Protein Structure & Functions

Chapter 4: Protein Structure & Function

General Protein Functions

Proteins are essential macromolecules performing a vast array of functions within living organisms. These include:

• Enzymes: Catalyze biochemical reactions, speeding them up significantly.

• Structural Proteins: Provide physical support and shape to cells and tissues (e.g., collagen, keratin).

• Transport Proteins: Move molecules across membranes or throughout the body (e.g., hemoglobin, membrane transporters).

• Motor Proteins: Generate movement within cells and tissues (e.g., myosin, actin).

• Storage Proteins: Store amino acids or other molecules (e.g., ferritin).

• Signal Proteins: Transmit signals between cells, acting as messengers (e.g., hormones, growth factors).

• Receptor Proteins: Detect and respond to signals, often binding to signal proteins.

• Transcription Regulators: Control gene expression by binding to DNA.

• Special Purpose Proteins: A broad category for proteins with unique or specialized roles not covered by the above categories.

Amino Acids: The Building Blocks of Proteins

Amino acids are the monomeric units that make up proteins.

Amino Acid Structure

Each amino acid shares a common fundamental structure, consisting of:

• An amino group ($\text{H}_2\text{N-}$).

• A carboxyl group ($\text{-COOH}$).

• A central alpha carbon ($\alpha\text{C}$) to which the amino and carboxyl groups, a hydrogen atom, and a side chain are attached.

• A unique side chain (also called an R-group), which varies among different amino acids and determines their specific chemical properties.

Categorization of Amino Acids by Side Chains

Amino acids are categorized based on the chemical properties of their side chains, which dictate their behavior in proteins and their interactions.

• Negatively Charged Amino Acids:

  • Aspartic acid (Asp, D)

  • Glutamic acid (Glu, E)

• Positively Charged Amino Acids:

  • Arginine (Arg, R)

  • Lysine (Lys, K)

  • Histidine (His, H)

• Uncharged Polar Amino Acids: (These contain polar groups that do not ionize at neutral pH but can form hydrogen bonds)

  • Asparagine (Asn, N)

  • Glutamine (Gln, Q)

  • Serine (Ser, S)

  • Threonine (Thr, T)

  • Tyrosine (Tyr, Y)

• Nonpolar Amino Acids: (These have hydrophobic side chains)

  • Alanine (Ala, A)

  • Glycine (Gly, G)

  • Valine (Val, V)

  • Leucine (Leu, L)

  • Isoleucine (Ile, I)

  • Proline (Pro, P)

  • Phenylalanine (Phe, F)

  • Methionine (Met, M)

  • Tryptophan (Trp, W)

  • Cysteine (Cys, C)

Peptide Bonds: Linking Amino Acids

Amino acids are joined together in specific sequences to form polypeptide chains through covalent bonds called peptide bonds.

Peptide Bond Formation

• A peptide bond forms between the carbon in the carboxyl group ($\text{-COOH}$) of one amino acid and the nitrogen of the amino group ($\text{-NH}_2$) of another amino acid.

• This reaction is a condensation reaction (or dehydration synthesis), where a molecule of water is removed.

• The resulting chain has a repeating polypeptide backbone (N-C$\alpha$-C-N-C$\alpha$-C…).

• The beginning of the polypeptide chain, with a free amino group, is called the amino terminus (or N-terminus).

• The end of the polypeptide chain, with a free carboxyl group, is called the carboxyl terminus (or C-terminus).

• The amino acid sequence of this chain ultimately determines the protein's unique three-dimensional shape and function.

Protein Folding and Noncovalent Interactions

The specific three-dimensional shape of a protein is critical for its function and is stabilized primarily by various noncovalent interactions between amino acid side chains and between parts of the backbone.

Types of Noncovalent Interactions

• Ionic Bonds (Electrostatic Attractions): Form between oppositely charged side chains (e.g., between a negatively charged aspartic acid and a positively charged lysine). These are strongest in environments with low dielectric constant (e.g., protein interior) and weaker in aqueous environments.

• Hydrogen Bonds: Weak interactions involving a hydrogen atom shared between two electronegative atoms (typically oxygen or nitrogen). In proteins, hydrogen bonds can occur:

  • Backbone to Backbone: Between atoms of two peptide bonds.

  • Backbone to Side Chain: Between atoms of a peptide bond and an amino acid side chain.

  • Side Chain to Side Chain: Between atoms of two amino acid side chains.

• Van der Waals Forces: Weak, short-range attractive forces that arise from transient fluctuations in electron clouds, creating temporary dipoles that induce complementary dipoles in nearby atoms.

• Hydrophobic Forces: A critical driving force in protein folding, particularly in an aqueous environment.

  • Nonpolar side chains tend to cluster together in the interior of the protein, forming a hydrophobic core region, minimizing their contact with water.

  • Conversely, polar side chains are typically found on the exterior of the protein, where they can form hydrogen bonds with water molecules, contributing to the protein's solubility and stability in an aqueous environment.

