Review for Protein Please do not memorize the answers You must understand the concepts Please do not share upload all and any lecture contents with other students who are not taking this course and at websites like Chegg and CourseHero as these sites will be monitored That is against copyright law of UNT and the book publisher so you WILL be reported and face consequences according to UNT s policies 1 Select the answer that best completes the following statement Chemical reactions in living systems occur in an environment within a narrow range of temperatures 2 Although covalent bonds are 10 100 times stronger than noncovalent interactions many biological processes depend upon the number and type of noncovalent interactions between molecules Which of the noncovalent interactions below will contribute most to the strong and specific binding of two molecules such as a pair of proteins optimal organic extracellular aqueous a b c d a b c d electrostatic attractions hydrogen bonds hydrophobic interactions Van der Waals attractions Please understand this Types of non covalent bonds forces 1 Electrostatic attractions 3 kcal mol in water forces that attract oppositely charged atoms 2 Hydrogen bonds 1 kcal mol in water a weak bond between an electronegative atom and a hydrogen bound to another electronegative atom 3 Van der Waals interactions 0 1 kcal mol in water fluctuations in the electron cloud surrounding an atom creates a transient dipole this dipole induces an opposing dipole in a nearby atom generating an attraction attraction between the nucleus of one molecule and the electrons of a nearby molecule 4 Hydrophobic forces not really a bond exclusion of non polar surfaces from the hydrogen bonded water network 3 Proteins are polypeptides built from amino acids which each have an amino group and a a carboxyl group attached to the central alpha carbon There are twenty possible side chains that differ in structure and are generally referred to as R In solutions of neutral pH amino acids are ioinized carrying both a positive and negative charge When a protein is made amino acids are linked together through peptide bonds which are formed by condensation reactions between the carboxyl end of the last amino acid and the amino end of the next amino acid to be added to the growing chain 4 As a protein is made the polypeptide is in an extended conformation with every amino acid exposed to the aqueous environment Although both polar and charged side chains can mix readily with water this is not the case for nonpolar side chains Explain how hydrophobic interactions may play a role in the early stages of protein folding and have an influence on the final protein conformation 5 A protein chain folds into its stable and unique three dimensional structure or conformation by making many noncovalent bonds between different parts of the chain Such noncovalent bonds are also critical for interactions with other proteins and cellular molecules From the list provided choose the class es of amino acids that are most important for the interactions detailed below A B C D forming ionic bonds with negatively charged DNA basic forming hydrogen bonds to aid solubility in water uncharged polar localizing an integral membrane protein that spans a lipid bilayer nonpolar tightly packing the hydrophobic interior core of a globular protein nonpolar acidic nonpolar basic uncharged polar 6 Fill in the blank spaces in the table below The first row has been completed for you 7 Indicate whether the following statements are true or false If a statement is false explain why it is false A large number of noncovalent interactions is required to hold two regions of a polypeptide chain together in a stable conformation True A single polypeptide tends to adopt 3 4 different conformations which all have equivalent free energy values G NO Just ONE conformation Please remember the different conformation 3D shape means the different function There is a single final fold for every polypeptide The fold adopted is the best conformation for which the free energy G of the molecule is at a minimum A B 8 A newly synthesized protein generally folds up into a stable conformation All the information required to determine a protein s conformation is contained in its amino acid sequence On being heated a protein molecule will become denatured as a result of breakage of noncovalent bonds 9 Explain 4 different protein structural levels and name the most important force s are involved in maintaining each structure Four Levels of Protein Structure Please know this o The primary structure of a protein is its unique sequence of amino acids Primary structure is like the order of letters in a long word Primary structure is determined by inherited genetic information Peptide bonds covalent bond o Secondary structure found in most proteins consists of coils and folds in the polypeptide chain The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone Typical secondary structures are a coil called an helix and a folded structure called o Tertiary structure is determined by interactions among various side chains R groups Tertiary structure the overall shape of ONE polypeptide results from interactions a pleated sheet between R groups These interactions include hydrogen bonds ionic bonds hydrophobic interactions and van der Waals interactions Strong covalent bonds called disulfide bridges may involve the protein s structure o Quaternary structure results when a protein consists of multiple polypeptide chains Quaternary structure results when two or more polypeptide chains form one macromolecule using hydrogen bonds ionic bonds hydrophobic interactions and van der Waals interactions 10 What are the noncovalent bonds held proteins fold Please answer this question 15 Any substance that will bind to a protein is known as its ligand Enzymes bind their substrates at the active site Enzymes catalyze a chemical reaction by lowering the activation energy because they provide conditions favorable for the formation of a high energy intermediate called the transition state Once the reaction is completed the enzyme releases the products of the reaction activation energy inhibitors products active site isomers substrates free energy ligand transition state high energy low energy 16 Allosteric enzymes have two or more binding sites True or False 17 The specificity of an antibody molecule is contained