Chapter 3 - Proteins

• What is the function of proteins?

  Enzymes (catalyze chemical reactions), structural integrity, control flow of info through membranes, regulate metabolite concentration, act as sensors and switches, cause motion, control gene function
• Structure of an amino acid?

  amino group, carboxyl group, and side chain
• What is the carbon backbone?

  Amino and carboxyl group of an amino acid
• Polar is hydrophilic
• Non-polar is hydrophobic
• Electrically charged side chains are hydrophilic and can be acidic (negatively charged) or basic (positively charged)
• Polar side chains are hydrophilic and have partial charges such as OH or the N on NH2
• Disulfide bonds are the strongest bond a protein can have
• Nonpolar side chains are hydrophobic
• Methionine is a nonpolar side chain that every protein starts with
• Joining 2 amino acids together creates a peptide bond
• Amino end is the N-terminus and the carboxyl end is the C-terminus
• Proteins are always read from the N-terminus to the C-terminus
• The protein primary structure is the sequence of amino acids and they are held together by Peptide bonds between carbon backbones. All proteins have a primary structure.
• Protein secondary structures are alpha helix, beta pleated sheet, and turns
• Combinations of secondary structure, motifs, are coiled coil, helix loop helix, and zinc fingers
• Quaternary Protein Structure is more than one polypeptide - some polypeptides can't function alone and must interact with other polypeptides
• Protein Secondary Structure - Alpha Helix

  H bonds between carbonyl O and amine H, 4 residues downstream, turns every 3.6 amino acids, rigid cylinder
• All proteins have secondary structure
• Ex. Secondary Structure - Alpha Helix

  Cell membrane proteins
• Protein Secondary Structure - Beta-Pleated Sheet

  H bonds between carbonyl O and amine H, 5-8 residues, toughness to proteins, either anti-parallel or parallel
• Ex. Secondary Structure - Beta-Pleated Sheet

  Transport proteins and receptors
• Protein Secondary Structure - Turns

  3-4 residues, Proline and Glycine utilized
• Motifs - Coiled Coil

  Structural framework in proteins, 2-3 alpha helices; Ex. keratin and myosin
• Motifs - Helix Loop Helix

  Involved in DNA binding, found in transcription factors
• Motifs - Zinc Fingers

  Alpha helix and 2 anti-parallel beta-pleated sheets, involved in DNA binding
• Proteins Tertiary Structure

  Interactions between R groups, All types of bonds, Found in all proteins
• Protein Tertiary Structure - Chaperones

  Help directly in folding, Stabilize proteins to prevent degradation
• Protein Tertiary Structure - Domains

  Contain specific protein functions, 100-200 residues
• Ex. Domains in Tertiary Conformation

  Kinase, DNA Binding, Membrane Binding, Catalytic, SH2/SH3
• Protein Quaternary Structure

  Can involve: carbon backbone and variable side chains

  Stabilized by: H bonds, Ionic bonds, Disulfide bonds. VDW forces, Hydrophobic interactions
• Not all proteins have quaternary structure - most proteins function at tertiary structure
• Hemoglobin requires quaternary protein structure
• Chromatography - separates proteins from sample
• SDS PAGE - separates proteins based on size
• SDS PAGE Advantages

  quick, inexpensive, easy
• SDS PAGE Disadvantages

  Not specific to any protein
• 2D Gel Electrophoresis - proteins separated by charge and then by size
• 2D Gel Electrophoresis Advantages

  Separate proteins based on 2 characteristics
• 2D Gel Electrophoresis Disadvantages

  More difficult than SDS PAGE alone and doesn't detect proteins specifically