Module 9: Biological Molecules & Lab Techniques
Part 1: Biological Molecules in Organic Chemistry
Carbohydrates
Carbohydrates are one of the most important classes of biological molecules. They serve as energy sources, structural components, and recognition molecules in cell signaling. Understanding their structure, stereochemistry, and reactivity is essential for both organic chemistry and MCAT-level biochemistry.
1. What Are Carbohydrates?
Carbohydrates are polyhydroxy aldehydes or ketones — molecules that contain:
- A carbonyl group (C=O) as either an aldehyde (aldose) or a ketone (ketose),
- And multiple hydroxyl groups (–OH).
$$\ce{(CH2O)_n} \quad \text{(where } n \geq 3 \text{)}$$
MCAT Insight: All monosaccharides are either aldoses or ketoses, and most are chiral molecules, meaning stereochemistry matters a lot.
Classification of Monosaccharides
By Carbon Number:
| Carbon Count | Name | Example |
|---|---|---|
| 3 | Triose | Glyceraldehyde |
| 4 | Tetrose | Erythrose |
| 5 | Pentose | Ribose |
| 6 | Hexose | Glucose, Fructose |
By Carbonyl Group:
| Carbonyl Type | Name | Example |
|---|---|---|
| Aldehyde | Aldose | Glucose |
| Ketone | Ketose | Fructose |
3. D and L Configuration
Carbohydrates are assigned D or L configuration based on the chiral center farthest from the carbonyl group.
- If the OH group on the last chiral carbon is on the right → D.
- If it’s on the left → L.
MCAT Favorite: Most naturally occurring sugars are D-isomers.
4. Fischer Projections and Epimers
Fischer Projections:
- Vertical lines = going into the plane (away from you).
- Horizontal lines = coming out of the plane (toward you).
- Aldehyde (CHO) is typically at the top.
Epimers:
Epimers are diastereomers that differ at only one chiral center.
Example:
- D-Glucose and D-Galactose differ at carbon 4 → C-4 epimers.
- D-Glucose and D-Mannose differ at carbon 2 → C-2 epimers.
MCAT Strategy: Be able to identify epimers from Fischer projections by spotting the one carbon where the OH/H groups are flipped.
5. Hemiacetal Formation & Ring Closure
Monosaccharides exist in equilibrium between linear (open-chain) and cyclic (ring) forms.
- Aldoses form hemiacetals by internal attack of an OH on the carbonyl.
- Ketoses form hemiketals.
This leads to the formation of 5-membered (furanose) or 6-membered (pyranose) rings.
Mechanism Summary:
- Nucleophilic OH group attacks the carbonyl carbon.
- A new C–O bond forms, creating a ring.
- The carbonyl becomes a new chiral center called the anomeric carbon.
6. Alpha and Beta Anomers
When the ring closes, two possible stereoisomers form at the anomeric carbon:
- α-anomer: OH group on anomeric carbon is trans (opposite side) to CH₂OH.
- β-anomer: OH is cis (same side) to CH₂OH.
MCAT Tip: Anomers are a special type of epimer — they differ only at the anomeric carbon.
7. Mutarotation
Mutarotation is the interconversion between α and β anomers in aqueous solution via the open-chain form.
$$\ce{α-D-glucose <=> open-chain <=> β-D-glucose}$$
MCAT loves this: mutarotation explains why glucose shows optical rotation even though it’s mostly in cyclic form.
8. Reducing Sugars
A sugar is called reducing if it has a free anomeric carbon — meaning it can be oxidized to a carboxylic acid.
- All monosaccharides are reducing sugars.
- Disaccharides like maltose (free anomeric carbon) are reducing.
- Sucrose is non-reducing because both anomeric carbons are locked in the glycosidic bond.
Benedict’s and Tollen’s Tests:
- Positive tests indicate reducing sugar (aldehyde or α-hydroxy ketone group is present).
- Used to detect glucose in urine (diabetes screening).
