Biochemistry Exam 2

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invariant residue
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residues that cannot be changes: too critical to protein function
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conservative residue
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substitutes amino acid with similar polarity
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unconservative residue
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substitues amino acid with different polarity: very detrimental
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draw a cis and trans peptide bond. Which is more stable?
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Trans is more stable. _/ vs //
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How many residues per turn in an α-helix?
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3.6
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°A per turn in a α-helix?
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5.4 or. 54 nm
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For coils _______ residues appear at the ________ creating __________
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hydrophobic, 1st and 4th, a hydrophobic core
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What bonds form α-keratin?
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Disulfide cross-links
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What determines folding?
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The primary structure: it automatically folds into its lowest energy, most stable structure.
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What are the two bond angles of secondary structure?
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phi and psi on C and N respectively
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Where are the side chains on an α helix?
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On the outside of the helix
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What residues absolutely cannot be part of a α helix and why?
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Pro, Ile and Tyr form regular bond angles and add steric interference.
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What forms every third amino acid in collage?
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Proline
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What are the two types of β sheet and which is the most stable?
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Parallel and antiparallel: antiparallel is more stable.
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What is a β turn? What are they usually composed of?
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Strands that turn and twist to connect secondary structures, usually compose of proline and glycine.
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What are really long polypeptide strands divided up into?
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domains
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What detrmines teritary structure?
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Hydrophobic portions turn inwards, hydrophilic portions face the solvent
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Hyper variable residues are what? What causes them?
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residues that change randomly and aren’t important for function, caused by genetic drift
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homologous
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evolutionarily related proteins
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Most mutations are…
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deletereous
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Phylogenetic tree
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a map of evolutionary history using a.a. sequence
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orthologous
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homologous proteins generated by speciation
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gene segment duplication
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2 copies of a gene that are passed to their progeny: one copy can evolve a new function while counterpart retains the old function
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paralogous
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when two different proteins evolve from gene duplication
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pseudogene
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a gene that cannot encode anything as a result from gene duplication
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What is the primary sequence of collagen?
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Gly-Pro-HHyp
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What is the secondary sequence of collagen?
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A left handed helical conformation in a right-handed twist due to proline hindering natural α-helix formation.
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What is the tertiary sequence of collagen?
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Same as the secondary due to only one secondary configuration.
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The quaternary sequence of collagen?
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The form of the right-handed twist with a trple helix: Gly is in the center forming hydrogen bonds with pro
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Why doesn’t polylysine form a α-helix? How could you force it to?
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Lys’s positive charge repels each other, but at 10.5 or higher pH it would be neutrally charged and would form an α-helix
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How does x-ray crystallography work?
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It maps electron densities of crystallized proteins
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Why don’t the terminal residues of a polypeptide chain show up on x-ray crystallography?
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Residues near the ends of a polypeptide experience fewer intramolecular bonds and are therefore disordered (highly mobile) making them difficult to map.
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domain
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evolutionarily conserved sequence of over 200 amino acids
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domain shuffling… why is this superior to gene duplication?
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proteins domains are shuffled in the genetic sequence. proteins evolve this way more rapidly
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What does the rate of protein evolution depend on?
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The amino acid relevance to structure and function
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Draw an antiparallel β sheet and a parallel β sheet
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parallel: ↑↑↑ antiparallel: ↑↓↑
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Primary structure
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the amino acid sequence
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secondary structure
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repetetive interactions within the backbone
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tertiary structure
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hydrophobic interactions between side-chains
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quarternary structure
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multiple protein subunits interacting
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Why doesn’t the peptide bond rotate?
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The carbonyl resonates with the amid, forming a rigid double bond.
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What direction does the α helix turn?
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right-handed
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H-bonding occurs between the carbonyl groups of the nth residue with the peptide of the ________ in a α helix
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(n+4)th residue
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what connects parallel β-sheets to each other?
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β-hairpin turns?
