near optimal efficiency. It is near 10⁸ to 10⁹ 1/Ms.

• 
• y=mx+b

• y axis = 1/V₀
• x axis = 1/[S]

y intercept= +1/Vmax

x intercept= -1/K_m

Slope= Km/Vmax

It is S vs. I. Both are competing for the same active site on the E. If one binds the other Cannot.

• Km.
• Remember equation for Km:

ES are not allowed to proceed to E+P because they are taken up by I, forming ESI. I has its own binding local.

Both are equally affected.

The inhibitor can either compete for the substrates binding site, or it can bind to it's own binding site, or change directly between the two. It exists both as EI and ESI.

Both are affected but unevenly.

• Apparent Km.
• Moving x intercept, but solid y intercept.
• change in Km, no change in Vmax.

• Vmax and Km by same amount.
• Moving y intercept, AND x intercept by same amounts.
• Change in Vmax, and equal change in Km.
• Parallel lines.

• Both Vmax and Km are changed, but not by same amount.
• The Plot could look like anything.

Rare! They make the RDS even Slower.

Vmax.

• Vmax.
• moving y axis, stable x axis.
• change in Vmax, no change in Km.

Chymotrypsin

Resonance stabilization. 

Step 2, The oxygen in water attacks the carbonyl carbon C=O⁺H as the double bond collapses, forming the -OH group. The Geometry changes from trigonal planar sp2 to tetrahedral sp3.

• 1. Chymotripsin.
• 2. Trypsin.
• 3. Elastase.

• Chymotripsin: Serine.
• Trypsin: Aspartic Acid.
• Elastase: Valine - Threonine.

• Tyr
• Arg
• Ala, Gly

It is Conserved.

Asp-His-Ser

Serine.

• form a hydrogen bond with His, greatly increasing the pKa of Histadines R group, thus increasing the basic nature of His N.
• pKa 6 --- pKa>12

Steal serines Hydrogen, inducing a H bond. making serine a strong nucleophile,

p-NO₂-phenol is released during the fast step. It absorbs light at 400nm. Acetate is released during the slow step, therefore after steady state released. The rise in p-NO₂-phenol before that point is the rate of attachement of S and E to form SE.

1/km decreases, ergo Km increases because an amino terminus is ionized as the pH rises.

Because at low pH the His is protonated, as the pH rises above the pKa of Histadines R group, the residue can perform it's catalytic function.

They are transition state analogues that have already adopted the tetrahedral geometry. They then do not change geometries and stop the mechanism. Bee and Snake venom are two examples of "irreducible complexity".

• 1. Allosteric Control.
• 2. Covalent Modification.
• 3. Protein Processing.

The Hemoglobin nonEnzyme.

• Allosteric regulation, and Km should be replaced with K_1/2.
• This is because the substrate serves as an activator for other protein subunits.

With one the product has no effect on inhibition, whereas the other the product concentration is the inhibitor.

Ubiquination, Phosphorylation. 

YES! totally, that's why we have phosphotases and deubiquitinases.

Communicate, produce cellular responses, modify proteins, Are critical through phosphorylation cascades.

There are examples of where it acts as a dimmer switch. More is better, less is worse. EX. Glycogen Synthase.

Inactive Precursor that must be cleaved to form an active enzyme. Ex. Chymotrypsonogen, or Pro-"enzyme"

For Chymotrypsinogen: Ile has protonated N terminus that forms salt bridge with Asp

An aldose has a terminal O=CCOH. A ketose has a chain O=C.

An AldoHexose.

a Ketohexose.

• Usually Aldoses or Ketoses.
• 3-7 carbons long.
• Mostly D.

Under aqueous conditions.

• 2ⁿ Where N is the number of Stereo Centers.

With the OH group UP.

The OH group is Down.

1:2 alpha:beta

• 5 membered Furanose
• 6 membered Pyranose

Furanose. Specifically 

Chitin: it is a beta chain that has GlcNAc groups coming off of it.

2 sugars held together with an O-glycosidic bond at the 1,4 carbons. May have a reducing end at the hemiacetal (C1) of sugar 2.

It is non-reducing

They store energy in plants.

Energy storage in Animal and Bacterial cells.

Structural, it is found in plants.

It is structural. It Forms on arthropods and yeasts.

alpha 1,4 linkage.

to increase the number of nonreducing ends.

It has beta 1,4 linkage, and it's linear form makes use of hydrogen bonds to strengthen the molecule, and limit the binding of water.

Fibrous proteins, and glycoaminoglycans (GAG).

It is a Heteropolysaccharide, made up of repeating, modified subunits. It has a rod-like helix due to the buildup of (-) charge.

A proteoglycan will have a core protein with a GAG attached. They can either be tethered to the cell membrane, or be cleaved off at a Ser residue.

They provide structural support, and Facilitate cell communication.

It is the name given to describe the 3 classes of glycoconjugates: Proteoglycans, glycoproteins, and glycolipids.

• Glycoproteins,
• Glycolipids.
• They are also smaller than the ECM associated Proteoglycan.

• Modifying Polarity,
• Destination Labels,
• Protein Quality Control.

• Modified Carbohydrate additions to Glycoproteins/lipids, that facilitate cell signaling. 
• -M6P-

• Lectins are the Membrane Bound Sugar Code Receptors. Nearly Infinite combinations.
• They move slowly until they find what will bind to them.

• N or O bonds.
• Asn; Ser are most common.

a Hemeacetal or a Hemeketal. The geometry changes from sp2 to sp3, and a new chiral center is introduced.

An Acetal or a Ketal. If the second alcohol is part of a sugar, than a glycosidic bond can form.

An two sugars that differ only in the arrangement of the hemeacetal or hemeketal are anomers. (Alpha vs. Beta)

Two sugars that differ only in the arrangement of 1 carbon.