Notes in 03AA&Proteins

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Status	Last Update	Fields
Published	07/30/2024	Distinguishes proteins from other macromolecules{{c1::Nitrogen}}
Published	07/30/2024	The {{c1::L}}-form of AAs is found in most proteins
Published	07/30/2024	All the 20 amino acids possess at least {{c1::two}} functional groups
Published	07/30/2024	When an AA is in an acidic environment, the {{c1::carboxylic acid}} group loses the \(\ce{H}\)
Published	07/30/2024	When an AA is in an basic environment, the {{c1::amine}} group gains the \(\ce{H}\)
Published	07/30/2024	Selenocysteine
Published	07/30/2024	1-Pyrrolysine
Published	07/30/2024	List the Amide containing AAs{{c1::Asparagine (from Aspartate)Glutamine (from Glutamate)}}
Published	07/30/2024	List the sulfur containing AAs{{c1::CysteineMethionine}}
Published	07/30/2024	List the hydroxyl containing AAs{{c1::SerineThreonineTyrosine}}
Published	07/30/2024	List the aromatic containing AAs{{c1::TyrosinePhenylalanineTryptophan}}
Published	07/30/2024	List the straight chain aliphatic containing AAs{{c1::GlycineAlanine}}
Published	07/30/2024	List the branched chain aliphatic containing AAs{{c1::LeucineIsoleucineValine}}
Published	07/30/2024	List the secondary AAs{{c1::Proline}}
Published	07/30/2024	List the Basic AAs{{c1::HistidineArginineLysine}}
Published	07/30/2024	List the Acidic AAs{{c1::Aspartate/Aspartic AcidGlutamate/Glutamic Acid}}
Published	07/30/2024	The {{c1::pK of an acid (pKa)}} is numerically equal to the pH of the solution when the molar concentration of the {{c2::acid::acid/base}} and its con…
Published	07/30/2024	Very acidic (low pH) solution: the {{c1::cat::cat/an}}ionic species would exist
Published	07/30/2024	Very basic (high pH) solution: the {{c1::an::cat/an}}ionic species would exist
Published	07/30/2024	{{c1::Isoelectric point (pI)}} is the pH wherein the AA has a net charge of {{c2::zero}} and exists as a {{c2::zwitter ion}}
Published	07/30/2024	For amino acids without ionizable R groups, the isolectric point (pI) is the average of the {{c1::pKa1 and pKa2}}
Published	07/30/2024	Amino Acid (AA) Net ChargeIf pH {{c1::≤::≥/≤}} pI, AA is {{c2::pro::de/pro}}tonated, {{c3::POSITIVE::+/-}} chargeIf pH {{c1::≥::≥/≤}} pI, AA is {{c2::…
Published	07/30/2024	My Suggestion: {{c1::YOU CAN'T ANKI THIS PART HAHAHAHAHA. Just read the trans for pKa shiz}}
Published	07/30/2024	Two amino acids may have the same ionization tendency (pK values){{c1::F::T/F}}
Published	07/30/2024	{{c1::Salting Out::AA and Protein Separation Method}}Principle: proteins are less soluble at {{c2::high::high/low}} salt concentrations
Published	07/30/2024	{{c1::Dialysis and Ultrafiltration::AA and Protein Separation Method}}Principle: eliminate ions and impurities through diffusion in a semi-permeable m…
Published	07/30/2024	{{c1::Chromatography::AA and Protein Separation Method}}Principle: Solutes travel with the mobile and stationary phase through a supporting medium. Di…
Published	07/30/2024	{{c1::Ion Exchange Chromatography::AA and Protein Separation Method}}Principle: Differential affinity of charged ions to the immobilized charged subst…
Published	07/30/2024	{{c1::Affinity Chromatography::AA and Protein Separation Method}}Principle: Polymer ligand specific to the target protein is bound to the column. Non-…
Published	07/30/2024	{{c1::Electrophoresis::AA and Protein Separation Method}}Principle: Separation of charged particles in an electric field. Different substances migrate…
Published	07/30/2024	{{c1::SDS Polyacrylamide Gel Electrophoresis (SDS-PAGE)::AA and Protein Separation Method}}Principle: Proteins are separated SOLELY based on the {{c2:…
Published	07/30/2024	{{c1::HIgh Performance Liquid Chromatography (HPLC)::AA and Protein Separation Method}}Separation based on {{c2::charge, size, and hydrophobicity::3 f…
Published	07/30/2024	A peptide bond exhibits partial double bond character due to the interaction between the electrons of the {{c1::double bond of carbonyl group and thos…
Published	07/30/2024	The {{c1::C-N peptide}} linkage and all atoms connected to them lie in a {{c2::planar}} configuration called the amide plane.
