Chapter 4 – Protein Structure and Function (Expanded Study Guide)

Proteins

The most versatile and essential macromolecules in living systems.

Functions of Proteins

Include structure, catalysis, transport, signaling, defense, and movement.

Amino Acids

The building blocks of proteins, there are 20 standard amino acids.

N-terminus

The amino group end of an amino acid chain.

C-terminus

The carboxyl group end of an amino acid chain.

Hydrophobic Amino Acids

Amino acids that cluster inside proteins (e.g., Val, Leu, Ile).

Hydrophilic Polar Amino Acids

Amino acids that interact with water (e.g., Ser, Thr, Gln).

Charged Amino Acids

Amino acids that form salt bridges to stabilize structure (e.g., Lys, Glu, Asp).

Primary Structure

Exact amino acid sequence of a protein.

Secondary Structure

Local folding patterns in proteins, such as α helixes and β sheets.

α Helix

A coiled structure in proteins stabilized by hydrogen bonds.

β Sheet

Strands of amino acids hydrogen-bonded side by side.

Tertiary Structure

Full three-dimensional conformation of one polypeptide.

Quaternary Structure

Complex formed by multiple polypeptides assembling together.

Chaperone Proteins

Assist in the correct folding of proteins.

Denaturation

Process by which proteins unfold due to heat or chemicals.

Renaturation

The process where some proteins can spontaneously refold.

Covalent Bonds

Strong bonds that stabilize proteins, such as disulfide bonds.

Disulfide Bonds

Covalent bonds between cysteine side chains that stabilize extracellular proteins.

Ligands

Specific molecules that proteins bind at their binding sites.

Antibodies

Y-shaped proteins with high specificity for binding antigens.

Enzymes

Biological catalysts that speed up chemical reactions.

Allosteric Proteins

Proteins that change shape when ligands bind to them.

Feedback Inhibition

A metabolic product that inhibits an earlier enzyme's activity.

Phosphorylation

A covalent modification that acts as an on/off switch for protein activity.

Protein Degradation

The process by which proteasomes remove misfolded or unneeded proteins.

Protein Machines

Large protein complexes that work in cycles, such as ribosomes.

Mass Spectrometry

Technique to measure peptide fragment masses for sequence deduction.

X-ray Crystallography

Method to determine high-resolution 3D structures of proteins.

Cryo-electron Microscopy

Technique to visualize large protein complexes at near-atomic resolution.

Fibrous Proteins

Elongated proteins that provide structural support (e.g., collagen).

Globular Proteins

Compact proteins that perform a variety of functions, including enzymes and antibodies.

Hydrophobic Effect

The tendency of nonpolar side chains to bury inside proteins to avoid water.

Domains

Independently folding units of proteins typically 40-350 amino acids long.

Protein Assembly

The process by which proteins form quaternary structures such as dimers and tetramers.

Structural Motifs

Commonly occurring structures in proteins, such as α helices and β sheets.

Protein Specificity

The ability of a protein to bind only to specific ligands based on shape and chemical interaction.

Protein Regulation

The control of protein activity through mechanisms like modifications and degradation.

Motor Proteins

Proteins that convert chemical energy into mechanical work, such as myosin and kinesin.

Historical Highlights of Protein Science

Key milestones include the coining of the term protein in 1838 and the first protein sequence in 1955.

Centrifugation

A purification technique that separates components by size and density.

Chromatography

A method to isolate specific proteins from mixtures.

Phase Separation

The process of proteins forming liquid-like compartments in cells.

Misfolded Proteins

Proteins that have failed to fold correctly, which can lead to diseases such as Alzheimer's.

Billions of Antibodies

The human immune system's capability to produce extremely diverse antibodies.

Directionality of Proteins

Proteins have a specific orientation due to their N-terminus and C-terminus.

Transition State

The high-energy state of substrates during chemical reactions that enzymes stabilize.

Hydrogen Bonds

Weak noncovalent bonds that contribute to the stabilization of protein structure.

Electrostatic Attractions

Interactions between charged groups that stabilize protein structures.

Van der Waals Forces

Weak forces that help proteins maintain their structure through close packing.

Coiled-coil Structure

Two helices twisted around each other, aligning hydrophobic stripes.

Amyloid Fibrils

Stable but pathological structures formed by stacked β sheets.

Protein Compartmentalization

The localization of proteins to ensure their proper function within the cell.

Negative Regulation

Process by which a product inhibits the action of an earlier enzyme.

Positive Regulation

Process by which a product stimulates the action of another enzyme.

Kinases

Enzymes that add phosphate groups to proteins.

Phosphatases

Enzymes that remove phosphate groups from proteins.

Signal Transduction

The process through which cells communicate by sending and receiving signals.

Cell Membrane Transport

The process utilized by proteins to move molecules across membranes.

Extracellular Matrix

A network outside cells that provides structural and biochemical support.

Hydrophilic Interactions

Interactions of polar side chains of amino acids with water.

Structural Integrity

The ability of proteins to maintain their shape under various conditions.

Biological Importance of Proteins

Proteins are crucial for virtually all cellular processes.

Protein Function

Determined by protein shape and the interactions it forms.

Proteomic Techniques

Modern methods used to study proteins, including mass spec and cryo-EM.

Functional Complexes

Quaternary structures formed by multiple interacting polypeptides.

Stabilization Mechanisms

Methods that proteins use to maintain their structure, such as disulfide bonds.

Protein Evolution

The changes proteins undergo over time, influenced by genetic mutations.

Pathological Proteins

Misfolded proteins associated with diseases.

Enzyme Action Models

Theoretical frameworks, such as the lock-and-key model, explaining enzyme specificity.

Protein Accessibility

The ability of proteins to interact with other molecules based on their structure.

Protein Interactions

The ways proteins influence each other’s function, often through binding.

Biotechnology Applications

Utilization of proteins in industries such as medicine, agriculture, and bioengineering.

Protein Solubility

The ability of proteins to remain dissolved in solution, influencing function.