Functions of proteins structural; transport & storage of small molecules; transmitting information between cells (i.e. hormones); defense against infection (antibodies); enzymes non-polar AAs... tend to be hydrophobic and located in the interior of proteins, where they are not in contact with water polar AAs... tend to be hydrophilic and located in the exterior of proteins, where they can interact with water Special importance of glycine provides the most flexibility to backbone bond rotation Special importance of histidine complexes with inorganics such as zinc & iron; can be uncharged or +charged and be involved in ion-exchange reactions Special importance of proline 2¡ amine; severely constrains peptide bond, will break alpha helix Special importance of cysteine forms S-S bonds; complexes with inorganics A protein's folded shape conformation Types of secondary protein structures alpha helix, beta sheet Types of minor secondary protein structures random coil, beta turn An alpha helix has this many AAs per turn 3.6 Alpha helices are stabilized by 1st, 4th AAs H-bonding Reverses the direction of the chain A beta turn does this Basic units of tertiary structure domains Examples of tertiary protein structure helix-loop-helix, zinc fingers, helix-turn-helix, leucine zippers Zinc fingers... are important structures in transcription factors Helix-turn-helix... involved in regulation of gene expression Covalent disulfide bonds 3D folding stabilized by disulfides; for secreted proteins, mostly; covalent linkage between cysteines The Anfinsen Experiment Demonstrated that only the AA sequence is needed to determine protein's folding state prosthetic groups are small molecules bound to proteins in which they play critical functional roles Examples of chemical groups protein modification acetylation, glycosylation, phosphorylation Protein Phosphorylation forward: kinases add phosphates to serine, tyrosine, threonine; backward: phosphatases remove phosphates cleave a portion of protein proteolysis chaperones assist in folding; protect intermediates until translation is complete Enzyme parameters catalytic power (Vmax): rate of cat v. uncat, specificity (Km): discrimination between substrates active site pocket (cleft/groove) in protein that binds substrate and catalyzes the reaction Types of active site interactions "lock & key," "induced fit" allosteric site regulatory site outside active site; binds regulatory effector; binding alters active site; changes activity; used in feedback inhibition types of protein binding regulation allosteric site; covalent modification (i.e. phosphorylation) totipotent these stem cells have unlimited capability, and can form embryonic cells pluripotent these stem cells can form most but not all tissues multipotent these cells are committed to form specific cell types (i.e. blood stem cells can form white blood cells) primary method of controlling gene expression transcription initation features of prokaryotic gene expression coupled transcription/translation; genes organized into operons operons multiple genes expressed as a single unit; generate polycistronic mRNAs; single regulatory step at transcription can control entire pathway of enzymes holoenzyme the complete and operative form of an enzyme with multiple protein subunits characteristics of a strong promoter matches consensus sequence; binds holoenzyme tightly; initiates often, genes highly expressed E. coli consensus sequences -10 (TATAAT), -35 (TTGACA) DNA footprinting Used to determine where a protein binds DNA; Under conditions that DNase makes one cut per molecule, get a bunch of fragments, add the protein, and then see where the protein is by looking for gaps in progression of fragment lengths. sigma subunit of RNA Polymerase is not necessary for activity, but is needed to identify correct site to initiate transcription. transcription termination symmetrical GC rich sequences followed by 4 or more A residues forms a stem-loop structure which disrupts RNA association transcription factors negative: repressors; positive: activators constitutive mutants express all 3 genes even when lactose was not present noninducible mutants failed to express any of the 3 genes when lactose was present cis-acting control elements regulatory DNA sequence that serves as a binding site & controls transcription of adjacent genes trans-acting control elements affect expression of genes located on other chromosomes in the cell