Biochemistry Basics for NMAT: NMAT Chemistry Review

Why Biochemistry Matters for the NMAT

Biochemistry shows up on the NMAT because it connects chemistry to living systems. Many NMAT questions test whether you can
apply core chemical principles—bonding, polarity, acids and bases, thermodynamics, kinetics, and equilibrium—to biological
molecules and processes. You do not need to memorize every pathway detail, but you do need a strong grasp of biomolecules
(carbohydrates, lipids, proteins, and nucleic acids), enzyme behavior, energy concepts (ATP, redox carriers), and basic
metabolism and regulation.

In NMAT-style problem solving, biochemistry often appears through interpretation: recognizing functional groups, predicting
solubility, understanding how pH affects molecules, or reasoning about how temperature and inhibitors affect enzymes.
If you treat biochemistry as “applied chemistry,” you will find it far more manageable.

Core Chemical Concepts You Must Bring Into Biochemistry

Before diving into biomolecules, keep these chemistry fundamentals ready:

• Polarity and intermolecular forces: hydrogen bonding, dipole-dipole interactions, ionic interactions, and hydrophobic effects.
• Acid-base behavior: pH, pKa, protonation states, buffers, and the idea that charge changes with pH.
• Thermodynamics: spontaneity (ΔG), equilibrium, and coupling (using a favorable process to drive an unfavorable one).
• Kinetics: reaction rate, activation energy, catalysts, and factors affecting rate (temperature, concentration).
• Redox: oxidation/reduction, electron carriers (NADH, FADH2 conceptually), and energy release from electron transfer.

Most biochemistry questions are built from these. When you feel lost, “translate” the biology back into chemistry terms.

Water: The Biochemical Solvent

Water is the stage for nearly all biochemical reactions. Its polarity and hydrogen bonding explain why many biomolecules
fold the way they do and why ions dissolve. Key properties of water that matter for NMAT:

• Polarity: makes water excellent at dissolving ionic and polar compounds.
• Hydrogen bonding: contributes to high boiling point and stabilizes biomolecular structures (like DNA base pairing).
• Hydrophobic effect: nonpolar molecules cluster together in water, driving membrane formation and protein folding.
• Autoionization: water produces H3O+ and OH−, forming the basis for pH.

Biological systems are extremely sensitive to pH because proton concentration changes charges on amino acids and other
functional groups, altering structure and function.

pH, pKa, and Buffers in Biological Systems

The NMAT frequently tests buffer reasoning and pH effects on biomolecules. A quick framework:

• pH: measures acidity (lower pH = more H+).
• pKa: the pH where a group is 50% protonated and 50% deprotonated.
• Buffer: a mixture of weak acid and its conjugate base that resists pH changes.

At pH values below pKa, groups tend to be protonated; above pKa, they tend to be deprotonated. This matters for amino acids:
some side chains gain or lose protons in physiological pH ranges, changing protein charge and enzyme activity.

Common biological buffers include bicarbonate in blood and phosphate in cells. On exams, focus less on memorizing names and
more on recognizing “weak acid + conjugate base” logic and how adding acid/base shifts equilibrium.

Carbohydrates: Structure and Function

Carbohydrates are polyhydroxy aldehydes or ketones and their derivatives. They serve as energy sources, storage molecules,
and structural components. NMAT questions often test recognition of functional groups, glycosidic bonds, and reducing vs
non-reducing sugars.

• Monosaccharides: glucose, fructose, galactose (basic examples).
• Disaccharides: formed via glycosidic bonds; example logic includes “two monosaccharides joined with loss of water.”
• Polysaccharides: starch, glycogen (storage); cellulose (structure).

Key exam idea: carbohydrates have many hydroxyl groups, making them generally polar and water-soluble. Large polymers can
be less soluble depending on structure and branching.

Lipids: Membranes, Energy Storage, and Signaling

Lipids are largely nonpolar molecules. They do not fit a single strict structural category, but share the common theme of
hydrophobic character. NMAT emphasizes their roles in membranes and energy storage.

• Fatty acids: long hydrocarbon chains with a carboxyl group. Saturated fats have no double bonds; unsaturated fats have one or more double bonds.
• Triglycerides: glycerol + three fatty acids; major energy storage form.
• Phospholipids: amphipathic molecules (hydrophilic head, hydrophobic tails) that form bilayers.
• Steroids: four-ring structures; include cholesterol and steroid hormones (conceptually).

A classic NMAT concept: unsaturated fatty acids introduce “kinks” that reduce packing, increasing membrane fluidity and
often lowering melting point. Saturated chains pack tightly, making membranes more rigid.