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What is the structure of keratin?
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Two α-helices in a left-handed coil
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Sequence of keratin and bonding patterns
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ABCDEFG -> A nd D interact hydrophobically, while the other residues are polar
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How do you determine whether keratin is hard or soft?
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Hard keratin has a lot of disulfide bonds
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The most abundant vertebrate protein
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collagen
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What does Hyp need for synthesis?
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Vitamin C is a cofactor for it.
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At what resolution can you resolve individual atoms?
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1.1 °A
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What is the caveat of using crystals in X-ray crystallography?
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You image a “snapshot” of a protein’s conformation at a particular time.
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What are the limitations of 2D NMR?
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Can only image very small proteins at a low resolution.
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Why are polar uncharged residues sometimes found inside a protein?
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They can form hydrogen bonds with each other, which reduces their overall polarity
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What are the exceptions (3) to the “hydrophobic sidechain location” rule?
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Proteins within a plasma membrane, salt bridges, protein may have important function
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βαβ
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↑α↑
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β-hairpin
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↑↓↑ connected by β hairpin turns
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αα
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two α helices crossed over each other
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Greek key
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↑↓↑↓ forms a “greek motif”
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motif
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a combination of secondary structures
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topology
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a combination of motifs
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β-barrel
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made of β-hairpins
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jelly roll
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made of greek keys
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αβ barrel
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made of βαβ motifs
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hyperthermophile
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bacteria that grow at temperatures near 100°C
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mesophile
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organisms that grow at “normal” temperatures
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What enables proteins of hyperthermophiles to withstand denaturation?
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salt brides, and a large hydrophobic core
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Are mesophilic proteins maximally stable?
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No. The marginal stability of proteins is favored by natural selection because it helps proteins have a greater structural flexibility
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What bonds (intramolecular) are found in collagen?
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H-bonds between gly and pro, van der waals and hydrophobic interactions.
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What are the pros of subunits?
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Fewer translational errors
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dimer
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two monomers connected
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homodimer
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two of the same dimer
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heterodimer
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two different dimers
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trimer
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three monomers connected
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How stable is a native protein?
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Only slightly more stable than the denatured protein
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What primarily stabilizes a protein?
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Hydrophobic interactions
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How does pH denature?
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By changing ionization states
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How does salt denature?
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By breaking H-bonds (chaotropes)
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How does a detergent denature?
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By interfering with hydrophobic interactions
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Steps of protein formation?
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Secondary structure > hydrophobic collapse (molten globule) > tertiary structure > domains > monomer > quarternary structure
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folding funnel
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as a protein folds it goes from a state of high entropy/high energy state to a low entropy/low energy state
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chaperones
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proteins that assist with folding and use ATP
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examples of misfolded protein diseases
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alzeihmers and mad cow
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Year marshall university was founded?
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1837
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Myoglobin forms what kind of O2 binding curve?
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A hyperbolic one
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What are the two binding formations?
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T and R (deoxy and oxy)
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What is Hemoglobin’s O2 binding curve?
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sigmoidal
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What is the basic structure of myoglobin?
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8 alpha helices
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Heme’s structure?
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5 pyrolle rings connected by methene bridges
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What happens if heme is oxidized?
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It cannot bind to O2 and turns brown
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Why is CO toxic?
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It has higher affinity for a heme than O2
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What is myoglobin’s primary purpose?
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To facilitate oxygen diffusion
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What is YO2?
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“fractional saturation” the fraction of ligands bound to O2 with a max value of 1
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What is pO2?
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The partial pressure of O2, a convenient way of denoting O2 concentration
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Equation for YO2 for myoglobin?
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YO2 = pO2 / (K + pO2)
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K =?
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K = p50. A lower value of K denotes tighter binding.
