Biochemistry - 20 Standard Amino Acids & Properties Flashcards

Question 1

Essential vs. Non-Essential Amino Acids

Accepted Answer

• **Essential** (cannot be synthesized *de novo*; must come from diet): Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Leucine, Lysine (**PVT TIM HALL**).
• **Non-essential**: Synthesized by the human body (e.g., Alanine, Aspartate, Glutamate, Serine).

Question 2

Non-polar, Aliphatic Amino Acids

Accepted Answer

Includes **Glycine (Gly, G)**, **Alanine (Ala, A)**, **Valine (Val, V)**, **Leucine (Leu, L)**, **Isoleucine (Ile, I)**, and **Proline (Pro, P)**. They contain hydrophobic hydrocarbon side chains that drive hydrophobic interactions in protein core folding.

Question 3

Aromatic Amino Acids & UV Absorption

Accepted Answer

• **Phenylalanine (Phe, F)**, **Tyrosine (Tyr, Y)**, and **Tryptophan (Trp, W)** contain aromatic rings.
• Tryptophan and Tyrosine absorb UV light at $\lambda = 280	ext{ nm}$, which is routinely used to estimate protein concentration.

Question 4

Positively Charged (Basic) Amino Acids

Accepted Answer

• **Lysine (Lys, K)** ($pK_a \approx 10.5$)
• **Arginine (Arg, R)** ($pK_a \approx 12.5$)
• **Histidine (His, H)** ($pK_a \approx 6.0$)

At physiological $pH \approx 7.4$, Lys and Arg carry a net positive charge ($+1$), while His is largely neutral or partially protonated.

Question 5

Negatively Charged (Acidic) Amino Acids

Accepted Answer

• **Aspartate (Asp, D)** ($pK_a \approx 3.9$)
• **Glutamate (Glu, E)** ($pK_a \approx 4.1$)

Both possess carboxylate side chains that are fully ionized (deprotonated) and carry a net $-1$ charge at physiological $pH$ ($7.4$).

Question 6

Polar, Uncharged Amino Acids

Accepted Answer

Includes **Serine (Ser, S)**, **Threonine (Thr, T)**, **Cysteine (Cys, C)**, **Asparagine (Asn, N)**, and **Glutamine (Gln, Q)**. Their side chains contain hydroxyl, thiol, or amide groups capable of forming hydrogen bonds.

Question 7

Unique Properties of Glycine (Gly, G)

Accepted Answer

Glycine is the smallest amino acid ($R = -H$) and the **only achiral** standard amino acid. Due to its minimal steric hindrance, it imparts high conformational flexibility to polypeptide chains and is abundant in collagen.

Question 8

Unique Structure and Secondary Impact of Proline (Pro, P)

Accepted Answer

Proline features a cyclic pyrrolidine side chain bonded to its backbone nitrogen, making it a secondary amino (imino) acid. This rigid structure introduces kinks, acting as a **helix breaker** in $\alpha$-helices and facilitating turns in $\beta$-sheets.

Question 9

Cysteine vs. Cystine & Disulfide Bonds

Accepted Answer

**Cysteine** contains a thiol (sulfhydryl, $-SH$) side chain ($pK_a \approx 8.3$). Under oxidizing conditions, two cysteine residues covalently cross-link via oxidation to form a disulfide bond, resulting in **cystine**.

Question 10

Histidine as a Physiological Buffer

Accepted Answer

Histidine's imidazole ring has a $pK_a \approx 6.0$, close to physiological $pH$ ($7.4$). Because it can easily accept or donate protons near neutral $pH$, Histidine frequently acts as a catalytic acid-base buffer in active sites.

