Biochemistry 1

Ionic Interactions

(salt bridges) - charge-charge interactions between a positively charged amino acid and a negatively charged amino acid

Proline Turns

*Can be considered as either disrupting 2* structure or as contributing to 3* structure.* -Neither alpha-helices, nor beta-sheets can contain proline internally without disruption of the 2* structure. -However, proline residues are often found at the beginning of alpha-helices and are very common (along with glycine) in the sharp turns at the end of two adjacent rows in a beta-sheet.

Disulfide Bonds

*Covalent bond* between the sulfurs of two cysteine residues

Hydrogen Bonding

*Non-covalent* bond between either backbone atoms (N-H or C=O) or side chains (amine groups, carboxyl groups, alcohol groups)

What aspect of a protein is primarily responsible the manner in which it folds?

*The primary sequence of a protein is primarily responsible for how it folds.* -There is evidence for this in the fact that simple proteins fold spontaneously without chaperone proteins. -Also, as peptides are exiting ribosomes, they immediately begin folding. This makes sense if you think about it: certain amino acids are found in certain secondary structures, and some groups of amino acids found together will almost always fold in the same way. -Mutations in key amino acids can completely destroy secondary and tertiary structure, while other mutations may alter only segments of folding.

Protein Hydrolysis:

*Trypsin and chymotrypsin cleave proteins on the CARBOXYL SIDE of specific amino acid residues:

What determines chemistry and folding of Proteins?

-*R Groups DETERMINE Chemistry* -Amino acid-R groups largely DETERMINE the chemistry of the amino acid, and the combination of *-R groups in a protein almost exclusively DETERMINES its chemistry and folding pattern*

Protein Denaturing Agents

-Acid -Heat -Urea -Mercaptoethanol

Enzymes vs. Catalysts

-Both increase the rate of reaction by lowering activation energy -Neither catalysts nor enzymes are consumed during a reaction; both can be recycled and used again. -Enzymes, however, are organic molecules, while catalysts can be inorganic molecules. -Enzymes are highly specific for a specific substrate or group of substrates, while catalysts can be more universal.

Six Molecular Interactions that contribute to Tertiary Protein Structure

-Hydrogen bonding -Disulfide bonding -Hydrophobic/Hydrophilic Interactions -ionic Interactions -Van der Walls Forces -Proline Turns

Structural Proteins (Be able to recognize)

-actin (thin filaments, microfilaments), -tubulin (microtubules), -keratin (hair and nails, intermediate filaments), -elastin (connective tissue, extracellular matrix).

Motor Proteins (Be able to recognize)

-myosin (power stroke, cellular transport), -kinesins and dyneins (vesicles, cellular transport, cell division, cilia, flagella)

Zwitterion

A dipolar version of an amino acid wherein positively and negatively charged functional groups cancel one another out, resulting in a neutral ion. -A zwitterion has both positive and negative charge. -Free amino acids will exist as zwitterions at neutral pH because both the amine group and the carboxyl group will be deprotonated (giving the amine group a positive charge and the carboxyl group a negative charge). -With the exception of amino acids that have charged -R groups (Asp, Glu, Lys, Arg, His), ALL of the amino acids exist as Zwitterions at a pH of 7.4. This can be very confusing because textbooks rarely draw them this way. Most texts draw them in their "non-ionized" form, with -COOH and -NH2 groups. That combination does not exist at physiological pH,oratANYpH!BelowapHofabout9 the amine group will be protonated: -NH3+. Above a pH of 9 the amine group will be - NH2 (as shown in most texts), but at that very high pH the carboxyl group will have long ago been deprotonated: -COO- (pH ~ 2). -The zwitterion itself is neutral.

