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66 Cards in this Set
- Front
- Back
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Polysaccarides are formed via?
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Condensation rxn's
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The bond that results from a condensation rxn of monosaccharides forming polysaccharides ?
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Glycosidic bond
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Lipids include?
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fatty acids, triglycerides, and phospholipids
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when water clusters around polar and ionic molecules, this is known as?
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hydration
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A hydrogen bond distance is defined as?
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The distance between the hydrogen bond donor and the hydrogen bond acceptor. (not between the hydrogen and the acceptor)
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Cells need to be buffered because?
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they need to maintain a specific ph, Usually close to 7, to keep biomolecules in their optimal odic state.
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Strong acids and bases completely dissociate in a dilute aqueous solution,True or False?
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True
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Which of the four is not considered part of the primary structure of a protein? 1-covalent bonds between amino acids, 2-hydrogen bonds formed between amino acids at distant positions with the peptide, 3-disulfide bonds, 4-covalent modifications to AA side chains.?
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2- hydrogen bonds that are formed between amino acids located at distant positions within the peptide are not part of primary structure.
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What is the importance of cysteine residues in the structure of proteins?
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Provides covalent links via disulfide bonds formation between parts of a protein molecule or between two different protein chains.
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how does SDS polyacrylamide gel electrophoresis work?
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SDS binds to the proteins proportional to the Molecular weight (about 1 sds every 2 AA) rendering the each protein having a large negative charge. the proteins are then ran through the electrophoresis using charge to allow proteins to flow through the polyacrylamide gel, separating them by MW(molecular weight).
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If the pH of a solution is below the pKa of a molecule (by more than 1 unit) then the molecule favors?
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protonation
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If the PH is above the pKa of a molecule (by more than one pKa unit) the the molecule favors?
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Deprotanation
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+/- 1 pKa unit; then the acid/base is?
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90-10% protonated/deprotonated
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+/- 0.5 pKa unit; then the acid/base is?
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75-25% protonated/deprotonated
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+/- 0.3 pKa unit; then the acid/base is?
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67-33% protonated/deprotonated
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Amino Acids polymerize via?
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condensation reactions (loss of H2O)
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when cysteine converts to cystine what has happened?
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The sulfa hydra groups of two cysteine R groups become linked forming a disulfide bond (primary structure).
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Name some factors that could be used to denature a protein?
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pH, Temperature, salts, Chemicals (HCl, detergents, Urea).
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Name two reagents used to reduce disulfide bonds?
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DTT, and BME (2-mercaptoethanol)
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Polyacrylamide gel electrophoresis can commonly be referred to as?
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PAGE
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SDS stands for?
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sodium dodecyl sulfate
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what are endopeptidases?
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enzymes that catalyze the cleavage of internal peptide bonds within the protein, adjacent to specific amino acids.
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Endopeptidase that cleaves peptide bonds at lysine(Lys,k) and Arginine (Arg, R).
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Trypsin
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Chemical that cleaves peptide chains at Methionine (Met, M)?
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Cyanogen Bromide (CNBr)
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HPLC stands for?
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High-Performance liquid Chromatography.
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separation and collection of peptide fragments is done by what process?
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reverse phase HPLC
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Frederick Sanger developed? and what does it do?
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1-floro-2,4-dinitrobenzene (FDNB). It attaches itself to the N-terminus of a residue and then hydrolyzes the peptide in order to determine what the residue at the N-terminis was. (this destroys the rest of the peptide).
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Edman degradation uses what type of machine to cary out its cycles?
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Sequenator
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Briefly explain how Edman degradation works?
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uses a chemical (phenylisothiocyanate) to attach to N-terminust and remove that peptide bond with its corresponding R group. without destroying the remaining polypeptied, that N-terminus Residue is then analyzed and this process is repeated until the entire polypeptide is sequenced (40-60 residues max).
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What is polymorphic?
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Having amino acid sequence variants with in a species population.
