Prepare for MCAT biochemistry with these amino acid flashcard questions and answers. This covers amino acid structures, properties, classifications, and metabolism.
Q: Glycine (Gly, G)Non-polar, hydrophobic
Answer: 19Tho there are 20 amino acids, there are only 19 R groups, since glycine doesn’t technically have one
Q: Alanine (Ala, A)Non-polar, hydrophobic
Answer: GlycineBecause it is not attached to 4 different groups, glycine does not have R/S configurations or D/L
Q: Valine (Val, V)Non-polar, hydrophobic
Answer: in their dipolar/zwitterion form (with a negative charge on the COO- and a positive charge on the NH3+)
Q: Leucine (Leu, L)Non-polar, hydrophobic
Answer: twists/bends, anywhere you can’t fit a larger side chainAlanine may also be found in these situations, as its methyl R group is also tiny in comparison to the other R groups.
Q: Isoleucine (Ile, I)Non-polar, hydrophobic
Answer: aliphatic – just Cs and HsGlycine (Gly, G)Alanine (Ala, A)Valine (Val, V)Leucine (Leu, L)Isoleucine (Ile, I)Proline (Pro, P)
Q: Proline (Pro, P)Non-polar, hydrophobic
Answer: Alanine (Ala, A)can be converted into pyruvate (and pyruvate can be converted into alanine) thru transamination. If we need to create aa’s from metabolic pathways or digest aa’s for energy, alanine is the necessary connection – for glycolysis, gluconeogenesis & TCA cycle
Q: Serine (Ser, S)Alcohol
Answer: NO, it’s isopropyl group makes it bulky
Q: Threonine (Thr, T)Alcohol
Answer: leucine (isobutyl side chain) & isoleucine (sec butyl side chain)molecules with same molecular formula, but differ in connection
Q: Phenylalanine (Phe, F)Aromatic
Answer: isoleucine
Q: Tyrosine (Tyr, Y)Aromatic
Answer: Methionine -a thioetherBecause the S is bound to C, the difference in polarity is not great enough to make it reactive
Q: Tryptophan (Trp, W)Aromatic
Answer: methionine
Q: Aspartate (Asp, D)Acid
Answer: hydrophobic (mostly Cs and Hs interacting with no polarity to interact with)
Q: Glutamate (Glu, E)Acid
Answer: phenylalanine (it is called phe bc it is a ‘phenyl’ group attached to ‘alanine’, however the methyl + benzene ring is technically a benzyl group)
Q: Histidine (His, H)Base
Answer: tryptophan — only amino acid with a bicyclo aromatic compound as its R groupIt is not polar bc, tho its N technically has a partial negative charge (giving the attached H a partial + charge) its electron pair participates in resonance with the 2 aromatic structures and thus is not interested in interacting with outside groups
Q: Lysine (Lys, K)Base
Answer: proline — important structural a.a. in polypeptides.
Q: Arginine (Arg, R)Base
Answer: proline – thus it cannot be in a linear polypeptide
Q: Asparagine (Asn, N)Amide
Answer: Alcohols:SerineThreonineAmides:AsparagineGlutamine>>Cysteine & Tyrosine (even tho they’re polar, are hydrophobic)
Q: Glutamine (Gln, Q)Amide
Answer: AspartateGlutamate
Q: Methionine (Met, M)Sulfur-containing
Answer: HistidineLysineArginine
Q: Cysteine (Cys, C)Sulfur-containing
Answer: Its -OH group has a partial – charge on the O and a partial + charge on the H
Q: How many R groups are there?
Answer: alcohols serine & threonine & tyrosineThe OH group allows H bonds to be formed rather than covalent bonds. The H bonds are weak and easily broken, or ‘reversed.’
Q: Only achiral amino acid
Answer: alcohols serine, threonine & tyrosineIf a protein has to be phosphorylated, you need to create a bond to that protein/enzyme, which can happen with an OH group. The H can be discarded and the O can form a bond with the phosphate group. This is key when you’re trying to turn an enzyme on or off
Q: How do amino acids exist at physiological pH?
Answer: Threonine (every aa except for glycine has a chiral a carbon, but not an additional one in their R group)
Q: Ideal places for glycine
Answer: SH group in cysteine – not quite acidic or basic, but under certain conditions there is an ionizable group – the proton can be removed, giving us an S-. The S- will be hydrophobic in this case.
Q: Non-aromatic (linear) side chain
Answer: cysteine2 cysteines can oxygenate their SH groups, allowing the resulting S- to bind to each other in a covalent bond — creating a disulfide bridge
Q: Link between amino acids & metabolism
Answer: disulfide bridge (between 2 cysteines, or ‘cystine’)helps stabilize the 3D structure of proteins/enzymes
Q: Would valine be found inside an alpha helix?
