Essential Cell Biology Third Edition Copyright Garland Science 2010 Structure Protein: Provides the cell with shape and structure (tubulin and actin) Enzymes: Catalyze covalent bond breakage or formation (pepsin) Transport Protein: Carries other molecules or ions (hemoglobin oxygen) Motor Protein: Generates movement in cells and tissues (Myosin) Storage Protein: Stores small molecules or ions (ferritin - iron in liver) Signal Protein: Carries signals from cell to cell (insulin glucose levels) Receptor Protein: Detects signals and transmits them to the cells response machinery (insulin receptor) Gene Regulatory Protein: Binds to DNA to switch genes on or off (transcriptional factors lactose repressor) A few examples of some general protein functions (I) The shape and structure of proteins Figure 4-1 Essential Cell Biology (Garland Science 2010) Amino acids are linked together by peptide bonds Oxygen Carboxyl group Amino group Hydrogen Nitrogen Carbon Figure 4-2 Essential Cell Biology (Garland Science 2010) A Protein is made of amino acids linked together into a polypeptide chain Figure 4-3 Essential Cell Biology (Garland Science 2010) Twenty different amino acids are linked together by peptide bonds Types of noncovalent bonds or interactions help proteins fold hydrogen bonds: When a hydrogen atom is sandwiched between electron-attracting atoms (oxygen or nitrogen). electrostatic attractions: between charged groups. van der Waals attractions: attractions between two atoms at very short distances. Hydrophobic interaction Three types of noncovalent bonds Figure 4-4 Essential Cell Biology (Garland Science 2010) Three types of non-covalent bonds help protein fold Figure 4-5 Essential Cell Biology (Garland Science 2010) Hydrophobic forces help proteins fold into compact conformations Figure 4-6 Essential Cell Biology (Garland Science 2010) Hydrogen bonds within a protein molecule help stabilize its folded shape Figure 4-7 Essential Cell Biology (Garland Science 2010) Denatured proteins can recovered their natural shapes to maintain a conformation of lowest energy Figure 4-8 Essential Cell Biology (Garland Science 2010) Prion diseases are caused by rare proteins whose misfolding is infectious Dr. Stanley Prusiner Nobel Prize in Medicine 1997 Discovery of Prions - a new biological principle of infection" . Figure 4-9 Essential Cell Biology (Garland Science 2010) Protein come in a variety of shapes and sizes 100 amino acids 3-D structure A ribbon model helices and sheets The helix is a common folding pattern of proteins The N-H of every peptide bond is hydrogen-bonded to the C=O of a neighboring peptide bond located four amino acids away in the same chain The helix is a common folding pattern The sheet is a common folding pattern of proteins The individual strands in the sheet are held together by hydrogen-bonding between peptide bonds in different strands, and side chains in each strand project alternately above and below the plane of the sheet Figure 4-11 Essential Cell Biology (Garland Science 2010) The helix is a regular biological structure Movie: The helix Figure 4-12 Essential Cell Biology (Garland Science 2010) A segment of helix can cross a lipid bilayer Hydrophobic hydrocarbon tails of phospholipid Intertwined helices can form a coiled-coil Nonpolar side chains Figure 4-14 Essential Cell Biology (Garland Science 2010) Sheet come in two varieties: Parallel and Antiparallel Pauling and Corey proposed the structures of helix and sheet. Linus Pauling won the Nobel Prize in Chemistry 1954 Figure 4-16 Essential Cell Biology (Garland Science 2010) Many proteins are composed of separate functional domains Figure 4-17 Essential Cell Biology (Garland Science 2010) Ribbon models show three different protein domains Figure 4-18 Essential Cell Biology (Garland Science 2010) Serine proteases comprise a family of proteolytic enzymes Identical amino acid sequence Active site: serine Figure 4-19 Essential Cell Biology (Garland Science 2010) Many protein molecules contain multiple copies of a single protein subunit Figure 4-20 Essential Cell Biology (Garland Science 2010) Some proteins contain two different subunits Hemoglobin contains two copies of -globin and two copies of -globin A heme molecule can bind one O2 Figure 4-21 Essential Cell Biology (Garland Science 2010) Protein can assemble into complex structures Figure 4-22 Essential Cell Biology (Garland Science 2010) An actin filament is composed of identical protein subunits Figure 4-23 Essential Cell Biology (Garland Science 2010) Single protein subunits can pack to form a filament, tube, or a spherical shell Figure 4-25a Essential Cell Biology (Garland Science 2010) Collagen is a triple helix formed by three protein