Protein Structure & Function: Amino Acids, Structures, Regulation & Separation, Quizzes of Cell Biology

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TERM 1 proteins DEFINITION 1 polymers of amino acids and perform their functions using a few key activities such as binding (to other proteins, ions, or small molecules-- the net goal is to produce conformational change), catalysis (enzymes-- rearrangement of covalent bonds), folding (to make a channel or pore) TERM 2 primary protein structure DEFINITION 2 The linear arrangement of amino acids linked together via a peptide bondcovalent amide bonds and disulfide bonds linking side chains TERM 3 polar amino acids DEFINITION 3 serinethreonineglutamineasparagine TERM 4 basic amino acids DEFINITION 4 ((positive charge))lysineargininehistidine TERM 5 acidic amino acids DEFINITION 5 ((negative charge))aspartateglutamate TERM 6 cysteine DEFINITION 6 sulfahydral group can form disulfide bridges TERM 7 These three amino acids have hydroxyl groups on them so they can be phosphorylated (key for regulation) DEFINITION 7 Tyrosinethreonineserine TERM 8 secondary protein structure DEFINITION 8 alpha helices and beta sheets60% of normal proteins will be in one of these two shapes, help together by hydrogen bonds that comes from NH2 and COO- TERM 9 Tertiary protein structure DEFINITION 9 overal conformation (of a polypeptide chain), stabilized by hydrophobic interactions, disulfide bridges (cysteine--> covalent bonds), H bonds TERM 10 structural motifs DEFINITION 10 particular combinations of secondary and tertiary structure (10-20 amino acids)-- allows for DNA bindingdepends on alpha helix and other bonding to keep helix in formationexample: in the major/minor helices TERM 21 Regulating Protein Activity DEFINITION 21 increase/decrease level of protein by (1) altering rate of synthesis or degredationchange the location or concentration of the substrate or cofactor (ie: calcium from before)regulate the instrinsic activity-- affinity of substrate binding (phosphorylation and GTP binding) TERM 22 Noncovalent modification to regulate protein function DEFINITION 22 Binding or dissociation of a molecule and a consequent change in conformation of a proteinBinding of calcium- calcium levels in the cell are tightly regulated, the average calcium concentration is 0.1uM inside the cell, outside is 1000uM (10,000x concentration difference--> need active transport using ATP to pump it out); also in the mitochondria and ER TERM 23 Calmodulin DEFINITION 23 has four different EF hands. Each one of them can bind to a calcium; when calcium is unbound you have alpha helices, when it is bound the helices fold around and form almost a circle and can then bind to the target peptide TERM 24 GTPase superfamile (noncovalent modification to regulate protein function) DEFINITION 24 in general, every time a protein is bound to GTP that protein is active, bound to GDP is inactive. The switching is done via a hydrolysis reaction in which GTP is hydrolyzed to GDP-- either an intrinsic activity of the protein-- very transient activation, may only last a few seconds, can be accelerated via GAPs, RGSs, or GDIsGaps- GTPase activation proteins, speeds up the rate of hydrolysisOnce protein is bound to the GDP, the GDP must be completely removed and replaced with a GTP -- this process is mediated by GEF (guanine exchange factor -- swaps GDP to GTP) TERM 25 Covalent modifications to regulate protein function DEFINITION 25 Phosphorylation- adds to hydroxyl group on Ser, THr, or Tyr residues-- an active R-OH has a protein kinase add a phosphate group from ATP (goes to ADP) and then it becomes active. To remove the phosphate group, a protein phosphatase comes in and using water, hydrolyzes the bond, leaving a Pi group and an inactive -OH bond - because these are covalent bonds it must be mediated by an enzyme TERM 26 Methods to separate and detect proteins DEFINITION 26 SDS-PAGE2D gel electrophoresisProteomic TERM 27 Electrophoresis DEFINITION 27 apply an electric field and separate proteins based upon their charge: mass ratio, the most common technique is called SDS-PAGE (SDS-polycrylamide gel electrophoresis)-- the detergent (SDS) takes the globular protein and essentially linearizes them, also puts the proteins in a state of negative charge TERM 28 SDS-PAGE DEFINITION 28 Stick protein A and protein B in wells (A is bigger- it has four negative charges, B is smaller and has 2 negative charges), the side where they put in (where the wells are) have a negative charge, the other side has positive, so the move towards the positive chargeIn theory, all of the proteins should have the same charge to pass ration -- larger proteins run smaller because they're retarded by the gel itself-- ge is like a mesh network, the smaller proteins can pass through easier so they are able to move faster TERM 29 2D gel electrophoresis DEFINITION 29 separates based upon mass and charge- the first separation is done by isoelectric focusing -- separation yb charge, it is loaded in a pH gradient and the protein will migrate to where the isoelectric point is -flip over and add SDS-- then it is spearated by size TERM 30 Proteomics DEFINITION 30 used to study a large subset of proteins TERM 31 Two DNA strands can separate from one another by: DEFINITION 31 Melting temperature (Tm)Ion concentration TERM 32 Melting temperature (Tm) DEFINITION 32 breaks the hydrogen bonds between AT and CG, it is the temperature at which half of the DNA within the test tube is broken up, and the other half is still together (Half of the DNA single strand, half double strand) TERM 33 Ion concentration DEFINITION 33 the phosphate groups are negatively charged, but positive around created a shielding shell around them -- the negative charges of the phosphates would typically cause steric repulsion, so in vitro, if you decrease the amount of positive charges, you create more repulsive forces and DNA is less stable TERM 34 Central dogma DEFINITION 34 DNA--> transcription-->RNA--> translation--> proteinsDNA is designed to be very stable, while RNA is designed to be not very stable at all TERM 35 three types of RNA DEFINITION 35 mRNA- transfer of genetic information (messenger)tRNA- read the mRNA and matches with the correct protein (transfer)rRNA- used, along with ribosomal proteins, to make ribosomes (ribosomal)