Chapter 3: Nucleic Acids, Proteins, and Enzymes3.1:Nucleic Acids are informational Macromolecules1) Nucleic acids (DNA and RNA) are polymers specialized for storage transmission, and use of genetic info2) Two types:a) DNAi) DNA and the proteins encoded by DNA determine metabolic functionsb) RNA3) Monomers are nucleotidesa) Consist of three components:i) Nitrogen-containing base(1) Two chemical forms: Pyrimidine (six membered single-ring structure) or Purine (fuseddouble-ring structure)ii) Pentose sugar(1) In DNA pentose sugar is deoxyribose, which differs from the ribose in RNA by the absence of one oxygen atomiii) 3 phosphate groups(1) Molecules consisting of only pentose sugar and nitrogenous base (no phosphate group) are called nucleosides(2) Nucleotides that make up nucleic acids contain just one phosphate group called nucleoside monophosphates4) Linkage of one nucleotide to the next is done through condensation rxn and phosphodiester linkage (joins nucleotides) (between sugar of one and phosphate of next)a) Nucleic acids grow in 5’ to 3’ direction5) Nucleotides can be oligonucleotidesa) Olgionucelotides include RNA molecules that function as “primers” to being the duplication of DNA;RNA molecules that regulate the expression f genes; and synthetic DNA molecules used for amplifying and analyzing other, longer nucleotide sequencesb) Polynucleotides more commonly reffered to as nucelic acids, include DNA nd most RNAi) can be very long, and are longest polymers in living world6) Differencesa) DNA: i) Double-strandedii) adenine (A), cytosine (C), guanine (G) and thymine (T)iii) sugar is deoxyriboseiv) structure is less flexible b/c lacks hydroxyl group at 2’ positionb) RNA: same as DNA but uracil (U) replaces thymine (T)i) sugar is riboseii) can form variety of structures7) Complementary base pairinga) DNA: A-T, C-Gb) RNA: A-U, C-Gc) Base pairs held by hydrogen bonds8) RNAa) Usually single-stranded, but many can fold up into 3-D structures, due to ribonucleotides in separate portions of moleculesb) Folded molecule by complementary base pairing, and structure determined by particular order of bases9) DNAa) Usually double-stranded, two separate polynucelotide strands of same lengthi) Form ladder that twists= double helixii) sugar phosphate groups form sides of ladder, bases with their H bonds form rungs on insideb) Uniform shape10) Processa) DNAi) Purely information moleculeii) Info encoded in sequence of bases carried in its strandiii) Functions:(1) DNA replication ( done by polymerization using an existing strand as base-pairing template)(2) DNA coped into RNA, transcription(a) Nucleotide sequence in RNA can be used to specify sequence of amino acids in polypeptide chain (translation)(b) Overall process of transcription and translation is gene expression(c) Note that:(i) DNA replication and transcription depend on the base pairing properties of nucleic acids(ii) DNA replication usually involves entire DNA molecule(iii) Complete set of DNA is called genome(iv)Sequences of DNA that encode specific proteins and transcribed into RNA are called genes3.2: Proteins are polymers with important structural and metabolic roles11) Major functions:a) Enzyme: catalytic proteins that speed up biochemical rxnsb) Defensive proteins: ex) antibodiesc) Hormonal and regulatory proteins: ex)insulin, control physiological processesd) Receptor proteins: recieve and respond to molecular signals from inside/outside org.e) Storage protein: store chemical building blocks (amino acids) for later usef) Structural proteins: provide physical stability and movementg) Transport protein: carry substances within org.h) Genetic regulator proteins:regulate when,how, and what extent a gene is expressed12) Proteins are polymers made up of monomers called amino acidsa) Polymeric proteins made by peptide linkagesb) Amino acids contain two functional groups: nitrogen-containing amino group and carboxylic acid groupc) Distinguished by R groups,side chain, identify amino acidsd) Only 20 amino acids occur extensively in proteins of all organismse) These 20 can be grouped according to properties of side chains (R groups):i) Charged Hydrophilic group:Five amino acids have electrically charged side chains, attractwater (hydrophilic), and attract oppositely charged ions of all sortsii) Polar hydrophilic group: Five amino acids have polar chains and tend to form H-bonds with water and other polar or charged substances, also hydrophiliciii) Hydrophobic group: Seven amino acids have side chains that are nonpolar hydrocarbons. In watery environment of cell, these hydrophobic side chains may cluster together in interiorof proteiniv) Special group:Cysteine,glycine, and proline(1) Cystein(a) Has terminal -SH group(b) Can react with other cysteine side chain to form a covalent bond called disulfide bridge (-S-S-)(i) Determines how polypeptide chain folds(2) Glycine(a) Side chains consist of single hydrogen atom(b) small enough to fit into tight corners in interior of a protein molecule, where larger side chain could not fit(3) Proline(a) Possess modified amino group that lacks hydrogen and instead forms covalent bond with hydrocarbon side chain, resulting in a ring structure(i) Limits both H-bonding ability and ability to rotate(ii) Proline often functions to stabilize bends or loops in proteins13) Amino acids can form short polymers of 20 or fewer amino acids, called oligopepties or simply peptides14) Common longer polymers called polypeptides or proteins15) Condensation rxn forms peptide linkagea) Polymerization occur in the amino to carboxyl direction16) Sequence of amino acids in a polypeptide chain constitutes the primary structure of a protein17) Secondary structure: consists of regular, repeated spatial patterns in different regions of a polypeptide chaina) H-bonding between N-H and C-O groups within and between chains is responsible for protein’ssecondary structureb) two basic types:i) alpha helix: right-handed coil that turns in the same direction as a standard wood screw(1) R groups extend outward from peptide backbone of helix(2) Coiling results from H-bonds in N-H group and C-O groupsii) beta pleated sheet: formed from two or more polypeptide chains that are extended and aligned(1) Stabilized by H-bonds in N-H groups and C-O groups on two chains(2) Many proteins contain both alpha and beta pletad sheets in different regions of same polypeptide chain18) Tertiary structure: Chain that is bent at specific sites