Notes in b. Proteins: Primary and Secondary Structure

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Published	07/28/2024	Purine mnemonic?
Published	07/28/2024	The {{c1::primary structure}} is required before ellucidating a proteins tertiary structure via X-ray chrystallography, NMR, or in silico methods…
Published	07/28/2024	SDS-PAGE stands for {{c1::sodium dodecyl sulfate polyacrylamide gel electrophoresis}}
Published	07/28/2024	What is the function of SDS in gel electrophoresis?
Published	07/28/2024	SDS-PAGE sorts proteins based on {{c1::size/mass, where small molecules move farther}}
Published	07/28/2024	Treating a sample with {{c1::beta mercaptoethanol}} reduces {{c2::disulfide bonds}}
Published	07/28/2024	A {{c1::western blot}} employs antibodies to detect proteins separated by SDS-PAGE
Published	07/28/2024	What are the general steps for a western blot?
Published	07/28/2024	Western blots are {{c1::more}} specific than ELISA
Published	07/28/2024	When trying to separate proteins based on both size and charge a {{c1::2-D Gel Electrophoresis}} can be used
Published	07/28/2024	The first step of a 2-d Gel electrophoresis is {{c1::isoelectric focusing}}. Then proteins are separated based on {{c2::mass}} by {{c3::SDS-PAGE}}
Published	07/28/2024	The second step of a 2-D Gel electrophoresis is {{c1::SDS electrophoresis}}.
Published	07/28/2024	A {{c1::SDS-PAGE}} is used to determine the number of different polypeptide chains in a protein
Published	07/28/2024	Disulfide bonds tend to be more important for internal or secreted proteins?
Published	07/28/2024	How many different cleavage methods must be used to allow for the determination of amino to carboxy terminal alignment for a set of peptides?
Published	07/28/2024	Edman degradation utilizes the compound {{c1::phenyl isothiocyanate}}
Published	07/28/2024	After {{c1::100}} residues, the reliability of edman degradation comes into question
Published	07/28/2024	What is the basic mechanism of edman degradation?
Published	07/28/2024	In mass spectrometry, separation is based on the {{c1::mass/charge (m/z)}}
Published	07/28/2024	Describe the process for tandem mass spectrometry.
Published	07/28/2024	Rotation can occur at the {{c1::alpha carbon}} within the peptide chain.
Published	07/28/2024	The {{c1::trans}} conformation is strongly favored in most peptide bonds.
Published	07/28/2024	When {{c1::proline}} is found in peptide bonds, it exists in both cis and trans form, with a {{c2::10% cis/90% trans}} split
Published	07/28/2024	Ramachandran diagrams describe the {{c1::steric interactions of a peptide based on phi/psi torsion angles}}
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Published	07/28/2024	Right handed alpha helixes are stabilized between the H bonds between each CO group and NH group {{c1::four}} residues ahead in the sequence
Published	07/28/2024	Where are the side chains found in an alpha helix?
Published	07/28/2024	There are {{c1::3.6}} residues per turn of an alpha helix
Published	07/28/2024	{{c1::Proline}} is the amino acid that breaks alpha helices
Published	07/28/2024	The {{c1::alpha helical coiled coil}} is an example of a quaternary structure which is built solely on the alpha helical secondary structure
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Published	07/28/2024	There are {{c1::4}} amino acids in a beta bend
Published	07/28/2024	Omega loops are typically {{c1::6-16}} residues in length
Published	07/28/2024	Omega loops are most often found at {{c1::the protein's surface}}
Published	07/28/2024	What are the major functions observed in omega loops?
Published	07/28/2024	Polyglutamine diseases are a result of?
Published	07/28/2024	A common polyglumatine disease is {{c1::Huntington Disease}}
Published	07/28/2024	Huntington Disease is inherited via an {{c1::autosomal dominant}} pattern of inheritence.
Published	07/28/2024	A normal huntington protein has {{c1::6-35}} glutamine repeats
Published	07/28/2024	A diseased huntington protein has {{c1::36-121}} repeated glutamines
Published	07/28/2024	ELISA is different than Western Blotting in that ELISA uses {{c1::antigens}} to detect {{c1::antibodies}}. ELISA also has high rate of {{c2:…
Published	07/28/2024	{{c1::Disulfide bonds}} must be removed for primary structure determination
Published	07/28/2024	{{c1::Proteolytic cleavage}} must be done with two reagents that have different specificity
Published	07/28/2024	The collagen helix is stabilized by repeated {{c1::proline}} and {{c1::hydroxyproline}} residues
Published	07/28/2024	Residue {{c1::2}} of either type of ß bend is often {{c1::Pro}} because it can readily {{c1::assume the required conformation}}
Published	07/28/2024	What are 2 effects of Polyglutamine diseases
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