Biochem 1

Nomenclature rules for sugars

"-ose" ending is given to all sugars. • "deoxy-" prefix is used if the normal location of an -OH group is replaced with hydrogen. • Aldose vs. Ketose (aldehyde vs. ketone)

feedback inhibition

(a.k.a., Negative Feedback): A specific type of non-competitive or allosteric inhibition that applies to multi-step reactions, synthetic pathways, or cascades. One of the products of a reaction later in the chain acts as an inhibitor for one of the enzymes earlier in the chain. see page 319 for picture

triacylglycerols

(a.k.a., triglycerides) • Glycerol backbone (HOCH2CHOHCH2OH) with three fatty acids attached via ester linkages.

Allosteric enzymes

- Enzymes whose activity is influenced by the reversible, non-covalent binding of another molecule. This could be a second subunit of the same enzyme, or it could be an activating or deactivating molecule. Threonine deaminase is an allosteric enzyme. It is inhibited by isoleucine, and it has two binding sites for it, one low affinity and one high affinity. When isoleucine binds the high affinity site, the binding affinity for the low affinity site increases. When isoleucine binds the low affinity site, the enzyme is deactivated. So enzyme activity is affected by non-covalent binding of isoleucine, initially by altering the binding affinity in the inhibition site, and then by actually being inhibited by the inhibitor.

X-int of linewaver berk plot:

-1/Km

What steps are necessary to cause a simple denatured protein to re-fold? Will this process work, unaided, for all proteins?

. It is often not possible to re-fold unfolded proteins. In cases where you can, proteins have been slowly denatured using a mild denaturant, something that will break hydrogen bonds and disulfide bonds but not other covalent bonds. When denaturing a protein that you want to re-fold, you want to denature slowly. Too quickly or too harshly and irreversible denaturing will occur, such as collapse of all hydrophobic amino acids into the center of the protein. To refold a denatured protein, you want to slowly remove the denaturant from solution. As you slowly wash away the denaturant, secondary structure will start to return, followed by tertiary and quaternary. This will not work with proteins that have been heat denatured, as this often disrupts hydrophobic interactions to the point that all hydrophobic residues collapse together. This will create hydrophobic interactions so strong that it cannot be unfolded. Other types of denaturation that are difficult or impossible to reverse: proteins that are subject to extremes in pH or harsh denaturants that may dissolve covalent bonds. If the first step of the reaction involves protonating the substrate, the active site amino acids will need to hydrogen bond with the atom gaining the proton. In this case, the amino acids will be accepting the hydrogen in the hydrogen bond (since the substrate is gaining its proton). Likely amino acids are aspartic acid and glutamic acid, since the carboxylic acid groups can readily bond with the new proton.

Y-int of lineweaver berk plot:

1/Vmax

each AA has minimum of how many acidic protons

2. 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

Diff between pyranose and furanose

6-member ring vs. 5-member ring

Zwitterion

A dipolar version of an amino acid wherein positively and negatively charged functional groups cancel one another out, resulting in a neutral ion.

Lineweaver-Burk Plots

A double-inverse graph of the Reaction Rate (v inverted to 1/v) and substrate concentration ([S] inverted to 1/[S]) graph described above.

cofactors:

A general term for any species required by an enzyme to function; coenzymes and prosthetic groups are both examples of cofactors.

M-M Saturation Curve

A graph of reaction velocity vs. substrate concentration [S]. This graph reveals the relationship between ½vmax and Km, as well as the overall concept of "saturation kinetics."

Solvation 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.

Phosphorylation

A phosphate group is added to a molecule. This is done by a kinase. Often the phosphate group is taken from an ATP molecule, although it can be taken from another molecule, or inorganic phosphate can be used. Phosphorylation functions to activate or inactivate molecules, depending on their particular pathways. For example, the tumor suppressor protein p53 is activated by phosphorylation, while phosphorylation of the src kinase is deactivating. De-phosphorylation is the removal of a phosphate group, and can also serve to activate or inactivate a protein or molecule. Often if a protein is activated by phosphorylation, it is inactivated by de-phosphorylation, and vice versa. De-phosphorylation is carried out by a phosphatase.

