Course number: BIOL 3090 Course title: Cell Biology Class 3 Protein structure and function Today, we wil learn 3 things: ?What is a hierarchy of a protein structure? ?How does a protein structure define the function? ?(What is a protein?s life cycle?) How is the protein structure linked to disease? Classification of Inherited Neurodegenerative Disorders Alzheimer's disease Alzheimer's disease afects over 4 milion people in the United States, resulting in over 10,00 deaths per year and costing the nation more than $60 bilion anualy. Martin, J. B. N Engl J Med 199;340:1970-1980 Lodish P72, Figure 3-14 The brain tissue of an Alzheimer?s-disease patient Nusbaum RL. N Engl J Med 203: 348: 1356-1364 Amyloid Precursor Protein enlarged view How to understand protein structures -CN3D- Proteins Structure hierarchy Lodish, P60 Figure 3-1 Primary Structure: Linear Arrangement of Amino Acids (polypeptide chain) Lodish, P60 Figure 3-2 Amino Acid (a)--- D,E,M,F,L,Y,W,A,V,I,R,H,N,C,etc (We will learn them in the class 6) Secondary Structure: folding of localized parts of a polypeptide chain Lodish, P60 Figure 3-3 ! helix " sheet/strand Lodish, P62 Figure 3-4 Stabilized by hydrogen bond Secondary Structure: folding of localized parts of a polypeptide chain Lodish, P60 Figure 3-3 ! helix " sheet/strand Lodish, P62 Figure 3-4 *Change of hydrogen bonds " amyloid Alzheimer's disease A change of the secondary structure of amyloid protein results in Alzheimer's disease Tertiary Structure: Combinations of secondary structures make a ?motif? Lodish, P62 Figure 3-6 Hydrophobic residues are in a regularly pattern?.. (Lodish P63) Wait! what are the hydrophobic residues? ?You have to memorize characters of each amino acid in the class 6 ? The motif in 3D? The information dictating the proper folded conformation of a nascent protein is contained within 1. chaperones that aid in folding 2. peptide bonds of the nascent protein 3. primary amino acids sequence of the nascent protein 4. 60S subunit of the ribosome synthesizing the protein 5. 40S subunit of the ribosome synthesizing the protein Tertiary Structure: Various combinations of motifs create a ?domain? Lodish, P65 Figure 3-7 Lodish, P65 Figure 3-8 Domains are conserved in many different proteins (Conserved Domain) Tertiary Structure: Overall folding of a polypeptide chain is stabilized by hydrogen bond and hydrophobic interactions Lodish, P63 Figure 3-5 Same protein but diferent views Proteins are designed to bind every conceivable molecule? The function of nearly all proteins depends on their ability to bind other molecules, or ligands, with a high degree of specificity?. Lodish P73 section 3.3 Quaternary Structure: made of more than two polypeptide chains The size of the molecules we will learn Lodish Page 19 Fig 1-20 CG movie: The inner life of a cell TV show: The miracle of life Quaternary Structure: made of more than two polypeptide chains Lodish p80 Fig. 3-23 This guy has a quaternary structure Lodish p81 Fig. 3-24 Quaternary Structure: made of more than two polypeptide chains Myosin II is made of 6 (hexamer) polypeptide chains! Analyze data A method used: ?SDS gel electrophoresis How to use and how to read? A tool to measure a function of a Car/Cell htp:/ww.images.gogle.com A480 kDa 250 kDa 200 kDa 300 kDa 25 kDa 15 kDa B C E F D Myosin II is a hexamer (6 peptides) composed of two heavy chains of approximately 200 kDa and two pairs of light chains of 20 and 17 kDa. The purification of myosin II protein was undertaken. A partially purified cell fraction containing the myosin II protein was subjected to SDS gel electrophoresis, which was stained with Coomassie blue. Which band(s) is myosin I protein(s)? 1.A only 2.B only 3.A, B, C, D, E, and F 4.B, C, D, E, and F 5.C, D, E, and F 6.C, E, and F A480 kDa 250 kDa 200 kDa 300 kDa 25 kDa 15 kDa B C E F D 200 kD 17 kD 20 kD I did not heat the samples before their loading. Which band(s) is myosin I protein(s)? 1.A only 2.B only 3.A, B, C, D, E, and F 4.B, C, D, E, and F 5.C, D, E, and F 6.C, E, and F A480 kDa 250 kDa 200 kDa 300 kDa 25 kDa 15 kDa B C E F D 200 kD 17 kD 20 kD
