3. Protein (some covered last class)a) Made from amino acids linked to form a higher order molecules(1) there are 20 amino acids and just four amino acids linked has 160000 possibilitiesb) The average protein has 300 amino acids, meaning that there are around 10390 possible amino acid combinations that can exist in one single protein(1) active part of research to find new proteins, there are so many possible combinations, so we still do not know how many are out therec) only have 20,000-80,000 proteins known in the cell, not nearly as many as possible.. Why?(1) In order to function, a protein must be(a) Stable- so that it doesn’t denature (could be in globular state or fibrous)(b) flexible- cant function if it can’t move in some way(2) very small percentage of proteins are both stable and flexible and those are the ones selected for (why we don’t have many proteins counted)d) made with peptide bonds- not flexible, dehydration reactione) the alpha carbon and the C-N bonds however freely rotatef) nomenclature:(1) free amino group= amino terminus (N terminous)(2) carboxyl group= carboxy terminus (C terminous)(3) the amino acid in protein is determined by the R groupg) go on to make higher order structures- take on one of 2 forms(1) globular- spherical, elongated (enzymes)(2) fibrous- long fiber (collagen)h) Peptide- as series of amino acids that has one N-terminus and one C-terminus – therefore it is a protein, but not all peptides are proteins cause it may not be activei) primary structure- sequence of amino acids from C terminus to N terminus,(1) no weak bonds are involved in primary structure, only covalent bondsj) secondary structure- when protein begins to fold: using H- bonding of the oxygen and hydrogen attached to the carbon closest to the peptide bond(1) made of a certain sequence of amino acids most of the amino acids that make up these 2 types are hydrophobic, imbedded on the interior of the globular protein, away from the aqueous media.(2) Many proteins stop here without tertiary or quaternary structure(3) 2 basic structures(a) Beta sheet – looks like crimped paper- strand turns back and binds to itself, continuing to fold on itself in a 2 dimensional plane (silk)(b) alpha helix- looks like a spiral slinky-like coil (lots of fibrous proteins are pure alpha helix, carotene, Achilles tendon- bundle of alpha helix)k) tertiary structure- less organized manner of folding, winding around itself with interactions between R groups with any type of bonding, covalent, and weak(1) Considered the final structure of any single protein(2) series of substructures can be made from many groupings of tertiary structures, all still part of a tertiary structure(a) benefits of domains would be that they are flexible, allowing them to do work and be a protein(b) some transmembrane proteins will have one domain transmembrane, one outside the cell and on within the cytoplasm- functionally all 3 domains can do separate things within one protein(c) typical domain does not exceed 150 amino acids(d) this is what we are talking about when saying proteins can make higher molecules- they have greater capabilities (some can walk around in cell)l) quaternary structure- weak bond interaction of the R groups on the surface of the protein of 2 peptides- 99% of the time are weak bonds(1) Has 2 or 3 peptides usually, RNA polymerase has 16 peptides in quaternary structure(2) can have multiple domains in one peptide(3) nomenclature;(a) monomer- one protein on its own(b) dimer- two proteins or peptides interacting together(c) trimer- 3 , tetramer- 4, polymer- many(4) Some have covalent bonds interacting between 2 R groups, rather than weak bonds, Cysteine makes sulfur- sulfur double bond linkages (disulfide bond, or disulfide bridge)(a) Usually the disulfide bridge is found in own protein (tertiary structure), but also can be found in quatinary structure(b) Not normally found in proteins in the cell, normally found in proteins that are exported from the cell- they provide extra stability for those proteins(c) EX. Insulin(5) Polymers- very large quaternary structure(a) chain of actin monomers- long filamentous layer made from many bound and wrapped around each other(b) viruses- large chain of proteins(c) Ultimate efficiency- proteins are made so that quaternary structures can be made with no energy cost (self assembly)m) Functionality(1) mainly binding to or interacting with other molecules(2) determined by the amino acids at that point of interaction (the binding site) – very specific(a) binding sites are in very specific locations in the protein(b) 3 types of binding sites(i) active – a ligand binds and the protein will modify it(ii) regulatory – ligand can bind there and change the protein’s shape or the way in which it moves (conformational change)(iii) structural- one binded to another in a chain(c) ligands- are something that binds to a protein binding site (can be anything)(d) enzymatic proteins are the work force of the cell(i) have many active and regulatory some structural sites(e) structural proteins hold up the structure of the cellBY 330 1st Edition Lecture 4Outline of Last Lecture F. Macromolecules 1. Weak Bonds (review)2. DNA3. ProteinOutline of Current Lecture 3. Protein (continued)Current Lecture3. Protein (some covered last class)a) Made from amino acids linked to form a higher order molecules (1) there are 20 amino acids and just four amino acids linked has 160000 possibilities b) The average protein has 300 amino acids, meaning that there are around10390 possible amino acid combinations that can exist in one single protein(1) active part of research to find new proteins, there are so many possible combinations, so we still do not know how many are out therec) only have 20,000-80,000 proteins known in the cell, not nearly as many as possible.. Why?(1) In order to function, a protein must be(a) Stable- so that it doesn’t denature (could be in globular state or fibrous)(b) flexible- cant function if it can’t move in some way(2) very small percentage of proteins are both stable and flexible and those are the ones selected for (why we don’t have many proteins counted)These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.d) made with peptide bonds- not flexible, dehydration reactione) the alpha carbon and the C-N bonds however freely rotatef) nomenclature:(1) free amino