Q29. Differentiate between a reducing sugar and a non-reducing sugar

A reducing sugar is one that is capable of reducing another molecule through an oxidation-reduction reaction (the sugar will become oxidized). To be able to participate in a redox reaction, the sugar must have an openchain form that has a free aldehyde group, and so it must be an aldose. Some ketoses are also reducing sugars, if they can isomerize to contain an aldehyde group. However, in that case, it is the aldehyde isomer and not the ketose form that is a reducing sugar. Disaccharides in which one of the subunits can linearize into an aldehyde are also reducing sugars. A non-reducing sugar is one that cannot participate in a redox reaction to reduce another molecule. To recognize a reducing sugar, look for an aldehyde group. The carbon with the double bonded oxygen should have a hydrogen attached in chain form. In ring form, the ring oxygen should be connected to one carbon with an R group attached and one carbon with an OH attached.

Provide a conceptual explanation for: substrate, active site, and enzyme-substrate complex.

A substrate is 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. An active site is 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. The enzyme-substrate complex is 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

Which vitamins are fat soluble and which are water soluble

A, D, E, and K - fat soluble all the rest - water soluble

AA with hydrophobic side chains

A, V, I, L, M, F, Y, W

are AA bases/acids - strong/weak?

AA are weak acids

Protein structure: primary

AA sequence

enzymes: lyases

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

alpha-glucose vs. beta-glucose =

ANOMERS • SAME molecule; different stereochemistry at the anomeric carbon

Protein Denaturing Agents:

Acid Heat Urea Mercaptoethanol

enzymes: ligases

Addition or synthesis of LARGE molecules, usually ATP-dependent (e.g., DNA Ligase)

AA characteristics: 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 (e.g., cysteine).

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

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. SEE Q16 answer for graphs

amino acid characteristics: alpha-carbon stereocenter

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

steroids - see q32

All steroids have 4 rings. see q31

What determines the chemistry in an AA?

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.

Q33. Which of the above lipids (fatty acids, triglycerides, phospholipids, steroids, terpenes, sphingolipids, waxes, glycolipids, and prostaglandins) are amphipathic?

Amphipathic molecules have both hydrophilic and hydrophobic properties (think of amphibians that live in both water and on land). They have both polar and non-polar structures. Amphipathic lipids are found in lipid bilayers, with the polar head groups on the surface and the non-polar tails within the membrane. Of the lipids drawn above, the following are amphipathic: fatty acids (carboxylic acid is polar), phospholipids (phospho group is polar), sphingolipids (oxygen and nitrogen are polar), and glycolipids (oxygens of the sugar are polar). Triacylglycerols, steroids, terpenes, and waxes are hydrophobic and not amphipathic.

Zymogen

An inactive enzyme precursor. Prothrombin is a zymogen. It is an inactive enzyme precursor that isactivated by prothrombinase, which converts prothrombin to thrombin, a vital enzyme in the blood coagulation cascade. Zymogens are incredibly important in the body. They are often the precursors for enzymes that are needed quickly but that would be detrimental if active all the time. Others include chymotrypsinogen and trypsinogen, precursors to proteases, and pro-caspaces, which are essential to the apoptosis pathway. You don't want free, activated proteases in a cell, because they would degrade random proteins, and you definitely don't want the apoptosis pathway activated randomly. However, with zymogens, cells essentially have these enzymes "on call." They are already synthesized and ready to use, they just need to be activated when needed.

What are anti-oxidants?

Anti-oxidants inhibit the oxidation of other molecules. They do this by being oxidized themselves.

Positively charged side chain amino acids - write 3 letter codes, 1 letter codes, and structures

Arg R, His H, Lys K

negatively charged side chain amino acids - write 3 letter codes, 1 letter codes, and structures

Aspartic acid asp(D), Glutamic Acid glu(E)

quaternary protein structure:

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

Describe the differences between a catalyst and an enzyme.

Both catalysts and enzymes increase the rate of a reaction by lowering the activation energy. Enzymes, however, are organic molecules, while catalysts can be inorganic molecules. Neither catalysts nor enzymes are consumed during a reaction; both can be recycled and used again. Enzymes are highly specific for a specific substrate or group of substrates, while catalysts can be more universal. Catalysts are often just metal ions or other small molecules that activate the substrate. Reactions using enzymes are millions of times faster than without, while reactions with catalysts are typically not increased by the same magnitude. All enzymes are catalysts, but not all catalysts are enzymes.

