Term
| Which carbon is the R group in amino acids attached to? |
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Definition
| IUPAC carbon #2, the alpha carbon |
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Term
| Amino acid diversity is dependent upon which aspect of the molecule? |
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Definition
| The R group - the rest of the molecule is considered the "backbone" |
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Term
| Which isomeric characterization comprises all amino acid constituents? |
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Definition
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Term
| Carboxylic acids are categorically which type of acid in aqueous solution? |
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Definition
| Bronsted-Lowry acids, donating a proton from pH (and thus pKa ranges) of 2-5. at pH of 2 or less, the carboxylic acid in the amino acid will be protonated, and at a pH of 5 or more, the carboxylic acid will be deprotonated |
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Term
| How does the amino group in an amino acid behave in aqueous solution? |
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Definition
| As a base - at pH ranges of 8 or less, the amino group remains protonated (NH3+), while at pH ranges of 9-10 or more, it becomes deprotonated (NH2). |
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Term
| Zwitterion concentration is peaked from ______ to ______ pH range. |
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Definition
| ~3 - ~8 or 9. This is because as the pH increases, the carboxylic acid gets deprotonated first (COO-) while the amino group remains protonated. Then, as it increases still, the amino group finally gets deprotonated. |
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Term
| Physiologic pH is 7.35-7.45, so which form (ionization) is most commonly observed in proteins in each functional group at this pH? |
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Definition
| The Zwitterion - the carboxylic acid is deprotonated, and the amino group remains protonated |
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Term
| The only secondary amino acid of the 20 is? |
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Definition
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Term
| The 3 aromatic amino acids are: |
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Definition
| Phenylalanine, Tyrosine, and tryptophan |
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Term
| The 2 alcoholic amino acids are: |
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Definition
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Term
| The 2 thiol amino acids are: |
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Definition
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Term
| The 3 basic amino acids are: |
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Definition
| Lysine, Arginine, and Histidine |
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Term
| What is the IUPAC name for Aspartame? |
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Definition
| N-L- α – Aspartyl-L-phenylalanine 1-methyl este |
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Term
| What is the abbreviated name for Aspartame? |
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Definition
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Term
| Two Cysteines linked together by a disulfide bond are called? |
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Definition
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Term
| Insulin is the smallest protein with ____# of amino acids, and it is held together in its tertiary structure by 3 cystine ________ linkages between the A and B chains |
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Definition
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Term
| What characteristic about the peptide bond limits the rotational ability of the molecule? |
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Definition
| the resonance contributes double bond character to the peptide linkage and this limits the rotational ability of that bond |
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Term
| Sigma bonds in the polypeptide backbone allow for rotation that gives rise to _________ _______________ |
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Definition
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Term
| What gives rise to secondary structures? |
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Definition
| bond angles in the primary structure |
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Term
| Alpha helices and beta sheets are stabilized by what kinds of bonds in the secondary structure? |
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Definition
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Term
| Water soluble proteins fold into shapes where the hydrophobic aspects of the tertiary structure are __________ and the hydrophilic aspects are __________ |
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Definition
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Term
| Beta-mercaptoethanol denatures proteins in what way? |
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Definition
| disrupting disulfide bonds |
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Term
| urea denatures proteins in what way? |
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Definition
| disrupting hydrogen bonds (secondary structure) |
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Term
| Anfinson's experiments with tertiary structure and dialysis demonstrated what? |
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Definition
| By adding beta mercaptoethanol, the tertiary structure was disrupted. by adding concentrated urea, the hydrogen bonds of the secondary structure were disrupted. then, removing these denaturing agents through dialysis proved that, in order for the ribonuclease to refold into its functional tertiary shape, the hydrogen bonds must form first to form the correct secondary structure, and then the disulfide bonds must form last to form the correct tertiary structure. if the disulfide bonds form first, then the protein will be stabilized in a shape that is not consistent with its functional shape, and its activity will be lost. thus, the urea must be removed from the solution first, allowing the hydrogen bonds to form, and then the beta mercaptoethanol can be removed allowing the disulfide bonds to form (tertiary structure) |
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Term
| Name 4 factors that can be used to ID a specific protein. |
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Definition
