mbb 201 section 4 protein structure and function

sturcture levels of proteins \ primary:amino acid sequience, secondary: stable arranglemennts of amino acids, tertiary sturcture: folded structure of peptide, quaternary structure: arangment of multiple peptides;

what are the 5 categories of r groups \ nonpolar(hydrophobic), polar, uncharged, acidi, and basic;

alpha helix properties \ 1.alpha helix - spiral shape, peptide backbone, r groups face outwards, 3.6 residues/turn, stabilized by h bonds, h bonds between every fourth amino acid, linking c=o of one peptide to the n-h of another, a helices can by hydrophobic or philic, can be right or left handed, ;

how do r groups affect a helix stability \ electrostatic or steric interaction between adjacent side chains 3-4 residues away can affect the stability of an a helix;

whats two molecules usually aren’t found in alpha helices? \ 1.proline- the nitrogen of proline is in a rigid ring which intereres sterically with th ebackbone, proline in a peptide bond lacks an amid hydrogen to form hydrogen bonds(helix breaker) 2.glycine - very flexible, allows for conformations that do not suit alpha helices , glycine is so small that it annot protect the backbone hydrogen bonds from the aqueous environment;

how do side chains affect protein localization \ amphiphatic helices: one side is hydrophobic, the other is hydrophilic, allows membrane associateion, helices with a region of hydrophobic residues flanked by hydrophilic residues can allow membrane spanning;

what are beta sheets \ -the form rigid structures at the core of many proteins, theyre composed of beta strands, and stabilized with interstrand hydrogen bonds, beta sheets can be anti parallel or parallel depending on relative orientation of the strands, arroes always point towards c terminus;

what are the properties of beta sheet properties \ -can be twisted, the R groups are perpendicular from the plane of the sheet, the beta sheets are generally not found to be transmembrane, unless they are part of a beta barrel structure, hydrophobic side chains line the outer surface of the beta barrel, common in thransmembrane channel proteins;

whats the protein tertiary structure \ 3d arangement of all atoms in a protein, generated by the folding and packing of secondary structure elements usually stabilized by non covalent interactions, usually between r groups or r groups and backbones rather than H bonding between c=o and n-h of the backbone;

what noncovalent interactions helpwith protein folding \ 1.hydrogen bonds 2. vanderwaals interactions 3. electrostatic interactions, 4. hydrophobic interactions;

what are disulfied bonds \ theyre the covalent bonds that can also help stabilize a proteins conformation, theyre very very strong, they dont form in the cytosol becasue of the high concentration of reducing agents , the can only form between two cysteine side chains in proteins;

whats quaternary structure \ referes to protein complexes with more than one polypeptide chain, each indiv. polypeptide chain in the protein is called a subunit, the level of organization concerned with subunit interactions and assembly, bonds and forces maintaining quaternary structure are the same as those responsible for tertiary structure;

what are protein domans\ - distinct, stable, structural units that often have separate functions asn fold as independent compact units, they can move as a single entity with respect to the entire protein, one domain is typically made of a single stretch of primary sequence, proteins may have on or more domains, proteins with similar functions often share a common domain;

whats an example of how different domains of a protein are often associated with different functions \ src kinase - an important signaling protein, possesses four functional domains, each with a different function, each domain is made from the same single stretch of primary sequence ;

what are fibrous proteins \ dominated by single repeating element of secondary structure (highly ordered), possess properties that give strength and or flexibility important for structural functions (ex alpha keratin, silk elastin, collagen);

globular proteins \ most proteins are globular proteins, roughly spherical in shape and often contain several types of secondary structure (ex myoglobin, lysozyme, cytochrome c)functions : enzymes, motor proteins, regulatory proteins;

waht is alpha keratin \ - a fibrous protein, right handed helix, coiled coil composed of two alpha keratin chains is left handed ;

whats a native state \ the most stable conformation that a protein tends to fold in ;

what is denaturation \ disrutpion of the native struture of a protein by breaking the weak bonds responsible for 2 and 3 degree structures ;