Special AA

C, U, G, P

KNOW THE FORMULA FOR HOW BLOOD PH IS REGULATED

CO2 + H2O ⇄ H2CO3 ⇄ H+ + HCO3-

Protein folding: 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.

Chelating agent

Chelating agents are chemical compounds whose structures permit the attachment of their two or more donor atoms (or sites) to the same metal ion simultaneously and produce one or more rings.

what are coenzymes? how are they diff than prosthetic groups

Coenzymes are organic molecules that are required by an enzyme to function, but are not usually covalently bound. They are differentiated from prosthetic groups because they are loosely bound to the enzyme, whereas prosthetic groups are tightly bound (usually, but not universally, via a covalent bond).

What form are sugars found in humans? L or D?

D-sugars = all human body sugars; L-sugars do NOT occur naturally in humans. Love my Dsert

see q7

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?

Difference between essential and non-essential AA

ESSENTIAL = Your body cannot synthesize this amino acid. You must ingest it. ▪ NON-ESSENTIAL = Your body can synthesize this amino acid on its own.

how many H+ does NADH push through membrane? What about FADH2?

Each pair of electrons from NADH result in translocation of 10 protons while FADH2 electrons result in translocation of 6 protons.

Carbohydrates formulas

Empirical formula of all monosaccharides = (CH2O)n ; polysaccharides = Cn(H2O)x

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 than 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.

What is better for long-term storage? Carbs or fats?

Fats

Protein folding: salt bridges

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

Tertiary

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

Know the difference between these glucose polysaccharides: -glycogen -starch -cellulose

Glycogen: Branched, alpha-linked glucose polymer, used for energy storage in animals Starch: Branched, alpha-linked glucose polymer, used for energy storage in plants Cellulose: beta-linked glucose polymer, used for energy storage in plants, indigestible to animals without help from symbiotic bacteria.

where does glycolysis/TCA cycle happen?

Glycolysis occurs in the cytoplasm and the products from that pathway will be the final electron acceptors to produce lactic acid. Because this occurs in the cytoplasm rather than the mitochondria, Answer C is correct. When oxygen is present, the products of glycolysis are trafficked to the mitochondria for oxidative phosphorylation

What are some ROS?

H202, oxygen radicals. check this. may be more

hemoglobin structure

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

Interactions that contribute to tertiary protein structure

Hydrogen bonding - non-covalent bond between either backbone atoms (N-H or C=O) or side chains (amine groups, carboxyl groups, alcohol groups) 2. Disulfide bonds - covalent bond between the sulfurs of two cysteine residues 3. Hydrophobic/hydrophilic 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. 4. Ionic interactions (salt bridges) - charge-charge interactions between a positively charged amino acid and a negatively charged amino acid 5. Van der Walls forces - intermolecular forces that repel atoms away from each other (steric hindrance) 6. 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 involves 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

Protein folding: hydrogen bonds

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

Protein folding: 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.

What determines how a protein will 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). Proteins with low hydrophobicity do not fold into a stable structure, but can retain function (e.g., Intrinsically Disordered Proteins).

Irreversible inhibition

Inhibitor binds covalently to the enzyme and/or the active site, disabling the enzyme for either a prolonged period of time, or permanently. IT WILL INHIBIT THE ENZYME COMPLETELY!! NO RXN!

Protein folding: Electrostatic interactions

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

How carbohydrate rings close: the reaction

Intramolecular Nucleophilic Substitution: The -OH group on the chiral carbon that is furthest from the carbonyl carbon (the same one used to determine D/L) acts as the nucleophile, attacking the carbonyl carbon (electrophile). The carbonyl oxygen is protonated to form a hydroxyl group.

Easier to overdose on fat-soluble or water-soluble vitamins?

It is much easier to overdose on fat soluble vitamins than water soluble vitamins. Ingesting large amounts of water soluble vitamins is generally not harmful because they will quickly be dissolved and excreted through the urine. Fat soluble vitamins, however, will be stored in fat tissue and membranes. Ingesting large amounts of these vitamins can lead to an overdose because disposal of the excess is more difficult.

where can and can't ketones be used as fuel?

Ketone bodies can be used as fuel in the brain, the heart, and muscles (so Answers A, C, and D are incorrect), but they cannot be used in the liver because it lacks the necessary enzymes to convert ketone bodies to ATP. This is because ketone bodies are produced in the liver when blood glucose is low.

