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Module 1

  1. What are the five principal components of the basic chemical structure of a free amino acid:
    • 1) Alpha carbon (Cα)
    • 2) Alpha carbon hydrogen (H)
    • 3) Amino group (NH3+1)
    • 4) Carboxylate group (COO-1)
    • 5) An R group (also called a side chain, which may or may not be ionizable)

  2. Define ionizable (as it pertains to amino acids)
    Ionizable: the side chain of the amino acid can lose or gain electrons, in an aqueous solution, resulting in a net charge. This is dependent on pH
  3. How many ionizable functional groups does a free amino acid have?
    minimum of 2 ionizable functional groups to a maximum of 3
  4. Define imino acid and state the only imino acid
    In chemistry, an imino acid is any molecule that contains both imino (>C=NH) and carboxyl (-C(=O)-OH) functional groups.

    proline
  5. Draw Proline
    • One of the 20 protein amino acids, it is also known as an imino acid
  6. Which atoms comprise the biological molecules?
    Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), Phosphorous (P) and Sulfur (S)

    CHNOPS (acronym)
  7. Which of the six atoms that make up biological molecules have a formal charge of 0?

    Which of the six atoms that make up biological molecules have a formal charge that can toggle between +1 and 0?

    Which of the six atoms that make up biological molecules have a formal charge that can toggle between a formal charge of 0 and -1
    Carbon (C), Hydrogen (H) and Phosphorous (P) ALWAYs have a formal charge of 0

    Nitrogen (N) can toggle between a formal charge of +1 and 0 

    Oxygen (O) and Sulfur (S) can toggle between a formal charge of 0 and -1
  8. State the formula for formal charge and state the valence electron count for all 6 of the biological atoms
    [valence electrons] - [1/2 (bonding electrons) + (lone electrons)]

    • Carbon: 4
    • Hydrogen: 1
    • Nitrogen: 5
    • Oxygen: 6
    • Phosphorous: 5
    • Sulfur: 6
  9. There are ____ genetically encoded (through mRNA codon) amino acids. For brevity we use one-letter assignment(s) and it is always used in scientific literature. All of the alphabets from A-Z are used, list the exceptions. **Memorize the amino acid codes
    • 20 amino acids
    • B, J, O, U, X and Z are the exceptions