Isoelectric Focusing (separation of proteins by isoelectric point)

A gel is created with stable pH gradient. A protein in a region of the gel with a pH lower than its isoelectric point will be positively charged (because it will be fully protonated) and so will move toward the negative cathode. -A protein in a region with a pH higher than its isoelectric point will be negatively charged (because it will be fully unprotonated) and so will move toward the positive anode. -As the protein moves through increasing pH in the gel, the protein's charge will decrease until it reaches the pH of its pI, at which point it will become neutral. -At this point the protein will cease to move through the gel, because it has no charge and so has no pull toward either electrode. -This causes proteins to form very sharp bands at the pH equal to each protein's pI.

Salvation Layer

A layer of water that surrounds a dissolved protein. -The water molecules in this layer interact closely with each other and with the protein's surface. -The water in the hydration layer is more ordered that the bulk water in the general area and is considered not to participate with the bulk (a.k.a., unstructured) water when considering colligative properties.

Substrate

A molecule that is acted upon by an enzyme. A substrate could be a small molecule, a protein, a lipid, DNA, etc. The key here is that a substrate is a molecule that is converted to a product by an enzyme.

Fischer Projection

A representation of a three-dimensional molecule drawn in two dimensions. -A tetrahedral carbon is represented as two crossed lines, and the groups attached to that carbon are displayed. -The horizontal line is extending "out" of the paper, toward you, and the vertical line is behind the plane of the paper, away from you. -Because of this, Fischer projections can be rotated 180° but not 90° or 270°. 180° rotation just flips the molecule over: the same R groups are extending forward or backward.

Protein Folding

A translated protein assumes secondary structure almost instantly, and then folds into its globular or structural tertiary state, driven by the interactions described below.

Lyase

AB->A+B[cleavage or synthesis; NO H2O, NOT hydrolysis]

Ligase

Addition or synthesis of LARGE molecules, usually ATP-dependent (ex DNA Ligase)

Absolute Configuration

All amino acids are designated as either L- or D-, depending on the side on which the amine group is located in a Fischer Projection (L = Left; D = Right). -*All native human amino acids are L-amino acids.* -*L- and D- do NOT correlate directly with R and S* and should be considered as separate stereochemical designations. Most L-amino acids are S, but some L-amino acids are R

Alpha-carbon Stereocenter

All human amino acids, except one, are chiral at the carbon because the carbon contains four different substituents: an -R group, a hydrogen, a carboxylic acid, and an amine.

Secondary Protein Structure

Alpha Helices and Beta Sheets - helix coils and beta sheets result in polymers that will occupy different volumes per residue

Proteins

Amino acid polymers; amino acids are often called *residues*

Primary Protein Structure

Amino acid sequence

Immune System Proteins ( Be able to recognize)

Antigens, antibodies

Trypsin

Arginine, Lysine

Quaternary Protein Structure

Association of multiple folded proteins into a multi-subunit complex.

Proline Turns

Because of proline's unusual cyclical shape, introducing a proline into an alpha helix or beta sheet will cause a kink. -Proline turns are also found at the end of most strands involved in beta sheets. -The sharp turn helps the chain redirect in such a way that the next segment is running antiparallel to the previous segment in the sheet formation.

Important

Charged side chains will be found on the surface of globular proteins if they are NOT paired with a complementary molecule. -However, they CAN be found inside the hydrophobic core if they are paired up with a complementary side chain of opposite charge. A similar complementarity exists between acid and base side chains because they can undergo an acid-base neutralization reaction. Finally, none of these rules of thumb are absolutes. -One will occasionally find hydrophobic residues on the surface (i.e., proline is relatively common), but the majority of hydrophobic -R groups will be internal and the majority of hydrophilic -R groups will be on the surface: This is a perfectly safe generalization for the MCAT

Hemoglobin = Classic example of quaternary structure.

Consists of four protein chains, two alpha subunits and two beta subunits. -Each subunit contains one heme capable of binding one O2 molecule. -*Positive Cooperativity = Ligand affinity increases with the binding of each subsequent ligand.* -In the case of hemoglobin, affinity for the first oxygen is relatively low, but increases for the second, third, and fourth oxygen to bind. This affinity remains in effect during offloading of oxygen at the tissues. -Therefore, the first oxygen (highest cooperative affinity) dissociates at the slowest rate, but each subsequent oxygen is released more easily.

