AP Biology Book Notes Chapter 3 v Nucleic acids Ø Polymers specialized for the storage transmission and use of genetic information Ø Two types DNA Encodes hereditary information Used to specify the amino acid sequences of proteins DNA and the proteins encoded by DNA determine metabolic functions RNA Ø Composed of nucleotides which consist of three component Nitrogen containing base Three phosphate groups A pentose sugar v Nucleotides Ø Pyrimidine single ring structure Ø Purine double ring structure Ø The pentose sugar and the phosphate provide the hydroxyl function groups for the linkage of one nucleotide to the next Done through condensation reaction the resulting bond is a phosphodiester linkage Ø Oligonucleotides Include RNA molecules that function as primers to begin the duplication of DNA RNA molecules that regulate the expression of genes and synthetic DNA molecules used for amplifying and analyzing other longer nucleotide sequences Ø Polynucleotides More commonly referred to as nucleic acids DNA and most RNA Can be very long and indeed are the longest polymers in the living world Some DNA molecules in humans contain hundreds of millions of nucleotides v DNA Ø Hydroxyl group makes DNA less flexible than RNA Ø Four bases Adenine Thymine Cytosine Guanine RNA has Uracil instead of thymine Ø Complementary base pairing A + T C + G Ø Bonds are relatively easy to break when energy is applied Ø Usually double stranded
DNA carries genetic information in its sequence to determine structure Ø Informational molecule Ø Can be reproduced exactly done through polymerization using and existing strand as a base pairing template Ø DNA to RNA called transcription Then can specify sequence of amino acids in polypeptide chain this is translation Process of transcription and translation is called gene expression Ø DNA replication and transcription depends on the base paring properties of nucleic acids Ø DNA replication usually involves the entire DNA molecule Ø DNA base sequence reveals evolutionary relationships closely related living species should have more similar base sequences than species that are more distantly related v RNA Ø Usually single strand, but can still fold into three dimensional structures because of hydrogen bonds Folding occurs because of complimentary base pairing and structure thus depends on the order of the pairing v Amino acids Ø Building blocks of proteins Two functional groups nitrogen containing amine group and the carboxylic acid group Ø Only 20 amino acids occur extensively in the proteins of all organisms Ø Can form short polymers of 20 or less amino acids called oligopeptides or peptides Longer = polypeptide/protein Proteins and peptides form via the sequential addition of new amino acids at the end of the chain condensation reaction forms a peptide linkage (peptide bond) Ø The precise sequence of amino acids in a polypeptide chain constitutes the primary structure of a protein Ø Higher level protein structure is determined by primary structure Primary structure or a protein is established by covalent bonds but higher levels of structure are determined by weaker forces including hydrogen bonds and hydrophobic and hydrophilic interactions Ø Secondary structure Consists of regular repeated patterns in different regions of a polypeptide chain Two types The (a) alpha helix is a right handed coil The R groups extend outward from the peptide backbone of the helix
Coiling results from the hydrogen bonds that form between the N- H group on one amino acid and the C=O group on another within the same turn of the helix The (b) beta pleated sheet Formed from two or more polypeptide chains that are extended and aligned Stabilized by hydrogen bonds between N- H groups and the C=O groups on the two chain May form between spate polypeptide chains or between different regions of a single polypeptide chain that is bent back on itself Tertiary structure In many proteins the polypeptide chain is bent at specific sites and then folded back and forth resulting in this structure Results in the polypeptide s definitive 3- D shape including buried interior as well as surface that is exposed to the environment Proteins exposed outer surfaces present functional groups capable of interacting with other molecules in the cell. These molecules might be other proteins or smaller chemical reactants The interactions between R groups determine tertiary structure Ø Tertiary and secondary structures derive from primary structure Quaternary structure Many functional proteins contain two or more polypeptide chains called subunits each folded into its own unique tertiary structure Results form the ways in which these subunits bind together and interact Ø Increase in temperature cause more rapid molecular movements and thus can break hydrogen bonds and hydrophobic interactions Ø Alterations in the concentration of H+ can change the patterns of ionization of the exposed carboxyl group and amino groups thus disrupting the patterns of ionic attractions and repulsions Ø High concentrations of polar substances such as urea can disrupt the hydrogen bonding that is crucial to protein structure Ø Nonpolar substances may also denature a protein incases where hydrophobic groups are essential for maintaining the proteins structure Ø Denaturing can be irreversible when amino acids that were buried in the interior od the protein become exposed at the surface of vice versa causing new structure to form or causing different molecules to bind to the protein v Catalysts Ø Substances that speed up a reaction without themselves being permanently altered Ø Does not cause a reaction to occur that would not proceed without it but it increases the rate of reaction Ø No catalyst can make a reaction that would not otherwise occur Ø Most are enzymes
