Week 3 – 9/8-9/10Week 3 – 9/8-9/10Amino Acid and Protein Structures-Amino Acids – 20 amino acid building blocks are used for protein synthesis. -Common structural Features: Central carbon(alpha-carbon) linked to a hydrogen, a primary amino group, and a carboxylic acid. The fourth linkage is to a variable side chain called the R group. R groups can be characterized by shape, size, and chemical composition. Four main groupings: neutral-nonpolar, neutral-polar, acidic, and basic. -Neutral Nonpolar side chains are composed of simple carbon chains or aromatic rings and make principally hydrophobic contacts. -Neutral Polar side chains include OH, SH, NH, and imidazole – they make primarily H-bond interactions. -Cysteine is special because it can form disulfide bond with itself in proteins: -CH2-S-S-CH2-Formation of a Peptide Bond-Peptide bonds are primary covalent, planar amide linkages. - N--->C-Rotation around this linkage is limited – all the other linkages in the peptide backbone that are single bond can rotate freely (but have to keep in mind steric hindrance)Polypeptide-Linear polymers ~100-1000 A.A. residues in length.-Average A.A. has a molecular weight of 110 Daltons, so most proteins have a mass in the range of ~10-100 DA-Adjacent A.A’s are covalently bonded by peptide bondsThe side chains determine the folding of polypeptides. • Polar amino acids tend to be on the protein surface.• Non-polar (hydrophobic) amino acids tend to be internal.• Two cysteines can form covalent disulfide bonds.• Hydrogen bonding between the C=O group of one peptide bond with the N-H group of a different peptide bond.Protein Structures:• Primary structure: The linear sequence of amino acids from the N- to C-terminus. • Secondary structure: Arrangement of segments of the polypeptide chain into regular structures.• Tertiary structure: The overall three-dimensional conformation (shape) of thepolypeptide resulting from folding of secondary structures and unstructured regions.• Quarternary structure: The association of two or more polypeptides (called subunits) to form a functional protein (complex). Structures may be: di-mers, tri-mers, etc., homo-mers or hetero-mers, Example: homodimer 2ndary structure:-alpha helix and beta sheets are the major forms of the secondary structures. H-bonding between the C=O group of one peptide bond and the N-H group of another occurs in a-helices and b-sheets.• -Alpha helix: H-bonding occurs between the C=O group of peptide bond n and the N-H group of peptide bond n+3.• -There are 3.6 amino acids and 5.4 Å per turn and diameter of 2.3 Å (the DNA helix is about 20 Å in diameter).• Proline, however, lacks this structure so it cannot participate as a donor in the H-bonding to stabilize the helix. (it has cyclic chem. structure) It is a helix-breaking residue. -Beta Sheets: Stabilization comes from alighnment of regions of polypeptide such that H-bond can form b/w C=O of one strand and NH on the adjacent one. -R groups project upwards and downwards in alternation because adjacent A.A’s are related by a roation of 180 degrees. -2 types: Parallel and Antiparallel-Parallel: the strands are arranged in the same orientation with respect to their N- and C-termini-Antiparallel: adjacent strands alternate in orientation with respect to their N- and C-termini.Turns Join the Stretches of Secondary Structure-Turns are loops of A.A’s that link alpha helices and beta strands but don’t exhibit a defined secondary structure themselves. Usually short, because they cause a number of unfulfilled H-bonds. -Adjacent antiparallel beta strands are joined by these hairpin loops.-Glycine and proline are frequently found in turns, because glycine has no side chain and proline has a natural bend in itscarbon backbone. Locally Connected Secondary Structures can form Motifs-a “motif” is a theme/design/figure that is recurring/repetitive- Coiled Coils(left): Occur when alpha helices supercoil around each other in a left-handed direction to form compact and highly stable structures. One example = leucine zipper family of DNA-binding proteins. They have two subunits that come together to form a dimer through the use of a coiled-coil region. -Another example is the Zinc –Finger.Many proteins are composed of modular domains• Very large single proteins often fold into domains, a part of the structure that appears independent form the rest as if it would be stable in solution on its own. Or a continous segment of protein that independently maintains its own structure/function. • Domains are part of the tertiary structure.• Different domain “modules” may be combined to create a protein with two or more discrete functions.Determination of Protein Structure-Secondary structures and motifs can sometimes be predicted from the primary sequence.-X-ray crystallography can provide a high-resolution (~ 2 Å) structure of proteins, but is technically challenging, time-consuming, and many proteins resist analysis. NMR is alsouseful but limited to small proteins (< 20 MDa). -Comparison of the primary sequence to known sequences of proteins for which the three-dimensional has been previously determined can reveal the likely structure of the unknown protein.Protein Functions• -Catalysis (metabolism, macromolecule synthesis, modification of protein structure/function).• DNA binding/regulation (DNA compaction, replication, transcription, recombination, etc.).• Structural (cell structure, scaffolds for enzymes, etc.)• Signaling (hormones, intracellular signal transduction).• Recognition (cell-cell interactions, immune response).DNA Binding Proteins-They mediate many of the central processes in biology. There are weak bonds that position proteins along DNA and RNA molecules.• May interact with specific DNA sequences, or non-specifically.• The most common structure of a protein that interacts with DNA is the a-helix• Interactions with the negatively charged phosphate backbone of DNA mediate non-specific interactionsProtein Conformation• Native conformation-the normal folding structure of a protein.• Denaturation-the partial or complete disruption or unfolding of the native protein conformation. Treatment with heat, detergent, or strong salts(ions) cause denaturation.• Renaturation-restoration of the native conformation. May be accomplished by heating to completely denature and then slowly cooling to allow proper refolding. Cells have proteins