Notes in Pharm 116-L02

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Published	09/15/2023	Peptide Group bond is both {{c1::Planar & Rigid}}.
Published	09/15/2023	The reason why a peptide bond is planar and rigid is because: {{c1::resonance between the carbonyl group with the lone pairs on nitrogen that relocali…
Published	09/15/2023	Most peptide bonds assume the {{c1::trans}} conformation.
Published	09/15/2023	The main chain is considered the {{c1::backbone}} where the {{c1::side groups}} are sticking out of the chain.
Published	09/15/2023	{{c1::Primary structure}}: {{c2::linear squence of amino acids in a polypeptide chain}}.
Published	09/15/2023	{{c1::Secondary structure}}: {{c2::local spatial arrangement of a polypeptide's backbone atoms without regard to conformations of its side chains}}
Published	09/15/2023	{{c1::Tertiary structure}}: {{c2::three-dimensional structure of an entire polypeptide, including its side chains}}.
Published	09/15/2023	{{c1::Quaternary structure}}: {{c2::spatial arrangement of two or more polypeptides (subnits)}}
Published	09/15/2023	Three types of secondary structures: {{c1::α-helix}}; {{c1::β-sheets}}; {{c1::Reverse turns (β-bends)}}
Published	09/15/2023	α-helix are right-handed spiral (coils) with {{c1::side chains extended outward}}.
Published	09/15/2023	α-helix has {{c1::3.6}} residues per turn. The distance the helix rises per turn = {{c1::5.4 Angstrom}}.
Published	09/15/2023	An average α-Helix has an average length of {{c1::12}} residues which is equal to around {{c1::3}} helical turns and a length of {{c1::18}} angstrom.
Published	09/15/2023	α-Helix is stabilized by {{c1::H-Bonds}} within the backbone.
Published	09/15/2023	H-bonds occur in the α-helix in the {{c1::peptide C=O bond of the nth residue points along the helix axis towards the peptide N-H group of the (n+4)th…
Published	09/15/2023	In an α-helix, the optimum distance for H-bonds is around {{c1::2.8 angstrom}}.
Published	09/15/2023	(Extra)
Published	09/15/2023	Three conditions that disrupts α-helix formation: {{c1::Electrostatic repulsion}}; {{c1::Steric repulsion}}; {{c1::Proline}}.
Published	09/15/2023	β-sheets contain {{c1::2 to 22}} polypeptide strains with an average of {{c1::6}} strands.
Published	09/15/2023	Like α-helix, there is {{c1::H-bonds}} between strands in β-sheets.
Published	09/15/2023	Each strand in β-sheet may contain up to {{c1::15}} residues where there is an average of {{c1::6}} residues.
Published	09/15/2023	When writing amino acids in residue, the format for writing the name is starting from the {{c1::N-terminus}} to the {{c1::C-terminus}}.
Published	09/15/2023	β-sheets can be antiparallel where the N to C runs {{c1::opposite of that of the other strand or antiparallel}}.
Published	09/15/2023	β-sheets can be Parallel where the N to C {{c1::strands run parallel or same way to eachother}}.
Published	09/15/2023	β-sheets can contain mixtures of parallel and antiparallel strands but parallel sheets containing less than {{c1::5}} strands are rare. Why? Dist…
Published	09/15/2023	β-sheets take a zigzag structure --> {{c1::pleated sheet}}: where side chains extend to {{c1::opposite sides of the sheet}}.The distance of one res…
Published	09/15/2023	Reverse turns or β-bends connect some units of secondary structure and the common amino acids seen in these turns are: {{c1::Gly and Pro}}.They a…
Published	09/15/2023	Compare β-bends in parallel and antiparallel β-sheets.
Published	09/15/2023	Why are Gly or Pro common in turns?
Published	09/15/2023	{{c2::Structural Motifs}} are: {{c1::combinations of secondary structure (i.e. Supersecondary structure) present in tertiary structures}}.
