Protein Structure and Function Lecture Flashcards

Chemical Reactions and Peptide Bond Formation

  • Dehydration Reaction Mechanism:

    • Two individual amino acid molecules are fused together to produce a single larger molecule.
    • Exactly one water molecule (H2OH_2O) is lost per dehydration reaction to form the linkage.
    • Contrast with hydrolysis reactions:
    • Hydrolysis uses one water molecule (H2OH_2O) to break one molecule apart into two smaller molecules.
    • Dehydration synthesizes polymers by releasing water.

  • Peptide Bond Nature:

    • The covalent bond formed between two neighboring amino acids via a single dehydration reaction is termed a peptide bond.
    • Successive dehydration reactions link amino acids into a continuous chain called a polypeptide.

Structural Determinants of Protein Function

  • Structure Dictates Function Principle:

    • The precise three-dimensional structure (3D architecture or 3D shape) of a protein dictates its biological role and activity both inside and outside of the cell.
    • A functional protein consists of one or more polypeptide chains that are precisely combined, folded, twisted, and coiled together to produce a unique structure with a unique job.
    • Disruption or loss of a protein's specific 3D shape leads directly to a loss of its biological function.

  • Structural Representation Models:

    • Space-Filling Model: Represents individual constituent atoms or amino acids as packed balls/spheres to visually map overall protein structure.
    • Ribbon Model: Depicts the overall folding pattern and ribbon-like trajectory, resembling praise and worship flags used in church.
    • Wireframe Model: Displays structural details as intersecting lines, looking like a bunch of barbed wire sitting around used to build a cow fence on a ranch or farm.
    • Simplified/Crude Representation Models:
    • Tube-like Model: Commonly used to depict transport proteins that move substances into or out of a cell.
    • Globular Model: Used to illustrate enzymes—catalytic proteins that accelerate or speed up chemical reactions. Substrate molecules (reactants) attach to the enzyme glob to form products.
    • Blob Model: Used to depict secreted signaling proteins like insulin.

Physiological Examples and Protein Specificity

  • Insulin and Blood Glucose Regulation:

    • Production Site: Synthesized and secreted by specialized cells in the pancreas called pancreatic beta cells.
    • Mechanism: Released into the bloodstream to bind target cells, causing those cells to absorb or "swallow" excess blood glucose.
    • Clinical Significance:
    • Regulates blood sugar levels in the human body.
    • Chronically elevated blood sugar levels cause diabetes mellitus (Type 1 or Type 2 diabetes).
    • Diabetes results in numerous negative health consequences, highlighting the importance of functional insulin.

  • Antibodies and Immune Defense:

    • Role: Specialized immune system proteins circulating through the bloodstream in blood plasma, designed to protect the body from foreign invaders.
    • Examples of Invaders: Influenza (flu) virus or pathogenic bacterial cells capable of causing disease in humans.
    • Binding Specificity: Custom-designed to track and bind to specific foreign targets like heat-seeking missiles.
    • Pathology Prevention: Binding neutralizes and destroys the flu virus so it cannot infect human cells and cause flu-like symptoms or make a person sick.

Amino Acid Anatomy and Functional Groups

  • Standard Amino Acid Structure:

    • Every amino acid contains three essential functional groups attached to a central structure:
    • Amino Group: Functional group starting with "A" (mnemonic: wanting an "A" in class).
    • Carboxyl Group: Carboxylic acid group starting with "C" (mnemonic: avoiding a "C" in class).
    • R Group (Side Chain): Variable group (mnemonic: "R" sound like a pirate saying "Arrr").

  • The Polypeptide Backbone:

    • Formed by repeating amino and carboxyl functional group constituents across joined amino acids.
    • Excludes the variable R groups / side chains.

Levels of Protein Structure

  • Primary Structure:

    • Definition: The specific linear sequence and order of amino acids within a polypeptide or protein.
    • Genetic Control: Dictated by the sequence of monomer units (nucleotides) in DNA.
    • Notation: Represented by single-letter codes or three-letter abbreviations (e.g., Pro for proline, Phe for phenylalanine, His for histidine in transthyretin protein).
    • Analogy: Similar to the specific order of letters in a book or in a long word.
    • Impact: Changing the amino acid sequence can alter the protein's 3D shape and destroy its function.

  • Secondary Structure:

    • Definition: Localized folding or coiling patterns within a protein.
    • Driving Force: Formed exclusively by hydrogen bonds between the carboxyl and amino functional groups that make up the polypeptide backbone.
    • Primary Configurations:
    • Alpha Helix (Coil): A spiral staircase-like structure resembling the 3D double-helix geometry of DNA.
    • Beta Pleated Sheet (Fold): A flat, sheet-like structure flat like the surface of a desk.

  • Tertiary Structure:

    • Definition: The overall three-dimensional shape of a single polypeptide chain resulting from interactions among variable R groups (side chains).
    • Exclusion: Independent of interactions within the polypeptide backbone constituents (amino and carboxyl groups).
    • Types of R Group Interactions:
    • Hydrogen Bonding: Attraction between a partially positive hydrogen atom (covalently bonded to a first electronegative atom) on one R group and another electronegative atom on a neighboring R group.
    • Ionic Bonding: Electrostatic attraction between a full negative charge on one R group and a full positive charge on an opposing R group.
    • Hydrophobic Interactions: Nonpolar/hydrophobic R groups cluster together in the protein interior away from water ("like dissolves like").
    • Van der Waals Interactions: Weak forces created when neighboring R groups balance opposing partial electrical charges to distribute charge evenly.
    • Disulfide Bridges: Strong covalent bonds formed between two sulfur atoms in a row (prefix "di-" meaning two) that bridge neighboring R groups.

