Online gaming, II Refer to the previous exercise. How large a sample would you need to take to estimate p within 2% at a 99% confi dence level? Show your work.
Chapter 4 Study Guide Protein structure and function Proteins are the building blocks from which cells are assembled and make up most of the cell’s mass. Enzymes promote intracellular chemical reactions. Proteins embedded in the plasma membrane form the channels and pumps that control the passage of nutrients and other small molecules into the cell. Other proteins carry messages from one cell to another, or act as signal integrators that relay info from membrane to nucleus. Shape and Structure The shape of a proteins is stabilized by noncovalent interaction between different parts of the molecule. A protein molecule is made of long chains of amino acids held together by covalent peptide bonds. Carbon of a carboxyl group shares electrons with nitrogen of amino group Condensation reaction because water is eliminated Proteins are also called polypeptides because of this. The polypeptide backbone is made of the core atoms (-N-C-C-). This backbone has an N-terminus and a C-terminus. The side chains are not involved in the peptide bonds. These side chains is what gives the amino acid its unique properties Nonpolar – hydrophobic Polar – hydrophilic Bonds that help fold proteins Disulfide bonds Hydrogen bonds Backbone-backbone Backbone-side chain Side chain-side chain Electrostatic attractions – between charged groups Van der waals attractions – between atoms at a short distance Weak force: Hydrophobic interaction Causes nonpolar sides to be forced together and stay on the inside of the protein Polar sides arrange on the outside of protein to make hydrogen bonds to water A protein can be denatured or unfolded by treatment with solvents that disrupt the noncovalent interactions holding it together. Example : Urea Implications with incorrect folding Form aggregates that can damage cells and tissues. Contribute to Alzheimer’s and Huntington’s disease. Prions: can convert the properly folded version of the protein into the abnormal conformation. Chaperone proteins- assist folding of proteins by binding to partially folded chains and help them fold. Different Shapes and Variety Range in size from 30 amino acids to 10,000, the majority of proteins are between 50 and 2000 amino acids long A-Helix Result from hydrogen bonds between N-H and C=O groups in the polypeptide backbone Side chains are not involved in bonds (BACKBONE-BACKBONE) A hydrogen bonds is made between every fourth amino acid; C=O of one amino acid to N-H of another amino acid. About 0.54 nm at each turn These are abundant in cell membrane proteins; transport and receptor proteins Backbone is hydrophilic and is hydrogen bonded to itself Coiled-coil structure where the hydrophobic side chains on one side face inward. In a trans-membrane region, the hydrophobic amino acids are on the exterior Beta Sheets Result from hydrogen bonds between N-H and C=O groups in the polypeptide backbone when they are side by side. Side chains are not involved (BACKBONE-BACKBONE) When the neighboring segments run in different directions = antiparallel When the neighboring segments run in same direction = parallel Relevant with aggregates in neurodegenerative diseases These can form channels in membranes Anti-Parallel Parallel Levels of Organization Primary Structure- amino acid sequence Secondary Structure- alpha helices and beta sheets Tertiary structure- 3 dimensional confirmation Quaternary structure- more than one polypeptide chain is formed into a complex (more than one domain) Protein domain: a segment of a polypeptide chain that can fold independently Usually contains between 40 and 350 amino acids Usually have different functions than other domains Example: CAP has two domains; one binds to DNA and other binds to cAMP. Unstructured Regions Called intrinsically disordered sequences are often found as short stretches linking domains. Binds around target proteins with high specificity and low affinity. Increases the frequency of encounters between domains. They can help scaffold proteins bring together proteins in signaling pathways. Families of proteins The amino acid sequences are very similar and their three-dimensional conformations are almost identical. They have different functions. Large proteins can have more than one polypeptide chain. Noncovalent bonds can bind proteins to eachother to produce larger structures. Each polypeptide chain in such a structure is called a subunit. Each subunit may contain more than one domain. In one case, there can be a dimer where two identical chains join together between two identical binding sites. This is called a dimer. Example of this is the CAP protein. Other structures One binding site Dimer 2 binding sites Turns into a helical protein filament (example actin filament) 2 binding sites in a certain way Closed ring Tubes, virus coats (shells) Covalent Cross-Linkages (Disulfide bonds) To maintain structure, proteins are often stabilized by covalent cross-linkages. Tie two amino acids in the same chain together Join together many polypeptide chains Disulfide bonds are formed before a proteins is secreted by an enzyme in endoplasmic reticulum that links two –SH groups from cysteine side chains that are adjacent in the folded protein. They do not form in the cell cytosol. Function All proteins bind to other molecules. The binding shows great specificity. Any substance that a protein binds to is called a ligand. Weak noncovalent interactions join the ligand and the protein Hydrogen, electrostatic attractions, van der waals, and hydrophobic forces Adenylyl Cyclase (Enzyme) turns ATP into cAMP. Antibodies Immunoglobulin proteins produced by the immune system in response to foreign molecules. Each antibody either binds to the molecule and inactivatie it or mark it for destruction. Antibody binds to antigen. Antibodies are Y shaped with two antigen-binding sites. They have a heavy chain and a light chain. When they come together Types of enzymes Hydrolase- catalyze a hydrolytic cleavage reaction Nuclease- breaks down nucleic acids Protease- breaks down proteins Ligase- joins two molecules together Isomerase- rearrange bonds in a single molecule Polymerase- polymerization Kinase- adds phosphate group to molecules Phosphatase- removes a phosphate group Enzymes Enzymes binds to substrates and convert them to chemically modified products. Speed up reactions.