Published	09/15/2023	name of Motif
Published	09/15/2023	(name of motif)
Published	09/15/2023	(name of motif)
Published	09/15/2023	(name of motif)
Published	09/15/2023	Tertiary structure is formed due to {{c1::association of secondary structure units within a single polypeptide chain to give a three-dimensional struc…
Published	09/15/2023	a73bfa9d1146480d9be520cfba069c92-oa-1
Published	09/15/2023	Protein structure determination by:1. {{c1::X-Ray crystallography}}2. {{c1::2D NMR spectroscopy}}
Published	09/15/2023	The {{c1::Protein Data Bank (PDB)}} is the {{c2::repository for structural information (PDBid).}}
Published	09/15/2023	(Protein Classification)
Published	09/15/2023	(Protein classification)
Published	09/15/2023	(protein classification)
Published	09/15/2023	In the image, X-ray structure of {{c1::β-barrel}} for the human retinol binding protein.
Published	09/15/2023	Domains are formed from large {{c1::polypeptides}}.
Published	09/15/2023	{{c2::Domain}} is: {{c1::a globular cluster of secondary/supersecondary structures usually found in polypeptides with > 200 residues.}}
Published	09/15/2023	Most domians consist of {{c1::40 to 200}} residues and have an average diameter of {{c1::25}} angstrom.
Published	09/15/2023	Quaternary Structure: {{c1::noncovalent association of two or more polypeptide chains (subunits) to form a native protein structure}}. (add-on of more…
Published	09/15/2023	{{c1::Disulfide bond (Cys-Cys)}} is the only covalent bond that can occur in quaternary structure.
Published	09/15/2023	Define what homo- and hetero-Tetramer mean.
Published	09/15/2023	Explain Image.
Published	09/15/2023	2 advantages of Quaternary structure:1. {{c1::defects can be repaired by simply only replacing the flawed subunit}}2. {{c1::provides the structural ba…
Published	09/15/2023	Fibrous proteins have {{c1::repeating secondary structures}}; and two examples are {{c1::Keratin and Collagen}}
Published	09/15/2023	α-Keratin have a {{c1::Coiled Coil}} secondary structure and are rich in {{c1::Cys}} residues.Found in: outer epidermis; hair (~14% Cys); horn; nails;…
Published	09/15/2023	79908e1a32984342b7015006ef9cca2e-oa-1
Published	09/15/2023	Explain what is happening
Published	09/15/2023	Collagen is the most abundant {{c1::vertebrate}} protein charactized by {{c1::strong, insoluble fibers}} in a {{c1::triple helix}} structure.
Published	09/15/2023	Collagen is the major stress-bearing component of connective tissues such as {{c1::bone, teeth, cartilage, tendon, and the fibrous matrices of skin an…
Published	09/15/2023	Collagen side chains are covalently cross-linked by reaction of {{c1::Histidine}} and {{c1::activated-Lysine}}. It is almost devoid of {{c1::Cys}} res…
Published	09/15/2023	Collagen Amino acid composition:- {{c1::30% Gly}}- {{c1::15% to 30% Pro and 4-hydroxyprolyl (Hyp)}}- Others
Published	09/15/2023	e2c72bef520848bab7f9dae87f07afba-oa-1
Published	09/15/2023	{{c1::Scurcy}} is caused by {{c2::ascorbic acid (Vitamin C)}} deficiency which results in {{c3::poor collagen fibers}}.
Published	09/15/2023	Scurcy can indicate/result in:1. {{c1::Low activity of Prolyl hydroxylase}}2. {{c1::Low amount of Hyp}}3. {{c1::Weak collagen fibers}}
Published	09/15/2023	When enzymes act on specific substrates there is noncovalent forces to allow for {{c1::reversible binding}}.There is might also be {{c1::hydrophobic g…
Published	09/15/2023	In this equation, calculate kd and ka binding affinity constants. Explain what they mean.