D and L Amino Acids

D - and L- amino acids are mirror images of one another, and they are not identical compounds. Think of your left and right hands. -They are mirror images, but you cannot superimpose one upon the other because they are arranged in a fundamentally different way. L - amino acids are predominant in nature, although a few D - amino acids are used by some bacteria. -By convention, if the carboxylic acid group in a fisher projection is placed at the top and the -R group is placed at the bottom, then L-amino acids will have the amine group on the left and D- amino acids will have the amine group on the right. This is ONLY true if the fisher projection is oriented exactly as described with the -COOH at the top.

Double Bond character and Rotation

Double bond character = RIGID peptide bond with limited rotation. -*limited rotation at the peptide bond!!!*

Essential Amino Acids

ESSENTIAL = Your body cannot synthesize it, *you must ingest it*

Amino Acid Acidic Protons

Each amino acid has a minimum of two acidic protons: -COOH and -NH3+ -Some amino acids (discussed below) have acidic side chains, and therefore three acidic protons. -Per the above statements, each amino acid has either two or three pKa values. -The amino acid acts as a buffer when the pH is near the pKa of one of the acidic protons

MNEMONIC

Enzymes help reactions *O*ver *T*he *HILL* (i.e., the Energy of Activation)

How do enzymes affect each of the following? a) reaction rate, b) energy of activation, c) equilibrium, d) Keq, e) yield, and f) percent yield.

Enzymes increase reaction rate, lower activation energy, and do NOT affect equilibrium, Keq, yield, or percent yield. -However, without an enzyme, it could take years, even centuries or millennia, for a reaction to reach equilibrium and thus reach the yield that could be achieved in seconds with the enzyme present.

Entropy and Protein Folding

Even when water interacts with a dissolved polar solute, this interaction is less entropically favorable that those same water molecules interacting with only other water molecules. -However, the driving thermodynamic force that favors protein folding results from the fact that non-polar regions require a much GREATER ordering of water molecules to accomplish solvation. -Therefore, transitioning from solvation of non-polar regions to solvation of a mostly polar or charged globular protein surface, represents a net increase in entropy. -In fact, it is enough to overcome the decreased entropy associated with the protein being in a folded rather than an unfolded state. This favorable increase in entropy is a major contributor to the overall conformational stability of the folded protein. -there is less organization of water molecules when non-polar molecules fold and polar molecules are exposed (higher entropy and more disordered bulk water -When you put a nonpolar molecule in water, the water molecules around that nonpolar surface become much more ordered (organized) than in the bulk liquid. These water molecules, therefore, become "ice-like" -- highly organized -- in an effort to maximize their hydrogen bonds (and minimize the unfavorable effects of disrupting the hydrogen bonds to the water molecules in order to interact with the nonpolar surface). The "ice-like" structure of the water molecules is not simply one layer thick because the order in the first layer is propagated to surrounding layers. That means that everywhere there is a nonpolar side chain, there is a mini iceberg surrounding it. We have already learned that the entropy of ice is lower than the entropy of water. The entropy of water surrounding a nonpolar surface is lower than the entropy of "bulk water". If the protein can bring the hydrophobic side chains together, then the water molecules surrounding the nonpolar side chains are released into bulk water, which, like ice melting, results in increased disorder

Salt Bridges

Formed when acidic and basic -R groups undergo a *neutralization reaction resulting in a salt.*

Enzyme-Substrate Complex

Formed when the substrate is bound in the active site. Once the enzyme-substrate complex is formed, the substrate will be converted to product (going through the transition state first). This is represented by the basic kinetics formula: E+S ↔ ES--> EP↔E+P

Strecker Synthesis

Forms amino acid from aldehyde with desired r group for the a.a. https://www.youtube.com/watch?v=_pXRH6h_vJw&feature=youtu.be&list=PL_uKI3obn00apPhD2qtTUl1W-I1NqKs4Q Forms racemic mixture (nitrile attacks from both sides) incoming ammonia-> amine forms in place of carbonyl -> alpha amine nitrile attacks imine -> carboxylic acid forms with acid (ammonia leaving group)

Molten/Denatured

Full unfolded

Globule State

Fully Folded

Tertiary Protein Structure

Geometric, *three-dimensional folding of the alpha helices, beta sheets, and other moieties* to form a functional globular or structural protein.