Kinesins and Dyneins

Kinesins = Move along microtubules from (—) to (+) end [center of cell to periphery; nerve cell body ---> dendrite] Dyneins = Move along microtubules from (+) to (—) end [periphery to center of the cell; nerve cell dendrite ---> cell body] K move out. D moves in

At 1/2Vmax, Km=?

Km = [S] @ ½Vmax

distinguishing D and L for sugars

L = the furthest -OH group from the carbonyl is always to the LEFT in a Fischer projection • D = the furthest -OH group from the carbonyl is always to the RIGHT in a Fischer projection. SAME bond-to-bond connectivity, but DIFFERENT stereochemistry at all chiral centers

keto-enol tautamerization of monosaccharides

Like other ketones and aldehydes, sugars can alternate between keto and enol forms.

Prostaglandins

Lipid mediators that have autocrine (self-target) and paracrine (target = cell in immediate vicinity) functions throughout the body. • UNLIKE endocrine hormones: Produced and released throughout the body; NOT only in specialized glands. Act locally, rather than traveling to a distant target via the bloodstream Based on arachidonic acid

definition of lipids

Lipids are a class of biomolecules with a rather inexact definition. Many sources define the term "lipid" by giving a list of the biomolecules classified as such. These include fats, oils, waxes, sterols, fat-soluble vitamins, glycerides (mono-, di-, and tri-), phospholipids, and terpenes. For the MCAT, focus on the two major identifying characteristics of lipids: 1) Lipids are biomolecules 2) Lipids are hydrophobic.

which direction are proteins made?

N to C

Coenzymes:

Non-protein species NOT permanently attached to the enzyme but required by the enzyme to function.

Prosthetic groups

Non-protein species that ARE permanently attached to the enzyme and are required by the enzyme to function.

peptide conventions:

Peptides are Written, Read, AND Synthesized from N-terminus ----> C-terminus

Phospholipids

Phosphatid = The most basic phospholipid, with two fatty acid moieties and ONLY a phosphate group—which is attached directly to the glycerol backbone. Most phospholipids in biological membranes have other functional groups attached to the phosphate head. You may also see this term as part of a named phospholipid, as in phosphatidylcholine.

What do plants and animals use as their long term energy storage?

Plants: starch (a carbohydrate) Animals: fat

hemoglobin cooperativity

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.

Positive feedback

Positive feedback - the product of a reaction acts as an agonist for the reaction. For example, the product could itself be an activator of the reaction, so that the more product you have in solution, the more likely the reaction will happen. The product could also be part of the synthesis pathway for the substrate, so that the more product you have, the more substrate will be made, increasing the forward reaction. Positive feedback is relatively rare in the human body, but it does exist. In blood coagulation, upon damage to a blood vessel, the glycoprotein FVII is released. An activation cascade of coagulation factors occurs, resulting in prothrombin being activated to thrombin. Thrombin activates FVII, resulting in an increase to the activation cascade, leading to more thrombin. Negative feedback is much more common, and an example was given in question 25.

pKa's for some AA

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] USEFUL BC IT REVEALS ORDER OF DEPROTONATION

Simple protein

Protein that contains only amino acids and no non-protein cofactors or prosthetic groups. If it is a simple protein that is an enzyme, it is called an apoenzyme.

conjugated protein

Protein that is associated with its cofactors, either covalently or via intermolecular attractions. Hemoglobin is a conjugated protein because it contains the nonprotein heme group. If it is a conjugated protein that is an enzyme, together with its cofactors it is called a holoenzyme.

things to know with AA

R group structure • -R group chemistry • -R group hydrophilicity vs. hydrophobicity (polar vs. non-polar) • -R groups with charges (negative = acidic; positive = basic) • -R groups that are aromatic • amino acid names • amino acid three-letter abbreviations • amino acid single-letter abbreviations.

List Polar and Non-polar amino acids

RHKDENSTQ

How polypeptide chains form:

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).

Why is Km significant

Relative measure of an enzyme's affinity for its substrate. The magnitude of Km is INVERSELY proportional to substrate-enzyme binding affinity. The lower the Km, the stronger the binding affinity.