Proteins and Amino Acids: The Workhorses of the Cell

Proteins perform most cellular functions: enzymes, transporters, structural elements, and signaling molecules. They are
polymers of amino acids linked by peptide bonds.

Each amino acid has an amino group, a carboxyl group, a hydrogen, and an R group attached to the alpha carbon. The R group
determines properties: nonpolar, polar, acidic, or basic. For NMAT, you do not need to memorize every amino acid structure,
but you should understand how side chains affect protein folding and charge.

• Peptide bond formation: condensation reaction between carboxyl and amino groups (water released).
• Protein structure levels: primary (sequence), secondary (alpha helices/beta sheets), tertiary (3D folding), quaternary (multiple subunits).
• Forces stabilizing structure: hydrogen bonds, ionic interactions, hydrophobic interactions, and disulfide bonds.

Protein denaturation can occur with heat, extreme pH, or chemicals. Denaturation disrupts higher-level structure but does not
break peptide bonds under mild conditions.

Enzymes: Catalysts and NMAT Favorites

Enzymes are biological catalysts that speed up reactions by lowering activation energy. They do not change the overall
ΔG or the equilibrium constant; they simply help the system reach equilibrium faster.

Key NMAT points:

• Active site: region where substrate binds and reaction occurs.
• Specificity: enzymes are selective for substrates due to shape and chemical environment.
• Optimal conditions: each enzyme has an optimal pH and temperature; extreme conditions reduce activity by denaturation.
• Michaelis-Menten ideas (conceptual): increasing substrate increases rate until saturation.

Inhibitors are common test material:

• Competitive inhibition: inhibitor resembles substrate and competes for active site; can often be overcome by increasing substrate concentration.
• Noncompetitive inhibition: inhibitor binds elsewhere and reduces enzyme activity; increasing substrate does not fully restore maximum activity.

You may also encounter cofactors and coenzymes (metal ions or organic helpers) that enable enzyme function. The takeaway:
some enzymes require additional components to work.

Nucleic Acids: DNA and RNA Essentials

Nucleic acids store and transmit genetic information. DNA and RNA are polymers of nucleotides, each composed of a sugar,
a phosphate group, and a nitrogenous base.

• DNA sugar: deoxyribose; RNA sugar: ribose (has an extra hydroxyl group).
• Base pairing: A pairs with T in DNA (A pairs with U in RNA); G pairs with C.
• Hydrogen bonding: stabilizes base pairing; stacking interactions also contribute to stability.
• Phosphodiester bonds: link nucleotides in the backbone, giving nucleic acids a negative charge.

The negative charge of the phosphate backbone makes nucleic acids very polar and water-friendly, but also means they interact
strongly with cations and proteins.

ATP and Energy Coupling

ATP (adenosine triphosphate) is the main energy currency of cells. NMAT questions often test conceptual understanding:
ATP hydrolysis releases usable free energy, not because “bonds contain energy” in a simplistic way, but because the products
are more stable (reduced electrostatic repulsion, resonance stabilization, and favorable hydration).

Cells use energy coupling: an unfavorable process (positive ΔG) can proceed if coupled to ATP hydrolysis (negative ΔG),
making the overall ΔG negative. This is a core thermodynamics application.

Metabolism Overview: Catabolism vs Anabolism

Metabolism is the sum of all chemical reactions in the body. It is often organized as:

• Catabolism: breakdown of molecules to release energy (often producing ATP and reduced carriers like NADH).
• Anabolism: building molecules, requiring energy input (often using ATP).

On the NMAT, you are more likely to see broad pathway logic rather than detailed step memorization. For example:
breaking down glucose produces energy; building macromolecules costs energy.

Glycolysis, Krebs Cycle, and Electron Transport: High-Level Concepts

You may encounter these terms. A high-level, test-friendly summary:

• Glycolysis: glucose is converted into smaller molecules (like pyruvate), producing some ATP and electron carriers.
• Krebs (Citric Acid) Cycle: further oxidation of carbon compounds, generating more electron carriers and some energy.
• Electron Transport Chain (ETC): electron carriers donate electrons through membrane complexes, building a gradient used to make ATP.

The key chemistry idea is redox: electrons move from higher-energy carriers to lower-energy acceptors, releasing energy.
That energy is captured in a gradient (often proton-based) and then converted into ATP.

Biochemical Regulation: Feedback and Allosteric Control

Living systems must control reaction rates. Two common regulation patterns appear in NMAT-style questions:

• Feedback inhibition: the end product of a pathway inhibits an earlier enzyme to prevent overproduction.
• Allosteric regulation: a molecule binds at a site other than the active site, changing enzyme shape and activity.