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p50=? for myoglobin + definition
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p50 is when YO2=K, which is when 50% of binding sites are occupied.2.8 torr for myoglobin
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Sigmoidal curves signify…
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Cooperative interaction between binding sites
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Hyperbolic curves signify…
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Noncooperative interactions between binding sites
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Which subunits form the most contacts in hemoglobin?
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alpha to beta
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Hill equation
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YO2 = pO2^n/K^n + pO2^n
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hill constant
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for hemoglobin, = 3. If 1, there is no cooperativity
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Removing CO2 via hyperventilation does what to O2 distribution?
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Removing CO2 also removes protons from the blood, increasing the pH, increasing O2 affinity to hemoglobin, which will reduce distribution of O2 to muscle tissue.
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How many hemes are in hemoglobin?
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4
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How does O2 induce a conformational change?
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In the T state, the heme is “puckered” towards His F8. When O2 binds to His F8, to avoid a steric collision, the heme becomes planar. This in turn changes the tertiary structure, and because of the tightly coupled nature of Hb all of the subunits change to the R form, increasing affinity for O2
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The bohr effect
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ion-pair formation increases the pK of the ion-pair which increases proton affinity
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At high pHs, what happens to O2 affinity? Physiological significance?
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at high pHs, there is greater affinity for O2. At capillaries there is increased CO2 due to respiration. The CO2 decreases the pH, decreasing hb affinity for O2 allowing it to release O2 to tissues.
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BPG
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BPG decreases O2 affinity for the deoxy state at low pO2 (which has a large gap in the middle of it) so that the deoxy state doesn’t immediately rebind to O2 in capillaries.
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What causes sickle-cell anemia?
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a single glu instead of val in the 6th position of the beta subunit
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What does Hb-S do?
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it deforms erthythrocytes into a sickle shape because it is water-soluble in the T form
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Why does sickle cell anemia make one resistant to malaria?
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Deformed sickle cells are taken up by the spleen which have plasmodium inside them.
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Draw a sarcomere
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A sacromere has a M disk in the middle with thick filaments coming out. the length of the thick filaments is the A band. There are thin filaments attached to a Z disk. the length of the thin filaments is the I band. The space between the thin filament ends and the thick filament ends is the H zone
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Thick filaments are made of… Thin filaments are made…
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myosin…. actin
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Structure of myosin
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similar to alpha keratin, it is a long filament with a globular head
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What causes myosin’s conformational changes?
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the hydrolysis of ATP
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What are the two ends of actin?
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+ and -. The + end binds to the Z disc
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Tropomyosin and troponin do what?
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They regulate muscle contraction by blocking myosin binding to actin in absence of Ca2+
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Walk me through cross-bridge cycling….
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Actin starts out bound to myosin. ATP attaches to myosin, so myosin detaches to actin. Myosin hydrolyzes ATP in ADP and Pi. This causes the myosin head to cock towards the Z disc. Pi increases myosin affinity to actin, so the myosin binds to an actin monomer closer to the Z disc than previously. The myosin head then “power strokes” which moves the thin filament towards the M disc. ADP is released.
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Walk me through treadmilling.
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Subunits are added to actin microfilaments at the (+) end at the same rate that they are removed from the (-) end allowing cellular movement in one direction.
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Why can myosin molecules move more than 100 angstroms per power stroke?
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The myosin molecules do not power stroke simultaneously
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Why is actin polar while keratin is not?
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Actin goes “tail to head” in a long filament, while keratin does the reverse.
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IgM
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first secreted, most effective
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IgG
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most common
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IgE
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parasites and allergies
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IgD
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unknown function
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structure of immunglobulin?
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2 heavy chains (50-75 kD) and 2 light chains (25 kD)
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immunoglobulin fold structure?
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3-4 antiparallel beta sheets linked by a disulfide bond. 3 loops are hypervariable
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What accounts for diversity in antibody sequences
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somatic recombination occurs in B lymphocyte development, also, somatic hyper mutation during B-cell proliferation to increase antibody affinity

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