Summary Table: Monosaccharide Key Concepts
| Term | Definition |
|---|---|
| Aldose | Monosaccharide with an aldehyde group |
| Ketose | Monosaccharide with a ketone group |
| Epimer | Diastereomer differing at one chiral center |
| Anomer | Isomer differing at the anomeric carbon (α vs. β) |
| Reducing Sugar | Sugar with a free anomeric OH; can be oxidized |
| Mutarotation | Interconversion between α and β forms |
| Pyranose/Furanose | 6-membered / 5-membered ring forms of sugars |
Disaccharides and Polysaccharides
Carbohydrates do not only exist as simple monosaccharides. They can link together via glycosidic bonds to form disaccharides, oligosaccharides, and polysaccharides. The type of linkage, branching, and stereochemistry determine their chemical reactivity and biological role — all of which are tested on the MCAT.
1. Glycosidic Bond Formation
A glycosidic bond is a covalent bond formed between the anomeric carbon of a sugar and another molecule (which could be another sugar, a base, or an alcohol).
Formation Reaction:
- Dehydration reaction (loss of water)
- The anomeric OH reacts with an alcohol group (typically another sugar’s –OH)
$$\ce{Monosaccharide-OH + Monosaccharide-OH -> Disaccharide + H2O}$$
MCAT Note: This is a condensation reaction (water is lost), and the reverse process — hydrolysis — breaks the bond.
2. Naming Glycosidic Linkages
Linkages are named based on:
- The anomeric configuration (α or β),
- The carbons involved in bonding (usually 1→4, 1→6, etc.)
Examples:
- α(1→4) linkage: Anomeric carbon (C1) of the first sugar is in alpha form and bonded to the OH on C4 of the second sugar.
- β(1→4) linkage: Same as above but the anomeric carbon is in beta configuration.
3. Important Disaccharides to Know
Sucrose
- Glucose + Fructose
- Linkage: α(1→2)β
- Non-reducing (both anomeric carbons involved)
$$\ce{α-D-glucose + β-D-fructose -> sucrose + H2O}$$
Lactose
- Galactose + Glucose
- Linkage: β(1→4)
- Reducing sugar (free anomeric OH on glucose)
Maltose
- Glucose + Glucose
- Linkage: α(1→4)
- Reducing sugar
| Disaccharide | Monomers | Linkage | Reducing? |
|---|---|---|---|
| Sucrose | Glucose + Fructose | α(1→2)β | ❌ No |
| Lactose | Galactose + Glucose | β(1→4) | ✅ Yes |
| Maltose | Glucose + Glucose | α(1→4) | ✅ Yes |
MCAT Strategy: You’re often tested on whether a disaccharide is reducing, and what type of linkage it uses.
4. Polysaccharides
These are long chains of monosaccharide units linked via glycosidic bonds. Structure and function vary based on the type of sugar, type of linkage, and degree of branching.
Starch
- Storage form of glucose in plants
- Made of α(1→4) linked glucose
- Two types:
- Amylose: unbranched
- Amylopectin: branched via α(1→6) every ~30 units
Glycogen
- Storage form of glucose in animals
- Similar to amylopectin but more highly branched — α(1→6) branches every ~10 glucose units
- Allows rapid release of glucose (important for MCAT metabolism passages)
Cellulose
- Structural carbohydrate in plants
- β(1→4) linked glucose
- Unbranched and linear, forms hydrogen-bonded fibrils
- Humans cannot digest cellulose due to lack of cellulase enzyme
| Polysaccharide | Monomer | Linkage | Branching | Digestible? |
|---|---|---|---|---|
| Amylose | Glucose | α(1→4) | No | Yes |
| Amylopectin | Glucose | α(1→4), α(1→6) | Yes (moderate) | Yes |
| Glycogen | Glucose | α(1→4), α(1→6) | Yes (high) | Yes |
| Cellulose | Glucose | β(1→4) | No (linear) | No (in humans) |
5. Hydrolysis of Glycosidic Bonds
- Glycosidic bonds can be hydrolyzed under acidic conditions or by enzymes (e.g., amylase, lactase).
- Enzymes are highly specific for the type of bond:
- Lactase hydrolyzes β(1→4) bonds in lactose
- Maltase hydrolyzes α(1→4) bonds in maltose
MCAT Trap: Enzyme specificity means lactase cannot digest maltose, and vice versa.