This ties to equilibrium and kinetics: regulation changes effective enzyme activity, shifting how fast products form under
cellular conditions.

Laboratory and Test-Relevant Biochemistry Skills

Some NMAT questions involve interpreting simple lab ideas:

• Solubility: polar/charged molecules dissolve well in water; nonpolar molecules dissolve better in nonpolar solvents.
• Protein denaturation: heat/pH changes disrupt folding, often decreasing enzymatic activity.
• pH effects: ionizable groups change charge; this affects binding, folding, and catalysis.
• Basic separation logic: size, charge, and polarity influence separation methods (conceptually).

Even without deep lab technique knowledge, you can answer many questions by reasoning from chemistry: what binds to what,
what dissolves where, and how charge changes with pH.

Common NMAT-Style Biochemistry Question Themes

• Functional groups: identifying alcohols, carboxylic acids, amines, phosphates, and how they behave.
• Acid-base and buffers: predicting protonation states and buffer responses.
• Enzyme behavior: interpreting effects of temperature, pH, substrate concentration, and inhibitors.
• Macromolecule properties: predicting solubility and interactions from structure.
• Energy concepts: ATP coupling, redox logic, and why electron transfer can produce energy.

High-Yield Tips for Studying Biochemistry for the NMAT

• Master concepts over memorization: understand why molecules behave as they do based on polarity, charge, and bonding.
• Practice pH thinking: always ask “what is protonated/deprotonated at this pH?”
• Enzyme questions are predictable: review inhibition types and saturation logic.
• Use quick comparisons: saturated vs unsaturated fats, DNA vs RNA, catabolism vs anabolism.
• Translate biology into chemistry: if a question mentions “binding,” think intermolecular forces; if it mentions “rate,” think kinetics.

Mini Summary

Biochemistry for the NMAT is best approached as applied chemistry. Focus on water and pH, biomolecule structures and
properties, enzyme behavior, and energy concepts like ATP and redox. Learn the big-picture logic of metabolism and
regulation, and practice interpreting common question patterns. With a chemistry-first mindset, most biochemistry topics
become consistent and testable rather than overwhelming.

Problem Set 1: Biomolecules and Functional Groups

Question 1. Which biomolecule class is most directly associated with forming cell membranes?

A. Carbohydrates
B. Lipids
C. Proteins
D. Nucleic acids

Question 2. A molecule contains many –OH (hydroxyl) groups and is highly soluble in water. It is most likely a:

A. Carbohydrate
B. Triacylglycerol (triglyceride)
C. Steroid
D. Nonpolar lipid

Question 3. The bond that links amino acids together in a protein is a:

A. Glycosidic bond
B. Phosphodiester bond
C. Peptide bond
D. Hydrogen bond

Question 4. Which best describes a phospholipid?

A. Entirely nonpolar; dissolves well in hexane only
B. Entirely polar; dissolves well in water only
C. Amphipathic; has both hydrophilic and hydrophobic regions
D. A polymer of nucleotides

Question 5. DNA and RNA are polymers of:

A. Amino acids
B. Fatty acids
C. Nucleotides
D. Monosaccharides

Answer Key 1

Answer 1. B. Lipids

Answer 2. A. Carbohydrate

Answer 3. C. Peptide bond

Answer 4. C. Amphipathic; has both hydrophilic and hydrophobic regions

Answer 5. C. Nucleotides

Problem Set 2: Water, pH, pKa, and Buffers

Question 1. A solution with pH 3 is how many times more acidic (in terms of [H+]) than a solution with pH 6?

A. 3 times
B. 10 times
C. 100 times
D. 1000 times

Question 2. If pH is lower than the pKa of an acid group, that group will be predominantly:

A. Deprotonated
B. Protonated
C. Neutralized by water
D. Oxidized

Question 3. Which pair forms a buffer system?

A. Strong acid + strong base
B. Weak acid + its conjugate base
C. Weak base + strong acid only
D. Salt + water only

Question 4. A protein has many acidic side chains. At a very low pH, its overall charge is most likely to become:

A. More negative because acids lose protons
B. More positive because groups become protonated
C. Neutral because all charges disappear
D. Unchanged because proteins are not affected by pH

Question 5. A buffer resists changes in pH primarily because it:

A. Removes all H+ from solution instantly
B. Contains components that can react with added H+ or OH−
C. Prevents water from ionizing
D. Converts strong acids into strong bases

Answer Key 2

Answer 1. D. 1000 times (10⁶⁻³ = 10³)

Answer 2. B. Protonated

Answer 3. B. Weak acid + its conjugate base

Answer 4. B. More positive because groups become protonated

Answer 5. B. Contains components that can react with added H+ or OH−

Problem Set 3: Enzymes and Inhibition

Question 1. Enzymes speed up reactions by:

A. Increasing ΔG of the reaction
B. Lowering activation energy
C. Increasing equilibrium constant (K)
D. Changing reactants into different products

Question 2. Which statement is true about enzymes?

