Regrouping amino acids for the MCAT

amino acids MCAT

In my high school and undergraduate career, I often learned about amino acids based on their chemical properties; that is, on the basis of their polarity, acidity, or basicity. Those classifications, while important, don’t capture the full story. For the MCAT, I’ve found it helpful to think about some of the different functional properties of amino acids, which you’ll find are commonly tested on the C/P and B/B sections of the test. 

Aromatic Amino Acids

There are 3 aromatic amino acids: phenylalanine (Phe, F), tryptophan (Trp, W), and tyrosine (Tyr, Y). Due to their aromaticity, these amino acids are able to absorb UV light. Tryptophan, which has a max absorption of 280 nm, is responsible for most of the UV-light absorbing properties of proteins. Peptides and amino acids can be quantified by measuring their UV absorption at 280 nm (remember Beer’s law, which connects light absorption to concentration). 

Screen Shot 2022-04-20 at 12.14.09 PM

Phosphomimetics

A phosphomimetic amino acid is an amino acid that “mimics” the properties of a negatively-charged phosphate group. On the MCAT, you will often see the term “phosphomimetic” come up in studies examining the effects of mutations or constitutive phosphorylation on protein function. For example, if one wants to study the effect of constitutive phosphorylation of a residue on the function of a protein, you could replace the normally phosphorylated amino acid (such as serine) with a phosphomimetic amino acid. The two phosphomimetic acids are aspartic acid (Asp, D) and Glutamic Acid (Glu, E), which are both negatively charged at physiologic pH. 

Note that aspartic acid and glutamic acid amino acids would be negatively charged at physiologic pH of 7.4.

Phosphorylated Amino Acids

Phosphorylation of an amino acids most commonly occurs when a nucleophilic hydroxyl group attacks an electrophilic phosphorus atom found in a phosphate group (often the terminal phosphate group in ATP, the gamma phosphate). Three hydroxyl-containing amino acids are commonly phosphorylated: tyrosine (Tyr, Y), serine (Ser, S), and threonine (Thr, T). Specific kinases (serine/threonine and tyrosine kinases) phosphorylate these residues.

Screen Shot 2022-04-20 at 12.20.10 PM

Secondary Structure Breakers

Certain amino acids, namely proline (Pro, P) and glycine (Gly, G) cannot be found within an alpha helix and/or beta pleated sheet. Proline has a pyrrolidine ring R group that confers increased rigidity to the amino acid. Within a polypeptide, proline’s pyrrolidine ring limits backbone hydrogen bonding and thus secondary structure formation. Glycine, which has a hydrogen as an R group, is generally too structurally flexible for incorporation into an alpha helix and beta sheet. Note that either amino acid can be found in the turns between secondary structures.

Screen Shot 2022-04-20 at 12.23.45 PM

Disulfide Bond Forming Amino Acids 

Finally, cysteine (Cys, C) is the only amino acid that can form a covalent disulfide bond with another cysteine amino acid. Cysteine’s sulfhydryl (thiol) group can be oxidized in certain environments to form a disulfide bond. Disulfide bonds can be reduced to re-form the individual sulfhydryl groups on each cysteine. Experimentally, we often use reducing agents such as dithiothreitol or 2-mercaptoethanol to break disulfide bonds within or between polypeptide chains. 

 

Screen Shot 2022-04-20 at 12.24.31 PM

 

Comments

topicTopics
academics study skills MCAT medical school admissions SAT expository writing college admissions English MD/PhD admissions GRE GMAT LSAT chemistry writing strategy math physics ACT biology language learning test anxiety graduate admissions law school admissions MBA admissions interview prep homework help creative writing AP exams MD study schedules summer activities career advice history personal statements academic advice premed philosophy secondary applications Common Application computer science organic chemistry ESL PSAT economics grammar test prep admissions coaching law statistics & probability supplements psychology SSAT covid-19 legal studies 1L CARS logic games reading comprehension Spanish USMLE calculus dental admissions parents research Latin engineering verbal reasoning DAT excel mathematics political science French Linguistics Tutoring Approaches chinese DO MBA coursework Social Advocacy academic integrity case coaching classics diversity statement genetics geometry kinematics medical school skills IB exams ISEE MD/PhD programs PhD admissions algebra astrophysics athletics biochemistry business business skills careers data science letters of recommendation mental health mentorship quantitative reasoning social sciences software engineering trigonometry work and activities 2L 3L Academic Interest Anki EMT English literature FlexMed Fourier Series Greek Italian MD vs PhD Pythagorean Theorem STEM Sentence Correction Zoom admissions advice algorithms amino acids analysis essay architecture argumentative writing art history artificial intelligence cantonese capacitors capital markets cell biology central limit theorem chemical engineering chromatography climate change clinical experience cold emails community service constitutional law curriculum dental school distance learning enrichment european history finance first generation student fun facts functions gap year harmonics health policy history of medicine history of science information sessions institutional actions integrated reasoning intern international students internships investing investment banking logic mandarin chinese mba meiosis mitosis music music theory neurology operating systems phrase structure rules plagiarism poetry pre-dental presentations proofs pseudocode school selection simple linear regression sociology software study abroad teaching tech industry transfer typology units virtual interviews writing circles