Published	07/30/2024	TRUE OR FALSE: In the amide plane, the carbonyl hydrogen and the oxygen of the nitrogen are also depicted in the trans position within the amide plane…
Published	07/30/2024	TRUE OR FALSE: The peptide bond only accepts protons, and not release.{{c1::FALSE - The peptide bond is uncharged and does not ionize, it cannot bear …
Published	07/30/2024	Peptide Pure Single Bonds{{c1::Psi}} bond - bond that connects the alpha-carbon & {{c2::carbonyl-carbon}}{{c1::Phi}} bond - bond th…
Published	07/30/2024	A polypeptide chain can be seen to have a backbone that consists of a series of amide planes linked with the {{c1::alpha-carbon}} atoms.
Published	07/30/2024	R-groups attached to the alpha carbon are always depicted in the {{c1::same::same/opposite}} direction based on the orientation of the succeeding side…
Published	07/30/2024	Protein Classification based on Composition{{c1::Simple}} - yield only amino acids when hydrolyzed{{c1::Conjugated}} - consists of protein covalently …
Published	07/30/2024	Conjugted Proteins based on Composition{{c1::Glycoproteins}} - carbohydrate component aside from amino acid{{c1::Lipoproteins}} - has lipid component …
Published	07/30/2024	Globular or Fibrous ProteinGlobular - Tightly folded water-{{c1::s}}oluble with dynamic functionFibrous - Elongated water-{{c1::ins}}oluble with struc…
Published	07/30/2024	The principal determinant in the primary level of protein structure is the {{c1::amino acid sequence}}
Published	07/30/2024	In sickle cell anemia, a single amino acid in the {{c1::beta}}-chain is altered, where {{c2::valine::AA}} instead of {{c2::glutamate::AA}} is at posit…
Published	07/30/2024	{{c1::Free rotation}} in a primary polypeptide chain is only possible in {{c1::the Psi and Phi}} bonds.
Published	07/30/2024	The stabilizing factor of the secondary structure of proteins is the {{c1::hydrogen}} bond between the {{c2::H of the amino}} group, and {{c2::O of th…
Published	07/30/2024	Types of Secondary Protein Structures{{c1::alpha helixbeta-pleated sheetsturns and bendsloops}}
Published	07/30/2024	The alpha-helix secondary structure is {{c1::right}}-handed or turns {{c1::clock}}wise and covers {{c2::3.6}} AAs per turn
Published	07/30/2024	The alpha helix structure is stabilized between the carbonyl oxygen of one AA residue and the amino hydrogen of the {{c2::4th}} residue down the chain
Published	07/30/2024	{{c1::proline and glycine::AA/s}} can disrupt the regular pattern of folding of the alpha helix and beta-pleated sheets and cause {{c2::bends}}.
Published	07/30/2024	The {{c1::beta-pleated sheets}} are formed when 2 or more segments of a polypeptide chain line side by side with each other, with its peptide backbone…
Published	07/30/2024	{{c1::Bends or Reverse Turns}} are short segments of amino acids that reverse the direction of the main polypeptide chain or connect regions of more r…
Published	07/30/2024	{{c2::B-bends or B-turns}} are the most common type of bends and they interconnect {{c1::antip}}arallel B-sheets at a hairpin turns
Published	07/30/2024	{{c1::Loops or Extended Bends}} are regions with beyond the minimum number of AA residues to connect adjacent regions of secondary structures of prote…
Published	07/30/2024	{{c2::Structural Motifs}} - Super secondary structures of proteins held by favorable {{c1::non-c::non-c/c}}ovalent interactions between side chai…
Published	07/30/2024	The arrangement of atoms in the tertiary level of proteins is due to the interactions between {{c1::side chains within the polypeptide}}.