Relationship between freezing point and melting point

Remember that freezing point is the same thing as melting point. It is a "point" at which two different processes both begin: freezing and melting. Freezing is the phase change from liquid to solid while melting is the phase change from solid to liquid. These processes take place at the same temperature

Basic mechanism of g-protein cascade

Researchers know a lot about G-proteins. Keep it simple here and focus on the basic story of a generalized G-protein response. First, a hormone or signal molecule binds to an integral protein on one of its extracellular domains—this protein is called a G-protein-coupled receptor or GPCR. This causes a conformational change that activates a cytosolic domain of that same integral protein. Near the GPCR, or at least along the cytosolic face of the membrane, is a G protein made up of an alpha, beta, and gamma subunit. The alpha subunit binds both GTP and GDP. When GDP is bound, the protein is "off" and when GTP is bound it is "on." Usually, but not always, the activated receptor protein acts as a catalyst for the replacement of GDP by GTP, activating the alpha subunit of the G protein. The activated alpha subunit then separates from the beta and gamma subunits. The activated alpha subunit acts as an agonist for another enzyme, often adenylyl cyclase. Adenylyl cyclase is an enzyme that catalyzes the conversion of ATP to cAMP plus two molecules of inorganic phosphate (ATP cAMP + 2Pi). Cyclic AMP just happens to be an agonist for Protein Kinase A, which phosphorylates proteins—usually enzymes. Many enzymes are turned on or off through being phosphorylated or dephosphorylated. The cascade can be shut down in various ways. Often the beta and gamma subunits re-bind with the alpha subunit, deactivating them. In other cases GPCR is phosphorylated one or more times, which deactivates it. DO NOT MEMORIZE THIS. The MCAT will not test you on names or other specifics. However, it does illustrate how cascades work and having a general familiarity with G protein signaling pathways will be a tremendous help on any passages or questions about G proteins, which have been fairly common.

Peptide bond has resonance?

Resonance between the pi electrons of the C=O bond and the nitrogen lone pair of the C-N bond yields 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 and can't rotate

Competitive inhibition: Reversible? Where/when does inhibitor bind? Does Vmax and or Km change? if so, how?

Reversible. Competitive: Inhibitor binds at the active site; The inhibitor resembles the substrate in shape; the inhibitory effect can be overcome by increasing the concentration of the substrate. • Vmax = NO CHANGE • Km = INCREASES

Non-competitive inhibition: Reversible? Where/when does inhibitor bind? Does Vmax and or Km change? if so, how?

Reversible. Non-Competitive: Inhibitor binds away from the active site and changes the shape of the enzyme. The inhibitor has an equal affinity for both the enzyme-substrate complex (E-S) and the enzyme (E). • Vmax = DECREASES • Km = NO CHANGE A noncompetitive inhibitor interacts with the enzyme at a site other than the active site and the enzyme's function is at least partly compromised regardless of the substrate level; in other words, it will consistently inhibit the reaction EVEN IF the substrate concentration is high. This makes a noncompetitive inhibitor the best option for continuous inhibition

Uncompetitive inhibition: Reversible? Where/when does inhibitor bind? Does Vmax and or Km change? if so, how?

Reversible. Uncompetitive: Inhibitor binds ONLY with the enzyme-substrate complex. • Vmax = DECREASES • Km = DECREASES

Mixed inhibition: Reversible? Where/when does inhibitor bind? Does Vmax and or Km change? if so, how?

Reversible. Mixed: Inhibitor has unequal affinity for the E-S and the E, favoring one over the other. • Vmax = DECREASES • Km = DECREASES if inhibitor = greater affinity for E-S over E • Km = INCREASES if inhibitor = greater affinity for E over E-S

AA with polar uncharged side chains

S,T,N,Q

Michaelis-Menten: Draw a graph of Reaction Rate vs. [Substrate] and label the axes. Label and describe Vmax. Label and describe Km. Describe the meaning of the term "saturation kinetics" in terms of your graph.

See Q22 answer

protein separation techniques: 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.

Protein Separation Techniques: ▪ Isoelectric Point

Separating proteins by isoelectric point is called isoelectric focusing. 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.

what determines if a substrate will bind in 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.

Saponification

The hydrolysis of an ester (e.g., triglycerides, phospholipids, etc.) Triacylglycerols and phospholipids are both ESTERS. Fatty acids are the only lipids that have a -COOH group. Students often refer to triacylglycerols as "fatty acids attached to glycerol," and many books even call them "fatty acid tails." This has led some students to be confused. Once a fatty acid attaches to glycerol, it is an ester.

isoelectric point

The isoelectric point (pI) is 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. 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.

