Proteins and Experimental Thinking

BIOL-UA 11 - Class 3: Proteins and Experimental Thinking

Announcements

• Attendance:

  • Requires one Wi-Fi-connected device.

  • Use the PollEverywhere App.

  • Contact instructor after class this week only if issues arise.

  • Must answer $80\%$ of questions.

• Problem Set: Due Friday at $5\ \text{PM}$.

• Study Path: Students should work on their Study Path.

Flash Review: Chemistry of Water and Nucleic Acids

Class 3 Focus Areas

• Building blocks: Amino acid components.

• Protein organization levels: How they are held together.

• Structure-function relationships: The link between a protein's shape and its biological role.

• Thinking about data: How experimental evidence informs our understanding of molecules.

Structure-Function Relationships in Proteins

• Protein building blocks (amino acids): Their structure allows for a vast array of $3D$ shapes.

• Functional diversity: These diverse shapes enable proteins to perform numerous functions within the cell, including:

  • Transport of substances.

  • Providing structural support.

  • Enabling movement.

  • Participating in defense mechanisms.

  • Catalyzing chemical reactions.

• Examples: The bacterial flagellar protein (for movement) and the PIEZO1 channel work due to their specific $3D$ structures.

Amino Acids: Diverse Building Blocks of Proteins

• Amino acid components: Each amino acid has a central carbon (alpha-carbon), an amino group ($H_3N^+$), a carboxyl group ($COO^-$), a hydrogen atom, and a unique side chain (R group).

• R Group diversity: Amino acids vary significantly in their R group.

• Impact of R Groups: The chemical properties of the R group dictate interactions both within the protein itself and with other cellular components.

  • Non-polar R Groups: These are hydrophobic and typically contain hydrocarbon chains or rings. Examples include Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine (special case as it's often the start codon, though it's non-polar), Phenylalanine, Tryptophan, and Proline.

  • Polar, Uncharged R Groups: These are hydrophilic and contain functional groups with electronegative atoms (like oxygen or sulfur) that can form hydrogen bonds but are not ionized at physiological pH. Examples include Serine, Threonine, Cysteine (unique for disulfide bonds), Asparagine, and Glutamine.

  • Charged R Groups: These are hydrophilic and either gain or lose a hydrogen ion in solution, becoming charged (acids or bases). Their charge is influenced by the solution's pH. This is in addition to the charges already present on the amino acid backbone ($H_3N^+$ and $COO^-$).

• Key Learning Points for Amino Acids:

  • Do not need to memorize specific names or structures of all amino acids.

  • Must know the basic components of an amino acid (backbone and R group).

  • Must know the four general types of side groups (non-polar, polar uncharged, positively charged, negatively charged).

  • Should be able to determine if a side group is hydrophilic or hydrophobic based on its chemical structure.

  • Should be able to predict if a charged side group will act as an acid (proton donor) or base (proton acceptor).

Protein Structure Levels

Primary Structure

• Definition: The unique, linear sequence of amino acids in a polypeptide chain.

• Formation: Amino acids are joined together by a dehydration reaction (water removal) to form peptide bonds.

• R Groups: Side chains (R groups) are not modified during peptide bond formation.

• Characteristics: Results in a $1D$ unbranched string of amino acids, with R groups projecting outwards.

• Directionality: Has a distinct N-terminus (amino end) and C-terminus (carboxyl end).

• Genetic Basis: The specific order of amino acids is genetically encoded.

Secondary Structure

• Definition: Local folded structures that form within a polypeptide due to interactions between backbone atoms.

• Common Forms: Primarily alpha helices (a coiled structure) and beta sheets (a pleated, sheet-like structure).

• Bonds Responsible: Formed by hydrogen bonds between the carbonyl oxygen ($C=O$) of one amino acid's backbone and the amino hydrogen ($N-H$) of another amino acid's backbone. Crucially, these interactions involve only the backbone, not the R groups.

• Other Regions: Can also include unstructured or random coil regions.

Tertiary Structure

• Definition: The overall $3D$ shape of a single polypeptide chain, resulting from interactions between the R groups.

• Bonds/Interactions (from strongest to weakest):

  • Covalent Disulfide Bridges: Strongest; form between the sulfhydryl groups of two cysteine amino acids ($S-S$ bond). These are distinct from typical non-covalent interactions.

  • Ionic Bonds: Strong attractions between oppositely charged R groups (e.g., between an acidic and a basic amino acid).

  • Polar/Hydrogen Bonds: Weaker attractions between polar uncharged R groups or between a polar R group and a charged R group.

  • Hydrophobic Interactions (van der Waals forces): Weakest; occurring when non-polar R groups cluster together in the protein's interior to minimize contact with water.

Quaternary Structure

• Definition: The arrangement of multiple polypeptide chains (subunits) into a single functional protein complex.

• Composition: Can involve multiple copies of the same protein subunit or different protein subunits assembled together.

• Forces: Held together by similar types of non-covalent interactions (ionic, hydrogen bonds, hydrophobic interactions) and sometimes disulfide bridges as seen in tertiary structure.

Folding and Unfolding Proteins

• Native State: Proteins typically fold into a specific $3D$ conformation that is stable and functional.

• Hydrophobic Core: Hydrophobic residues (non-polar R groups) are characteristically buried in the interior of the protein, away from the aqueous cellular environment.

• Denaturation: Heat, extreme pH changes, or certain chemicals can cause proteins to denature (unfold), losing their specific $3D$ structure and, consequently, their function.

• Aggregation: If proteins refold incorrectly after denaturation, especially if hydrophobic regions are exposed to the aqueous environment, they can aggregate. This involves hydrophobic parts of multiple proteins sticking together.

• Sickle Cell Disease Example: A single amino acid change in hemoglobin alters its structure, causing hydrophobic residues to be exposed on the surface. This leads to protein aggregation, forming long fibers that distort red blood cells into a sickle shape, with disastrous effects.

Determining Large Molecule Structures

• Challenge: Determining the precise $3D$ arrangement of complex molecules like proteins (e.g., $C<em>{16}H</em>{18}N<em>2O</em>4S$ or $C<em>{256}H</em>{381}N<em>{65}O</em>{77}S$) is incredibly difficult.

• Methods:

  • X-ray Crystallography: Involves crystallizing the protein, then using X-ray diffraction patterns from the crystal. Mathematical techniques, specifically Fourier Transforms, are used to convert the diffraction pattern into an electron density map, from which the atomic structure is determined.

  • Cryo-electron Microscopy (Cryo-EM): Involves rapidly freezing biological samples, then imaging them with an electron microscope. Many $2D$ images are computationally combined to reconstruct a $3D$ model.

Visualizing Protein Structure

• Models: The images and animations of proteins we observe are computational models, not direct photographs.

• Purpose of Models: These models are designed to highlight useful structural features and functional aspects for human understanding.

• Cellular View: It's important to differentiate what humans