Published	07/30/2024	The {{c1::quaternary}} level of proteins is formed by the {{c2::non-c::non-c/c}}ovalent binding of multiple polypeptide chains into a single mole…
Published	07/30/2024	TRUE OR FALSE: Quaternary level proteins are stabilized by similar interactions occuring in the secondary structure.{{c1::FALSE: similar with TERTIARY…
Published	07/30/2024	CLASSIFICATION OF QUATERNARY PEPTIDES:According to {{c1::number of subunits}} - dimer, trimer, tetramer, oligomerAccording to {{c1::similarity of subu…
Published	07/30/2024	Protein denaturation does not destroy the {{c1::primary}} structure of proteins
Published	07/30/2024	Proteins can spontaneously refold after denaturation, and cooling under precisely controlled conditions with the help of chaperonins will favor renatu…
Published	07/30/2024	{{c1::Insoluble aggregates}} may be formed when the uncontrolled cooling of denaturated protein kinetically traps the energy within, leading to refold…
Published	07/30/2024	Have you read the summary? {{c1::CHECK THIS::Yes/No}}
Published	07/30/2024	Amino acids have ionizable weakly acidic alpha-carboxyl and weakly basic alpha-amino groups and some ionizable R group. This makes them {{c1::amphoter…
Published	07/30/2024	pK for most AAs:pKa1 (a-{{c1::\(\ce{COOH}\)}} group): {{c2::~2}}pKa2 (a-{{c1::\(\ce{NH3+}\)}} group): {{c2::~9-10}}pKa3/R for those who…
Published	07/30/2024	The acetyl group in most acetylation/acylation reactions comes from {{c1::Acetyl CoA}}
Published	07/30/2024	Benzolyation{{c2::Phenols}} → {{c2::benzoic acid}} + AA \(\ce{NH2}\)Representative example: {{c1::Glycine::AA}} + Benzoic Acid = {{c3::Hippu…
Published	07/30/2024	Formaldehyde Reaction{{c2::2::n}} moles of formaldehyde + AA \(\ce{NH2}\) = {{c3::N-dimethylol derivative}}
Published	07/30/2024	MethylationRepresentative Example: {{c1::epsilon}} \(\ce{NH2}\) group of lysine is methylated by {{c1::lysine methyltransferase (KMT)::enzym…
Published	07/30/2024	Ninhydrin ReactionNinhydrin + FREE AA \(\ce{NH2}\) = {{c2::hydrindantin intermediate::intermediate}} → {{c2::Ruhemann’s Purple}}{{c3::Prolin…
Published	07/30/2024	Peptide bond formationLinkage is found in the {{c1::primary level::level}} of protein structure.Reaction of AA \(\ce{NH2}\) with a free carb…
Published	07/30/2024	{{c1::Biuret Reaction::reaction}}Useful to quantitate {{c2::the amount of peptide bonds}} in a solution{{c1::copper-containing biuret::reagent}} + \(\…
Published	07/30/2024	{{c1::Van Slyke Reaction::reaction}}Quantitative determination of amino groups in proteins by measuring {{c2::Nitrogen gas (\(\ce{N2}\))}} releas…
Published	07/30/2024	Reactions used in Protein Sequencing:{{c1::Dansyl chloride reactionEdman's reactionSanger's DNFB reaction}}
Published	07/30/2024	Dansyl Chloride Reaction Dansyl chloride + AA \(\ce{NH2}\) = {{c2::sulfanomide derivative::derivative}} ({{c1::blue-green::color}} fluo…
Published	07/30/2024	{{c1::Edman's Reaction::reaction}} {{c2::Phenylisothiocyanate (PITC)}} + AA \(\ce{NH2}\) = {{c2::cyclical phenylthiocarbamoyl derivativ…
Published	07/30/2024	Sanger's DNFB Reaction{{c1::2,4-Dinitrofluorobenzene (DNFB)}} + AA \(\ce{NH2}\) = {{c3::dinitrophenyl-amino acids}} ({{c2::yellow::colo…
Published	07/30/2024	{{c1::Oxidative deamination::reaction}}Representative Example: {{c2::Glutamate}} + {{c3::\(\ce{H2O}\)}} by {{c2::glutamate dehydrogenase}} →&nbsp…