Summary: What to Know for the MCAT
- Recognize the types of glycosidic bonds (α vs. β, 1→4 vs. 1→6).
- Know which disaccharides are reducing (lactose, maltose) vs. non-reducing (sucrose).
- Be able to compare polysaccharide structures (e.g., glycogen vs. cellulose).
- Understand that enzyme specificity determines digestibility.
Lipids
Lipids are a diverse group of hydrophobic or amphipathic organic molecules that play essential roles in energy storage, membrane structure, insulation, and signaling. Unlike carbohydrates and proteins, they are not defined by a specific repeating unit but rather by their solubility properties and general chemical features.
- Fatty Acids
Structure
Fatty acids consist of:
- A hydrocarbon tail (nonpolar)
- A carboxylic acid head (polar, acidic)
General Formula:
$$\ce{R-COOH}$$
Where R is a long alkyl chain (typically 12–20 carbons).
Saturated vs. Unsaturated
| Type | Structure | Properties |
|---|---|---|
| Saturated | No C=C double bonds | Solid at room temp, pack tightly (e.g., butter) |
| Unsaturated | One or more C=C double bonds | Liquid at room temp, kinked, less tightly packed (e.g., olive oil) |
MCAT Tip: Cis double bonds introduce kinks → reduce van der Waals interactions → lower melting point.
2. Triglycerides (Triacylglycerols)
Triglycerides are energy storage molecules formed by esterifying 3 fatty acids to glycerol.
Structure:
$$\ce{Glycerol + 3 R-COOH -> Triacylglycerol + 3 H2O}$$
- The reaction is a condensation reaction (loss of water).
- Stored in adipose tissue as fat droplets.
Energy Density: Triglycerides store ~2x more energy per gram than carbohydrates because they are more reduced (fewer oxygens, more hydrogens).
3. Phospholipids
Phospholipids are amphipathic molecules with:
- Two hydrophobic fatty acid tails
- One hydrophilic phosphate head (often modified with additional polar groups)
Key Type: Phosphatidylcholine
- Glycerol backbone
- Two fatty acids
- Phosphate + choline
MCAT Favorite: Phospholipids form lipid bilayers — key to cell membrane structure.
4. Micelles, Liposomes, and Bilayers
In aqueous environments, amphipathic lipids self-assemble:
- Micelles: spherical droplets with hydrophobic tails inward
- Bilayers: flat sheets, hydrophobic interior
- Liposomes: spherical bilayers enclosing an aqueous compartment
Know this self-assembly is driven by the hydrophobic effect — entropic stabilization in water.
5. Steroids
Steroids are a class of non-saponifiable lipids with a four-ring fused backbone (three 6-membered rings + one 5-membered ring).
Examples:
- Cholesterol: structural component of membranes, precursor to steroid hormones
- Testosterone, Estrogen: derived from cholesterol
- Cortisol, Aldosterone: adrenal corticosteroids
Cholesterol increases membrane fluidity at low temps and decreases it at high temps — this dual effect stabilizes membrane dynamics.
6. Saponification
Saponification is the base-catalyzed hydrolysis of triglycerides into:
- Glycerol
- Fatty acid salts (i.e., soap)
$$\ce{Triglyceride + 3 NaOH -> Glycerol + 3 R-COO^- Na^+}$$
MCAT Tip: Soaps are amphipathic → form micelles that trap grease in aqueous environments.
Summary Table: Lipid Classes and Functions
| Lipid Type | Structure | Function |
|---|---|---|
| Fatty Acids | Long hydrocarbon + COOH | Fuel, building block |
| Triglycerides | 3 FA + glycerol | Energy storage |
| Phospholipids | 2 FA + phosphate + glycerol | Membrane bilayers |
| Steroids | Four fused rings | Hormones, membrane fluidity |
| Saponified soaps | Fatty acid salts | Detergents, emulsification |
Proteins and Amino Acids
Proteins are polymers of amino acids, joined via amide (peptide) bonds. They perform virtually every function in the body: catalysis (enzymes), structure (keratin, collagen), signaling (hormones), transport (hemoglobin), immunity (antibodies), and more.