casues of protein denaturation \ temp change, extrene ph, detergents and organic sovents, urea or guanidinium chloride, reducing agents;

whats a chaperone protein \ help some eptides to fold into their final conformation, some bind to newly synthesized or paritally folded chains and help them fold, others form isolation chambers which prevents the polypeptide chain from aggregating with either other molecules or itself in the cytoplasm.;

what diseases could arise from the misfolding of proteins \ alzheimers disease, huntingtons, creutzfeld jakob disease, mad cow disease;

why are some parts of a protein in intrinsically disordered sequences bc they have functional importance such as binding, scaffolding, tethering, and flexibility;

whats a protein family \ a group of proteins where each member has an amino acid sequence and 3d conformation that closely resembles each other, they arise over time during evolution (ex: elastase and chymotrypsin, members of the serine protease family, despite their similarity they differe in the substreate specificity, they cleave to different proteins );

whats a binding site \ a region of protein that associates with a ligand, formed by a specific arrangement of amino acid side chains that may not be immediately adjacent to one another in thepolypeptied chain, the specific interactions between the binding site amino acids and the ligand dictates specificity;

what are antibodies \ y shaped molecule composed of two heavy chains and two light chains, the bind specifically to a target molecule called an antigen;

what are enxymes \ biological catalysts that speed up the rate of reactio byreducing the activation energy, they bind to substrates to for an enxyme substrate complex, afte the rxn has proceeded the enxyme will be in contact with the product as an unzyme produc complex and will eventually release a product;

whats lysozyme \ an enxyme that severs polysaccharide chains that form cell walls in bacteria, helps perform a hydrolysis reaction, helps the reaction overcome the activation energy, multiple non covalent interactions are formed inducing a strained conformation in one of the monosaccharieds to make it resemble a transition state;

steps in the transition state \ 1. enzyme binds to two substrate molecules and orients them precisely to encourage a rxn to occur between them 2. binding of substrate to enxzyme rearranges electrons in the substrate creatin partial positive and negative charges that favour a rxn 3, enxyme strains the boudn substrate molecule forcing it toward a trasition state to favour a rxn;

whats retinal \ binds to the protein rhodopsin, retinal changes shape upon absorption of a photon;

whats heme \ it binds to the protein hemoblobin and allows reversible binding of oxygen ;

what are the levels of control for a protein \ -regulation of gene expression, regulation of protein degredation, -confining proteins to specific comopartments - regulating protein activity directly;

what are allosteric proteins, \ proateins that can exist in two or more slightly different conformations, thir activity can be regulated by a shift from one conformation to the other;

how do allosteric proteins change from one conformation to the other \ the binding of a molecule to a site other than the catalytic site;

how would the chang einconformation affect the function of the protein? \ changing conformation may affect ability of the protein to bind a ligand or affect the activity of teh protein if it is an enzyme, they can bind inhibitors and activators. ;

positive regulation \ binding makes it more active;

protein kinase \ enzyme that catalyzes the addition of a phosphate (phosphorylation- it can either activate or inhibit protein activity);

protein phosphatase \ enxyme that catalyzes the removal of a phosphate (dephosphorylation);

phosphorylation \ involves the enzyme catalyzed transfer of the terminal phosphate of atp to the hydroxyl group of serine, threonin or tyrosine, can also create docking site, its important for intracellular signaling proteins and the binding of a signla causes phosphorylation of tyrosine residues which allows other proteins to bind;

what other covalent modifications can be made that can control the location and interaction of a given protein \ -addition of an acetyl group, - attaching (poly odr mono) ubiquitin, -addition of fatty acids,;

GTp vs GDP \ for some proteins the phosphate is transferred from GTP instead of ATP, GTP-on, GDP-off;

what are motor proteins \ generate forces responsible for muscle contractions and most other eukaryotic cell movement;

what are protein machins \ proteins often work in tandemwith other proteins to function as a large multiprotein complex, hydrolysis of nucleoside triphosphates drives an ordered series of conformational changes in individual subunits which ultimately affects the entire complex (ex DNA replication, protein synthesis, vesicle budding, transmembrane signaling etc);