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26 Cards in this Set
- Front
- Back
Protein folding Gen Info
1. Primary Structure 2. Secondary Structure 3. Tertiary Structure 4. Quarternary Structure |
Gen: Stabilized by non-covalent bonds (H-bonds) Folding occurs to energetically favorable state.
1. Amino Acid residues 2. Beta sheets and Alpha Helices, turn 3. Folded petptide 4. Assembled polypeptide subunits - usually bury the majority of hydrophobic side chains |
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Oxygen binding by myoglobin
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Myoglobin binding mechanism means it needs really low pO2 to unbind. Typical capillary O2 concentration is 30mmHg. Typically during vigorous exercise will dip below 10mmHg. Allowing myoglobin to release O2.
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Oxygen binding by hemoglobin
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Small change in oxygen concentration results in a large change in oxygen binding. Cooperative Binding.
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Bohr Effect
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Lowering pH favors the T-State. Tissues in need of O2 have lower pH. Releasing more O2.
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CO2 - Hemoglobin -
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80% of CO2 travels in plasma as HCO3- > catalyzed by carbonic anyhdrase
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2,3- BPG
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Upregulated by glycolysis, in higher altitude. 2,3 BPG binds to partially deoxygenated hemoglobin, allosterically upregulating bound O2
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Transcription
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RNA Polymerase I II III - add onto the 3' end of nascent product.
Read template strand.mRNA builds in a 5' to 3' direction. Complimentarity - anti parallel double stranded helix. |
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DNA Binding Proteins
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Short recognition molecules on DNA.
Interact with each other. (More at the party longer they stay) Not necessarily enhancers or silencers. They just bind, then the complex they form will recruit co-activators or co-repressors Multiple factors therefore cooperate to increase or decrease the probability that a polymerase will be recruited and transcription will occur. Allows the level of transcription to be controlled over a wide range of values. |
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Beta globin locus
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Regulated so that subsets come on and then are repressed in a developmental pattern.
A single enhancer or control locus is the key to regulation. |
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Mutations in genes can occur....
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-Promoter mutations lead to decreased transcription
-Splice site recognition or splice junction mutations lead to inappropriate splicing of the primary transcript into mRNA -Exon mutations lead to decreased translation, decreased protein stability, or altered protein function |
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Consider where mutations occur in gene and how that would play out clinically.
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Hemoglobin as an example.
Things to consider: missense mutations in introns and exons. Splice-site mutations, promoter mutations, nonsense mutations, frameshift mutations, more? |
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Discuss the regulation of Transcription
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Discuss 4 ways to regulate transcription and how they interact.
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Complex Diagrams and how to easily understand them
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Diagramming Example
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We can use the wiring diagram to generate hypotheses:The effect of the HDAC inhibitor suggests that some cancers result from altered expression of tumor suppressor genes.
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Explain the delta-ALA Synthase Mechanism
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Vitamin B6 = Pyridoxal Phosphate (PLP)
Binds to Lysine248 of delta-ALA-Synthase. Activates Glycine to neutrophillically attack succinyl CoA |
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Enzyme Catalysis: Substrates bind to enzyme ________.
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active sites
Where chemical transformations occur. |
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Active site amino acids often act as_____ and_____ in the reaction.
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acids and bases
enzyme activity is often pH dependent |
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Reaction specificity depends on _________.
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active site structure.
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Many reactions require more chemical capabilities than amino acids can provide. These are called:
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cofactors or coenzymes. (often vitamins and minerals) B6 and B5 in delta ALA is an example.
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Enzyme Catalysis: Define - Transient intermediate
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During reaction intermediates can form which contain covalent bonds.
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Define - Catalysis
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lowering the free energy of the transition state.
Enzymes alter the kinetics, not the thermodynamics of the reaction. Thus the speed at which the products and substrates reach equilibrium. |
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Define: Vmax
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the rate at which a particular enzyme, at a particular concentration, catalyzes a reaction when it is saturated with substrate.
varies with the concentration of the enzyme present |
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Define: Km
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The concentration of substrate required for a particular enzyme to catalyze the reaction at half the maximal rate. This is a constant and does NOT vary with enzyme concentration.
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Define: kcat
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turnover number for an enzyme
kcat is independent of enzyme concentration. |
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Define: kcat (again)
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