Published	09/15/2023	Proteins are dynamic structures meaning they are {{c1::flexible}} and rapidly {{c1::fluctuating}} molecules whose structural mobilities are functional…
Published	09/15/2023	The average molecular weight (MW) of an amino acid is {{c1::110 Daltons}}.To calculate the average MW of protein: {{c1::(# amino acids) * 110 Daltons}…
Published	09/15/2023	Side chain location of Nonpolar residues such as {{c1::Val}},{{c1::Leu}},{{c1::Ile}},{{c1::Met}},and {{c1::Phe}} occur mostly in the {{c1::interior of…
Published	09/15/2023	Location of side chains of charge polar residues such as {{c1::Arg}}, {{c1::His}}, {{c1::Lys}}, {{c1::Asp}}, {{c1::Glu}} are usually located on {{c1::…
Published	09/15/2023	Location of side chains of uncharged polar groups such as {{c1::Ser}}, {{c1::Thr}}, {{c1::Asn}}, {{c1::Gln}}, {{c1::Tyr}} are usually on {{c1::protein…
Published	09/15/2023	In this slide, identify the 5 amino acids that are not mentioned.
Published	09/15/2023	8f3b116340a44f6892012e368a8e2a38-oa-1
Published	09/15/2023	Protein stability depends on Hydrophobic effect because:- Has greatest influence on protein stability due to {{c1::increase in entropy of the water mo…
Published	09/15/2023	Protein stability depends on hydrogen bonds because:- H-bonds are central features of {{c1::protein structures}}- H-bonds make {{c1::only minor}} cont…
Published	09/15/2023	Protein stability depends on ionic interactions (ion pair or salt bridge):- {{c1::Minor contribution}} to stability of native protein----- Loss of Ent…
Published	09/15/2023	Protein stability depends on disulfide bonds:- Cross-link {{c1::extracellular proteins}}.- disulfide bonds are rare in {{c1::intracellular proteins}} …
Published	09/15/2023	Protein Stability depends on Metal Ions because:- Stabilize {{c1::small protein structural motifs}} (Zinc Finger)- Zinc Finger: {{c1::25-60}} residues…
Published	09/15/2023	The Zinc Finger functions as interaction modules that bind {{c1::DNA}}, {{c1::RNA}}, {{c1::proteins}}.
Published	09/15/2023	Protein can be denatured by:- {{c1::Heat (most protein unfold or melt at temp < 100C)}}- {{c1::Acid/Base (pH cariations affect protein charge and H…
Published	09/15/2023	What does Polyphenol oxidase (PPO) do in fruits?
Published	09/15/2023	Decrease browning of fruits by inactiving PPO (Polyphenol oxidase). This is done by:{{c1::Heat}}; {{c1::reducing the pH on the surface of the fruit}};…
Published	09/15/2023	Explain what is happening.
Published	09/15/2023	ccb8dc18e1af466fa967694726836530-oa-1
Published	09/15/2023	ccb8dc18e1af466fa967694726836530-oa-2
Published	09/15/2023	Protein Renaturation occurs only when {{c1::primary}} structure is intact. This is because the protein {{c1::primary}} structure dictates its three di…
Published	09/15/2023	When does hydrophobic collapse occur in the protein folding process?
Published	09/15/2023	Molecular chapterones are "ATPases"ATPases are enzymes that {{c1::catalyze the hydrolysis of ATP to ADP and Pi}}.
Published	09/15/2023	Heat shock proteins or HSP is an important chapterone that is required to {{c1::recover heat-denatured proteins or to prevent misfolding under conditi…
Published	09/15/2023	Hsp synthesis is increased at {{c1::elevated temperatures}}.
Published	09/15/2023	Hsp90 also stabilized a number of proteins required for {{c1::tumor growth}}. Thus being a target for {{c1::cancer therapy}}.
Published	09/15/2023	{{c1::Molecular chapterones}}: essential proteins that bind to unfolded and partially folded polypeptides chains where they:1. {{c2::Assist in the fol…
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