A. They change the reaction’s equilibrium position
B. They are consumed during the reaction
C. They increase reaction rate without changing ΔG
D. They make endergonic reactions spontaneous without coupling

Question 3. In competitive inhibition, the inhibitor typically:

A. Binds irreversibly to the enzyme’s active site and destroys it
B. Binds to the active site and competes with the substrate
C. Binds to an allosteric site and prevents substrate binding completely
D. Increases Vmax and decreases Km

Question 4. If you increase substrate concentration and the inhibition effect largely disappears, the inhibitor is most likely:

A. Competitive
B. Noncompetitive
C. Uncompetitive only
D. A cofactor

Question 5. An enzyme has maximum activity at pH 7. If placed at pH 2, its activity will most likely:

A. Increase because acids always speed up enzymes
B. Decrease due to changes in protonation and possible denaturation
C. Stay the same because enzymes are stable at all pH values
D. Stop permanently because peptide bonds will instantly break

Answer Key 3

Answer 1. B. Lowering activation energy

Answer 2. C. They increase reaction rate without changing ΔG

Answer 3. B. Binds to the active site and competes with the substrate

Answer 4. A. Competitive

Answer 5. B. Decrease due to changes in protonation and possible denaturation

Problem Set 4: Proteins, Folding, and Interactions

Question 1. Which interaction is most associated with the hydrophobic effect in protein folding?

A. Clustering of nonpolar side chains away from water
B. Formation of phosphodiester bonds
C. Repulsion between opposite charges
D. Breaking of all hydrogen bonds in water

Question 2. Disulfide bonds form between side chains that contain:

A. Phosphate groups
B. Sulfur atoms (thiol groups)
C. Extra hydroxyl groups
D. Aromatic rings only

Question 3. Secondary protein structure (alpha helices and beta sheets) is stabilized mainly by:

A. Ionic bonds between R groups
B. Hydrogen bonds along the backbone
C. Peptide bond breaking
D. Disulfide bonds only

Question 4. Which change is most likely to denature a protein?

A. Mild temperature decrease from 25°C to 20°C
B. Extreme pH change from pH 7 to pH 1
C. Adding a small amount of inert salt at low concentration
D. Storing the protein briefly at room temperature

Question 5. At physiological pH (~7.4), a side chain with pKa = 10.5 is most likely:

A. Deprotonated (neutral or negative depending on group)
B. Protonated
C. Always neutral regardless of pH
D. Oxidized

Answer Key 4

Answer 1. A. Clustering of nonpolar side chains away from water

Answer 2. B. Sulfur atoms (thiol groups)

Answer 3. B. Hydrogen bonds along the backbone

Answer 4. B. Extreme pH change from pH 7 to pH 1

Answer 5. B. Protonated (pH < pKa, so protonated predominates)

Problem Set 5: Nucleic Acids and Bioenergetics

Question 1. In DNA, adenine (A) pairs with:

A. Cytosine (C)
B. Guanine (G)
C. Thymine (T)
D. Uracil (U)

Question 2. The bond that links nucleotides together in DNA/RNA is a:

A. Peptide bond
B. Phosphodiester bond
C. Glycosidic bond (between monosaccharides)
D. Disulfide bond

Question 3. Compared with DNA, RNA typically:

A. Contains ribose and uracil
B. Contains deoxyribose and thymine
C. Is always double-stranded
D. Has no phosphate groups

Question 4. ATP hydrolysis is often used to drive an unfavorable reaction because cells use:

A. Buffering
B. Energy coupling
C. Denaturation
D. Competitive inhibition

Question 5. Which statement best describes the role of enzymes in ATP-coupled processes?

A. Enzymes create ATP from nothing by changing ΔG laws
B. Enzymes help couple reactions by organizing reactants and lowering activation energy
C. Enzymes increase ΔG to make reactions faster
D. Enzymes stop the need for substrates

Answer Key 5

Answer 1. C. Thymine (T)

Answer 2. B. Phosphodiester bond

Answer 3. A. Contains ribose and uracil

Answer 4. B. Energy coupling

Answer 5. B. Enzymes help couple reactions by organizing reactants and lowering activation energy

NMAT Chemistry Review: NMAT Study Guide