CARBON AND MOLECULAR DIVERSITY The structure and function of macromolecules: Proteins and Nucleic Acids Chapter 5

Objectives Describe the properties of a Protein Understand how proteins are structured. Be able to explain each level of organization affects the shape and specificity of the protein Describe the properties of a Nucleotide Describe the differences in structure between major nucleic acids and how the structure correlates with function

PROTEINS: MOLECULAR TOOLS OF THE CELL. Amino acids: the monomer building block of Proteins A Polypeptide is a structural term used to describe a polymer of amino acids Protein is a functional term applied to one or more polypeptides that perform a task within a cell Functions of proteins may include: –Structural, Storage, Transport, Hormonal, Receptor, Contractile, Defensive, Enzymatic

STRUCTURE OF AMINO ACID. Hydrogen atom. Carboxyl group. Amino group. Variable R group.

Peptide Bond: The covalent bond between two amino acids formed via condensation synthesis.

Proteins are Flexible Leads to complex three dimensional shapes

So what. Why should we care? Flexibility within the polypeptide chain allows for potential interactions between various regions of the polypeptide and/or with other polypeptides. This leads to diverse chemical structures, each potentially capable of performing a different role within the cell.

FUNCTION DEPENDS ON SPECIFIC CONFORMATION. Primary level of organization –Sequence of amino acids, numbered from the amino end Secondary level of organization –H bond interactions between the amino acid Tertiary level of organization –“R” group interactions Quaternary level of organization –subunit interactions

Protein Structure Primary level of organization –Defined as the sequence of amino acids –Numbered from the amino end –Each protein has a unique combination of amino acids

Protein Structure Secondary level of organization –H bond interactions between the amino and carbonyl groups of amino acids –  helix, H bonds between every 4th AA –Pleated sheet, H bonds between protein regions lying parallel to each other

 helix: H bonds between every 4th AA Pleated sheet: H bonds between protein regions lying parallel to each other; drawn as arrows in models

Protein Structure Tertiary level of organization –“R” group interactions, bonds Disulfide bridges Ionic bonds H bonds Hydrophobic interaction between nonpolar AA –reinforced by van der Waals

Protein Structure Quaternary level of organization –subunit interactions

Changes in Protein Conformation Denaturation: loss of a protein’s shape –Principally influenced by pH: Disrupts H-bond interactions Temperature: May break disulfide bonds Protein folding is sometimes assisted by molecular chaperone proteins

NUCLEIC ACIDS: INFORMATIONAL POLYMER Nucleic acids are polymers of monomer units called nucleotides Nucleic acids store and transmit hereditary information: gene Two major forms of nucleic acid polymers: DNA and RNA

Nucleotide Structure Three parts to the monomer –Phosphate group –Sugar Ribose Deoxyribose –Nitrogenous base: Pyrimidine Purine

Nucleic Acids Polymers Nucleotide polymers are created via phosphodiester linkages between the phosphate of one nucleic acid and the sugar of another

Synthesis is 5’-3’ Because of the action of the enzymes involved in the attachment of the monomer units, nucleic acid synthesis always occurs from 5’ toward 3’ end

Monomer Unit Created During Synthesis The nucleotide monomer is created during polymerization from a higher energy molecule: The nucleoside triphosphate.

Nucleic Acids DNA: A pyrimidine on one chain is attracted to its complimentary purine on the adjacent chain. H bonds form between the purines and pyrimidines keeping the two nucleotide polymers together.

RNA Structure RNA is also synthesized from nucleosides where Ribose is the sugar and the nitrogenous base Uracil replaces that of Thymine Unlike DNA, RNA functions as a single polymer but may “double up” on itself via complimentary base pairing