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Intro Biology I - CH.3 : Protein Structure and Function

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  • How do amino and carboxyl groups behave in water?

    They ionize to form NH3+ (amino) and COO- (carboxyl), which helps amino acids stay in solution and affects their reactivity

  • What are the four main components bonded to the central carbon in an amino acid?

    Amino group (NH2), carboxyl group (COOH), hydrogen atom (H), and an R-group.

  • What determines the unique properties of each amino acid?

    • The R group (side chain), which varies in polarity, charge, and functional groups.

  • How are amino acids classified based on their side chains?

    • Into charged (acidic or basic), uncharged polar, and nonpolar amino acids.

  • What type of bond links amino acids to form proteins? How does it work?

    • A peptide bond, a covalent bond formed between the carboxyl group of one amino acid and the amino group of another via a condensation reaction.

  • What are the three key features of the peptide-bonded backbone?

    • R-group orientation (side chains extend outward)

    • Directionality (N-terminus to C-terminus),

    • Flexibility (the peptide itself cannot rotate, but the single bonds on either side can).

  • Define protein

    • complete, functional amino acid chain.

  • What is the primary structure of a protein?

    • The unique linear sequence of amino acids in a polypeptide chain (20 types of amino acids available)

  • How can a single amino acid change affect a protein?

    • It can radically alter the protein's function, as seen in sickle-cell anemia where glutamic acid is replaced by valine.

  • What forms the secondary structure of proteins?

    • Hydrogen bonds between the carboxyl group of one amino acid and the amino group of another, forming α-helices (twirls) and β-pleated sheets (sheets)

  • What causes the tertiary structure of a protein?

    • Interactions between R-groups, including hydrogen bonds, hydrophobic interactions, van der Waals forces, covalent disulfide bonds, and ionic bonds.

      • Cause backbone to bend and fold -- three-dimensional shape

  • What is quaternary structure in proteins?

    • The association of two or more polypeptide subunits into a single functional protein complex.

  • What are dimers, homodimers, and heterodimers?

    Dimers are proteins with two polypeptide subunits (how do I know it's two polypeptides? -- two different polypeptide chains associated with each other, but not continuous.)

    • Homodimers consist of two identical polypeptide subunits

    • Heterodimers consist of two different subunits.

  • What is a molecular machine? What role do molecular chaperones play in protein folding?

    • Multiple-protein machine that carry out a particular function

    • They facilitate proper folding and prevent inappropriate interactions between unfolded proteins.

  • What happens to a protein when it is denatured?

    • It loses its folded structure and becomes unable to function normally.

  • How can protein misfolding be infectious?

    Prions are misfolded proteins that induce normal proteins to adopt the infectious misfolded form, causing diseases like mad cow disease

  • List some diverse functions of proteins in cells.

    • Catalysis - speed up chemical reactions

    • Structural support

    • Movement

    • Signaling - convey signals btw cells

    • Transport - allow molecules to enter & exit cells or carry them throughout body

    • Defense - antibodies attack pathogens

  • What is the role of enzymes in biological reactions?

    • Enzymes are protein catalysts that hold substrates in precise orientation at the active site to speed up reactions.

  • What is the significance of the active site in an enzyme?

    It is the specific location where substrates bind and the chemical reaction occurs

  • Why is the primary structure important for higher levels of protein structure?

    • Because the amino acid sequence determines how the protein will fold into secondary, tertiary, and quaternary structures.

  • What is an amino acid?

    • Building blocks of proteins (monomers of protein and polypeptides.

  • What is a polypeptide? Tripeptide? Oligopeptide? Dipeptide?

    • Long chain of more than 20-50 amino acids

    • A chain made of 3 amino acids

    • A chain made of 2-20 amino acids

    • A chain made of 2 amino acids

  • What three attributes of life must protein possess?

    • Information

    • Replication

    • Evolution

  • What do R-groups usually contain?

    Functional groups; although, sometimes just carbon and hydrogen atoms --determine core structure & function

  • What affects the solubility of an amino acid? Types?

    Nature of R-group

    • Polar & charged groups - interact w/ water -- hydrophilic

    • Non-polar -- hydrophobic

  • How can you determine the R-group type of amino acid?

    • Does side chain have - charge?

      • Yes -- acidic

    • Positive charge?

      • Yes -- basic

    • If uncharged, does it have an oxygen atom?

      • Yes? - uncharged polar

     If all the answers are no -- non-polar amino acid

  • What is the N-terminus? The C-terminus? How do they interact?

    • Peptide bonds end with a free amino group

    • End with a free carboxyl group

  • Are amino acid chains flexible or inflexible?

    Flexible

  • In a peptide chain, what are the backbone, peptide bonds, and R groups?

    • Backbone = repeating N–C–C chain. Peptide bonds = C–N (or N-C) links. R groups stick off the backbone.

  • Where does the R-group attach to an amino acid? The hydrogen?

    • Both attach to the central carbon (Ca; the middle of N C C pattern)

              R         R

               I          I

    • ex: N C C N C C

               I          I

              H         H

  • What is typically the amino group? The carboxyl group?

    • NH (in water : NH+) - LEFT

    • COOH ( in water: -COO-) - RIGHT

  • How do amino acids polymerize? What is the bond?

    The carboxyl group of one amino acid bond with the amino group of the second amino acid = PEPTIDE BOND

    • Covalent bond resulting from condensation reaction

  • What types of R-group interactions occur in tertiary structure?

    • Hydrogen bonds — btw polar side chains with opp partial charges.

    • Hydrophobic interactions — hydrophobic side chains avoid H20.

    • Van der Waals — weak electrical attractions btw nearby hydrophobic side chains.

    • Disulfide bonds — cov. bonds btw sulfhydryl grps.

    • Ionic bonds — btw grps w/ full, opp charges

  • When do proteins fold & how does it work? Why does this happen? Is it often spontaneous or non-spontaneous?

    • Protein folding occurs when interactions between amino acid R groups (ex: hydrogen bonds, ionic interactions, etc.) cause the chain to bend and fold into a specific 3D shape. This shape allows the protein to perform its function.

    • Folded molecule = more stable; less potential energy

    • Spontaneous

  • Denatured vs. Misfolded protein

    • Denatured = shape is disrupted/lost → basically “destroyed” shape

    • Misfolded = wrong shape → the protein is still folded, but incorrectly