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- https://bio.libretexts.org/Courses/Ouachita_Baptist_University/Reyna_Cell_Biology/02%3A_2-(T2-first_lecture)_Protein_Structure/2.02%3A_Composition_Sequence_and_Conformational_Analysis_of_Proteinsdescribe in general terms the procedures and chemical steps in the determinations of the following for proteins: presence of certain specific amino acids amino acid composition N and C terminal amino ...describe in general terms the procedures and chemical steps in the determinations of the following for proteins: presence of certain specific amino acids amino acid composition N and C terminal amino acid specific amino acid necessary for binding and activity amino acid sequence Thumbnail: Structure of human hemoglobin. The proteins α and β subunits are in red and blue, and the iron-containing heme groups in green. Contributors and Attributions Henry Jakubowski (College of St.
- https://bio.libretexts.org/Courses/Ouachita_Baptist_University/Reyna_Cell_Biology/02%3A_2-(T2-first_lecture)_Protein_Structure/2.01%3A_Amino_Acids/2.1.08%3A_A8._Reactions_of_HistidineThe nitrogen atom in a secondary amine might be expected to be a stronger nucleophile than a primary amine through electron release to that N in a secondary amine. Opposing this effect is the steric h...The nitrogen atom in a secondary amine might be expected to be a stronger nucleophile than a primary amine through electron release to that N in a secondary amine. Opposing this effect is the steric hindrance by the two attached Cs of the N on attach on an electrophile . However, in His, this steric effect is minimized since the 2Cs are restrained by the ring. With a pKa of about 6.5, this amino acid is one of the strongest available bases at physiological pH (7.0).
- https://bio.libretexts.org/Courses/Ouachita_Baptist_University/Reyna_Cell_Biology/02%3A_2-(T2-first_lecture)_Protein_Structure/2.01%3A_Amino_Acidsstate the charge on amino acid side chains using the Henderson Hasselbach equation and the approximate charge by inspection at any given pH draw mechanisms and identify products for the reaction of nu...state the charge on amino acid side chains using the Henderson Hasselbach equation and the approximate charge by inspection at any given pH draw mechanisms and identify products for the reaction of nucleophilic side chains Lys and Cys with common chemical modification agents and extend this understanding to reactions of His. The proteins α and β subunits are in red and blue, and the iron-containing heme groups in green.
- https://bio.libretexts.org/Learning_Objects/Visualizations_and_Simulations/Interactive_Figures/Interactive_Biochemistry_Graphs/Uncompetitive_Inhibition_-_Lineweaver-Burk_Plots
- https://bio.libretexts.org/Courses/Ouachita_Baptist_University/Reyna_Cell_Biology/02%3A_2-(T2-first_lecture)_Protein_Structure/2.02%3A_Composition_Sequence_and_Conformational_Analysis_of_Proteins/2.2.04%3A_B4._Analysis_of_Protein_Secondary_StructureThe percent and type of secondary structure can be determined using circular dichroism (CD) spectroscopy. (The links below come from an animated tutorial on Electromagnetic Waves and Circular Dichrois...The percent and type of secondary structure can be determined using circular dichroism (CD) spectroscopy. (The links below come from an animated tutorial on Electromagnetic Waves and Circular Dichroism by András Szilágyi ) In this method, right and left circularly polarized light illuminates a protein, which, since it is made of all L-amino acids, is chiral. (The mirror image would be a protein of the same sequence made of D-amino acids.) Circularly polarized light can be made when plane polari…
- https://bio.libretexts.org/Courses/Ouachita_Baptist_University/Reyna_Cell_Biology/02%3A_2-(T2-first_lecture)_Protein_Structure/2.05%3A_G._Predicting_Protein_Properties_From_Sequences/2.5.03%3A_G3._Prediction_of_HydrophobicityIn this system, empirical measures of the hydrophobic nature of the side chains are used to assign a number to a given amino acid. For a water-soluble protein, a continuous stretch of amino acids foun...In this system, empirical measures of the hydrophobic nature of the side chains are used to assign a number to a given amino acid. For a water-soluble protein, a continuous stretch of amino acids found to have a high average hydropathy is probably buried in the interior of the protein. A hydrophathy plot for chymotrypsinogen (sum of hydropathies of seven consecutive residues) shows many stretches that are presumably buried in the interior of the protein.
- https://bio.libretexts.org/Courses/Ouachita_Baptist_University/Reyna_Cell_Biology/02%3A_2-(T2-first_lecture)_Protein_Structure/2.01%3A_Amino_Acids/2.1.10%3A_A10._General_Links_and_ReferencesThe Amino Acid Repository from the Image Library of Biological Molecules. Contains a great data base of properties about amino acids. Amino Acid Information form Rockefeller University. References Chi...The Amino Acid Repository from the Image Library of Biological Molecules. Contains a great data base of properties about amino acids. Amino Acid Information form Rockefeller University. References Chin, J. An expanded eukaryotic genetic code. pg 964 (2003) Schultz, P. et al. JACS, last week January, 2003 A New Twist on Chirality (how homochirality in amino acids may have developed). Science. 292, pg 2021 (2001) Contributors and Attributions Henry Jakubowski (College of St. John's University)
- https://bio.libretexts.org/Courses/Ouachita_Baptist_University/Reyna_Cell_Biology/02%3A_2-(T2-first_lecture)_Protein_Structure/2.03%3A_Understanding_Protein_Conformation/2.3.04%3A_C4._Common_Motifs_in_ProteinsGiven the number of possible combinations of 1°, 2°, and 3° structures, one might guess that the 3D structure of each protein is quite distinctive. This is true. However, it has been found that simila...Given the number of possible combinations of 1°, 2°, and 3° structures, one might guess that the 3D structure of each protein is quite distinctive. This is true. However, it has been found that similar substructures are found in proteins. For instance, common secondary structures are often grouped together to form a motifs called super-secondary structure (SSS).
- https://bio.libretexts.org/Learning_Objects/Visualizations_and_Simulations/Interactive_Figures/Interactive_Biochemistry_Graphs/Fx_Sat_Y_vs_Lo_for_any_L
- https://bio.libretexts.org/Courses/Ouachita_Baptist_University/Reyna_Cell_Biology/02%3A_2-(T2-first_lecture)_Protein_Structure/2.01%3A_Amino_Acids/2.1.09%3A_A9._In_Vivo_Post_Translational_Modification_of_Amino_AcidsAmino acids in naturally occurring proteins are also subjected to chemical modification within cells. These modifications alter the properties of the amino acid that is modified, which can alter the s...Amino acids in naturally occurring proteins are also subjected to chemical modification within cells. These modifications alter the properties of the amino acid that is modified, which can alter the structure and function of the protein. Most chemical modifications made to proteins within cells occur after the protein is synthesized in a process called translation. Here is a list of post-translational modification from the Swiss Institute of Bioinformatics:
- https://bio.libretexts.org/Courses/Ouachita_Baptist_University/Reyna_Cell_Biology/05%3A_(Test_2)Transport_and_Kinetics/5.01%3A_Passive_and_Facilitated_Diffusion/5.1.02%3A_A2._Facilitated_DiffusionFacilitated diffusion is the process of spontaneous passive transport (as opposed to active transport) of molecules or ions across a biological membrane via specific transmembrane integral proteins.