Protein folding: Hydrophilic Surface:

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

Why would nitrogen be in your urine?

The primary reason nitrogen would be in the urine is because excess proteins are in the urine, perhaps because they are being broken down somewhere in the body. If you have nitrogen in your urine you are likely 1) diabetic (because you cannot get sugar into your cells and thus must break down proteins for energy), 2) starving to death (you cannot get enough food, so you must break down your body's own proteins), 3) are experiencing severe damage to organs, cell lysis, etc., or 4) are on an Atkins diet, eating more protein than your body can process.

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.

what determines reaction mechanisms in the enzyme pocket

These mechanisms 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 (At the very least, you can narrow it down to a few possibilities).

how to do protein hydrolysis:

Trypsin and chymotrypsin cleave proteins on the CARBOXYL SIDE of specific amino acid residues: • Trypsin = arginine, lysine • Chymotrypsin = phenylalanine, tryptophan, tyrosine

Protein folding: 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.

What are lineweaver burk plots used for

Used to calculate Vmax and Km experimentally Used to Identify Enzyme Inhibition: We will cover enzyme inhibition in the following section. Each type of inhibition has a characteristic impact on Km and vmax. Because these two values can be easily calculated from the x- and y-intercepts of a LineweaverBurk plot, the type of enzyme inhibition can be easily deduced. To do so, you must have two trials, one with, and one without, the inhibitor. By comparing these two results you can observe the IMPACT of the inhibitor on Km and vmax, and therefore deduce the type of inhibitor.

M-M Equation: what it gives you

Used to calculate the rate of a reaction at a given concentration of substrate. V = Vmax[S]/(Km + [S])

what's unique about proline and alpha helices?

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.

Diff between vitamins and minerals?

Vitamins are relatively small, organic molecules that are essential nutrients required in small amounts for proper metabolism. Many cofactors and coenzymes are derived from vitamins, such as NAD discussed in the previous question (derived from the vitamin niacin). Humans have lost the ability to synthesize vitamins in sufficient quantities in our bodies, and so we must acquire them through our diet. Water soluble vitamins are the ones most often required for synthesis of cofactors. Fat soluble vitamins are needed for diverse biological functions, such as vitamin A, which is converted to retinal and used as a coenzyme in visual proteins. Other fat soluble vitamins act as antioxidants, aid in maintaining blood pressure, and play a role in blood clotting. Nicotinamide Adenine Dinucleotide (NAD) 2Fe-2S iron-sulfur cluster Minerals inorganic elements or compounds necessary for bone formation (calcium and phosphate), ion gradients (sodium and potassium), oxygen transport (iron-containing heme), muscle contraction (calcium), ATP processing (magnesium), production of stomach acid (chlorine), etc. Minerals are gained through diet and are needed in very small quantities, making them micronutrients.

When you see PROTEIN or ENZYME THINK

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

What is y-intercept on lineweaver burk plots?

Y-Intercept = 1/Vmax

what is a prosthetic group?

a non-protein cofactor that is tightly bound to an enzyme and is necessary for its function. THink: a prosthetic leg isnt like the rest of the body but is attached. a prosthetic group isnt a protein like the enzyme is but is attached and necessary for function. While coenzymes are always organic non-protein molecules, prosthetic groups can be either organic or inorganic

Structural Proteins

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

What are agonists/antagonists?

agonist binds and activates receptor. antagonist binds and deactivates receptor.

what is an allosteric regulator

allosteric effectors are molecules that bind to an enzyme at a site other than the enzyme's active site and regulate its function. THEY BIND NON-COVALENTLY!! enzymes can and do function without allosteric modulators, they just function differently under that regulation (e.g., increased or decreased reaction rate, binding affinity, etc.) THINK OF HEMOGLOBIN

allosteric regulation

allosteric regulation (or allosteric control) is the regulation of an enzyme by binding an effector molecule at a site OTHER THAN the enzyme's active site.

another name for amino acids

another name for residues

Immune System proteins

antigens, antibodies

What constitutes a nucleotide?

any molecule that contains a sugar backbone, a nitrogenous base and a phosphate group. Cyclic AMP, ADP, ATP, GTP, GMP GDP, NADH, FADH2 and the DNA and RNA subunits are all examples.

