Lysine, $\text{H}_2\text{N}(\text{CH}_2)_4\text{CH}(\text{NH}_2)\text{COOH}$, is _______. (Note: one or more of the following options may be correct.) (i) $\alpha$-Amino acid (ii) Basic amino acid (iii) Amino acid synthesised in the body (iv) $\beta$-Amino acid

Lysine, H₂N(CH₂)₄CH(NH₂)COOH, is ____. (Note: one or more of the following options may be correct.) (i) α-Amin

NCERT Exemplar · Q58

\text{H}_2\text{N}(\text{CH}_2)_4\text{CH}(\text{NH}_2)\text{COOH}

(i)

\alpha

-Amino acid

(ii) Basic amino acid

(iii) Amino acid synthesised in the body

(iv)

\beta

-Amino acid

Uttarakhand UbseMCQ· 1mImportance★★★★★

83% · 91/110 Questions

🔒 Locked · start free trial →

You're viewing a preview — the full solution, concept, methods & PYQ mapping are locked.

Start your 14-day free trial to unlock the full solution →

Concept understanding — Amino Acid Classification

Amino Acid Classification: From Intuition to Precision

Imagine you're building with LEGO blocks. You have many different pieces — some are long, some are short, some have bumps on the side, some are flat. But all of them have one thing in common: they all click onto the same base plate. That's exactly what amino acids are like. They are the building blocks of proteins, and every single one of them shares a common "base plate" — a core structure — but differs in a side chain that gives each its unique personality.

The Common Core: What Every Amino Acid Shares

Every amino acid has a central carbon atom (called the $\alpha$ -carbon) bonded to four groups:

An amino group ( $-NH_2$ )
A carboxyl group ( $-COOH$ )
A hydrogen atom ( $-H$ )
A variable side chain (called the R group)

The R group is what makes each of the 20 standard amino acids different. It's like the unique shape and colour of each LEGO piece. The classification of amino acids is really just a way of grouping them based on what their R groups are like.

The Big Picture: Why Classify?

You classify things to understand their behaviour. In a crowded room, you might group people by height, or by what they're wearing. Similarly, amino acids are classified to predict how they will behave in water, how they interact with each other, and what role they play in a protein's structure. The most fundamental classification is based on polarity — essentially, how the R group interacts with water.

The Five Major Classes (with Intuition)

1. Nonpolar (Hydrophobic) Amino Acids

Intuition: These R groups are like oil. They hate water. They prefer to hide inside a protein, away from the watery environment of the cell.

What they look like: Their R groups are made mostly of carbon and hydrogen — no charged or polar groups. They are "greasy."

Examples: Glycine (the smallest, just a hydrogen), Alanine, Valine, Leucine, Isoleucine, Methionine, Proline (has a ring that connects back to the amino group), Phenylalanine, Tryptophan.

Note

Proline is unique — its R group forms a ring that includes the amino nitrogen, making it rigid and often causing "kinks" in protein chains.

2. Polar, Uncharged Amino Acids

Intuition: These R groups are like sugar. They dissolve in water but carry no net electric charge. They are "friendly" with water but don't have a full positive or negative charge.

What they look like: Their R groups contain oxygen, nitrogen, or sulfur atoms that can form hydrogen bonds with water.

Examples: Serine, Threonine, Cysteine (has a sulfur atom that can form disulfide bonds), Asparagine, Glutamine.

Watch out

Cysteine is often grouped here, but its sulfur atom can form a special covalent bond (disulfide bridge) with another cysteine. This is a strong, permanent link — not a weak interaction like hydrogen bonds.

3. Positively Charged (Basic) Amino Acids

Intuition: These R groups carry a positive charge at physiological pH (around 7.4). They are like magnets with a "+" sign — they attract negatively charged things.

What they look like: Their R groups contain an extra amino group ( $-NH_2$ ) that picks up a proton ( $H^+$ ) to become $-NH_3^+$ .

Examples: Lysine, Arginine, Histidine.

Important

Histidine is special — its charge changes near physiological pH. This makes it a common player in enzyme active sites where it can act as a proton donor or acceptor.

4. Negatively Charged (Acidic) Amino Acids

Intuition: These R groups carry a negative charge at physiological pH. They are like magnets with a "−" sign — they attract positively charged things.

What they look like: Their R groups contain an extra carboxyl group ( $-COOH$ ) that loses a proton to become $-COO^-$ .

Examples: Aspartic acid, Glutamic acid.

5. Aromatic Amino Acids

Intuition: These have a ring structure (a benzene ring) in their R group. They absorb ultraviolet light — a property used to measure protein concentration.

What they look like: They contain a planar, ring-shaped structure.

Examples: Phenylalanine, Tyrosine, Tryptophan.

Tip

Tyrosine and Tryptophan absorb UV light at 280 nm. This is how scientists measure protein concentration in a lab — a quick and dirty method.

--- …

Why this formula?