Answer: tyrosineits OH is competing with a large aromatic ring – it’s not big enough to make up for the rest of the stable side chain
Q: constitutional isomers
Answer: Asparagine (Asn, N) & Glutamine (Gln, Q)Their NH2 groups should be basic, due to lone pair of electrons on N, but sp2 Ns are far less basic than sp3 – bc electrons that would reach out & attack a proton are too busy resonating onto the carbonyl group.
Q: In addition to having a chiral a carbon, has a second chiral C in the R group
Answer: Asparagine (Asn, N) & glutamine (Gln, Q)The fact that they have a N in both their side chain & R group, and thus act as a N storage for living molecules. The N groups can be removed thru transamination.
Q: considered an aliphatic, hydrophobic, non-polar side chain despite having a sulfur atom
Answer: aspartate (an acidic aa)oxaloacetate (OAA) – an intermediate in the TCA cycle
Q: used as a start codon when translating from mRNA to a polypeptide
Answer: glutamate (an acidic aa)a-ketoglutarate (intermediate in the TCA cycle)
Q: Traits of aromaticity
Answer: aspartate & glutamateAt physiological pH, COOH groups exist as COO- – giving these aa’s carboxylate groups rather than carboxyl groups.
Q: technically has a benzyl group as its R group
Answer: Asparagine > aspartatic acid > OAAGlutamine > glutamate acid > a-ketoglutarate
Q: has largest & most complex R group
Answer: outside – they are happy to face the hydrophilic environmentquaternary & tertiary structure
Q: has an R group bound to the N in the amino side chain
Answer: They form ionic bonds between their negative side chain & a positive ion elsewhere, such as protonated basic amino acids. These ionic bonds are called ‘salt bridges’ and stabilize the overall 3D structure of the protein
Q: due to its ring, it introduces a ‘kink’ into polypeptide chains – forces groups toward each other and away from the ring in its R group
Answer: the NH2 is protonated to NH3+, which is how it occurs at physiological pH
Q: polar neutral amino acids — hydrophilic due to a partial + or – charge that allows them to interact with water
Answer: salt bridges (ionic bonds, just like acidic aa’s)outside
Q: acidic amino acids
Answer: arginine (Arg, R)A N that can resonate is actually sp2 hybridized, thus the only N that cannot resonate is the one participating in a double bond. This means its electrons aren’t distracted by resonance, making it the most basic N, the one that gets protonated. At physiological pH, there is a 2nd H added to it, giving it a + charge.
Q: basic amino acids
Answer: salt bridgeoutside
Q: What makes serine polar/hydrophilic?
Answer: Which N is busy participating in resonance, or more importantly, aromatic resonance?Which N doesn’t need its pair of electrons, making them available to attack a proton?If the lone pair of electrons are needed for the N to participate in resonance, it’s aromatic.The N not next to a double bond cannot participate in resonance unless it donates its electrons, making them ‘busy.’ The lower N already participates in resonance thru its pi bond, thus its lone pair is not needed & can be used to attack a proton.
Q: Used for temporary, reversible binding — bio molecules often create temporary bonds while a rxn is taking place or while sthg is being moved.
Answer: ~6This is important bc it is only 1 pH unit away from physiological pH. This means that histidine is easily protonated & deprotonated in biological molecules, making it ideal in active sites of enzymes – when it’s protonated or deprotonated, it will interact differently with side chains, potentially changing the conformation and therefore, the function
Q: Have the ability to phosphorylate
Answer: R or SD or LR/S do not directly relate to D/L. A D amino acid may be R or S.
Q: has chirality in its side chain
Answer: sp3tetrahedral109.5°4 unique substituents
Q: has a slight amount of polarity (due to minimal difference in negativity in its R group) but not great enough to want to interact with water
Answer: Rank substituents from high to low priorityPut the lowest priority in the back (bc we’re only looking at the 3 highest)Determine whether you go CW or CCW to go from 1 to 2 to 3
Q: has the ability to form a covalent bond with another of the same aa
Answer: S > O > N > C > HIf faced with 2 of the same, cross that out & go to the next atom.
Q: only covalent bond seen in tertiary/quaternary structures is _. What is the purpose of this type of bond?