Question 11

Isoelectric Point ($pI$) Calculation

Accepted Answer

The $pI$ is the $pH$ at which an amino acid has a net electrical charge of zero (zwitterion).
• **Neutral amino acids**: $pI = \frac{pK_{a1} + pK_{a2}}{2}$
• **Acidic side chains**: $pI = \frac{pK_{a, 	ext{carboxyl}} + pK_{a, 	ext{side chain}}}{2}$
• **Basic side chains**: $pI = \frac{pK_{a, 	ext{amino}} + pK_{a, 	ext{side chain}}}{2}$

Question 12

Peptide Bond Geometry & Resonance

Accepted Answer

Peptide bonds form via condensation between an $\alpha$-carboxyl and $\alpha$-amino group. Resonance delocalization gives the $C-N$ bond partial double-bond character $(\sim 40\%)$, making it **planar**, **rigid**, and restricted to **trans** geometry in most residues.

Question 13

Backbone Dihedral Angles (Ramachandran Plot)

Accepted Answer

Protein backbone flexibility is defined by rotation around two single bonds per residue:
• **Phi ($\phi$)**: Angle of rotation around the $N-C_\alpha$ bond.
• **Psi ($\psi$)**: Angle of rotation around the $C_\alpha-C$ bond.
A **Ramachandran plot** maps allowed $(\phi, \psi)$ angles to prevent steric overlap.

Question 14

Purely Ketogenic Amino Acids

Accepted Answer

**Leucine (Leu, L)** and **Lysine (Lys, K)** are purely ketogenic. They degrade strictly into acetyl-CoA or acetoacetate and **cannot** be converted into glucose via gluconeogenesis.

Question 15

Amphibolic (Glucogenic & Ketogenic) Amino Acids

Accepted Answer

Five amino acids yield precursors for both glucose and ketone body synthesis: **Isoleucine (Ile)**, **Phenylalanine (Phe)**, **Threonine (Thr)**, **Tryptophan (Trp)**, and **Tyrosine (Tyr)** (Mnemonic: *PhITTT*).

Question 16

Non-Intuitive Single-Letter Codes

Accepted Answer

• **D**: Aspartic acid
• **E**: Glutamic acid
• **F**: Phenylalanine
• **K**: Lysine
• **N**: Asparagine
• **Q**: Glutamine
• **R**: Arginine
• **W**: Tryptophan
• **Y**: Tyrosine

Question 17

Branched-Chain Amino Acids (BCAAs) & Clinical Tie-in

Accepted Answer

**Leucine**, **Isoleucine**, and **Valine** are BCAAs degraded primarily in muscle rather than liver. Defective oxidation of BCAAs by the branched-chain $\alpha$-keto acid dehydrogenase complex causes **Maple Syrup Urine Disease (MSUD)**.

Question 18

Neurotransmitter & Hormone Precursors

Accepted Answer

• **Tyrosine** $\rightarrow$ L-DOPA $\rightarrow$ Dopamine $\rightarrow$ Norepinephrine $\rightarrow$ Epinephrine, Melanin, $T_3/T_4$
• **Tryptophan** $\rightarrow$ Serotonin $\rightarrow$ Melatonin, Niacin ($NAD^+/NADP^+$)
• **Histidine** $\rightarrow$ Histamine
• **Glutamate** $\rightarrow$ GABA

Question 19

Typical $pK_a$ Values of Amino Acid Functional Groups

Accepted Answer

• $\alpha$-carboxyl group: $pK_a \approx 2.0$
• $\alpha$-amino group: $pK_a \approx 9.0 - 10.0$
• Asp/Glu side chain ($-	ext{COOH}$): $pK_a \approx 4.0$
• His imidazole: $pK_a \approx 6.0$
• Cys thiol ($-	ext{SH}$): $pK_a \approx 8.3$
• Lys amino ($-	ext{NH}_3^+$): $pK_a \approx 10.5$
• Arg guanidino: $pK_a \approx 12.5$

Question 20

Methionine & One-Carbon Metabolism

Accepted Answer

**Methionine (Met, M)** is a sulfur-containing non-polar amino acid encoded by the universal start codon (**AUG**). It reacts with ATP to form **S-adenosylmethionine (SAM)**, the primary methyl donor in methylation reactions.

Biochemistry - 20 Standard Amino Acids & Properties

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