cytosine guanine. are they aromatic?

are cytosine and guanine aromatic? Yes

Trypsin

arginine, lysine

what are eukaryotic membranes composed of?

carbohydrates, proteins, phospholipids and steroids

Hemiacetals vs. Hemiketals in sugars

cyclical aldehydes vs. cyclical ketones

D sugars compared to their L sugar are?

enantiomers

glucose vs galactose: anomers or epimers?

epimers. DIFFERENT molecules; an example of diastereomers • NOTICE that the enantiomers and anomers have the SAME name (glucose in all of these examples), whereas the epimers have DIFFERENT names (glucose/galactose)

waxes

ester with long hydrocarbon r groups extending from both sides

keratin structure and where found

found in hair and nails = alpha helices.

globule

fully folded

molten

fully unfolded (denatured).

Common monosaccharides to know

glyceraldehyde dihydroxyacetone ribose deoxyribose glucose fructose galactose mannose

• Binding Proteins

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

enzymes: hydrolases

hydrolysis

Two theories of enzyme specificity are: ______and _______ . Which of these two theories has been largely dismissed by scientists? Why has it been dismissed?

induced fit and lock and key. The induced fit model predicts that the active site's empty structure is not an exact fit for the substrate, and may be rather nondescript. 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. The lock and key model 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. 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.

What constitutes tautomerism?

isomers of a compound which differ only in the position of the protons and electrons. The carbon skeleton of the compound is unchanged. A reaction which involves simple proton transfer in an intramolecular fashion is called a tautomerism.

common disaccharides to know

lactose = galactose + glucose (beta-linked) maltose = glucose + glucose a1-4 sucrose = glucose + fructose. GLC a1-b2 FRC

alpha linkage

linked through an oxygen that is on the OPPOSITE SIDE of the plane from the CH2OH group (i.e., trans).

beta linkage

linked through an oxygen that is on the SAME SIDE of the plane as the CH2OH group (i.e., cis).

protein structure: secondary

local 3d configuration of peptide chain (beta sheet or alpha helix)

polypeptide

longer chain of AA

corn rule for amino acids

look down h to alpha c bond. clockwise is l. counterclockwise is d.

polymerization

monosaccharide--->disaccharide--->polysaccharide

Enzyme names

most enzyme names include a clear indication of the enzyme's substrate and the enzyme class. Ex. Galactokinase

Motor proteins

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

how to quickly estimate pI's for AA

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

molten globule

partially folded

chymotrypsin

phenylalanine, tryptophan, tyrosine

Rules for aromaticity

planarity and adherence to the 4n + 2 rule. and sp2 hybridized.

Hemoglobin is what level of structure?

quaternary. Each subunit of a protein is its own amino acid polypeptide.

enzymes: isomerases

rearrangements

enzymes: oxidoreductases

redox reactions

what does anhydrase mean?

removal of water molecule

Beta Sheets

secondary structure. 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.

Alpha helices

secondary structure. 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).

glycolipids

see internet

Lipids to Know for the MCAT: Be generally familiar with each structure, be able to draw it in linebond form, recognize each functional group it contains, and predict where it is likely to be found or used in the human body. THIS INFO IS FOR THE NEXT FEW FLASHCARDS

see other side

MNEMONIC: Enzymes help reactions Over The HILL (i.e., the Energy of Activation)

see page 316

see q 24-26

see q24-26 answers

Draw a mechanism for each of the reactions outlined on the previous page: a) oxidation/sulfur-linkage of two cysteine residues, b) formation of a peptide bond, c) hydrolysis of a peptide bond, d) Strecker Synthesis and e) Gabriel Synthesis. Use real amino acid species and show electron flow wherever possible.

see q9 answers

oligopeptide

small chain of AA

fibroin structure and where found

the molecule that makes up silk = beta sheets.

reduction potential

the potential for that molecule to be reduced

Breaking chemical bonds requires considerable activation energy, which is often the defining parameter affecting the reaction rate

this is why H202 is stable in water. High activation energy.

terpenes - see q32

this pic is isoprene. terpenes are made from connected isoprenes.

enzymes: transferases

transfer of a functional group

What is x-intercept on lineweaver burk plots?

• X-Intercept = -1/Km