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| Mikhail Tswett first separated colorful plant pigments by what |
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| Chromatographic methods to separate amino acid mixtures |
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| ion exchange, and high performance liquid |
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| can form disulfides and can be easily alkylated |
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| Proteins or peptides can be quantified by rxn with |
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| Copper based reagents give a what color |
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| the peptide bond is usually found in what conformation |
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| Because of the 40% double bond character of peptide bonds |
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| the 6 atoms of the peptide group are always planar |
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| short polymers of amino acids |
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| highest pKa and highest isoelectric point |
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| lowest pKas and lowest isoelectric points |
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| structural and normally H20 insoluble (ex collagen) |
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| are compact H2O soluble and used for transport or metabolism (ex. mycoglobin) |
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| hydrophobic/ hydrophilic and are used for cell signaling and transport (ex: bacteriorhodopsin) |
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| the shape they take based on the individual amino acids attractive / repulsive forces and their steric conformation |
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| Two shapes secondary structures can take in peptides |
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| 3D formation when secondary structures aggregate or fold into more complex structures |
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| Association of 2 or more polypeptide chains thatalready have their oen tertiary structures |
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| Quaternary structure are usualy held by |
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| non-convalent attractions by convalent disulfide bridges |
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| Loss of its native conformation |
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| 2 alpha and 2 beta subunits, each one with a heme group |
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| angle denotes about the C(alpha) - N bond |
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| Angle denoted about the C(alpha)- C bond |
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| Alpha helices are stabalized by |
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| Alpha helices are mostly this but not always |
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| Aromatic Amino acids absorb |
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| The sequence of a.acids in a protein |
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| is encoded by the nucleotide sequence of DNA |
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| Amino acids in a protein is read |
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| from the amino terminus to the carboxyl terminus |
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| real amino acid sequencing and sequencing the corresponding DNA in the gene is two ways to |
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| two polypeptide chains A and B held together by two disulfide bonds |
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| Eddman reagent (most common), PTH derivatives, Sanger's or Dansyl Cl |
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| determining the N terminus |
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| enzymatic analysis (carboxypeptidase) |
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| cleaves any residue except Pro, Arg, and Lys |
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| Carboxypeptidase B (hog pancreas) |
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| only works on Arg and Lys |
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| Mixture of Carboxypeptidase B and A cleave all but |
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| Extreme pH, 8M urea, 6M guanidine HCL, high salt do what |
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| Cleavage of disulfide bridges use |
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| Sulfhydryl reducing agents (metacaptoethanol, dithiothreitol, or dithioerythritol) |
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| alkylating agent that prevents reforming of disulfide bridges, |
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| Trypsin, chymotrypsin, clostripain, staphylooccal V8 protease |
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| cleavage on the C side of Lys, and Arg |
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| Like Trypsin but attack Arg more than Lys |
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| cuts the C-side of Phe, Tyr, Trp |
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| Staphylococcal V8 protease |
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| C side of Glu, Asp, in phosphate buffer |
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| Specific for Glu, in acetate or bicarbonate buffer |
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| Staphylococcal V8 protease |
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| Only reacts on methionine residues |
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| Produces a peptide with a C terminal homoserine lactone |
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| Observations of what can be used to build phylogenetic trees |
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| Proline and glycine are prevalent in |
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| Carbonyl C of one residue is H-bonded to the amine proton of a residue 3 residues away |
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| PLay a structural role in nature, mechanically strong, usually insoluble, most of the chain is organized and approximately parallel to a single axis |
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| hair,fingernails, claws and horns |
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| Primary structure consists of 7-residue repeats( a-b-c-d-e-f-g) where a and d are nonpolar |
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| Seuqences consists of alpha residues capped with non-helical N and C termini |
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| breaks the disulfide bridges |
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| Ellman's test is to test for |
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| In the formation all the glycines are on one side and the alanines and serines are on the other side |
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| Basic unit of collagen is |
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| Glycine, Serine, Asparagine, Glutamine, Tyrosine, Cysteine, Threonine |
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| Leucine, Proline, Methionine, Tryptophan, Isoleucine, Phenylalanine, Valine, Alanine |
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| Histidine, Arginine, Lysine |
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| Where the proline content is unusually high |
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| The composition of collagen is not suited for alpha or beta sheets but rather |
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| 40 nm gaps in collagen fibers arae called ____ and they contain carbohydrate and are thought to be nucleation site for bone formation |
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| most polar rediues face outward of the protein and interat with the solvent |
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| Most hydrophobic resides face the interiorof the protein and interact with each other |
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| yields two DNA molecules identical to the original one |
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| sequence of bases in DNA is recorded as a sequence of complementary bases in a single-stranded mRNA molecule |
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| three bases codons on the mRNA correspondind to a specific a.acid, directing the building of proteins |
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| Bases are linked via what bond |
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| Carbond of the glycosidic bond is |
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| what makes nucleosides more water soluble than free bases |
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| vascodilator, muscle relaxant, produces sleepines |
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| central to energy metabolism |
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| drives carbohydrate metabolism |
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| the basis of structure and function of ribosomes |
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| IN eukaryotes the mRNA is called the |
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| WHat is spliced and thrown away in the euk. mRNA |
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| Ribosome are mainly____ than proteins |
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| 3' terminal sequence in tRNA |
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| Hydrolyzed by a dilute base |
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| depurinated by dilute acid |
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| SNAKE venom phosphodiesterase is a |
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Definition
| a cutter ( cuts to the left of the P-bond) |
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Definition
| b cutter (cuts to the right of the P-bond) |
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| These RE cleave DNA chain at selected sites |
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| RE with no ATP requirement |
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| Type two RE can leave what kind of ends when cut |
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| A and T share how many H bonds |
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| C and G shared how many H bonds |
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| The right hand forms of DNA |
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| A DNA (shortest and broad) |
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| Z DNA (longest and thinnest) |
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| Found in rich G:C regions. G goes to syn and C goes to ani conformation |
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| G:C H-bonds can be preserved in the transition from |
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Definition
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Term
| when DNA is heated it UV absorbance increases by |
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Definition
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| Hyperchromic shift reflects |
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Definition
| unwinding of the DNA double helix |
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| Ezymes that can reduce or introduce supercoiling |
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Definition
| topoisomerases or gyrases |
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Definition
| cut one DNA strand, pass the other one through and rejoin them |
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| using ATP cuts both strands |
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| topoisomerase that introduces neg. supercoiling |
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Definition
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| Uses ATP to unwind DNA and put neg. supercoiling w/o breaking the strands. |
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Definition
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| # of base pairs in DNA/ bp per turn = |
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Definition
| histone and nonhistone chromosomal proteins |
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Definition
| regulators of gene expression |
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| Many non-canonical bp found in |
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Term
| DNA Pol 1 has what activity |
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Definition
| 5' to 3' polymerase, 3' to 5' exonuclease, and 5' to 3' exouclease activity |
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Term
| 5' exonuclease activity accomplishes |
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Definition
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| The real plymerase in E. coli is |
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Definition
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| Core enzyme has three subunits |
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Definition
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| THe alpha subunit in the core enzyme is the |
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Definition
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| The epsilon subunit is the |
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Definition
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| What DNA pol uses a RNA primer 12 nucleotides long |
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Definition
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| What polymerase excises the primer and refills with DNA |
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