Amino Acid Classification: Why the Groupings Make Sense

Amino acids are the building blocks of proteins, and their classification isn't arbitrary — it's based on the chemical properties of their side chains (R-groups). Understanding why these groups behave as they do is key to mastering biochemistry for exams.

The Core Idea: The R-Group Dictates Everything

Every amino acid has a common backbone:

Amino group ( $\text{NH}_2$ )
Carboxyl group ( $\text{COOH}$ )
Hydrogen atom ( $\text{H}$ )
Variable side chain ( $\text{R}$ )

The R-group determines:

Polarity
Charge at physiological pH (~7.4)
Hydrogen bonding ability
Hydrophobicity/hydrophilicity

The Five Major Classes (and Why They Exist)

1. Nonpolar, Aliphatic (Hydrophobic) R-Groups

Examples: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline

Why they're nonpolar:

The R-group consists of only carbon and hydrogen (hydrocarbon chains).
Carbon and hydrogen have similar electronegativity ( $\chi_C \approx 2.55$ , $\chi_H \approx 2.20$ ), so no significant dipole forms.
Water is polar; "like dissolves like" — these side chains avoid water and cluster in protein interiors.

Key exam point: Methionine has a sulfur atom, but the $\text{CH}_3\text{SCH}_2\text{CH}_2-$ group is still nonpolar because the C–S bond is nearly nonpolar.

2. Aromatic R-Groups

Examples: Phenylalanine, Tyrosine, Tryptophan

Why they're special:

Contain benzene rings (conjugated $\pi$ systems).
The delocalized electrons make them planar and rigid.
Phenylalanine is purely hydrophobic (no polar groups on ring).
Tyrosine has an –OH group → can form hydrogen bonds (partially polar).
Tryptophan has an indole ring with a nitrogen — can donate H-bonds.

Why they absorb UV light: The conjugated $\pi$ system has a small HOMO-LUMO gap, absorbing at ~280 nm — used to measure protein concentration.

3. Polar, Uncharged R-Groups

Examples: Serine, Threonine, Cysteine, Asparagine, Glutamine

Why they're polar but uncharged:

Contain electronegative atoms (O, N, S) that create partial charges.
Serine/Threonine: –OH group can donate and accept hydrogen bonds.
Cysteine: –SH group can form disulfide bonds ( $\text{–S–S–}$ ) — critical for protein structure.
Asparagine/Glutamine: –CONH $_2$ group has both carbonyl oxygen (H-bond acceptor) and amide hydrogen (H-bond donor).

Why they're uncharged at pH 7: The –OH, –SH, and –CONH $_2$ groups do not ionize significantly at physiological pH.

4. Positively Charged (Basic) R-Groups

Examples: Lysine, Arginine, Histidine

Why they're basic (proton acceptors):

Lysine: Has an $\epsilon$ -amino group ( $\text{–CH}_2\text{CH}_2\text{CH}_2\text{CH}_2\text{NH}_2$ ). The lone pair on nitrogen accepts a proton: $\text{–NH}_2 + \text{H}^+ \rightleftharpoons \text{–NH}_3^+$ pKa ≈ 10.5 → protonated at pH 7.
Arginine: Guanidino group ( $\text{–NH–C(NH}_2\text{)=NH}$ ) is resonance-stabilized when protonated — extremely basic (pKa ≈ 12.5).
Histidine: Imidazole ring has pKa ≈ 6.0 — unique because it can be neutral or positively charged near physiological pH, making it a key catalytic residue in enzymes.

5. Negatively Charged (Acidic) R-Groups

Examples: Aspartic Acid, Glutamic Acid

Why they're acidic (proton donors):

Contain a second carboxyl group ( $\text{–COOH}$ ).
At pH 7, the carboxyl group loses its proton: $\text{–COOH} \rightleftharpoons \text{–COO}^- + \text{H}^+$ …

Start your 14-day free trial to unlock the full solution →

Lysine is a basic, $\alpha$ -amino acid that cannot be synthesised in the human body. The correct options are (A) and (B).

Lysine is one of the 20 standard amino acids, and its structure tells you almost everything you need to know. The formula given is $\text{H}_2\text{N}(\text{CH}_2)_4\text{CH}(\text{NH}_2)\text{COOH}$ . Let’s break down what each part means and why the options fall the way they do.

The key idea: an $\alpha$ -amino acid has the amino group ( $-\text{NH}_2$ ) attached to the carbon atom next to the carboxyl group ( $-\text{COOH}$ ). That carbon is called the $\alpha$ -carbon. In lysine, the central carbon in $\text{CH}(\text{NH}_2)\text{COOH}$ is that $\alpha$ -carbon — it carries both the carboxyl and one amino group. So it’s an $\alpha$ -amino acid, not a $\beta$ -amino acid (where the amino group would be on the second carbon away).