Draw a titration curve for the titration of a solution of phenylalanine with sodium hydroxide. Label the following: half-equivalence point, equivalence point, end point, pI, and buffer region (Hint: Some terms may apply more than once). Describe the relative concentrations of each species at each of the above-stated points along the curve. Draw a similar titration curve for aspartic acid titrated with sodium hydroxide. In what ways does this titration curve differ?

Half-equivalence point and buffer region: concentration of NaOH is much lower than phenylalanine; Equivalence point and pI: concentration of NaOH is equal to phenylalanine; End point: concentration of NaOH is much higher than phenylalanine. Aspartic acid has a double curve because the side chain is charged. Because of this, as the pH rises due to the OH- in solution (from the dissociation of NaOH), two different equivalence points are reached, as the two acid groups are deprotonated. The two points are at different pH values because they have different pKa values.

Hydrogen Bonds

Hydrogen bonding between -R groups also *encourages folding and stabilizes the folded protein.*

Beta Sheets

Hydrogen bonding between ALL of the carbonyl oxygens in one row and the amide hydrogens in the adjacent row. - ALL residues involved in hydrogen bonding! -R groups are directed perpendicular to the plane of the beta sheet, on both sides. -Beta sheets assume a pleated conformation. This is necessary for the carboxyl and amide moieties to line up properly so that every residue is participating in two hydrogen bonds. -Anti-paralell or paralel -Ex: *Fibroin silk molecule*, the molecule that makes up silk = beta sheets.

Alpha Helices

Hydrogen bonding between the carbonyl oxygens and the amide hydrogens that are exactly FOUR residues apart, *including the residues involved in the hydrogen bond (i.e., A-B-B-A arrangement where A and A share a hydrogen bond).* -Each amino acid forms a hydrogen bond with the fourth amino following it in the chain. -R groups are directed exactly away from the alpha helix cylinder (i.e., perpendicular to a plane tangent to the surface of the alpha helix). -Ex: *Keratin* found in hair and nails = alpha helices.

Hydrolases

Hydrolysis

How will a protein fold?

Hydrophobic -R groups fold INTO the protein core (hydrophobic environment), and hydrophilic -R groups are more common on the surface of the protein (hydrophilic environment).

Hydrophobic Core

Hydrophobic -R groups fold into the interior of a globular protein to escape water. -They often bring some smaller polar groups with them, which interact in a complementary way to stabilize the folded protein further.

Hydrophobic/Hydrophillic Interactions

In soluble proteins, the hydrophobic amino acids will collapse into the protein core. -In membrane proteins, the hydrophilic membranes will be either outside the membrane in the cytoplasm or inside the core of the protein, away from the membrane bilayer, with hydrophobic amino acids located within the membrane bilayer.

Which amino acids are most likely to be part of an enzyme active site where the first step of the catalyzed reaction involves abstraction of a proton from the substrate? What if the first step is protonation of a functional group on the substrate?

In the first case, it is most likely that an amino acid is involved that features a basic side chain. This would be histidine, arginine or lysine. In fact, histidine in particular, is frequently a part of enzyme active sites for this very reason. -In the second case, the active site amino acids will need to hydrogen bond with the atom losing the proton. The amino acids will be donating the hydrogen to the hydrogen bond (since the substrate is losing its proton). Likely amino acids are lysine and arginine, because the amine groups can readily hydrogen bond with the substrate which is now likely negatively charged (due to losing a proton). By contrast, if the first step were protonation we would be looking for amino acids with acidic side chains, such as glutamate or aspartate.

