Next Step MCAT Super Review: Amino Acids

Next Step MCAT Super Review: Amino Acids Welcome to Super Review! Introduction AA Study Strategies AA Content Review Peptide Bond AA Separation & Purification MCAT Passage What Next? How Can Next Step Help?MCAT Super Review: Amino Acids

Introduction to Super Review Thanks for coming to Next Step Super Review!Before Getting Started Here’s how it works 1. If you have a microphone, make sure itis turned on and easily available. These sessions are meant to be:Problem-focused2. Locate the hand-raise button on thetoolbar on your screen.Specific to your needs (so ask questions!)3. Locate the Question box on the toolbar.Interactive4. Let me know if you’re having anytechnical issues! Today’s focus: review of amino acids This is NOT a lecture! You can benefit most by:Raising your hand and speakingCommenting in the Question/Chat boxParticipating!If on wireless connection: Close any other internet resource-heavy processes Ask other users on network to do same Sit as close to router as possibleMCAT Super Review: Amino Acids

We will have some great free resources and discounts available for you at the endof the presentation. Stick around and give us some feedback on our short survey aswell!nextsteptestprep.com888-530-NEXT

In General: Biochem Study StrategiesA big-picture approach to biochem How is biochem tested on the MCAT? How doyou get the most bang for your buck in termsof studying?Focus on: Principles Physiological function Interconnections with other subject mattero Amino acids & acid-base chemistryo Carbohydrates & stereochemistryo Metabolism & physiologyWhat have your biochem experiences been like?What strategies work for you?MCAT Super Review: Amino Acids

Amino Acid Study StrategiesYou may have heard that amino acids are among the most high-yield MCAT topics! Today, let’s startlearning what you need to know. High-yield topics Chemical properties Electrical charge properties / acid-base behavior Biological location on proteins Biochemical lab techniques (isoelectric focusing, etc.) Abbreviations!MCAT Super Review: Amino Acids

Amino Acid Study StrategiesWhen studying, ask yourself Why does this matter physiologically? Biomolecules: how does AA identityconnect to biological function? What pathways may relate to AAmetabolism? Are there any neurological or endocrineuses for this AA?Do not lose the forest for the trees!MCAT Super Review: Amino AcidsAdapted from quinn.anya under CC BY-SA 2.0

General Structureside chain AAs only differ in their R groups 20 standard AAs α-amino acids Is this structure chiral? Yes, EXCEPT “amino”basicglycine“acid” COOH

Amino Acid Configuration – D or L? Misconception: D R, L S In reality, D/L and R/S are separate systemsL-glyceraldehyde3S2R1L-alanineL-cysteine

Classifications – Polar vs Nonpolarcan’t H-bond Note: classifications are based only on side chains Backbone is always the same! Nonpolar hydrophobicvaline Generally have hydrocarbon R groups Location: interior of globular proteinscan H-bond Polar hydrophilic Includes polar uncharged AND polar charged AAs acidic / basiccharged very polarthreonine

Classifications – Acidic and Basic Acidic side chains contain COOH (-OH, -SH) Basic side chains contain nitrogen and canbecome protonatedamide neutral Lys amine His imidazole Arg guanidinium Be careful: is this a basic side chain?asparagine

Acidic / Basic AAs – Be Careful! Lysine exists in a certain 0.5 M solution in thestate pictured here. Which group(s) on thismolecule can act as bases? (gain a proton) Amines? already protonated!can act as acids Remember: protonation state depends on pHlysine

Aromatic Side Chains10 π electrons 4(2) 2 Phenylalanine Tyrosineconjugated Tryptophan Histidine* (contains an aromatic ring) Conjugation UV light absorptionplanar ring structure

Sulfur-Containing AAs – Why Are They Special? Disulfide linkages crucial part of 3 structureoxidizedmethionine no S-S bondsreduced Cysteine vs cystinecysteine S-S bondsImage adapted from Benjah-bmm27 [Public Domain]

