Topic 2 Biology

Cell Chemistry Basics

• Covalent Bonds

  • Polar Covalent Bonds

    • Electrons shared unequally due to differences in electronegativity

    • Creates partial charges

  • Nonpolar Covalent Bonds

    • Electrons shared equally

    • No partial charges

• Electronegativity

  • Ability of an atom to attract electrons

  • Oxygen and nitrogen are highly electronegative

  • Determines whether a bond is polar or nonpolar

• Ions

  • Atoms that gain or lose electrons —> full charge

  • Ionized molecules are polar and interact strongly with water

Amino Acid Structure

• General Structure

  • Each amino acid has central alpha carbon

  • Amino group

  • Carboxyl group

  • Hydrogen atom

  • R group (side chain) —> determines chemistry and behavior

• pH effects

  • Amino group: usually positively charged

  • Carboxyl group: usually negatively charged

• R Groups

  • Nonpolar (hydrophobic)

    • Rich in C-C and C-H bonds

    • Tend to cluster inside proteins or in membranes

  • Polar charged

    • Form hydrogen bonds

    • Often found on protein surfaces

  • Polar uncharged

    • Positively charged

    • Negatively charged

    • Interact via ionic bonds

Peptide Bonds & Polypeptides

• Peptide Bond Formation

  • Catalyzed by the ribosome (rRNA is the catalyst)

  • Forms between

    • Carboxyl carbon of one amino acid

    • Amino nitrogen of the next

  • Dehydration (condensation) reaction

    • OH- removed from carboxyl group

    • H+ removed from amino group

    • Water released

  • Bond is covalent and strong

• Polypeptide Chain

  • Has directionality

    • N-terminus —> free amino group (start)

    • C-terminus —> free carboxyl group (end)

  • Amino acids are numbered from N—>C

Levels of Protein Structure

• Primary Structure

  • Linear amino acid sequence

  • Held together by peptide bonds

  • Determines all higher levels of structure

• Secondary Structure

  • Local folding patterns stabilized by hydrogen bonds in the backbone

  • Independent of R-group identity

    • Alpha Helices

      • Coiled structure

      • H-bonds form between backbone atoms

      • R groups stick outward

    • Beta Sheets

      • Extended strands aligned side-by-side

      • H-bonds between backbone atoms of adjacent strands

      • Can be parallel or antiparallel

• Tertiary Structure

  • Overall 3D shape of a single polypeptide

  • Driven by R-group interactions

    • Bonds Involved

      • Hydrogen bonds:

        • between polar R groups and/or backbone

      • Ionic bonds:

        • between oppositely charged R groups

      • Van der Waals forces:

        • Very weak, transient interactions

        • Important when many occur together

        • Common between hydrophobic R groups

      • Disulfide bonds

        • Covalent bonds between two cysteine R groups

        • Stabilize protein structure

        • Not present in all proteins

  • Quaternary Structure

    • Proteins made of multiple polypeptide subunits

    • Subunits held together by:

      • Hydrogen bonds

      • Ionic bonds

      • Van der Waals forces

      • Occasionally disulfide bonds

Protein Models

• Backbone model

  • shows path of polypeptide chain

• Ball-and-stick (wireframe)

  • shows all atoms and bonds, good for seeing interactions

• Ribbon model

  • Highlights α-helices, β-sheets, loopsSpace-filling model:

• Space-filling model

  • Shows surface shape, packing, and how the protein actually occupies space

Structure Determines Function

• Correct folding = correct function

• Misfolded proteins

  • Do not function properly

  • Sent to the proteasome for degradation

  • Accumulation overwhelms cell systems

Environmental Effects on Protein Folding

• Heat

  • Increased temperature → more molecular motion

  • Weakens non-covalent bonds

  • Can cause denaturation (unfolding)

• Light

  • High-energy light disrupts non-covalent interactions

• pH

  • Alters charge of R groups

  • Disrupts ionic and hydrogen bonds

• Salt

  • Shields charges

  • Interferes with ionic interactions

• Detergents

  • Disrupt hydrophobic interactions

  • Often cause protein unfolding