Electrostatic Interactions

Interactions between charged -R groups both *encourage the act of folding itself, and stabilize the protein in its folded state.*

While true that L- and D- do not correlate directly with R and S, among all 20 of the common amino acids there are only two cases in which an amino acid cannot be said to be BOTH L- and S. Name the two exceptions and explain why, specifically, they are exceptions.

L and D refer to the glyceraldehyde molecule that the amino acid could theoretically be synthesized from (D-glyceraldehyde or L- glyceraldehyde). -R and S refer to the absolute stereochemistry of the molecule. To designate a molecule as R or S, you must rank each R group of a chiral carbon for priority based on atomic number of the atom connected to the carbon. -The lowest priority R group is pointed away from you. You then consider the priority of the other three R groups. If that priority descends in a clockwise fashion, the molecule is R. If it descends counterclockwise, then the chiral center is S. -For almost all the amino acids, the L designation and the S designation occur together. This makes sense, because if they all could theoretically derive from the same glyceraldehyde molecule, they would all end up with the same stereochemical orientation. -Two amino acids, however, differ from this rule. One is glycine. The tetrahedral carbon of glycine is not a chiral center, because it has two hydrogens attached and so does not have four different R groups. Because it does not have a chiral center, glycine cannot be designated as either R or S. -Cysteine is the other oddity. Because cysteine has a sulfur at the second position in its side chain, the side chain has a higher ranking than other side chains when considering whether to designate it as R or S (due to cysteine's higher atomic mass). This means that L - cysteine will be R - cysteine, because the sulfur has changed which direction the priorities of the R groups turn.

Polypeptide

Longer chain of amino acids

Dynein

Move along microtubules from (+) to (—) end [periphery to center of the cell; nerve cell dendrite cell body]

Kinesins

Move along microtubules from (—) to (+) end [center of cell to periphery; nerve cell body dendrite]

Enzymes

PROTEINS -*Biological catalysts* -*organic molecules* - increase the rate of reaction by lowering activation energy -not consumed in a reaction, can be recycled and used again -Enzymes are highly specific for a specific substrate or group of substrates, -The most notable difference is that, as proteins, enzymes are far more sensitive than inorganic catalysts to environmental conditions such as temperature and pH

Molten Globule

Partially Folded

Peptides are Written, Read, AND Synthesized from ____-terminus -> ___-terminus

Peptides are Written, Read, AND Synthesized from N-terminus -> C-terminus Think of it as N always attacks C...

Chymotrypsin

Phenylalanine, Tryptophan Tyrosine ALL ARROMATIC AMINO ACIDS

The Lock and Key Model of Enzyme Specificity

Predicts that the active site of an empty enzyme is an exact fit for its substrate; the substrate is the key, and the enzyme active site is the lock. -*incorrectly emphasizes that the stabilization of reactants serves to increase reaction rate* -This model is not favored by scientists because it predicts a very rigid, inflexible active site. -*Energetically, this would be unfavorable, and sterically for many enzymes this would be unlikely or impossible, based on where the active site is located*. -While this model is unlikely to be correct for most enzymes, there are a few for which the energy profiles of binding, as well as their 3D structures, indicate that the active site is more rigid than most enzymes.

Induced Fit Theory of Enzyme Specificity

Predicts that the active site's empty structure is not an exact fit for the substrate, and may be rather nondescript. -*emphasizes a stabilized transition state, or the lowering of activation energy, serves to increase reaction rate.* -As the substrate begins binding the pocket, small but specific conformational changes occur, such that the final shape and charge characteristics of the active site are not in place until the substrate is completely bound. -This is the favored theory: induced fit means that as the substrate binds, the affinity for the substrate increases. -The resulting conformational changes will induce a higher affinity for the transition state, stabilizing it and lowering activation energy.