chains that wrap around one another Cross-linked Figure 4-26 Essential Cell Biology (Garland Science 2010) Disulfide bonds help stabilize a favored protein conformation (II) How proteins work Figure 4-27 Essential Cell Biology (Garland Science 2010) The binding of a protein to another molecule is highly selective Figure 4-28a Essential Cell Biology (Garland Science 2010) The folding of the polypeptide chain creates a cavity on the protein surface Figure 4-28 Essential Cell Biology (Garland Science 2010) Binding site allow a protein to interact with specific ligands Figure 4-29 Essential Cell Biology (Garland Science 2010) An antibody is Y-shaped and has two identical binding sites for its antigen Table 4-1 Essential Cell Biology (Garland Science 2010) Some common functional classes of enzymes Figure 4-30 Essential Cell Biology (Garland Science 2010) Lysozyme cleaves a polysaccharide chain S: substrate, E: enzyme, P: product The lysozyme cuts the polysaccharide by catalyzing the addition of a water molecule to one of the sugar-sugar bonds. Figure 4-31 Essential Cell Biology (Garland Science 2010) In the active site of lysozyme, bonds are bent and broken Movie: Lysozyme cleaves a polysaccharide chain Figure 4-32 Essential Cell Biology (Garland Science 2010) Enzymes can encourage catalysis in several ways (III) How proteins are controlled Figure 4-34 Essential Cell Biology (Garland Science 2010) Feedback inhibition regulates the flow through biosynthetic pathways B is the first metabolite in a pathway that gives the end product Z. Z inhibits the first enzyme for its synthesis and thereby controls its own concentration in the cell. Figure 4-36 Essential Cell Biology (Garland Science 2010) Feedback inhibition triggers a conformational change The multisubunit enzyme, aspartate transcarbamoylase, catalyzes an important reaction that begins the synthesis of the pyrimidine ring of C, U, and T nucleotide. One of final products of this pathway, cytosine triphosphate (CTP), binds to the enzyme to turn it off whenever CTP is plentiful. Figure 4-37 Essential Cell Biology (Garland Science 2010) An increase of ligand (ADP) concentration activates the enzymatic reaction for oxidation of sugars ADP can bind only to the enzyme in its closed conformation and thereby lowers the energy of the closed conformation, locking nearly all of the enzymes in the active form. Figure 4-38a Essential Cell Biology (Garland Science 2010) Protein phosphorylation is a very common mean of regulating protein activity Figure 4-38b Essential Cell Biology (Garland Science 2010) Protein phosphorylation is a very common means of regulating protein activity Figure 4-39 Essential Cell Biology (Garland Science 2010) GTP-binding proteins form molecular switches Figure 4-40 Essential Cell Biology (Garland Science 2010) A large conformational change is produced in EF-Tu in response to nucleotide hydrolysis The GTP-binding protein EF-Tu binds tRNA on the ribosome and plays a role in the elongation of a polypeptide chain during protein synthesis. In its GTP-bound form, EF-Tu binds a tRNA molecule tightly. The hydrolysis of bound GTP causes a large conformational changes within the protein and leads to release of the tRNA. An allosteric mortor protein, driven by ATP hydrolysis, moves in one direction An orderly transition among three conformations is driven by the hydrolysis of a bound ATP molecule. By repeated cycles of the conformation changes, the protein moves continuously to the right along the thread. Figure 4-44a Essential Cell Biology (Garland Science 2010) The modification of a protein at multiple site produce a regulatory code that controls the protein behavior Acetylation Ubiquitylation Phosphorylation Figure 4-44b Essential Cell Biology (Garland Science 2010) Some of the covalent modifications that control the activity and degradation of the protein p53 Acetylation Ubiquitylation Phosphorylation (IV) How proteins are studied Figure 4-45 (part 1 of 2) Essential Cell Biology (Garland Science 2010) Mass spectrometry can be used to identify proteins by determine the precise masses of peptides Two-dimensional electrophoresis Figure 4-45 (part 2 of 2) Essential Cell Biology (Garland Science 2010) Mass spectrometry can be used to identify proteins by determine the precise masses of peptides Figure 4-46 Essential Cell Biology (Garland Science 2010) The structure of a protein can be determined by X-ray crystallography Figure 4-48 Essential Cell Biology (Garland Science 2010) Cells in culture often display properties that reflect their origin Fibroblasts Oligodendrocytes (Neurons) Myoblasts Epithelial cells Tobacco cells Affinity chromatography can be used to isolate the binding partners of a protein of interest