1. Structure of Amino Acids
All 20 standard amino acids share a general structure:
$$\ce{H2N-CHR-COOH}$$
Where:
- NH₂ is the amino group (base)
- COOH is the carboxylic acid group (acid)
- R is the side chain (defines the identity and properties)
- α-carbon is the central carbon (chiral in all but glycine)
MCAT Note: All natural amino acids are L-isomers and α-amino acids, meaning the amino group is attached to the α-carbon (carbon next to the COOH group).
2. Zwitterion Form and pKa Behavior
At physiological pH (~7.4), amino acids exist as zwitterions:
- The amino group is protonated: \ceNH3+\ce{NH3^+}\ceNH3+
- The carboxyl group is deprotonated: \ceCOO−\ce{COO^-}\ceCOO−
This makes the molecule overall neutral but with both positive and negative charges.
3. Acid-Base Properties & Isoelectric Point (pI)
Each amino acid has at least two ionizable groups, with characteristic pKa values:
- pKa₁ (COOH) ≈ 2
- pKa₂ (NH₃⁺) ≈ 9–10
The isoelectric point (pI) is the pH at which the molecule has no net charge.
Formula (for neutral amino acids):
$$\text{pI} = \frac{\text{pKa}_1 + \text{pKa}_2}{2}$$
Acidic amino acids (Asp, Glu) and basic ones (Lys, Arg, His) have side chain pKa values and thus different pI formulas.
4. Peptide Bond Formation
Amino acids link via peptide bonds formed through condensation reactions between:
- The amino group of one amino acid and
- The carboxylic acid of another
Reaction:
$$\ce{H2N-CHR-COOH + H2N-CHR’-COOH -> H2N-CHR-CONH-CHR’-COOH + H2O}$$
This results in a dipeptide, and water is lost.
MCAT Tip: Peptide bonds are planar and exhibit partial double bond character due to resonance, making them rigid and non-rotatable.
5. Levels of Protein Structure
| Level | Definition | Stabilized by |
|---|---|---|
| Primary | Linear sequence of amino acids | Peptide (covalent) bonds |
| Secondary | Local folding (α-helices, β-sheets) | Hydrogen bonds between backbone atoms |
| Tertiary | 3D folding of entire polypeptide | R-group interactions: H-bonds, hydrophobic forces, disulfide bridges |
| Quaternary | Multiple polypeptides forming a complex | Same as tertiary (non-covalent + disulfide) |
6. Denaturation
Protein denaturation is the disruption of secondary, tertiary, or quaternary structure — not primary.
Causes include:
- Heat
- pH changes
- Detergents
- Reducing agents (break disulfide bonds)
- Organic solvents
Denaturation affects function but does not break peptide bonds.
7. Classification of Amino Acids (Side Chain Properties)
| Group | Examples | Properties |
|---|---|---|
| Nonpolar (Hydrophobic) | Gly, Ala, Val, Leu, Ile, Met, Pro, Phe | Avoid water, found in interior of proteins |
| Polar Uncharged | Ser, Thr, Asn, Gln, Tyr, Cys | Participate in H-bonding |
| Acidic | Asp, Glu | Negatively charged at physiological pH |
| Basic | Lys, Arg, His | Positively charged at physiological pH |
Know which side chains are charged, which form disulfide bonds (Cys), and which are aromatic (Phe, Tyr, Trp).
MCAT Summary: Protein Concepts to Master
- Peptide bond formation = condensation reaction between NH₂ and COOH
- Zwitterions dominate at pH ~7.4
- pI = average of pKa’s → varies with acidic/basic residues
- Denaturation ≠ hydrolysis
- Know structure and function of all 20 amino acids (names, 1-letter codes, side chain features)
Nucleic Acids
Nucleic acids — DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) — store and transmit genetic information. Structurally, they are polymers of nucleotides, and their behavior can be understood through basic organic chemistry: nucleophilicity, hydrogen bonding, and phosphodiester linkage formation.
1. Nucleotide Structure
Each nucleotide is composed of:
- A nitrogenous base (purine or pyrimidine)
- A pentose sugar (ribose or deoxyribose)
- A phosphate group
General Formula:
$$\ce{Base – Sugar – Phosphate}$$
- If the phosphate is absent, the molecule is a nucleoside (base + sugar).
