What determines Protein Structure?Unique shape endows each protein with a specific function.A Polypeptide chain of a given Amino Acid sequence can spontaneously arrange itself into a 3D shape determined and maintained by the interactions responsible for secondary and tertiary structure.Folding occurs as the protein is being synthesized in the crowded environment of the cell, aided by other proteins.Protein structure also depends on the physical and chemical conditions of the proteins environment.pHSalt ConcentrationTemperatureOther aspects of the environment are alteredThe weak chemical bonds and interactions within a protein may be destroyed, causing the protein to unravel and lose its native shapeA change called denaturationThis protein is misshapen, the denatured protein is biologically inactive.Most protein become denatured if they are taken from an aqueous (polar) environment and put into a nonpolar solvent.Examples: ether or chloroformIn these cases the polypeptide chain refolds so that its hydrophobic regions face outward toward the solvent.Other denaturing agents:ChemicalsDisrupt Hydrogen BondsDisrupt Ionic BondsDisrupt Disulfide BridgesThese maintain a proteins shapeExcessive heatAgitates the polypeptide chain enough to overpower the weak interactions that stabilize the structure.Example: Egg whites become opaque when cooked because the denatured proteins are insoluble and solidify.Also explains why high fevers can be fatal: Proteins in the blood can denature at very high body temperatures.Test-Tube ProteinDenatured protein in a test tube that has been denatured by heat or chemicals can sometimes return to its functional shape when the denaturing agent is removed.The information for building specific shape is intrinsic to the proteins primary structure.The sequence of amino acids determines a proteins shapeWhere an alpha helix can formWhere beta pleated sheets can existWhere disulfide bridges are locatedWhere ionic bonds can formProtein folding in the cellProteins go through many intermediate structures on their way to a stable shape.Looking at the mature structure doesn’t reveal the stages of folding required to achieve that form.Making it difficult to determine set rules for protein folding.Crucial to protein folding are chaperonins (also called chaperone proteins).Protein molecules (complex) that assist in the proper folding of other proteins.They don’t specify the final structure of a polypeptideKeep the new polypeptide segregated from “bad influences” in the cytoplasmic environment while it folds spontaneously.Other molecular structures interact with the chaperonins and check whether proper folding has occurred.These structures either refold the protein or mark them for destruction.Misfolding of polypeptides is a serious problem in cells.Many diseases, such as Alzheimer’s, Parkinson’s, and mad cow disease, are all associated with an accumulation of misfolded proteins.A single protein has thousands of atomsMethods of viewing proteinsX-Ray crystallographyUsed to determine the 3D shapes of molecules.Allowed scientists to view the 3D shapes of proteins.Nuclear magnetic resonance (NMR) spectroscopyDoesn’t require protein crystallizationBioinformaticsPredict the 3D structures of polypeptides from their amino sequence.Nucleic acids store, transmit, and help express hereditary information.Amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance known as a gene.Genes consist of DNADNA belongs to the class of compounds call nucleic acids.Nucleic acids are polymers made of monomers called nucleotides.The Roles of Nucleic AcidsTwo Types of Nucleic AcidsDeoxyribonucleic acid (DNA)Genetic material that organism inherit from their parents.Each chromosome contains one long DNA moleculeCarrying several hundreds of genes.When a cell reproduces itself by diving, its DNA molecules are copied and passed along from one generation of cells to the next.Encoded in the structure of DNA if the information that programs all the cells activities.The DNA is NOT directly involved in running the operations of the cell.Proteins are required to implement genetic programsExample: computer software by itself cant print a bank statement…a printer is needed.The molecular hardware (the tools for biological function) consist mostly of proteins.Example: the oxygen carrier in red blood cells is the protein hemoglobin, not the DNA that specifies its structure.Ribonucleic Acid (RNA)Each gene along a DNA molecule directs synthesis of a type of RNA called messenger RNA (mRNA).The mRNA molecule interacts with the cells protein synthesizing machinery to direct production of a polypeptide.Folds into all or part of a protein.Conveys genetic instructions for building proteins from the nucleus to the cytoplasm.They enable living organisms to reproduce their components from one generation to the next,Unique among molecules, DNA provides directions for its own replication.DNA directs RNA synthesis and through RNA controls protein synthesis.Flow of genetic information DNARNAProteinRibosomesSites of protein synthesisTiny structuresEukaryotic CellLocated in the CytosolDNA stays in the nucleus.Prokaryotic CellUse the same process, just DNA isn’t in a nucleus.The components of Nucleic AcidsMacromolecules that exist as polymers called polynucleotides.Consists of monomers called nucleotides.In general composed of three partsA nitrogen containing (nitrogenous) baseA five carbon sugar (pentose)One or more phosphate group(s)Each monomer has only one phosphate groupThe portion of a nucleotide without any phosphate groups is called a nucleoside.Building a nucleotideNitrogenous basesOne or two rings that include nitrogen atoms(called bases because the nitrogen atoms tend to take up an H+ from solution, thus acting as a base)Two families of nitrogenous basesPyrimidines and purinesPyrimidinesOne six-membered ring of carbon and nitrogen atomsMembers areCytosine (C)Thymine (T)Uracil (U)PurinesLarger than pyrimidinesSix-membered ring fused to a five-membered ring.Members areAdenine (A)Guanine (G)Differ in chemical groups attached to ringsAdenine, guanine, and cytosine are found in both DNA and RNA.Thymine ONLY in DNAUracil ONLY in RNAAdding a sugar to the Nitrogenous baseDNAThe sugar is deoxyriboseCompared to ribose, it lacks an oxygen atom in the second ring.Hence the name deoxy-RNARiboseTo distinguish the numbers of the sugar carbons (from those sugars used for the ring atoms of