Order of Deprotonation

Proceeding from acidic to basic (low to high pH): 1) -COOH Group pKa ~ 2 2) -R Group, ACIDIC pKa ~4 [Asp=3.7;Glu=4.5] 3) -R Group, His pKa ~ 6 4) -NH3+ Group pKa ~ 9 5) -R Group, BASIC pKa ~ 11-12 [Lys = 10.7; Arg = 12]

Proteins with low Hydrophobiciy

Proteins with low hydrophobicity *do not fold into a stable structure*, but can retain function (e.g., *Intrinsically Disordered Proteins*).

Oxidoreductases

REDOX reactions

Peptide Bond Formation

Reaction Type: Dehydration Synthesis and Acyl Substitution -The amine group nitrogen *(nucleophile)* from the NEW amino acid attacks the carbonyl carbon *(electrophile)* on the C-TERMINUS of the growing peptide chain (aided by the enzymatic function of the ribosome).

Isomerase

Rearrangements

Peptide Bond Resonance

Resonance between the pi electrons of the C=O bond, and the nitrogen lone pair of the C-N bond, yield two resonance structures for any peptide bond. The actual structure is a hybrid of the two, and therefore: *BOTH the C=O bond and the C-N bond in a peptide bond have DOUBLE BOND character*.

Separating Proteins by Gel Electrophoresis

Separating proteins by electrophoresis will separate proteins based on size. -To perform electrophoresis, proteins are placed in a solution with a detergent to denature them and to coat them uniformly with a negative charge. This gives proteins a uniform charge to mass ratio. -*Proteins are then run through a gel of polyacrylamide, which will slow down the migration of larger proteins more than smaller ones*. -The gel is run from the *negative to the positive* electrode, so the proteins are pulled toward the positive pole due to the negative charge from the detergent. The smallest proteins will run furthest into the gels, while the largest proteins will stay near the top.

Myoglobin

Single Unit protein Does not exhibit cooperatively for O2 (only one binding site) Higher affinity for O2

Stabilizing Non-polar Substrates

Stabilized by alanine, glycine, valine, leucine, isoleucine, proline, methionine, phenylalanine, and tryptophan, via hydrophobic interactions.

Stabilizing Positively Charged Substrates

Stabilized by aspartic acid, glutamate, asparagine, and glutamine, via positive-negative charge interactions, -and via hydrogen bonding with the carboxyl group of asparagine and glutamine.

Stabilizing Negatively Charged Substrates

Stabilized by lysine, arginine, serine, threonine, tyrosine, and asparagine, via positive-negative charge interactions, -and via hydrogen bonding with the alcohol group of serine, and threonine, or with the amine group of tyrosine and asparagine.

Will a substrate bind an active site?

The answer depends on the existence of complementary charges on the -R groups, and/or the hydrophilicity or hydrophobicity of the -R groups.

To which acid-base titration term is the isoelectric point most similar? a) half-equivalence point, b) equivalence point, c) end point, or d) buffer region? Why?

The isoelectric point is most similar to the equivalence point in acid-base titration. In acid-base titration, the equivalence point is the point at which all of the starting solute is neutralized by the titrant. -At that point the acid and the base are present in equal quantities. -This is similar to the isoelectric point, because in both cases the acid and the base are both neutralized at that specific pH, rendering a net charge of zero.

Hydrophilic Surface

The majority of the -R groups on the *surface of a globular protein are either polar or charged.*

Isoelectric Point

The pH at which a molecule carries no net charge. For amino acids and other organic molecules, the molecule is often in the form of a zwitterion. -For molecules that have two pKas, the equation for pI is: pI = (pKa1 + pKa2)/2. -At pH lower than the pI, the molecule will have a net positive charge. - At a pH higher than the pI, the molecule will have a net negative charge. This can be utilized to separate molecules based on their pIs by varying the pH in a gel.