Last But Not Least - ProlineR group What’s unique about this structure? Side chain is connected to α-amino group! Introduces “kinks” in 2 protein structure These “kinks” often found on protein surfaceamino groupα carbon

MCAT Practice1. In a hair “permanent,” hair is relaxed via alkali agentswhich act to reduce the disulfide bonds between keratinproteins. What is the most likely function of thesereagents?A) The agents form new disulfide bonds between Thrresidues.B)The agents form new disulfide bonds between Serresidues.C) The agents break disulfide bonds between Cysresidues.D)The agents break disulfide bonds between Metresidues.MCAT Super Review: Amino Acids

Amino Acids and ChargeZwitterion: form where some groups are charged butoverall charge of molecule is 0pKa pH for a given functional group where half of allmolecules are protonatedGlycine (and many others) arezwitterions at physiological pH10.53 When solution pH pKa: group is deprotonated When solution pH pKa: group is protonated8.952.18MCAT Super Review: Amino Acids

Example: using pKa to predict net chargeAspartic acid has three pKa values: 2.10, 3.86,and 9.82. Which pKa corresponds to which group?-1 At pH 5, net charge 3.86α-2 At pH 11, net charge 2.109.82Image adapted from Sten André [Public Domain]

Isoelectric point (pI) What is it? The pH at which an entire AA or protein isneutral In some ways, like “the pKa of the entiremolecule” When pH pI: AA is negative When pH pI: AA is positiveImage adapted from Benjah-bmm27 [Public Domain]

Isoelectric point: how is it calculated?net charge 2 If AA has two pKas: just average them! If AA has three pKas: average the two mostrelevant For basic AAs, two most basic For acidic AAs, two most acidic Consider lysinenet charge 1Images adapted from NEUROtiker [Public Domain]net charge 1net charge 0

MCAT Practice2. Which chromatography technique would mosteffectively separate Ile from Lys at pH 6.7?3. Which of the following scenarios is most likely toproduce a neutral zwitterion?A) Cation-exchange chromatographyB) Anion-exchange chromatographyC) Size-exchange chromatographyD) Nickel affinity chromatographyA) Alanine at pH 5B) Tyrosine at pH 12C) Lysine at pH 4D) Glycine at pH 1MCAT Super Review: Amino Acids

MCAT Practice4. A professor attempts to purify glycine from a solutionusing anion-exchange chromatography. At which pHwould he observe the largest amount of glycine adheringto the column?A) 1.5B) 6.5C) 8.0D) 10.0MCAT Super Review: Amino Acids

Peptide Bond Forms via nucleophilic attack Nucleophile amino group Nucleophile carbonyl C Peptide bond amide linkageMCAT Super Review: Amino Acids

Primary Protein Structure Linear amino acid sequence Amino acids now termed: residues Typically written from N-terminal to Cterminal Main type of bond found in 1 structure? Covalent? (chemical bond) Hydrogen?Gly-His-LysGHKImage adapted from Ed (Edgar181) [Public Domain]

MCAT Practice5. Due to the planar properties of the peptide bond,proteins can easily assume various organized structures (forexample, beta sheets). All of the following arecharacteristics of the peptide bond EXCEPT:6. Ion-exchange chromatography with a positivelycharged stationary phase is used to separate twopolypeptides. Which amino acid is LEAST likely to befound in the polypeptide that elutes first?A) its rotation is restricted.B) it has multiple resonance forms.C) it frequently breaks and reforms to allowstructural fluidity.D) it exhibits partial double bond character.A) AB) HC) PD) DMCAT Super Review: Amino Acids

MCAT Practice7. Which of the following amino acid sequenceswould incur the greatest entropic penalty if itwere used to replace Tyr-Cys-Met in the surfaceregion of a protein?A) His-Gly-GlyB) Ala-Gly-SerC) Leu-Val-PheD) Met-Thr-Glu8. At pH 1, what will be the net electrical charge onTyr?A) -1B) 0C) 1D) 2MCAT Super Review: Amino Acids

