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67 Cards in this Set
- Front
- Back
There are over _ AA but only _ are coded only by DNA to appear in proteins
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300
20 |
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AA structure
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Carboxyl group
Amino group H Side chain |
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All AA have an alpha Carbon except proline due to it's
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Side pyrroline ring which includes both alpha amino and alpha carbon forces a bend in a polypeptide
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AA geometry
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Tetrahedral
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AA are stereoisomers, meaning they can rotate plane-polarized light. Aka _
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Enantiomers
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Though they come in L/D, majority are in the _ form
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L
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Aliphatic groups AA
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Alanine, valine, leucine, isoleucine, glycine, methione
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Aliphatic
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Saturated hydrocarbon side chains, hydrophobic (found in membrane)
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Aromatic groups AA
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Phenylalanine, tyrosine, tryptophan
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Aromatic
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Aromatic side chains, nom polar, hydrophobic, found in all membrane, buried in the protein core
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Neutral, Polar AA
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Serine, Threonine, Cysteine, Proline, Asparagine, Glutamine
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Neutral, Polar
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Hydroxyl or amide, reversible phosphorylation
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Acidic AA
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Asphartate, Glutamatic
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Acidic
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Neg charged, carboxylic ionized at pH 7
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Basic AA
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Lysine, Aginine, Histidine
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basic
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Pos charged, protonated at pH 7
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Amphoteric
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Basic and acid groups
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Zwitteron
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Dominant at pH 7. Neutral; charges cancel each other out
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Titrated to acidic
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Alpha amine is protonated, pos charged
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Titrated to basic
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Alpha carboxyl is deprotonated
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Overall charge of protein depends on basic/acidic actual charge on protein varies with _
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PH of the solution
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Henderson-Hasselbalch Equation
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HA <-> H+ + A-
Conjugate acid <-> conjugate base |
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Dissociation Constant (ka)
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Of weak acid. Equilibrium constant for The dissociation reaction. Half is dissociated.
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PH =
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-log[H]
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Isoelectric
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Intermediate b/t pk1and pk2; net charge 0
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Buffers
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Solutions that minimize a change in [H]; acid-base conjugate pair
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Maximal buffeting capacity
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Occurs at pH=pka
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Side chain reactivity of Cystine
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Oxidized 2cystines to form disulfide bonds, reduced by thiol reagents; bonds form protein structures
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Vasopressin vs. Oxytocin Spot #3
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Phe to IIe
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Vasopressin vs. Oxytocin Spot #8
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Arg to Leu
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1st Order
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Sequence of AA linked together by covalent peptide bonds. Planar.
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2nd Order
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Structure of polypeptide chain, determined by H-bond interactions b/t carbonyl oxygen of one and the amide of another.
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2nd Order is determined by _ nature of the peptide bond
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Planar
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Planar structure is stabilized by resonance b/t the C and N, confers _ restricting rotation
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Partial double band character on the peptide bond
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Ramachandran Plot
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Shows regular arrangement of AA that are located near to each other in the linear sequence
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A helix
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Stabilized by intra-H bonds formed b/t carbonyl oxygen and hydrogen attached to amide Hydrogen. 3.6 AA per turn
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A helix H bonds binding
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N + 4; H bonds to peptide 4 residues ahead
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B sheet
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H bonds formed b/t C=O of one peptide bond and the N of another. Inter-H bonds pleated b/c C-C bonds are tetrahedral. not planar.
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B turn
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Segments in which the polypeptide changes directions (Glycine and Proline)
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3rd Order
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Spontaneous stabilized by side chain interactions (non covalent)
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4th Order
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Formed by interactions b/t peptide chains. Held together by covalent forces.
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monomeric proteins
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proteins consist of a single polypeptide chain
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multimeric proteins
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proteins that consist of two or more polypeptide chains
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eghomodimer
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structurally identical
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heterodimer
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structurally totally unrelated
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Hemoglobin is held together by
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hydrophobic interaction, H-bonds and ionic interactions
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Hemoglobin structure
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a2b2 heterotetramer. Binding of O2 increases affinity for O2.
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cytochrome oxidase
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multimeric proteins. oxidase in the mitochondrial electron transport chain and the pyruvate dehydrogenase complex.
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Protein Denaturation
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results in the unfolding and disorganization of the protein’s structure and is commonly defined as any noncovalent change in the structure of a protein.
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Protein Denaturation effects these proteins structures
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the secondary, tertiary or quaternary structure of the molecules
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The most common observation in the denaturation process is the precipitation or _ of the protein
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coagulation
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Denaturing agents
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excess heat, chaotropes such as urea and guanidine hydrochloride, organic solvents, such as alcohol, mechanical mixing or shearing, strong acids or bases, such as HCl or NaOH, detergents, such as sodium dodecylsulfate and heavy metal ions such as lead and mercury that typically react with free sulfhydryl groups.
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Protein Purification
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cells are disrupted by grinding or homogenization in buffered isotonic solutions at physiological pH to minimize degradation.
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The Anfinsen Experiment
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determined how the primary structure of a protein determines its 2* & 3* structure
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The analysis of primary structure, or sequence analysis, reveals the effects of _ and _
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genetic mutations and shows homologies within families of proteins
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There are three major steps in the analysis of primary structure
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1) Amino acid composition
2) Fragment sequencing 3) Fragment linking |
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Amino acid composition is determined by quantitative analysis following _ by complete acid hydrolysis which cleaves all peptide bonds liberating the individual amino acid residues.
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protein digestion
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Fragment sequencing: Specific hydrolysis by chemicals or proteolytic enzymes cleaves peptide bonds at specific residues to produce small, easy-to-manage peptide fragments. This is followed by _
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Edman degradation of each fragment to identify each of the amino acid residues and their sequence in the peptide.
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Trypsin hydrolyzes the carboxyl side of _ and _
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K and R residues
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Chymotrypsin hydrolyzes the carboxyl side of
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aromatic residues (F, Y and W).
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Cyanogen bromide cleaves on the carboxyl side of
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M
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Edman degradation involves the sequential removal and identification of N-terminal amino acid by reaction with _; it is used for peptide sequences up to 50-60 residues long.
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phenylisothiocyanate
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Fragment linking
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Cleavage of the protein at different points produces overlapping fragments
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Methods for studying primary structure
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Mass spectrometry
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Mass spectrometry
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used to identify molecular mass and sequence of polypeptides
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Methods for studying secondary structure
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CD spectra
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Methods for studying tertiary structure
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X-ray crystallography
NMR |