Chapter 3 3.1 Amino acids and their polymerization I. Amino acids are molecules that are composed of just 20 different building blocks• Have a common structure with a central carbon atom1. H-a hydrogen atom2. NH2-an amino functional group3. COOH-a carboxyl functional group4. A distinctive “R-group”(side chain)• Charges on functional groups are important:1. They help amino acids stay in solution, where they can interact with one another and with other solutes2. They affect the amino acids chemical reactivity II. Nature of side chains• Vary from a single hydrogen atom to large structures containing carbon atoms linked into rings• Share same core structure but each of the 20 R-groups is unique. Properties of amino acids vary bc their R-groups vary• See figure 3.2 page 43 to see 20 R-groups• Several found in amino acids contain carboxyl, sulfhydryl, hydryl, or amino functional groups. Under right conditions can participate in chemical reactions1. Amino acids with a sulfhydryl group (SH) can form disulfide (S-S)• Some are devoid of functional groups (only carbon and hydrogen atoms). Rarely participate in chemical reactions and depend primarily on their size andshape rater than reactivity• The nature of R-group affects the polarity and solubility of an amino acid in water1. Hydrophobic: they do not interact with water. Nonpolar side chains lack charged or highly electronegative atoms capable of forming hydrogen bondswith water2. Hydrophilic: polar or charged interact with water. Dissolve in water easily.• Amino acid side chains can be grouped into 4 different general types: acidic, basic, uncharged polar, and nonpolar• If given a structural formula for an amino acid you can determine which type of amino acid it is by asking 3 Qs:1. Does the side chain have a negative charge? If so it has lost a proton so it must be acidic2. Does the side chain have a positive charge? If so it has taken on a proton, so it must be basic3. If the side chain is uncharged, does it have an oxygen atom? If so the highly electronegative oxygen will result in a polar covalent bond and thus isuncharged polar.4. If answer is no to all three then it is a nonpolar amino acid III. How do amino acids link to form proteins?• Amino acids link together to form proteins and amino acid monomers can polymerize to form proteins• A molecular subunit such as an amino acid, a nucleotide, or a sugar is called a monomer. When a large # of monomers are bonded together, the resultingstructure is called a polymer• Polymerization: process of linking monomers together• Macromolecule: used to denote a very large molecule that is made up of smaller molecules joined together1. Proteins=macromolecules=polymers (consist of linked amino acid monomers)• Theory of chemical evolution: monomers in the prebiotic soup polymerized to form larger and more complex molecules (don’t spontaneously self-assembleinto macromolecules)• Input of energy required for monomers to link together and form macromolecules• Monomers polymerize through condensation reactions, also known as dehydration reactions: newly formed bond results in the loss of a water molecule• Hydrolysis: breaks polymers apart by adding a water molecule. It reacts with the bond linking the monomers, separating one monomer from the polymerchain (dominates)• Peptide bond: the C-N covalent bond that results from this condensation reaction (fig 3.5)• Peptide bonds are unusually stable compared to linkages in other types of macromolecules. The degree of electron sharing is great enough that it sharessome characteristics of a double bond• 3 key points to note about the peptide bonded backbone:1. R-group orientation: side chains extend out from backbone to interact with each other or water2. Directionality: an amino group on one end of the backbone and a carboxyl group on the other.3. Flexibility: peptide cant rotate but single bonds on either side can. Making whole flex• Oligopeptide(peptide): type of polymer resulted from fewer than 50 amino acids linked together• Polypeptides: polymers that contain 50 or more amino acids• Protein: any chain of amino acid residues OR complete, often functional form of the molecule3.2 What do proteins look like?• Can serve diverse functions in cells bc they are diverse in size and shape as ell as in the chemical properties of their amino acid residues.• Two proteins shapes has a clear correlation with their function:1. TATA box-binding protein has a groove where DNA molecules fit. The groove interacts with specific regions of a DNA molecule2. Porin has a hole that forms a pore. Fits in cell membranes and allows certain hydrophilic molecules to pass through• Most proteins do not have shapes that correlate with function1. Trypsin protein has an overall globular shape that tells little about its function: bind and cleave peptide bonds of other proteins• No matter how large or complex a protein may be, its underlying structure can be broken down into just 4 basic lvls of organization.• Primary Structure: unique sequence of amino acids in a protein/polypeptide1. With 20 types of amino acids available and length ranging from two amino acid resides to tens of thousands the # pf primary structure that arepossible is practically limitless2. Fundamental to the higher lvls of protein structure: secondary, tertiary, and quaternary3. Stabilized by peptide bonds• Secondary Structure: formation of α-helices (polypeptides backbone is coiled) and β-pleated sheets (segments of a peptide cahin bend 180 and then foldin the same plane) in a polypeptide1. Stabilized by hydrogen bonding btw groups along the peptide-bonded backbone; thus, depends on primary structure2. Large # of hydrogen bonds in these structures makes them highly stable.3. Distinctly shaped by C=O group (hydrogen bond btw oxygen) and hydrogen on N-H groups• Tertiary Structure: most overall shape of a polypeptide results from interaction btw R-groups or btw R-groups and the backbone to make a 3D shape(depends on primary structure) (includes secondary)1. 5 types of interactions involving side chains: i. hydrogen bonding ii. hydrophobic interactions iii. van der waals interactions iv. covalent bonding v. ionic bonding• Quaternary Structure: shape produced by combinations of polypeptides (combo of tertiary)1. Some proteins contain multiple polypeptides that interact to form a single structure2. Protein structure is hierarchical; quat is based on