Key Concepts Most cell functions depend on proteins Proteins are made of amino acids Amino acids vary in structure and function The structure of a protein can be analyzed at four levels 1 Amino acid sequence 2 Substructures called helices and pleated sheets 3 Interactions between amino acids that dictate a protein s overall shape 4 Combinations of individual proteins that make up larger multiunit molecules In cells most proteins are enzymes that function as catalysts 2011 Pearson Education Inc The Structure of Amino Acids All proteins are made from just 20 amino acid building blocks All amino acids have a central carbon atom that bonds to NH2 COOH H and a variable side chain R group In water pH 7 the amino and carboxyl groups ionize to NH3 and COO respectively this helps amino acids stay in solution and makes them more reactive 2011 Pearson Education Inc 2011 Pearson Education Inc The Nature of Side Chains The 20 amino acids differ only in the unique R group attached to the central carbon The properties of amino acids vary because their R groups vary 2011 Pearson Education Inc Functional Groups Affect Reactivity R groups differ in their size shape reactivity and interactions with water 1 Nonpolar R groups hydrophobic do not form hydrogen bonds coalesce in water 2 Polar R groups hydrophilic form hydrogen bonds readily dissolve in water Amino acids with hydroxyl amino carboxyl or sulfhydryl functional groups in their side chains are more chemically reactive than those with side chains composed of only carbon and hydrogen atoms 2011 Pearson Education Inc 2011 Pearson Education Inc 2011 Pearson Education Inc Monomers and Polymers Many mid size molecules such as amino acids and nucleotides are individual units called monomers They link together polymerize to form polymers such as proteins and nucleic acids Macromolecules are very large polymers made up of many monomers linked together Thus proteins are macromolecules consisting of linked amino acid monomers 2011 Pearson Education Inc 2011 Pearson Education Inc Assembling and Breaking Apart Polymers Polymerization requires energy and is nonspontaneous Monomers polymerize through condensation dehydration reactions which release a water molecule Hydrolysis is the reverse reaction which breaks polymers apart by adding a water molecule In the prebiotic soup hydrolysis is energetically favorable and thus would predominate over condensation However polymers clinging to a mineral surface are protected from hydrolysis and thus polymerization of the amino acids into proteins may have occurred spontaneously 2011 Pearson Education Inc 2011 Pearson Education Inc The Peptide Bond Condensation reactions bond the carboxyl group of one amino acid to the amino group of another to form a peptide bond A chain of amino acids linked by peptide bonds is called a polypeptide Polypeptides containing fewer than 50 amino acids are called oligopeptides peptides Polypeptides containing more than 50 amino acids are called proteins 2011 Pearson Education Inc 2011 Pearson Education Inc Polypeptide Characteristics Within the polypeptide the peptide bonds form a backbone with three key characteristics 1 R group orientation Side chains can interact with each other or water 2 Directionality Free amino group on the left is called the N terminus Free carboxyl group on the right is called the Cterminus 3 Flexibility Single bonds on either side of the peptide bond can rotate making the entire structure flexible 2011 Pearson Education Inc 2011 Pearson Education Inc 2011 Pearson Education Inc What Do Proteins Do Proteins are crucial to most tasks required for cells to exist Catalysis enzymes speed up chemical reactions Defense antibodies and complement proteins attack pathogens Movement motor and contractile proteins move the cell or molecules within the cell Signaling proteins convey signals between cells Structure structural proteins define cell shape and comprise body structures Transport transport proteins carry materials membrane proteins control molecular movement into and out of the cell 2011 Pearson Education Inc What Do Proteins Look Like Proteins can serve diverse functions in cells because they are diverse in size and shape as well as in the chemical properties of their amino acids All proteins have just four basic levels of structure primary secondary tertiary and quaternary 2011 Pearson Education Inc Primary Structure A protein s primary structure is its unique sequence of amino acids Because the amino acid R groups affect a polypeptide s properties and function just a single amino acid change can radically alter protein function 2011 Pearson Education Inc 2011 Pearson Education Inc Secondary Structure Hydrogen bonds between the carbonyl group of one amino acid and the amino group of another form a protein s secondary structure A polypeptide must bend to allow this hydrogen bonding forming helices pleated sheets Secondary structure depends on the primary structure Some amino acids are more likely to be involved in helices others in pleated sheets The large number of hydrogen bonds in a protein s secondary structure increases its stability 2011 Pearson Education Inc 2011 Pearson Education Inc Tertiary Structure The tertiary structure of a polypeptide results from interactions between R groups or between R groups and the peptide backbone These contacts cause the backbone to bend and fold and contribute to the distinctive three dimensional shape of the polypeptide R group interactions include hydrogen bonds hydrophobic interactions van der Waals interactions covalent disulfide bonds and ionic bonds 2011 Pearson Education Inc R group Interactions That Form Tertiary Structures Hydrogen bonds form between hydrogen atoms and the carbonyl group in the peptide bonded backbone and between hydrogen and negatively charged atoms in side chains Hydrophobic interactions within a protein increase stability of surrounding water molecules by increasing hydrogen bonding van der Waals interactions are weak electrical interactions between hydrophobic side chains Covalent disulfide bonds form between sulfur containing Rgroups Ionic bonds form between groups that have full and opposing charges 2011 Pearson Education Inc 2011 Pearson Education Inc Quaternary Structure Many proteins contain several distinct polypeptide subunits that interact to form a single structure the bonding of two or more subunits produces quaternary structure 2011 Pearson Education Inc 2011 Pearson Education Inc