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NOTES: Ch 5, part 2 Proteins & Nucleic Acids 5.4 - Proteins have many structures, resulting in a wide range of functions ● Proteins account for more than 50% of the dry mass of most cells ● Protein functions include: Functions of Proteins ● structural support ● storage ● cell-to-cell communication / signaling ● movement ● transport ● response ● defense ● catalysis of reactions (enzymes) ● an enzyme is a type of protein that acts as a catalyst, speeding up chemical reactions Substrate (sucrose) Glucose Enzyme (sucrose) Fructose ● consist of 1 or more polypeptide chains folded and coiled into specific conformations ● Polypeptide chains = polymers of amino acids – arranged in specific linear sequence – linked by PEPTIDE BONDS – range in length from a few to 1000+ AMINO ACIDS ● building blocks of proteins ● structure of an amino acid – central carbon – hydrogen atom – carboxyl group – amino group – variable R group (side chain) Amino Acid Monomers ● Cells use 20 amino acids to make thousands of proteins a carbon Amino group Carboxyl group ● linked together by PEPTIDE BONDS (links the carboxyl group of 1 amino acid to the amino group of another; requires dehydration / condensation) PROTEIN STRUCTURE ● a protein’s function depends on its specific conformation (3-D shape) ● Four levels of protein structure: 1. Primary structure ● unique, linear sequence of amino acids (forms the “backbone” of a protein) – determined by genes – a slight change can affect a protein’s conformation and function (e.g. sickle-cell hemoglobin) – can be sequenced in the laboratory (insulin) 2. Secondary structure ● regular, repeated coiling and folding of a protein’s polypeptide backbone ● stabilized by H-bonds between peptide linkages in protein’s backbone (NOT the amino acid side chains) ● ALPHA HELIX = helical coil stabilized by H-bonding between every 4th peptide bond (3.6 amino acid/turn) ● BETA PLEATED SHEET = sheet of antiparallel chains folded into “accordion” pleats Spiders secrete silk fibers made of a structural protein containing beta-pleated sheets…able to stretch & recoil! 3. Tertiary Structure ● irregular contortions of protein due to bonding between side chains (R groups) resulting in 3-D shape Tertiary Protein Structure Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Ionic bond 4. Quaternary Structure ● association of 2 or more protein subunits to form a single functioning molecule (i.e. hemoglobin and collagen) Polypeptide chain b Chains Iron Heme Polypeptide chain Collagen a Chains Hemoglobin Protein Form and Function ● A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape ● The sequence of amino acids determines a protein’s three-dimensional formation ● A protein’s formation determines its function Protein Conformation ● determined by physical and chemical environmental conditions ● DENATURATION: process that alters a protein’s native conformation and hence its biological activity – heat – salt concentration – chemical agents that disrupt H-bonding – transfer to an organic solvent – pH changes (SDS is a detergent that denatures proteins.) Protein Denaturation: ● A denatured protein is misshapen and therefore biologically inactive The Protein-Folding Problem ● It is hard to predict a protein’s conformation from its primary structure ● Most proteins probably go through several states on their way to a stable conformation ● Chaperonins are protein molecules that assist the proper folding of other proteins Cap Hollow cylinder Chaperonin (fully assembled) Polypeptide Steps of Chaperonin Action: An unfolded polypeptide enters the cylinder from one end. Correctly folded protein The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. 5.5 - Nucleic acids store and transmit hereditary information ● The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a GENE ● Genes are made of DNA, a nucleic acid ● Two types of nucleic acids: 1) DNA 2) RNA The Roles of Nucleic Acids ● There are two types of nucleic acids: -Deoxyribonucleic acid (DNA) -Ribonucleic acid (RNA) ● DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis ● Protein synthesis occurs in ribosomes 1. DNA = Deoxyribonucleic acid ● encodes the instructions for amino acid sequences of proteins ● is copied and passed from one generation of cells to another 2. RNA = Ribonucleic acid ● functions in the actual synthesis of proteins coded for by DNA ● carries the encoded information to the ribosomes; carries the amino acids to the ribosome; a major component of ribosomes DNA RNA Protein Structure of Nucleic Acids ● polymers of monomers called NUCLEOTIDES ● Each nucleotide consists of: 1. Pentose (5-carbon sugar) -deoxyribose in DNA -ribose in RNA 2. Phosphate group (attached to #5 carbon on sugar) 3. Nitrogenous base -purines (double ring) -pyrimidines (single ring) The Structure of Nucleic Acids ● The portion of a nucleotide without the phosphate group is called a nucleoside ● nucleotides are joined together by phosphodiester linkages (between phosphate of one nucleotide and the sugar of the next) ● results in a backbone with a repeating pattern of sugarphosphate-sugarphosphate... 5 end Nucleoside Nitrogenous base Phosphate group Nucleotide 3 end Polynucleotide, or nucleic acid Pentose sugar The DNA Double Helix ● A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix ● One DNA molecule includes many genes ● The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion: A always with T, and G always with C DNA & Proteins as Tape Measures of Evolution ● genes and their products (proteins) document the hereditary background of an organism ● linear sequences of DNA are passed from parents to offspring; 2 siblings have greater similarity in their DNA than do unrelated individuals… DNA & Proteins as Tape Measures of Evolution ● it follows, that 2 closely related species would share a greater proportion of their DNA & protein sequences than 2 distantly related species would… ● that is the case!!! DNA & Proteins as Tape Measures of Evolution ● example: the β chain of human hemoglobin: ● this chain contains 146 amino acids -humans & gorillas differ in 1 amino acid -humans & frogs differ in 67 amino acids ● Molecular biology has added a new “tape measure” with which we can study evolutionary relationships!!