Answer: enantiomerswhen you swap 1 group to get the enantiomer (if you swap the position of the #3 and #4 substituents so that #3 is in the ‘away’ position, you will get the other enantiomer)
Q: has an OH group (polar) but the fact that it’s such a tiny component of the overall R group makes the overall amino acid hydrophobic/nonpolar
Answer: Rather than looking at the OH group, we put the COOH group at the top (just like sugars) and look at the NH2 group to determine D or L.If NH2 is to the right, it is DIf NH2 is to the left, it is L
Q: These two amino acids ‘should’ be basic but are not
Answer: L
Q: play a key role in synthesis of nitrogen-containing compounds
Answer: the acid-base interactionsThe acidic COOH will deprotonate to COO- and the basic NH2 will be protonated to NH3+. In nature, they won’t interact with each other, but rather with the solution.This a Zwitterion, or dipolar ion (2 charged groups on molecule). Acidic/basic side chains can have a 3rd charge in their R group
Q: If the N in asparagine is replaced by an O via transamination, we get _. If we remove the second N in the backbone, we get _
Answer: acids
Q: If we swap out an N for an O in glutamine via transamination, we get _. If we remove the N in the backbone, we get _
Answer: bases
Q: Conjugate bases of aspartic acid & glutamic acid
Answer: Look at it in its neutral form (NH2, COOH) and look for the pKa values – these will tell you at which pH it’s going to gain or lose a protonWhat is the pH of any ionizable group and will it be protonated or deprotonated based on the pKa?
Q: The side chains for aspartate & glutamate look exactly like those of asparagine & glutamine, except that the amides are swapped out for carboxylic acid groups. They are intermediates in the transamination series that asparagine & glutamine participate in. What are these rxns?
Answer: pKa = -logKapH = pKa + log[conjugate base]/[acid] <<Henderson-Hasselbach equationIn pH vs pKa, it is like a ‘battle’ for the proton. The higher value has a stronger desire for the proton. If the pH is higher, the solution wins, and if the pKa is higher, the molecule wins.
Q: Acidic aa’s (aspartate & glutamate) are typically found on the _ of proteins & enzymes bc _. They also play a key role in _ structures.
Answer: [H+][A-] / [HA]**Ka is proportional to the H+ concentration, which tells us the pH
Q: Why are acidic aa’s (aspartate & glutamate) key components of tertiary & quaternary structure? What are these bonds called?
Answer: the likelihood of a molecule to take or donate a proton from/to solution
Q: conjugate acid of lysine’s basic side chain
Answer: concentration of H+low [H+] = acidic = lots of H+ to be pumped onto molecules dissolved in solutionHigh [H+] = basic = lots of OH- to take protons away from molecules dissolved in solutionWe have to compare the acidity or basicity of the solution to the molecule’s desire to hold onto their H+?
Q: Basic amino acids are found in _ bonds & _ of proteins/enzymes
Answer: acidic solutionThe molecule is stronger and takes the proton away from solution – and will be protonated
Q: side chain has 3 Ns, each with a lone pair of electronsWhich N is the basic one, first to get protonated?
Answer: basic solutionThe solution is stronger and takes the proton from the molecule, deprotonating it
Q: Arginine partipates in _ ionic interactions & can be found on the _ of proteins/enzymes
Answer: ‘stale-mate’: buffer zoneThe solution wants the proton just as much as the molecule.
Q: Which is the basic N in histidine?
Answer: buffer zone >> 50:50 – half molecules will be protonated and half will be deprotonated.
Q: pKa of histidine side chain
Answer: still in the buffer zone, but the molecules will be slightly more or less protonated depending on direction (if pH is lower, you’ll have more protonated; if pH is higher, you’ll have more deprotonated – but still in that partially charged region)
Q: Chiral amino acids can be classified as _ or _ when looking at them in a 3D structure, or _ or _ when looking at them in a biological standard format
Answer: Acetic acid is happy to donate its proton depending on the solution. If dissolved in an acidic solution, we have too many protons & Le Chatelier’s principle says the rxn shifts to the left & we protonate acetic acid.If dissolved in basic solution, the base (OH-) is pulling protons out of equilibrium and the rxn shifts to the right – we deprotonate the acid
Q: A chiral carbon must be _hybridized, _ with a bond angle of _ and attached to _
Answer: pH is significantly lower than pKa. We have so many protons in solution that we will protonate every available acetate to get acetic acid. The charge = 0, a neutral molecule.
Q: To find the chirality, what do you do?
Answer: buffer: 50% protonated, 50% deprotonatedThe charge in this case (average charge) equals -0.5. We have a charge of 0 for the protonated form and a charge of -1 for the protonated form, thus the avg charge is -0.5.
Q: In ranking substituents of amino acids, what is the order of the 5 most common atoms seen?
Answer: more negativeless negative1 pH unit above or below
Q: R and S are _ of each otherWhat is the ‘swap’ method?
Answer: There is a 10:1 ratio of protonated to deprotonated
Q: How to find whether an amino acid is D or L
Answer: We have a very basic solution, with OH- more desperate for the proton than the acetic acid. OH- will take away all the protons, and we have acetate in solution for a charge of -1The pKa of the carboxy side chain will vary between amino acids, depending on what else is nearby, thus the specific charges will vary
Q: Biological amino acids prefer which form: D or L?