  10. What are the two classes the amino acids can be divided into:
    The hydrophobic (water fearing) and the hydrophilic (water loving)
  11. How many of the 20 amino acids are hydrophobic (briefly list them)? How many are hydrophilic (briefly list them)?
    • Hydrophobic: 9/20 (GAV LIM FWP)
    • Hydrophilic: 11/20 (CDESTY HKR NQ)
  12. The hydrophobic class can be further divided into two subcategories define and briefly list them
    • The aliphatic category: relating to or denoting organic compounds in which carbon atoms form open chains (as in the alkanes), not aromatic rings (GAV LIM P)
    • The hydrophobic aromatic category: also known as arenes or aromatics, are chemical compounds that contain conjugated planar ring systems with delocalized pi electron clouds instead of discrete alternating single and double bonds. Typical aromatic compounds are benzene and toluene. They should satisfy Hückel's rule. (F and W)
  13. Of the 11 hydrophilic amino acids, _______ and _______ are aromatic. Of those 11, make a list of the ones that can engage in hydrogen bonding, and a separate list of the ones that have an ionizable side chain
    • Histidine (H) and Tyrosine (Y)
    • Hydrogen bonding capable: DESTY HKR NQ
    • Ionizable side chain: CDESTY HKR
  14. Define Isomers and Stereoisomers
    • Isomers: Isomers are compounds with different physical and chemical properties but the same molecular formula. In organic chemistry, there are many cases of isomerism. For example, the formula C4H10 represents both butane and 2-methylpropane.
    • Stereoisomers:  have identical molecular formulas and arrangements of atoms. They differ from each other only in the spatial orientation of groups in the molecule. The simplest forms of stereoisomers are cis and trans isomers, both of which are created by the restricted rotation about a double bond or ring system. Butene, C4H8, exists in both cis and trans forms.
  15. Explain the rules of the Cahn-Ingold Prelog system
    • Rule 1. We look first at the atoms attached directly to the stereocenter. A substituent atom of higher atomic number takes precedence over one of lower atomic number. Consequently, the substituent of lowest priority is hydrogen. In regard to isotopes, the atom of higher atomic mass receives higher priority.
    • Rule 2. What if two substituents have the same rank when we consider the atoms directly attached to the stereocenter? In such a case, we proceed along the two respective substituent chains until we reach a point of difference. (pg 176-177 for examples and explanation)
    • Rule 3. Double and triple bonds are treated as if they were single, and the atoms in them are duplicated or triplicated at each end by the respective atoms at the other end of the multiple bond.
  16. For amino acids, we are mainly concerned with five elements. List them and state their atomic numbers. In addition why is the sixth atom is left off this list
    • Nitrogen (7), Oxygen (8), Carbon (6), Hydrogen (1), and Sulfur (16)
    • Phosphorous (15) is also biologically important, but it is ONLY found in post-translationally modified amino acids
  17. In the Cahn-Ingold prelog system, Four priority score #s are used: 1-4 (1 being the ______; 4 being the ______-typically reserved for ______). The higher the atomic #, the ______ the priority score. The lower the atomic #, the _____ the priority score
    • highest
    • lowest
    • hydrogen
    • higher
    • lower
  18. In the Cahn-Ingold prelog system, what does L and D stand for and what are they equivalent to?
    • Levorotatory (L) is equivalent to S (sinister)
    • Dextrorotatory (D) is equivalent to R (rectus)
  19. Show the stereoisomerism for the amino acids, what is the exception?
  20. Show the stereoisomerism for cysteine
  21. How do you calculate the number of stereoisomers of an amino acid?
    2n where n is the number of chiral centers
  22. Of the 20 amino acids, which ones have only 2 stereoisomers (explain and list them)
    • 17/20, they only have one chiral carbon, so 21 = 2 stereoisomers
    • A, C, D, E, F, H, K, L, M, N, P, Q, R, S, V, W and Y (exceptions I, T and G)
  23. How many amino acids have 4 stereoisomers (explain and list).
    • 2/20, they have 2 chiral centers, so 22 = 4
    • I and T 
  24. How many amino acids have 1 stereoisomer?
    • 1 out of 20 amino acid has NO chiral center, so 20 = 1 
    • It is Glycine
  25. Draw the aliphatic amino acids and Hydrophobic aromatic amino acids
    • Remember GAV LIM FWP
    • aliphatic: GAV LIMP and hydrophobic aromatic: F and W
  26. The uniqueness of each amino acid is attributed to its _____ _____
    side chain (aka the R group)
  27. Draw the Hydrophilic amino acids
  28. Make a table listing the 20 amino acids, stating their one-letter notation, three-letter notation, full name, pka, and name of their R group
  29. Draw the skeletal representations of the amino acids
  30. Draw the skeletal representation of the 20 amino acid side chains as they exist at a pH of 7.40
  31. What are the two types of bonds formed in biological systems? How is the polarity of the bonds determined?
    • The covalent and polar covalent bond
    • Bond polarity is determined as a function of the electronegativity difference between the two respective atoms involved in making the bond
  32. What is a hydrogen bond? Which atoms are required to create a hydrogen bond in biological systems?
    Not necessarily a bond but rather a weak favorable electrostatic attractive force between two atoms

    3 atoms are needed: Nitrogen (3.05), Oxygen (3.44) (both very electronegative) and hydrogen (2.20) (very electropositive)
  33. N-H and O-H bonds are incredibly _____; this creates a perfect setting for the propagation of a ______ ______
    • polar 
    • hydrogen bond
  34. How do you determine the number of hydrogen bond donors and the number hydrogen bond acceptors?
    • To be a hydrogen bond donor: 
    • 1) Must have hydrogen atom covalently bonded to a very electronegative atom

    • To be a hydrogen bond acceptor:
    • 1) Must have a lone pair on an electronegative atom (N and/or O)
    • 2) ONE lone pair equals to ONE acceptor