| Enzyme activity, metallic cofactor, color (fluouresence), binding affinity to certain substance |
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Term
| What step follows homogenization in protein purification? |
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Definition
| centrifugation - separating cellular contents by running centrifuge at different g-forces |
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Term
| HIghly soluble proteins must be spun at _______ g-forces to spin them out of solution. |
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Definition
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Term
| How does fetal Hb differ from adult Hb? |
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Definition
| There is a serine in place of the histidine, which is near the binding site for 2,3-BPG, significantly reducing the affinity for 2,3-BPG. Thus, a decreased affinity for 2,3-BPG gives rise to a higher affinity for oxygen, which effectively allows the fetus to draw oxygen across the placenta from the mother |
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Term
| What is the amino acid compositional change in sickle cell anemia? |
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Definition
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Term
| How does sickle cell anemia bring about higher reproductive fitness rates in regions rampant with malaria? |
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Definition
| the parasite needs high oxygen saturations to survive in the body, so sickle cells in the body that cannot be saturated with oxygen select for an ability to survive this parasite's infection |
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Term
| What is the amino acid compositional change in sickle cell anemia? |
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Definition
| the Hb has a valine substituted for glutamate at position #6 (valine is nonpolar hydrocarbon, whereas glutamate is highly polar). This is on the outside of the external portion of the Hb tetramer, and this results in "sticky" sites on the deoxy beta chains (weak van der waals forces bring valines together and stick together inappropriately). this only occurs during deoxy state though. then, once this "polymerized" form happens, then oxygen cannot bind to the red blood cell |
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Term
| How does sickle cell anemia bring about higher reproductive fitness rates in regions rampant with malaria? |
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Definition
| the parasite needs high oxygen saturations to survive in the body, so sickle cells in the body that cannot be saturated with oxygen select for an ability to survive this parasite's infection |
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Term
| How can the sickle cell trait be identified in the DNA? |
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Definition
| the Mstll restriction enzyme will cleave the gene at 3 sites with normal genes, but with sickle celled genes, only two cleavage sites are observed |
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Term
| What is the pKa of Glutamic and Aspartic Acid? |
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Definition
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Term
| What is the pKa of Cysteine? |
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Definition
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Term
| What is the pKa of Tyrosine? |
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Definition
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Term
| What is the pKa of Lysine? |
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Definition
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Term
| What is the pKa of Arginine? |
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Definition
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Term
| What are the 10 essential amino acids? |
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Definition
| Ile, Leu, Lys, Met, Phe, Tryp, Threo, Val, Arg, Histidine |
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Term
| What kind of reaction must take place in order to create a disulfide linkage between two cysteine's, making a cystine linkage? |
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Definition
| oxidation, and to reverse the reaction is reduction (sodium dodecylsulfate, lauryl sulfate, etc). |
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Term
| What is the difference between tertiary protein structure and quaternary structure? |
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Definition
| tertiary is overall (individual) protein shape and quaternary structure describes interactions between different individual proteins |
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Term
| Which atoms in a primary protein sequence participate in hydrogen bonds that stabilize the secondary structure? |
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Definition
| the carbonyl carbon and the amino nitrogen |
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Term
| At what positions in the protein primary sequence do hydrogen bonds form to make alpha helices? |
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Definition
| i + 4, so positions 1 and 5, 2 and 6, 3 and 7, etc... |
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Term
| Beta sheets in secondary structure can run both ________ and ________ to one another. |
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Definition
| parallel and antiparallel |
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Term
| In a beta sheet, which positions in the backbone will be hydrogen bonded to stabilize this structure? |
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Definition
| 1 and 2, 4 and 5, 7 and 8, 10 and 11, etc. (every 3rd position is not bonded to its adjacent strand) |
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Term
| How does differential centrifugation work? |
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Definition
| Take a sample and centrifuge for a certain time at a lower-end strength g-force, and the most dense cellular components will be the first to separate out. Then, steadily increasing the time and g-force for centrifugation for each of the previous centrifugation's supernatant will separate proteins out by decreasing density, then they can be assayed for function in various ways |
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Term
| In what order do cellular components spin out from centrifugation? |
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Definition
| nuclear fraction (low g-force, short time) -> mitochondrial fraction -> microsomal fraction (long time, high g-force) |
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