Amino Acids and Protein Structure

Enzymes

• Function: Catalyze chemical reactions (bond forming/breaking)

• Examples

  • DNA polymerase: copies DNA

  • Sucrase: Breaks down sucrose

Structural Proteins

• Function: Provide mechanical support to cells and tissues

• Examples

  • Collagen + Elastin: Form fibers in tendons and ligaments

  • Keratin: Forms fibers that strengthen epithelial cells

Transport Proteins

• Function: Carry small molecules or ions

• Examples

  • Hemoglobin: Carries oxygen throughout the body

Motor Proteins

• Function: Generate movement in cells and tissues

• Examples

  • Myosin: In skeleton muscle cells, provides the motive force needed for humans to move

Storage Proteins

• Function: Store amino acids and ions

• Examples:

  • Ferritin: Helps store iron in the liver by binding it to itself

Signal Proteins

• Function: Carry extracellular signals from cell to cell (Allows cells to communicate w/ each other)

• Examples

  • Insulin: Small protein that controls insulin levels in the blood

  • Nerve Growth Factor: Stimulates some types of nerve cells to grow axons

Receptor Proteins

• Function: Detect signals and transmit them to the cell’s response mechanisms

• Examples

  • Insulin receptor: Allows a cell to respond to the hormone insulin by taking up glucose

Transcription Regulators

• Function: Bind to DNA to switch genes on or off

• Examples

  • Lac repressor: In bacteria, silences the genes for the enzymes that degrade the sugar lactose

Antibodies

• A type of special-purpose proteins

• Structure: Contains four peptide-chains held together by disulfide bonds

• Function

• They appear when there are traces of viral cells in the body

• Antibodies bond to the receptors on the viral cells’ surfaces, preventing them from binding to host cells

• The appearance of antibodies on viral cells also alert phagocytes to the viral cells

  • causes degradation of viral cells to occur

Proteins - Definition

• One of the four macromolecules

• Consist of one or more peptide chains

  • Folded into specific 3D shapes that are determined by the sequence of amino acids

Twenty Amino Acids

• STRONGLY HYDROPHILLIC (5)

  • Consist of an R-group that is charged OR highly polar

    • Contains electronegative atoms like F.O.N.

  • These R-groups can form hydrogen bonds with water

• STRONGLY HYDROPHOBIC (7)

  • Consist of an R-group that is uncharged AND highly non-polar

  • Usually has H’s and C’s

  • Many feature branched or ring-like structures

• GENERALLY HYDROPHILIC (5)

  • R-groups that have polar bonds b/c of the appearance of electronegative atoms

  • However, R-groups can contain some hydrocarbon bonds that take away from the full potential of a highly polar molecule

• GENERALLY HYDROPHOBIC (3)

  • R-groups that consist largely of non-polar bonds

  • There can be some polar bonds but the effects aren’t as strong as those of the non-polar bonds

Protein Diversity

• The average length of a protein is 500 amino acids

• There are 20 different standard amino acids that can be used

Primary Level of Protein Structure

• Amino acids form to create polypeptide chains

  • Through use of peptide bonds

• Refers to the sequence of amino acids that define the protein

  • dictates what intramolecular interactions will occur in the SECONDARY + TERTIARY levels

Secondary Level of Protein Structure

• Refers to the backbone-backbone interactions that occur within a polypeptide chain due to hydrogen-bonding

• Formation of alpha-helices & beta-pleated sheets within a chain

• Alpha helices

  • Every N-H of each peptide bond is H-bonded to the C-O of a neighboring peptide bond located FOUR amino acids away in the SAME chain

  • Promote the formation of helical shapes

• Beta-pleated sheets

  • H-bonding can occur between individual segments of the same polypeptide chain or different polypeptide chains

  • ANTIPARALLEL

    • Adjacent strands run in opposite directions

    • Leads to stronger bonds b/c the ends of one strand directly meet up with the starts of the adjacent strand

    • Like a ladder

  • PARALLEL

    • Adjacent strands run in the same directions

    • Leads to weaker bonds b/c the starts and ends don’t directly meet-up, which causes loose bonding, resulting in zig-zag lines

Tertiary Level of Protein Structure

• Refers to the overall 3D-folding of a single polypeptide chain

• Driven primarily by interactions between the R-groups of the amino acids

• Types of Interactions That Can Exist

  • Ionic interactions between two charged amino acids

  • van der Waal attractions of nonpolar side chains

  • Hydrogen bonding between H’s and electronegative atoms