- If present, it’s a nucleotide.
2. Nitrogenous Bases
| Type | Base | Rings | Found In |
|---|---|---|---|
| Purines | Adenine (A), Guanine (G) | 2 | DNA & RNA |
| Pyrimidines | Cytosine (C), Thymine (T), Uracil (U) | 1 | T in DNA, U in RNA |
MCAT Tip: Purines = “PURe As Gold” (A and G); Pyrimidines = “CUT the Py” (C, U, T)
3. DNA vs. RNA
| Feature | DNA | RNA |
|---|---|---|
| Sugar | Deoxyribose (no 2′ OH) | Ribose (has 2′ OH) |
| Bases | A, T, G, C | A, U, G, C |
| Strandedness | Double-stranded | Single-stranded |
| Stability | More stable (no 2′ OH) | Less stable (prone to base hydrolysis) |
The 2′ hydroxyl group in RNA makes it chemically reactive under basic conditions → important in MCAT logic questions.
4. Phosphodiester Bond Formation
Nucleotides are linked via phosphodiester bonds, connecting the 3′ OH of one sugar to the 5′ phosphate of the next nucleotide.
Reaction:
$$\ce{Nucleotide-OH + Nucleotide-PPP -> Dinucleotide + PPi + H2O}$$
MCAT LOVES this: DNA and RNA synthesis is always 5′ → 3′, and new nucleotides are added to the 3′ end.
5. Base Pairing and Double Helix Structure
In DNA:
- A pairs with T via 2 hydrogen bonds
- G pairs with C via 3 hydrogen bonds
GC pairs are stronger → higher melting temperature (MCAT favorite in melting curve questions)
DNA strands are:
- Antiparallel (5′ to 3′ opposite 3′ to 5′)
- Held together by hydrogen bonding and base stacking
- Arranged in a right-handed double helix
6. Denaturation and Renaturation
Denaturation (melting):
- Caused by heat, pH, or organic solvents
- Disrupts hydrogen bonding, but not covalent phosphodiester bonds
Renaturation:
- Occurs when conditions return to normal
- Complementary strands reanneal
Melting temperature (Tm) increases with GC content
7. Important Biochemical Derivatives
| Molecule | Function |
|---|---|
| ATP (adenosine triphosphate) | Energy currency |
| NAD⁺, FAD | Electron carriers in metabolism |
| cAMP | Second messenger in signaling |
All of these are nucleotide-based molecules and retain the purine/pyrimidine + sugar + phosphate motif.
Summary Table: MCAT-Relevant Nucleic Acid Concepts
| Concept | Key Point |
|---|---|
| Nucleotide | Base + sugar + phosphate |
| Phosphodiester bond | Links 3′ OH to 5′ phosphate |
| Directionality | Synthesis = 5′ → 3′ |
| DNA vs. RNA | DNA lacks 2′ OH; RNA has uracil |
| Base pairing | A-T (2 H-bonds), G-C (3 H-bonds) |
| GC content | Higher GC = higher melting temperature (Tm) |
| Denaturation | Breaks H-bonds; reversible |
| ATP, NAD⁺, FAD, cAMP | Nucleotide-based biomolecules |
Part 2: Laboratory Techniques
Understanding lab techniques is essential for MCAT success. You’re expected not only to recognize what each method does, but also to interpret data, spot experimental flaws, and predict outcomes in passage-based questions.
This section will cover:
- Separation and Purification Techniques
- Spectroscopy Methods
- Chromatography Techniques
- Electrophoresis and Blotting
- Qualitative Tests and Identification
- MCAT Tips for Lab Data Interpretation
1. Separation and Purification Techniques
These methods exploit differences in physical properties (like polarity, boiling point, solubility, size) to separate compounds.
Distillation
Used to separate liquids based on boiling point differences.
| Type | Use Case |
|---|---|
| Simple Distillation | Compounds with ≥25°C difference in boiling point |
| Fractional Distillation | For mixtures with <25°C difference |
| Vacuum Distillation | For high-boiling point compounds (>150°C) |
MCAT Tip: More volatile compound (lower bp) is collected first.
Extraction
Separates compounds based on acid–base and polarity differences between aqueous and organic layers.