    *Please use octet rule as shown
  35. What are the 4 main categories of amino acids whose side chains can engage in hydrogen bonding at a physiological pH of ~7.40?
    • Only hydrogen bond acceptors
    • Only hydrogen bond donors
    • Predominantly a hydrogen bond donor 
    • Both Acceptors and Donors
  36. List the amino acids with side chains that can engage in hydrogen bonding under their respective groups
    • Only hydrogen bond acceptors
    • 1) Aspartate (Asp, D)
    • 2) Glutamate (Glu, E)

    • Only Hydrogen bond donor
    • 1) Lysine (Lys, K)

    • Predominantly a hydrogen bond donor
    • 1) Arginine (Arg, R)

    • Acceptors and Donors
    • 1) Histidine (His, H)
    • 2) Asparagine (Asn, N)
    • 3) Glutamine (Gln, Q)
    • 4) Serine (Ser, S)
    • 5) Threonine (Thr, T)
    • 6) Tyrosine (Tyr, Y)
  37. Make a table, listing the amino acids whose side chains are capable of hydrogen bond donating or accepting at pH of ~7.40. Then list the number of hydrogen bond acceptors, donors and total capacity of each
  38. Draw the structures of the side chains of the amino acids DESTY HKR NQ and state their hydrogen bonding capacity
  39. Briefly detail a strategy on how to learn the bonding capacities
    • First, learn how to draw the skeletal representation of each side chain very well
    • Then, learn the capacity by satisfying the octet around the respective N and O 
    • This way you don't need to memorize
  40. When do the side chains of an amino acid display resonance?
    When more than one lewis structure is needed/required to fully explain the bonding in a particular part of a molecule
  41. Make a list of the amino acids whose side chains display resonance
    • 1) Tryptophan (W)
    • 2) Histidine (H)
    • 3) Tyrosine (Y)
    • 4) Phenylalanine (F)
    • 5) Arginine (R)
    • 6) Glutamate (E)
    • 7) Aspartate (D)

    *WHY FRED
  42. Draw the resonance forms for:
    Phenylalanine
    Tyrosine
    Aspartate
    Glutatmate
    Arginine
  43. List the aromatic amino acids
    • Tryptophan (W)
    • Histidine (H)
    • Tyrosine (Y)
    • Phenylalanine (F)
  44. 1) Let Q be a donor and T be an acceptor. Draw out the skeletal forms of each of the side chains and determine the number of hydrogen bonds that can be drawn between the two side chains
    2) Let Y be a donor and S be an acceptor. Draw out the skeletal forms of each of the side chains and determine the number of hydrogen bonds that can be drawn between the two side chains
    • 1) (Glutatmine) QD = 2 | QA = 3 & (Threonine) TD = 1 | TA = 2 
    • 2 hydrogen bonds
    • 2) (Tyrosine) TD = 2 | TA = 1 & (Serine) SD = 1 | SA = 2
    • 2 hydrogen bonds

    *Both ties, when you don't have a tie like between K and Y you choose the lesser number: KD = 3 & YA = 2 would have two hydrogen bonds
  45. What is the formula for formal charge? Detail the two categories that are relevant for such calculations among CDESTY and HKR side chains state their overall charge and their charge when they deprotante
    [(Number of valence electrons)] - [(1/2(bonding electrons) + (lone electrons)]

    • Category 1: The SIDE CHAINS of protonated forms of cysteine, aspartic acid, glutamic acid, serine, threonine, and tyrosine have an overall side chain charge of: 0
    • When these side chains deprotonate, they form a charge of: -1
    • *remember CDESTY