Published	07/30/2024	{{c1::Schiff's Base Formation::reaction}}{{c2::Aldehyde}} + AA \(\ce{NH2}\) = {{c1::Schiff's base}} → {{c3::Amadori product}}
Published	07/30/2024	Glycine
Published	07/30/2024	Alanine
Published	07/30/2024	Valine
Published	07/30/2024	Leucine
Published	07/30/2024	Isoleucine
Published	07/30/2024	Methionine
Published	07/30/2024	Phenylalanine
Published	07/30/2024	Tryptophan
Published	07/30/2024	Proline
Published	07/30/2024	Serine
Published	07/30/2024	Threonine
Published	07/30/2024	Cysteine
Published	07/30/2024	Tyrosine
Published	07/30/2024	Asparagine
Published	07/30/2024	Glutamine
Published	07/30/2024	Aspartate/Aspartic acid
Published	07/30/2024	Glutamate/Glutamic acid
Published	07/30/2024	Lysine
Published	07/30/2024	Arginine
Published	07/30/2024	Histidine
Published	07/30/2024	Schiff's Base Formation Representative ExampleValine \(\ce{NH2}\) of the {{c1::beta-chain::Hb chain}} of Hb + aldehyde of {{c1::glucose}}, {…
Published	07/30/2024	{{c1::Transamination::reaction}} AA \(\ce{NH2}\) transfers to an {{c2::acceptor keto-acid}} = {{c3::new keto-acid}} + {{c3::new AA}}Represen…
Published	07/30/2024	The products of decarboxylation are {{c1::an amine + \(\ce{CO2}\)}}
Published	07/30/2024	Decarboxylation Representative Examples:Histidine → {{c1::Histamine}}Glutamate → {{c1::GABA}}
Published	07/30/2024	Ester formation Representative Example:{{c1::Alanine}} + {{c1::Ethanol}} = Alanine Ethyl Ester.
Published	07/30/2024	Amide Formation {{c1::Acidic}} AAs + {{c1::\(\ce{NH3}\)}} + {{c1::ATP}} = AmidesRepresentative Examples
Published	07/30/2024	{{c1::Hopkin's Cole or Glyoxylic Acid Test::reaction}}Reagent: {{c2::Glyoxylic acid in concentrated sulfuric acid}}Target Group & AA: {{c3:…
Published	07/30/2024	{{c1::Millon's Test::reaction}}Reagent: {{c2::Concentrated Nitric acid (\(\ce{HNO3}\)) + Mercury}}Target Group & AA: {{c3::Phenol (Tyr…
Published	07/30/2024	{{c1::Xanthoproteic Test::reaction}}Reagent: {{c2::Concentrated Nitric acid (\(\ce{HNO3}\)) + Heat}}Target Group & AA: {{c3::Aromatic group…
Published	07/30/2024	{{c1::Pauly's Test::reaction}}Reagent: {{c2::Sulfanilic acid + Sodium Nitrite (\(\ce{NaNO2}\)) + \(\ce{HCl}\) = Diazonium salt}}Targe…
Published	07/30/2024	{{c4::Sakaguchi Test::reaction}} Reagent: {{c2::Alpha-Naphthol (a-naphthol) + sodium hypobromite (\(\ce{NaBrO}\))}}Target Group & AA: …
Published	07/30/2024	{{c2::Nitroprusside Test::reaction}} Reagent: {{c2::Nitroprusside (\(\ce{NH4OH}\)) + Excess Ammonia (\(\ce{NH3}\))}}Target Group & AA:…
Published	07/30/2024	A string of amino acids can only be called a protein if: 1. {{c1::They have been translated by genetic code::genes}}2. {{c2::AA should be an L-is…
Published	07/30/2024	Practice naming Oligopeptides{{c1::Seryl-glycyl-tyrosyl-alanyl-leucine}}
Published	07/30/2024	{{c1::Aspartame::Biologically Important Peptide}}: dipeptide with methyl ester group used as a sweetener
Published	07/30/2024	{{c1::Glutathione::Biologically Important Peptide}}: Tripeptide made up of glutamate, cysteine, and glycine which is an antioxidant
Published	07/30/2024	{{c1::Insulin::Biologically Important Peptide}}: Made up of {{c2::51::n}} AA with 2 chains (A & B) that interlink with each other via inter- and i…
Published	07/30/2024	Peptide Antibiotics{{c1::Gramicidin}} - cyclical in nature{{c1::Isopenicillin N}}{{c1::Cyclosporin A}} - cyclical in nature
Published	07/30/2024	{{c1::Salt Formation::reaction}}Amino acid or Carboxyl group can react with acid or base to form an salt.