- Acidic compounds → deprotonated (water-soluble) in basic aqueous layer.
- Basic compounds → protonated (water-soluble) in acidic aqueous layer.
- Neutral organics remain in organic solvent.
Common Trap: Be sure to identify which layer is which (depends on solvent density — diethyl ether is on top; chloroform on bottom).
Recrystallization
Purifies solids by dissolving in hot solvent and slowly cooling.
- Impurities remain in solution.
- Pure compound crystallizes out.
Choose a solvent in which the compound is soluble when hot but insoluble when cold.
2. Spectroscopy Techniques
These techniques identify compounds based on how they interact with electromagnetic radiation.
Infrared (IR) Spectroscopy
Measures vibrational transitions in bonds.
| Bond Type | Wavenumber (cm⁻¹) | Appearance |
|---|---|---|
| O–H (alcohol) | 3200–3600 (broad) | Broad, strong |
| N–H (amine) | 3300 (sharper) | Medium, sharp |
| C=O (carbonyl) | ~1700 | Sharp, strong |
| C≡C, C≡N | 2100–2260 | Weak, sharp |
MCAT Tip: Always associate ~1700 cm⁻¹ with carbonyl groups.
NMR Spectroscopy (¹H NMR)
Reveals the chemical environment of hydrogen atoms.
| Region (ppm) | Group | Splitting Pattern |
|---|---|---|
| 0–3 | Alkyl H’s | Singlets, doublets, etc. |
| 3–5 | Electronegative groups (O, N) | Deshielded, downfield |
| ~7 | Aromatic H’s (benzene) | Multiplets |
| 9–10 | Aldehyde H | Singlet |
| 10–12 | Carboxylic acid H | Broad singlet |
n + 1 rule: A proton with n
nn neighboring hydrogens will split into n + 1 vpeaks.
UV-Vis Spectroscopy
Used for conjugated systems. More conjugation → lower energy transition → longer wavelength absorption.
MCAT may use this to test DNA base quantification or enzyme kinetics.
Mass Spectrometry
Ionizes molecules and breaks them into fragments.
- Gives molecular weight (M⁺ peak)
- Useful for identifying unknowns
3. Chromatography Techniques
Used to separate compounds based on polarity, size, or affinity.
Thin-Layer Chromatography (TLC)
- Stationary phase = polar (e.g., silica gel)
- Mobile phase = solvent (nonpolar)
- More polar compounds travel less (stick to silica)
Retention factor (Rf):
$$
Rf = \frac{\text{Distance traveled by compound}}{\text{Distance traveled by solvent front}}
$$
Column Chromatography
Same principle as TLC but on a larger scale.
- Can use polar or nonpolar stationary phases.
- Elution order depends on polarity.
Gas Chromatography (GC)
- Separates volatile compounds
- Mobile phase = inert gas (e.g., He)
- Stationary phase = liquid in a capillary tube
Lower boiling point = faster elution
4. Electrophoresis and Blotting
Gel Electrophoresis
- DNA/RNA: separated by size (smaller = faster)
- Proteins: separated by size (SDS-PAGE) or charge (native PAGE)
Blotting Techniques
| Blot | Detects | Probe Used |
|---|---|---|
| Southern | DNA | DNA probe |
| Northern | RNA | DNA probe |
| Western | Protein | Antibody |
Mnemonic: SNoW DRoP
Southern = DNA, Northern = RNA, Western = Protein
- Common Qualitative Tests
| Test | Detects | Positive Result |
|---|---|---|
| Benedict’s | Reducing sugars | Red/orange precipitate |
| Tollen’s | Aldehydes | Silver mirror |
| Iodoform | Methyl ketones | Yellow precipitate |
| Ninhydrin | Free amines (e.g. amino acids) | Purple color |
| Biuret | Proteins (peptide bonds) | Violet complex |
MCAT Strategy: Interpreting Lab Data
- Know what each technique measures, and what variable is being compared.
- Be ready to infer structure, identify contaminants, or evaluate purity.
- Common question types:
- TLC: Which spot is more polar?
- NMR: Which proton gives this peak?
- Gel: Which DNA strand moves faster?
- Distillation: Which compound elutes first?