Biochemistry 5201 Exam 1 Study Guide: Foundations, Water, Amino Acids, Protein Structure, and Techniques

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Functional Groups in Biological Molecules

Common Functional Groups

Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. In biochemistry, these groups are essential for the structure and function of biomolecules.

Hydroxyl (-OH): Found in alcohols and carbohydrates; increases solubility in water.
Carboxyl (-COOH): Present in amino acids and fatty acids; acts as an acid (proton donor).
Amino (-NH2): Found in amino acids; acts as a base (proton acceptor).
Phosphate (-PO42-): Key in nucleic acids and energy molecules like ATP.
Sulfhydryl (-SH): Found in cysteine; forms disulfide bonds in proteins.
Carbonyl (C=O): Found in ketones and aldehydes; important in sugars.

Example: The carboxyl and amino groups in amino acids allow them to act as zwitterions at physiological pH.

Classification of Life Based on Carbon and Energy Sources

Types of Organisms

Organisms are classified by how they obtain carbon and energy:

Autotrophs: Use inorganic carbon (CO2) as a carbon source.
Heterotrophs: Use organic carbon sources.
Phototrophs: Obtain energy from light.
Chemotrophs: Obtain energy from chemical compounds.

Example: Plants are photoautotrophs; humans are chemoheterotrophs.

Forces of Interaction and Bonding in Proteins

Types of Interactions

Protein structure and function depend on various forces:

Hydrogen Bonds: Stabilize secondary and tertiary structures.
Van der Waals Forces: Weak, but numerous; contribute to overall stability.
Electrostatic (Ionic) Interactions: Occur between charged side chains.
Hydrophobic Interactions: Drive folding by excluding nonpolar residues from water.
Disulfide Bonds: Covalent bonds between cysteine residues.

Example: The hydrophobic core of globular proteins is stabilized by hydrophobic interactions.

Water: The Solvent of Life

Main Features of Water

Water's unique properties make it essential for life:

Polarity: Water is a polar molecule, allowing it to dissolve many substances.
Hydrogen Bonding: Leads to high cohesion, surface tension, and specific heat.
Solvent Properties: Can dissolve ionic and polar compounds.
High Heat Capacity: Helps regulate temperature in organisms.

Example: Water's ability to form hydrogen bonds is crucial for protein folding and enzyme activity.

Colligative Properties

Definition and Examples

Colligative properties depend on the number of solute particles, not their identity:

Boiling Point Elevation
Freezing Point Depression
Osmotic Pressure
Vapor Pressure Lowering

Example: Adding salt to water lowers its freezing point, which is why salt is used to melt ice.

Henderson-Hasselbalch Equation, Buffers, and Amino Acids

Buffering Systems and pH

The Henderson-Hasselbalch equation relates pH, pKa, and the ratio of conjugate base to acid:

Equation:

Buffers: Resist changes in pH; important in blood (bicarbonate buffer system).
Amino Acids: Act as buffers due to their ionizable groups.

Example: The bicarbonate buffer system maintains blood pH around 7.4.

Thermodynamics in Biochemistry

Key Terms and Gibbs Free Energy

Thermodynamics describes energy changes in biochemical reactions:

Endothermic: Absorbs heat.
Exergonic: Releases free energy; spontaneous.
Gibbs Free Energy Equation:

Enthalpy (\(\Delta H\)): Heat content.
Entropy (\(\Delta S\)): Disorder.
Temperature (T): In Kelvin.
Product/Reactant Concentrations: Affect reaction direction and spontaneity.

Example: ATP hydrolysis is exergonic due to high negative \(\Delta G\).

High/Intermediate Energy Bonds

Properties and Energy Release

High-energy bonds, such as those in ATP, release energy upon hydrolysis:

Resonance Stabilization: Products are more stable than reactants.
Electrostatic Repulsion: Breaking bonds relieves repulsion between charged groups.
Hydration: Products are better solvated.

Example: The phosphoanhydride bonds in ATP are high-energy due to these properties.

Amino Acids: Abbreviations, Structures, Properties, and Titration

Key Features

One- and Three-Letter Abbreviations: E.g., Glycine (G, Gly), Alanine (A, Ala).
Structures at Different pH: Amino acids exist as zwitterions at neutral pH.
Hydrophobicity Trends: Nonpolar side chains are hydrophobic; polar/charged are hydrophilic.
Linkages: Peptide bonds connect amino acids; restrict rotation due to partial double-bond character.
Titration Curves: Show ionization of groups; pI (isoelectric point) is where net charge is zero.

Example: Lysine has a basic side chain and a higher pI than glutamic acid.

Protein Purification Techniques

Methods and Chromatograms

Protein purification separates proteins based on physical and chemical properties:

Ion Exchange Chromatography: Separates by charge.
Size-Exclusion Chromatography: Separates by size; larger proteins elute first.
Affinity Chromatography: Uses specific binding interactions.

Chromatogram: A plot of absorbance (y-axis) vs. elution volume or time (x-axis), showing peaks for different proteins.

Example: Affinity chromatography is used to purify His-tagged proteins using a nickel column.

Table: Amino Acid Abbreviations and Properties

Main Purpose: Classification and Properties

Amino Acid	One-Letter	Three-Letter	Property
Glycine	G	Gly	Nonpolar, smallest
Alanine	A	Ala	Nonpolar
Glutamic Acid	E	Glu	Acidic, polar
Lysine	K	Lys	Basic, polar
Serine	S	Ser	Polar, uncharged
Phenylalanine	F	Phe	Nonpolar, aromatic
Cysteine	C	Cys	Polar, forms disulfide bonds
Additional info: Other amino acids follow similar classification.

Additional info:

Protein purification chromatograms typically have absorbance (y-axis) vs. elution volume (x-axis), with peaks corresponding to different proteins.
Buffering systems in the human body include phosphate and protein buffers in addition to bicarbonate.
Colligative properties are important in maintaining osmotic balance in cells.