  • Quaternary Structure:

    • Definition: Spatial arrangement and bonding interactions resulting from the combination of multiple polypeptide chains into a single functional macromolecule.
    • Requirement: Present only in proteins made of two or more polypeptide chains (minimum of 2 required; absent in single-chain proteins).

Molecular Case Studies of Multi-Chain Proteins

  • Spider Silk:

    • Strength Profile: Pound for pound stronger than steel.
    • Molecular Basis: Held together by extensive hydrogen bonding networks between adjacent polypeptide chains.

  • Collagen:

    • Structure: Long, fibrous, stringy structural protein.
    • Subunit Composition: Consists of 3 distinct polypeptide chains intertwined/wrapped around one another like a rope.
    • Quaternary Status: Possesses quaternary structure due to the linkage of its 3 polypeptide subunits.

  • Hemoglobin:

    • Subunit Composition: Consists of 4 total polypeptide subunits:
    • 2 alpha (α\alpha) subunits / polypeptides.
    • 2 beta (β\beta) subunits / polypeptides.
    • Physiological Role: Attached to red blood cells to transport essential gases throughout the bloodstream:
    • Delivers oxygen (O2O_2) from lungs to peripheral cells (lack of O2O_2 leads to cell death).
    • Removes carbon dioxide (CO2CO_2) waste from cells to prevent toxic accumulation and cell death.

Pathology: Sickle Cell Disease

  • Etiology and Genetics:
    • An inherited genetic blood disorder caused by a single DNA mutation.
  • Molecular Mechanism:
    • Alters the primary structure (amino acid sequence) of hemoglobin.
    • At position number 6 of the hemoglobin polypeptide chain, normal glutamate is substituted by valine.
  • Pathological Consequences:
    • The single amino acid change modifies the 3D shape of hemoglobin.
    • Abnormal hemoglobin causes red blood cells to deform from their normal biconcave / inner tube shape into a crescent moon / sickle shape.
    • Deformed red blood cells form chains and clump together, blocking flow and reducing oxygen transport efficiency throughout the body.

Protein Denaturation, Renaturation, and Folding Diseases

  • Environmental Factors Affecting 3D Shape:

    • pH Variations: Changes in acidity or alkalinity alter electrostatic charges.
    • Salt Concentration: Excessively high salt concentrations disrupt delicate bonding.
    • Temperature Extremes: Temperatures that are too high or too low break weak bonds, causing proteins to unravel.

  • Denaturation and Biological Inactivity:

    • Definition: The process where a protein loses its 3D structure and unravels in response to environmental stressors.
    • Consequence: Denatured proteins become biologically inactive and fail to perform their functions.
    • Medical Example: Extremely high fevers can be fatal because high heat denatures hemoglobin on red blood cells, abolishing oxygen transport and causing widespread cell death.

  • Renaturation:

    • Process where a denatured protein regains its native 3D shape and function once the denaturing agent is removed (though refolding is not always possible).

  • Protein Folding and Neurodegenerative Pathology:

    • Emerging polypeptides usually pass through multiple intermediate 3D structures prior to achieving their final native folding state.
    • Protein misfolding is directly linked to severe neurological diseases, including:
    • Parkinson's disease
    • Alzheimer's disease
    • Mad cow disease

Analytical Techniques for Structural Determination

  • X-Ray Crystallography:

    • A protein sample is crystallized, and a beam of X-rays or electrons is shot at the crystal.
    • X-rays deflect/diffract off protein atoms onto a detector, producing an X-ray diffraction pattern used to elucidate the protein's 3D structure.

  • Cryogenic Electron Microscopy (Cryo-EM):

    • Cellular or protein samples are flash-frozen at cryogenic temperatures.
    • Beams of electrons are shot through the frozen sample to visualize structural details.
    • Major Advantage: Does not require proteins to be converted into crystal form.

  • Bioinformatics:

    • Computational approach utilizing software, algorithms, and database alignment to predict 3D protein structures directly from primary amino acid sequence data.

Central Dogma and Nucleic Acids

  • Genetic Determinants:

    • The amino acid sequence of a polypeptide is encoded by a gene (a unit of inheritance passed from parent to offspring).
    • Genes consist of DNA, a nucleic acid polymer made of nucleotide monomers.

  • Types of Nucleic Acids:

    • Deoxyribonucleic Acid (DNA): Provides the permanent genetic blueprint.
    • Ribonucleic Acid (RNA): Acts as an intermediate nucleic acid messenger.

  • Gene Expression Pathway:

    • Transcription: Information in DNA directs the synthesis of messenger RNA (mRNA).
    • Translation: mRNA sequence is translated into a specific polypeptide chain (protein synthesis).
    • Flow of Genetic Information:     DNA→mRNA→Protein\text{DNA} \rightarrow \text{mRNA} \rightarrow \text{Protein}