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enzymes that catalyze the hydrolytic cleavage of peptide bonds?
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Proteases (ex; trypsin, pepsin, cyanogen bromide).
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When sequencing large proteins FDNB is used for? (this is step 1)
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determining the N-terminus Amino Acid.
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Sequence positions that have no functional/structural role and are free to mutate are called?
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hypervariable residues.
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Critical sequence positions required for function, or to maintain 3D structure, do not change. these residues are called?
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Invariant residues.
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Sequence positions that can only change to residues with similar chemical properties are called?
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conservative residues.
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What is a homolog
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a gene/or protein sequence related to a second sequence by descent from a common ancestral sequence.
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Two constraints that limit proteins to their secondary structure are?
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The peptide bond (phi & psi), and the amino acid side chain (R group).
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How many residues are there per turn in a alpha helix?
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3.6
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Which amino acid largely disrupts an alpha helix and why?
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Proline, because the R-group of proline binds to its own nitrogen in the peptide bond, therefore it causes a kink in the alpha helix. Also because it bonds to the N in the peptide bond there is no existing N-H to hydrogen bond to a residue 4 AA away to stabilize the helix.
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How far away are positively charged and negatively charged amino acids found from one another within a alpha helix?
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Three (this for prevents the formation of an ion pair).
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how far away can interactions between amino side chains take place in a alpha helix?
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Three to four residues away.
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True or False- the Alpha helix has a Dipole moment?
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True
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Positively Charged amino acids are found at what end of an Alpha helix?
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the C-terminus
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Negatively charged amino acids are found at what end of an alpha helix?
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The N-terminus
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Which end terminus of an Alpha helix has a partial positive charge(electric dipole moment)?
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The N-terminus
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Which end terminus of the alpha helix has a partial negative charge (due to the electric dipole moment)?
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The C-terminus
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True or false? the last four amino acid residues on either side of an alpha helicie participate in hydrogen bonding?
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False
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Side chains point to which terminus in an alpha helix?
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The N-terminus (amino terminus)
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Describe amphipathic helicies?
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in amphipathic helices the one face of the helix is hydrophobic while the other is hydrophilic.
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Amphipathic helixes do not promote helix interactions, True or False?
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False.
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When a Amphipathic helix is in a aqueous solution what takes place?
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the hydrophilic portions of the helix interacts with the solution while the hydrophobic portions of the alpha helices interact with one another.
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When a amphipathic helix is interacting with a membrane what happens?
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the hydrophobic portions of the helices interact with the lipids of the membrane protein, while the hydrophilic portions are shielded on the inside and interact with on another.
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Two types of beta sheets, what are they?
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Anti-parallel and parallel
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How many residues per repeat in a beta sheet?
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2
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Where do hydrogen bonds take place in a beta sheet?
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between a carbonyl and nitrogen in the peptide-backbone, these can be distant in location of the peptide chain.
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Which part of the amino acids involved in a beta sheet are on the outside (sticking up and down in conformation)?
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the Side chains of each amino acid residue (R-groups).
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what is the average number of strands in a beta sheet?
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six
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average number of residues per strand in a beta sheet is?
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six
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True or False- Beta sheets can be either parallel or anti-parallel, but not a combination?
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False- beta sheets can be parallel, anti-parallel or a combination of the two.
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ideal phi, psi angles for anti-parallel β sheet? and hydrogen bonds are?
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-140, 135
Perpendicular |
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Ideal phi/psi angles for parallel beta sheets are? and hydrogen bonds are?
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-120,115
at 70 degree angles |
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In anti parallel beta sheets, beta turns are?
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hairpin (arrows point toward C-terminus)
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what type of residues (amino acids) are found in beta turns?
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Glycine and proline
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in type I and type II where does the hydrogen bond take place?
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between residue 1 an 4
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Type II has what amino acid at position 3
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Glycine
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in type I turns what amino acid is in position 2
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Proline
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