Ø Ribozyme provides a molecular structure that binds the reactants and can participate in the reaction itself Ø To speed up a reaction an energy barrier must be overcome Exergonic reaction releases energy Energy input required to reach transition state is activation energy Ø Enzymes bind specific reactants at their active sites Catalysts increase the rates of chemical reactions Most non- biological catalysts are nonspecific An enzyme usually binds to only one or a few closely related reactants and it catalyzes only a single chemical reaction In enzyme- catalyzed reaction the reactants are called substrates Substrate molecules bind to a particular site on the enzyme called the active site where catalysis takes place The specificity of an enzyme results from the exact 3- D shape and chemical properties of its active site The binding of the substrate to the active site of an enzyme produced an enzyme substrate complex Gives rise to product and free enzyme Ø During and after the formation of the enzyme substrate complex chemical interactions occur and contribute directly to the breaking of old bonds and the formation of new ones Ø Enzymes may Induce strain Once the substrate has bound to the active site the enzyme causes bonds in the substrate to stretch putting it in an unstable transition state Substrate orientation When free in solution substrates are moving from place to place randomly while at the same time vibrating rotating and tumbling they only rarely have the orientation to react when they collide The enzyme lowers the activation energy needed to start the reaction by brining together specific atoms so that bonds can form Adding chemical groups The R groups of an enzymes amino acids may be directly involved in the reaction Ø The binding of the substrate to the active site depends on the same relatively weak forces that maintain the tertiary structure of the enzyme, hydrogen bonds the attraction and repulsion of electrically charged groups and hydrophobic interactions Ø The rest of the macromolecules has three other roles It provides a framework so the amino acids of the active site are properly positioned in relations to the substrates It participates in the changes in protein shape and structure that result in induced fit It provide binding sites for regulatory molecules
Ø Some enzymes require ions or other molecules in order to function Cofactors inorganic ions that bind to certain enzymes Coenzyme carbon containing molecule that is required for the action of one ore more enzymes Relatively small compared to the enzyme it bonds with Does not permanently bind to the enzyme it binds to the active site changed chemically during the reaction and then separates from the enzyme to participate in other reactions Can participate in many different reactions with different enzymes Prosthetic group non- amino acid atoms or molecular groups that are permanently bound to their enzymes Ø Rate of reaction Directly proportional to the concentration of the substrate When all the enzyme molecules re bound to substrate molecules the enzyme is working at its maximum rate and active sites are said to be saturated The maximum rate of a catalyzed reaction can be used to measure how efficient the enzyme is v Metabolic processes Ø Enzymes may participate in anabolic pathways, producing complex molecules from simpler ones Ø Cell can regulate metabolism by amounts or activity of enzymes Ø Enzymes can be regulated by inhibitors Chemical inhibitors can bind to enzyme slowing down the rates of the reactions they catalyze Some occur naturally in cells, which regulate metabolism, artificial, ones can treat disease etc. The inhibitor can bind to the enzyme irreversible and the enzyme becomes permanently inactivated Reversible inhibition The competitive inhibitor is similar enough to the substrate that it can bind to the enzymes active site but different enough that the chemical reaction cannot occur Noncompetitive inhibitor binds to the enzyme at a site distinct from the active site and causes a change in the enzymes shape making the enzyme inactive, either the substrate cant bind or it reduces the reaction rate Ø Allosteric enzyme Occurs when the non- substrate molecule binds or modifies a site other than the active site or an enzyme inducing the enzyme to change its shape Covalent modification amino acid can be covalently modified by the addition of a phosphate (phosphorylation) if it occurs in a hydrophobic region it makes the region hydrophilic
Non- covalent bonding a regulatory molecule may bind non- covalently to an allosteric site which can either activate or inhibit the enzymes function Protein kinases enzymes that regulate responses to the environment by organisms Ø First step of metabolic processes is usually the commitment step Ø Feedback/end product inhibition a mechanism for regulating a metabolic pathway in which the end product of the pathway can bind to and inhibit the enzyme that catalyzes the first committed step in the pathway Ø Enzymes affected by their environments ph Generate H+ become anions Attract H+ become cations Reactions often reversible Law of mass action Implies that the higher of the H+ concentration the more the reaction will be driven to the left Changes in the H+ concentration can alter the level of hydrophobicity of some regions of a protein and affect shape Each enzyme has a tertiary structure and amino acid sequence that makes is optimally active at a particular ph Temperature Generally warming increases the rate of chemical reaction because of greater proportion of the reactant molecules have a enough kinetic energy to provide the activation energy for the reaction Temperatures that are too high inactivate enzymes can cause covalent bonds break Isozymes catalyze the same reaction but have different chemical compositions and physical properties Different isozymes within a given group may have different optimal temperatures