MCAT Practice10. One of the complications in certain forms ofschizophrenia is a loss-of-function mutation to peptidyltransferase. What process is most likely to be halted inthese patients?A) Binding of the mRNA template to the ribosomeB) Construction of the cellular ribosomeC) Construction of the primary structure ofneuroproteinsD) tRNA recognition of mRNA codons.Peptidyl transferase catalyzes peptide bond formationon the ribosome.Enzyme lowers the activation entropy of the reactiondue to positioning the two substrates, ordering waterin the active site, and providing an electrostaticnetwork that stabilizes the reaction intermediates.Any issue related to loss of peptide bonding is our bestanswer.Peptide bonds comprise the primary structure ofproteins.MCAT Super Review: Amino Acids

MCAT Practice11. Which substitution, of those below, is most likelyto cause a change in the tertiary structure of a protein?12. What structural characteristic marks the sidechain of the amino acid N?A) Val to MetB) Lys to LeuC) Ser to ThrD) Asp to GluA) A four-carbon chain attached to an aminethat makes the residue basic overallB) A sulfur atom in the form of a thioetherC) A simple one-carbon groupD) An amideMCAT Super Review: Amino Acids

Isoelectric focusing (IEF): the basicselectrons Separates AAs by pI Setup: electrophoresis on an “immobilized pHgradient” Acts like an electrolytic / galvanic cellnonspontaneousspontaneousImage adapted from Mrbean427 under CC BY-SA 3.0anodecathode

IEF: predicting direction of movementcathode Net positive AAs will move toward theanode Net negative AAs will move toward the Example: pI of glycine 5.97At pH 3At pH 5.97At pH 10 cathodestationary anode

MCAT Practice Passage Now we will take the opportunity to put all of our skills andknowledge to the test with an MCAT-style practice passage. Prepare to take notes along with our reading or to think about whatyou might highlight, just like you would on Test Day.MCAT Super Review: Amino Acids

MCAT Practice PassageThe artificial sweetener aspartame (Figure 1) is themethyl ester of the dipeptide of L-phenylalanine and Laspartic acid. There are two general approaches toprepare aspartame. The chemical approach involvesreacting the methyl ester of phenylalanine with an Nprotected anhydride of aspartic acid. The protectinggroup, either a benzyl or formyl group is then removedby mild acid hydrolysis. In addition to the desiredproduct, a beta structural isomer is also formed due toformation of a peptide bond with the wrong carboxylategroup, which must be removed since it produces a bittertaste.Figure 1 Structure of N-(L-α-Aspartyl)-L-phenylalanine,1-methyl ester (Note: pKa1 3.2; pKa2 7.7)A second enzymatic synthesis has been developed inwhich proteases catalyze the selective peptide bondformation and avoids the formation of the beta isomer.MCAT Super Review: Amino Acids

MCAT Practice PassageUpon ingestion, aspartame is broken down in theduodenum into its components, aspartic acid,phenylalanine and methanol, with the subsequentformation of metabolites such as formaldehyde andformic acid. Some research has raised concerns thataspartame may lead to the formation of certain cancersas a result of the formation of some of these potentiallytoxic compounds. A new drug, known as protein AT7(MW 5 104 amu), has been developed to counter thispossibility.MCAT Super Review: Amino Acids

MCAT Passage1. According to the passage, the pI of aspartame is mostnearly:A. 3.2B. 5.5C. 7.0D. 7.72. How many stereocenters are in aspartame?A. 1B. 2C. 3D. 4MCAT Super Review: Amino Acids

MCAT Passage3. The two amino acids that form the basis for thedipeptide structure of aspartame, aspartic acid andphenylalanine, are most accurately be classified as:4. Prior to its digestion in the small intestine, aspartamemust pass through the stomach. What is net charge onaspartame while in the stomach?A. hydrophilic and hydrophilic, respectively.B. hydrophobic and hydrophilic, respectively.C. hydrophilic and hydrophobic, respectively.D. hydrophobic and hydrophobic, respectively.A. -1B. 0C. 1D. 2MCAT Super Review: Amino Acids