Published	07/30/2024	AA Reactions MnemonicMemorize the reactions for R-groups:{{c1::Hopkins, Pauly, and Sakaguchi took Nine Million X-Rays (Hopkins-Cole, Pauly, Sakaguchi,…
Published	07/30/2024	An antibody is an example of a {{c3::tertiary}} level protein with the {{c2::Fab}} domain associated for antigen binding, and the {{c2::Fc}} domain fo…
Published	07/30/2024	List the Weakly Acidic AAs{{c1::CysteineTyrosine}}
Published	07/30/2024	AAs with ionizable R-groups are the{{c3::Acidic, Weakly acidic, and Basic}} AAs
Published	07/30/2024	In SDS Polyacrylamide Gel Electrophoresis (SDS-PAGE),Exposed {{c3::negative::+/-}} charge are used to separate different lengths of proteins using pol…
Published	07/30/2024	Reactions used in Protein Sequencing target the {{c2::terminal \(\ce{NH2}\)}} group
Published	07/30/2024	Reactions occuring in Amino Acid Metabolism{{c1::Oxidative deaminationSchiff's base formationTransamination}}
Published	07/30/2024	When displaying peptides...The N-terminus is on the {{c1::left::R/L}}The C-terminus is on the {{c1::right::R/L}}When naming residues, the suffixes are…
Published	07/30/2024	# of ResiduesName 2Dipeptide3Tripeptide{{c1::<10}}Oligopeptide{{c1::10-50}}Polypeptide{{c1::>50}}Protein
Published	07/30/2024	The {{c1::steric relationship}} between amino acids along bonds allow polypeptide folding to form the secondary structure of proteins
Published	07/30/2024	An polypeptide solution has the greatest buffering capacity when pH = {{c1::pK1 or pK2}}
Published	07/30/2024	Titration curve for Acidic and Basic AAspI for acidic AAs: pI = {{c2::1⁄2 (pK1 + pKR)}}pI for basic AAs: pI = {{c2::1⁄2 (pK2 …
Published	07/30/2024	{{c1::Column Gel Filtration or Size Exclusion Chromatography or Column Chromatography::AA and Protein Separation Method}}Principle: Proteins of differ…
Published	07/30/2024	{{c1::Chaperones::Auxillary Proteins}} - Helper protein that stabilizes transitory intermediates of folding proteins
Published	07/30/2024	{{c1::Disulfide Isomerases::Auxillary Proteins}} - Facilitate formation of disulfide bonds that stabilizes the protein’s native conformation
Published	07/30/2024	{{c1::Cis-Trans Isomerases::Auxillary Proteins}} - Convert cis to trans isomers and vice versa
Published	07/30/2024	Myoglobin is a prime example of a {{c2::tertiary}} protein structure, and it is formed by a {{c1::conjugated}} protein with a {{c1::non-protein heme}}…
Published	07/30/2024	Peptide bonds are {{c1::r::non-r/r}}igid
Published	07/30/2024	Tertiary level proteins are stabilized by the following:{{c1::H BondsHydrophobic InteractionsElectrostatic/Ionic InteractionsDisulfide BondsMetal Ion …
Published	07/30/2024	{{c1::Aromatic}} amino acids are often found in beta-pleated sheets, because these structures provide adequate space for rings of the R-group.
Published	07/30/2024	B-bends and b-turns contain {{c1::4}} amino acids with an internal H bond between the {{c1::1st}} and {{c1::4th}} amino acid, facilitating a tight 180…
Published	07/30/2024	Based on the direction of the interacting segment of the polypeptide chain, pleated sheets can be oriented as {{c2::parallel}} or {{c2::antiparallel}}…
Status	Last Update	Fields