Active Site

The part of an enzyme where the substrate is converted to product. -It is typically a small port or pocket that will hold only that enzyme's *highly-specific* substrate. -There are often cofactors associated with the active site, such as metal ions or small molecules that assist in the catalysis of the enzyme. The amino acids that form the active site have specific properties associated with both the type of substrate and the type of reaction being catalyzed (as discussed in questions 8 and 9). -The active site likely changes conformation as the substrate binds, as described by the induced fit model of enzyme kinetics.

Reaction Mechanisms in the Enzyme Pocket

They are entirely a function of the chemistry of the -R groups found in that pocket. You can usually predict accurately the amino acids present in a protein ligand or in an enzyme active site, just by knowing how the protein is functioning

Transferases

Transfer of a functional group (e.g.,kinases,aminotransferases)

Disulfide Bonds

Two oxidized cysteine residues form a disulfide (R-S-S-R) bond. -*This is the strongest type of protein folding interaction.* -Disulfide bonds between keratin alpha helices are what make hair more or less curly.

Proline and secondary Structures

Usually the first residue at the very end of an alpha helix, but rarely found inside the helix because it introduces a KINK/TURN. -This same KINK/TURN is desirable at the end of beta-sheets because the chain must make a 180 degree turn to align as a neighboring row in the beta sheet.

Van der Walls Forces

Van der Waals forces are due to instantaneous dipoles -intermolecular forces that repel atoms away from each other *(steric hindrance)*

Oligopeptide

Very small chain of amino acids

Amino Acids are ___________

WEAK ACIDS - amino acids exhibit the same general acid-base functionality covered in the General Chemistry 2 chapter.

When you see PROTEIN or ENZYME THINK

What amino acids are present and what is the chemistry of their -R groups?

Non-essential Amino Acids

Your body can synthesize the amino acid on its own

How do each of the following affect reaction rate for an enzyme-catalyzed reaction? a) pH, b) temperature, c) substrate concentration and d) enzyme concentration. Draw a graph of RXN rate vs. each of the variables listed above.

a) All enzymes have an optimal pH at which enzyme activity is highest. For most enzymes this is around 7, but the optimum pH can vary based on typical pH for that enzyme's environment. Pepsin, for example, has a pH optimum of about 2 (the normal pH of the stomach). Enzymes in lysosomes will also prefer a lower pH, as will the enzymes of acidophiles. Whatever the optimum is, movement in either direction causes a rapid decrease in rate because changes in pH will affect the hydrogen bonding of the enzyme itself, possibly altering the structure, and will likely disrupt the enzyme-substrate complex. b) Mildly increasing temperature will increase the rate of an enzyme catalyzed reaction. However, increasing the temperature too much will denature the enzyme, causing the reaction rate to drop precipitously. c) At low substrate concentrations, the reaction rate will increase rapidly. As more and more substrate is added, the rate increase will drop off, as described in question 23. d) Enzyme concentration shows a "saturation curve" similar to that for substrate concentration and similar logic applies. Adding enzyme when enzyme concentration is low will increase the rate, because there is plenty of substrate available for the newly added enzyme molecules to act upon. As saturation levels are reached, the rate increase will drop off because enzymes are less and less likely to encounter a substrate molecule.

Binding Proteins (Be able to recognize)

hemoglobin, calmodulin, troponin, tropomyosin, histones, transcription factors, cell adhesion molecules

Catalysts

increase the rate of reaction by lowering activation energy -not consumed in a reaction, can be recycled and used again -catalysts can be inorganic molecules. -while catalysts can be more universal (not as specific)

Estimating Isoelectric Point: acidic, basic and neutral amino acids

pI neutral = average of pKa-amine group and pKa-carboxyl group. pI acidic = average of pKa-acidic R group and pKa-carboxyl group. pI basic = average of pKa-amine group and pKa-basic R group.

Stabilizing Polar Substrates

stabilized by asparagine, glutamine, aspartic acid, glutamic acid, lysine, and arginine, via dipole interactions -and via hydrogen bonding with any amines or acid groups.

Hydrophobic effect

tendency of nonpolar side chains to become buried because that leads to increased entropy of water. *This effect is a major driving force for protein folding.*