Answer: The pH is significantly lower than pKa and is much more acidic (it has so many H+ that it doesn’t want any more). Thus, the methyl ammonium is more hungry for the proton and will be primarily protonated (CH3NH3+) – charge is +1
Q: The neutral form of amino acids cannot exist in nature bc of _
Answer: The pH is significantly greater than the pKa, thus methyl ammonium will exist primarily in deprotonated form (CH3NH2), with a neutral charge. It’s not neutral bc we started out with a positive charge; dropping one unit brings us to 0, or neutral.
Q: donate H+
Answer: pH is slightly less than pKa, making it slightly more acidic. However, we’re still in the buffer zone (pH within 1 unit of pKa). We will have slightly more CH3NH3+ than CH3NH2, with a charge somewhere between 0 and +1.
Q: accept H+
Answer: pH 1 is less than both pKa values. Thus the solution has more protons, and will give them to both the amine and carboxyl groups. Thus the groups exist as NH3+ and COOH. If we add both charges, we get +1 and 0, for a net charge of +1.
Q: How to find charge of an aa at any given pH
Answer: The carboxyl group will be partially protonated/partially deprotonated (half will have a -1 charge and half will be neutral, for an avg charge of -0.5). The amine pKa is greater, thus all will exist as NH3+ with a +1 charge.
Q: relationship between pH & pKa
Answer: We expect to see the Zwitter ion at physiological pH.This pH is greater than the carboxyl pKa, thus it will exist as COO- with a -1 charge. The pH is less than the amine pKa, thus it will exist as NH3+ with a charge of +1. This gives a net neutral charge for the moleculeAs we raise pH, we went from +1 and we’re dropping half a point. If we raise
Q: Ka =
Answer: iso = sameelectric = chargeIt is the pH at which the amino acid has a net charge of 0. For ex, amino acids such as glycine exist at a net charge of 0 at physiological pH, as the – charge on the COO and the + charge on the NH3 cancel each other out
Q: What does pKa tell us?
Answer: 2
Q: What does pH tell us?
Answer: 10
Q: When pH < pKa, what does that tell us?
Answer: pI = (pKa1 + pKa2) / 2Take the avg of the pKa valuespI(glycine) = (2.3 + 9.6)/2 round > (2+10)/2 = 6
Q: When pH > pKa, what does that tell us?
Answer: guess-&-check method: look at the pH and determine what charge each group will haveEx: tyrosine (pKa COO: 2.3, pKa NH3: 9.1, pKa OH: 10.1)Rank pKa values from low to high (2.3, 9.1, 10.1)_ 2.3 _ 9.6 _ 10.1 _Drop pH to well below the lowest pKa (pH = 1)(+1) 2.3 _ 9.7 _ 10.1At this pH, all groups will be protonatedAs you raise the pH between pKa units, the molecule loses a proton & the charge goes down by 1 (thus if we jump to a pH between 2.3 and 9.7, the charge of the molecule will decrease to 0)(+1) 2.3 (0) 9.1 (-1) 10.1 (-2)pH 1 pH 5 pH 9.6 pH 13pI is the avg of the 2 pKa values that are before & after 0 (2.3+9.1)/2 = 5.5
Q: When pH ~ pKa, what does that tell us?
Answer: goes down by 1
Q: If pH = pKa, what does that tell us?
Answer: R group of each functional group is the amino acid side chain)aldehyde (formaldehyde has R group H, thus it would be used to synthesize glycine; if you wanted to synthesize alanine, R group would be CH3) >React with NH3 / HCl (NH4Cl) >imine intermediate (amine double bound to C, the nitrogen version of a carbonyl) >React with HCN (or CN-) >Intermediate with N where we want it and a nitryl group which will be hydrolyzed in the final step >React with H3O+ (hydrolyze) >Amino acid product with alpha carbon, alpha amine, alpha carboxyl, and amino acid side chain
Q: If pH is within 1 unit of pKa, what does that tell us?
Answer: It is NOT in Zwitterion form, but rather has its carboxyl and amine groups protonated (net +1 charge)This is bc the final step is carried out in acid (H3O+), giving a very low pH where the carboxyl and amine groups both ‘win’ the proton
Q: What does the pKa of acetic acid (4.8) tell us?
Answer: Start out with a C chain that has amino acid side chainAdd backbone (add N, then carboxy)
Q: If acetic acid (pKa = 4.8) is dissolved in solution with pH 2, what happens?
Answer: So that we have an alpha H rather than a methyl group
Q: If acetic acid (pKa = 4.8) is dissolved in solution with pH 4.8, what happens?
Answer: to activate the O of the carbonyl which then activates the carbonyl CWhen O reaches for the H