Hierarchical Levels of Protein Structure

Protein structure is described through four hierarchical levels, each building upon the previous one.

1° Primary Structure (Primary)

• Shape: A linear chain of amino acids.

• Bonds: Covalent peptide bonds linking amino acids.

• Functional: Generally no, the protein is in an unfolded state and cannot perform its biological function.

2° Secondary Structure (Secondary)

• Definition: Localized folding of the polypeptide chain into regular, repeating structures, primarily stabilized by hydrogen bonds between atoms of the polypeptide backbone.

• Bonds: Hydrogen bonds between the $\text{C=O}$ group of one peptide bond and the $\text{N-H}$ group of another peptide bond, typically $4$ amino acids away.

• Functional: Generally no, as these are only local folds within a larger chain.

• $\alpha$ Helix:

  • A common spiral structure.

  • The $\text{C=O}$ group of each peptide bond is hydrogen-bonded to the $\text{N-H}$ group of the peptide bond $4$ amino acids away along the polypeptide chain.

  • The side chains project outwards from the helix.

  • Has a pitch of $0.54 \text{ nm}$.

• $\beta$ Sheet:

  • Forms when two or more polypeptide strands lie side-by-side.

  • Hydrogen bonds form between the $\text{C=O}$ and $\text{N-H}$ groups of adjacent strands.

  • Can be arranged in parallel or antiparallel configurations.

  • The distance between adjacent amino acid residues in a $\beta$ sheet is approximately $0.7 \text{ nm}$.

3° Tertiary Structure (Tertiary)

• Definition: The overall three-dimensional shape of a single polypeptide chain, including the folding of both secondary structures and the interactions between all amino acid side chains.

• Bonds: Stabilized by a combination of all noncovalent interactions (ionic, hydrogen, Van der Waals, hydrophobic forces).

• Functional: Often yes, many proteins are functional at this level, consisting of a single polypeptide chain.

• Protein Domain: A segment of a polypeptide chain that can fold independently into a stable, compact, and often functionally distinct structure.

4° Quaternary Structure (Quaternary)

• Definition: The arrangement of multiple polypeptide chains (subunits) to form a larger, functional protein complex.

• Bonds: Stabilized by noncovalent interactions (ionic, hydrogen, Van der Waals, hydrophobic forces) between the surfaces of the different polypeptide subunits.

• Functional: Yes, if a protein requires multiple subunits to be biologically active.

• Examples of Quaternary Structures:

  • Dimers: Two subunits coming together (e.g., CAP protein, where a single, identical binding site on each monomer interacts).

  • Tetramers: Four subunits (e.g., neuraminidase protein, which can involve interactions between two nonidentical binding sites on each monomer).

  • Larger assemblies like actin filaments, spherical shells, or hollow tubes (e.g., viral capsids, microtubules).

Protein-Ligand Binding

All proteins are designed to bind to other molecules, which are referred to as ligands.

• Specificity: Each protein typically binds to just one or a few specific molecules. This specificity arises from the precise complementary fit and arrangement of noncovalent interactions (hydrogen bonds, electrostatic attractions, Van der Waals forces, hydrophobic interactions) between the protein's binding site and the ligand.

• Binding Site: A region on the protein's surface formed by a specific arrangement of amino acid side chains, which is complementary in shape and chemical properties to the ligand.

• Duration of Binding: The interaction between a protein and its ligand can be short-lived (transient) or long-lasting, depending on the protein's function.

Enzyme Function: Catalysis

Enzymes are a special class of proteins that act as biological catalysts, dramatically speeding up specific biochemical reactions.

How Enzymes Work

• Binding to Substrate: Enzymes achieve their catalytic activity by binding specifically to substrate molecules at their active site.

• Chemical Alteration: Once bound, the enzyme chemically alters the substrate molecules, converting them into products.

• Lowering Activation Energy: The most crucial mechanism of enzyme action is to lower the activation energy ($E_a$) required for a reaction to proceed.

  • By stabilizing the transition state—an unstable, high-energy intermediate form of the substrate—the enzyme makes it easier for the reaction to occur, thus increasing the reaction rate.

Catalyzed vs. Uncatalyzed Reaction Graph (Conceptual Overview)

Imagine a reaction energy diagram where:

• The X-axis represents the reaction pathway or progress.

• The Y-axis represents the free energy ($G$) of the molecules.

• Reactant: The starting molecule(s) for the reaction, located at an initial energy level.

• Product: The molecule(s) formed after the reaction, located at a final energy level.

• $\Delta G$ (Change in Free Energy): The difference in free energy between the products and the reactants ($\text{Product } G - \text{Reactant } G$). This indicates whether a reaction is spontaneous (exergonic, negative $\Delta G$) or requires energy input (endergonic, positive $\Delta G$).

• Transition State: The highest energy point on the reaction pathway, representing the unstable intermediate state that reactants must pass through to become products.

• Activation Energy ($E_a$): The energy difference between the reactants and the transition state. It's the minimum energy required for the reaction to occur.

On such a graph:

• An uncatalyzed reaction would show a high