    • Category 2: The SIDE CHAINS of protonated histidine, lysine, and arginine have an overall side chain charge of : +1
    • When these side chains deprotonate, they form a charge of: 0
    • *remember HKR
  46. Draw the protonated and deprotonated configurations of CDESTY HKR and state the formal charge of each.
  47. Ionizable side chain charge assignment: 0, +1 or -1 (also includes _____ group and ______ group). The important valence electrons are ____ for nitrogen and ____ for oxygen
    • amino group and carboxylate group
    • 5
    • 6
  48. Formal charge for protonated CDESTY side chain: Find the formal charge of protonated sulfur and oxygen
    [6] - [1/2 (4) + 4] = 6 - 6 = 0
  49. Formal charge on a deprotonated CDESTY side chain: Find the formal charge of a deprotonated sulfur and oxygen
    [6] - [1/2 (2) + 6] = 6 - 7 = -1
  50. Formal charge on a protontated HKR side chain: Find the formal charge of protonated Nitrogen
    [5] - [1/2 (8) + 0] = 5-4 = +1
  51. Formal charge on a Deprotonated HKR side chain: Find the formal charge of the deprotonated nitorgen atoms within the respective side chains
    [5] - [1/2 (6) + 3] = 5 - 5 = 0
  52. Name two scenarios in Biochemistry in which assignment of formal charge is most important
    • Peptide and amino acid charge assignment 
    • Peptide and amino acid isoelectric point assignment
  53. State the protonated and deprotonated charge of the following amino acid side chain or functional group
  54. What are the three possible scenarios we encounter when calculating free amino acid charge?
    • Fully-protonated charge
    • Full-deprotonated charge
    • Zwitterionic charge
  55. How would you determine the overall charge on a fully-protonated and a fully-deprotonated FREE amino acid (considering the ENTIRE free amino acid). Separate your answer into the three categories
    • Category 1: includes GAV LIM FWP NQ 
    • Amino acids with non-ionizable side chains have an overall fully-protonated charge of: 1+
    • When these fully deprotonate, their charge is: -1
    • (Alanine, glycine, isoleucine, leucine, valine, phenylalanine, tryptophan, asparagine, proline, methionine and glutamine)

    • Category 2: includes CDESTY
    • Amino acids whose ionizable side chains contains a sulfur or oxygen have an overall fully-protonated charge of: +1
    • When these fully deprotonate, their charge is: -2
    • (Cysteine, aspartate, glutamate, serine, threonine and tyrosine)

    • Category 3: includes HKR
    • Amino acids whose ionizable side chains contains a nitrogen have an overall fully-protonated charge of: +2
    • When these fully deprotonate, their charege is: -1
    • (Histidine, lysine and arginine)
  56. At a pH of 7.40, ___/20 amino acids exist as zwitterions. List the exceptions that do not exist as zwitterions at a pH of 7.40.
    • 16/20
    • D, E, K, and R
  57. Which amino acids when fully protonated have the following sum charges: +1, +1 and +2. When fully deprotonated, which amino acids have the following sum charges: -1, -2 and -1
  58. Define isoelectric point
    The isoelectric point (pI, pH(I), IEP), is the pH at which a particular molecule carries no net electrical charge in the statistical mean.
  59. In order to calculate the isoelectric point (pl) of a free amino acid, you must be able to calculate or determine the _____ _____ charge.
    fully-protonated charge
  60. What is the formula for the isoelectric point (pl)? What do you do if you have a free amino acid with a non-ionizable R group? Which amino acid residues does this work for?
    pl = (pKa1 + pKa2)/2

    • average the α-carboxyl and α-amino pKa values
    • 11 residues conform to this scheme: GAV LIM FWP NQ
  61. The two pKa values involved in calculating the isoelectric point ALWAYS surround the ______ (or ______) state of a molecule
    zwitterionic or neutral state
  62. Finding the isoelectric point of a free lysine Pt I:
    Lysine is an example of an amino acid with a(n) _______ side chain (List all the amino acids in this category). For a free amino acid with an ionizable R group, ______ the 2 pKa values that flank the ______ (_______) charge state.
    • ionizable side chain
    • Cysteine, Aspartate, Glutamate, Histidine, Lysine, Arginine, Serine**, Threonine**, Tyrosine (9)
    • average
    • neutral (zwitterion)
  63. Finding the isoelectric point of a free lysine Pt II: 
    State the three pKa values for lysine, justify which two to use for the calculation of pl and finally calculate pl
    • Alpha carboxyl: ~2.20
    • Alpha amino: ~9.40
    • R-group (epsilon amino group): ~10.5

    • The 2 values that flank are 9.40 and 10.5. So, to get the pl of lysine, we average them as follows:
    • pl = (pKa1 + pKa2)/2 = (9.40 + 10.5)/2 = 9.95
Author
chikeokjr
ID
339417
Card Set
Module 1
Description
Module 1 Pt I
Updated

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