Now, why is it basic? Because there’s a second amino group at the end of the side chain: $(\text{CH}_2)_4\text{NH}_2$ . That extra $-\text{NH}_2$ can accept a proton, making the overall molecule basic. In fact, at physiological pH, lysine carries a net positive charge — it’s one of the three basic amino acids (along with arginine and histidine).

What about synthesis? The human body cannot make lysine. It is an essential amino acid, meaning it must come from the diet. So option (C) is false.

Let’s go step by step.

Identify the $\alpha$ -carbon. The general structure of an $\alpha$ -amino acid is $\text{R}-\text{CH}(\text{NH}_2)\text{COOH}$ . In lysine, the $\text{CH}(\text{NH}_2)\text{COOH}$ part matches exactly — the amino group is on the carbon adjacent to the carboxyl. So it is an $\alpha$ -amino acid. …

Start your 14-day free trial to unlock the full solution →

Here are the common mistakes students make on this question, along with how to avoid each.

Mistake 1: Confusing $\alpha$ -Amino vs $\beta$ -Amino Acids

The Mistake:

Students see the long carbon chain $(\text{CH}_2)_4$ and assume the amino group is far from the carboxyl group, incorrectly selecting β-amino acid (Option D) or rejecting α-amino acid (Option A).

Why it happens:

They focus on the total chain length instead of the position of the first amino group relative to the carboxyl carbon.

How to Avoid:

Always locate the carboxyl carbon first (the carbon of $-\text{COOH}$ ).
The α-carbon is the carbon immediately next to the carboxyl carbon.
In lysine, the structure is: $\text{H}_2\text{N} - \text{CH}_2 - \text{CH}_2 - \text{CH}_2 - \text{CH}_2 - \text{CH}(\text{NH}_2) - \text{COOH}$ The carbon attached to $\text{NH}_2$ and $\text{COOH}$ is the α-carbon.
Rule: If the amino group is on the α-carbon, it is an α-amino acid. The second amino group on the side chain does not change this classification.

Correct choice: (A) is correct. (D) is wrong.

Mistake 2: Misclassifying Lysine as Neutral or Acidic

The Mistake:

Students see two amino groups and one carboxyl group but forget the basicity of the side chain, marking lysine as neutral or acidic.

Why it happens:

They only count the groups without considering the pKa values or the net charge at physiological pH.

How to Avoid:

Amino acids are classified by the nature of their R-group (side chain).
Lysine’s side chain is $(\text{CH}_2)_4\text{NH}_2$ . This is a basic group (it can accept a proton).
At physiological pH (~7.4), the side chain amino group is protonated ( $-\text{NH}_3^+$ ), giving lysine a net positive charge.
Memory aid: Basic amino acids have extra nitrogen atoms in their side chains (Lysine, Arginine, Histidine).

Correct choice: (B) is correct.

Mistake 3: Assuming All Amino Acids Are Essential

The Mistake: …

Start your 14-day free trial to unlock the full solution →

←Previous questionQ57 — Amino acids are classified as acidic, basic or neutral according to th…→Next questionQ59 — Which of the following monosaccharides are present as five membered cy…

Q.Lysine, $\text{H}_2\text{N}(\text{CH}_2)_4\text{CH}(\text{NH}_2)\text{COOH}$ , is _______. (Note: one or more of the following options may be correct.)

Concept understanding — Amino Acid Classification

Amino Acid Classification: From Intuition to Precision

The Common Core: What Every Amino Acid Shares

The Big Picture: Why Classify?

The Five Major Classes (with Intuition)

1. Nonpolar (Hydrophobic) Amino Acids

2. Polar, Uncharged Amino Acids

3. Positively Charged (Basic) Amino Acids

4. Negatively Charged (Acidic) Amino Acids

5. Aromatic Amino Acids

Why this formula?

Amino Acid Classification: Why the Groupings Make Sense

The Core Idea: The R-Group Dictates Everything

The Five Major Classes (and Why They Exist)

1. Nonpolar, Aliphatic (Hydrophobic) R-Groups

2. Aromatic R-Groups

3. Polar, Uncharged R-Groups

4. Positively Charged (Basic) R-Groups

5. Negatively Charged (Acidic) R-Groups

Concept: Classification of Amino Acids

Method: Structural Analysis & Classification

Mistake 1: Confusing $\alpha$ -Amino vs $\beta$ -Amino Acids

Mistake 2: Misclassifying Lysine as Neutral or Acidic

Mistake 3: Assuming All Amino Acids Are Essential

Q.Lysine, H2N(CH2)4CH(NH2)COOH\text{H}_2\text{N}(\text{CH}_2)_4\text{CH}(\text{NH}_2)\text{COOH}H2​N(CH2​)4​CH(NH2​)COOH, is _______. (Note: one or more of the following options may be correct.)

🎓Unlock everything free for 14 days

Q.Lysine, $\text{H}_2\text{N}(\text{CH}_2)_4\text{CH}(\text{NH}_2)\text{COOH}$ , is _______. (Note: one or more of the following options may be correct.)

Unlock everything free for 14 days