Exam 3 biochem

A recurring theme in signal transduction is the capacity of a pathway to amplify the signal intracellularly. In response to the primary signal, cellular concentration of ______________ is often increased allowing these molecules to diffuse throughout the cell and amplify the signal.
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A recurring theme in signal transduction is the capacity of a pathway to amplify the signal intracellularly. In response to the primary signal, cellular concentration of ______________ is often increased allowing these molecules to diffuse throughout the cell and amplify the signal.
secondary messengers
A product of reaction "X", a thermodynamically unfavorable reaction, is consumed as a reactant in the favorable reaction "Y" such that the fre energy for the overall reaction of X->Y is -8.3 KJ mol^-1. This is an example of a(n) ________________ reaction.
coupled AND exergonic
A DNA double helix forms spontaneously in water and the structure is stabilized largely by _____________ and ________________.
hydrogen bonds and van der Waals forces
RNA polymerase requires a primer for synthesis.
false (only DNA requires this)
Although a small amount of ATP is generated during the first parts of glycolysis through ________________, the majority of ATP is subsequently generated during oxidative phosphorylation, a process powered by ___________________.
-generation of high phosphoryl-transfer molecules, an ion gradient
During oxidation-reduction reactions, a molecule that gains electrons has its oxidation state reduced while a molecule that loses electrons is said to be oxidzed.
-ture
-Reduction=gain electrons
-oxidation=lose
The essence of the intermediary metabolism is to harness the energy of carbon oxidation as ATP. The ultimate use of this energy is for biosynthesis, ________________, and _____________________.
mechanical work, active transport
ATP is the main currency fo intermediary metabolism since the hydrolysis of ATP to ADP is exergonic and the structure of the product leads to its high-phosphoryl potential. What are the four reasons that make this reaction thermodynamically favorable?
1. Inorganic phosphate has resonance and the double bond stabilizes the structure
2. increase in entropy (free energy)
3. electrostatic repulsion
4. stabilization by hydration
What is favored in the rxn: Phosphoenolpyruvate+ADP---> pyruvate+ATP ?
-the products (b/c phosphoenolpyruvate breakdown has greater exergonic rxn that ATP breakdown, so rxn moves away from Phosphoenolpyruvate
What is favored in the rxn: ATP+glycerol--->ADP+glycerol 3-phosphate ?
-the products
-ATP breakdown has greater free energy than glycerol 3-phosphate breakdown, so the rxn moves away from ATP
In nucleotide triphosphates, a nitrogenous base is attached to the ______________ carbon of the sugar and a triphosphate is attached to the ______________ carbon.C-1, C-5The primary amino acid sequence of proteins is encoded in DNA. mRNA is transcribed from the DNA coding strand and the message is brought to the ribosome for translation. The amino acid code is said to be degenerate because:64 potential codons encode 20 amino acids AND Most amino acids are coded by multiple codons__________________ encode protein domains and some new proteins arise over evolutionary time as a result of ________________.Exons, Exon shufflingAlthough __________________ formation between the DNA backbone and an incoming NTP is roughly neutral thermodynamically, hydrolysis of the inorganic pyrophosphate product drives DNA toward synthesis. These reactions are _________________.phosphodiester, coupledDNA synthesis goes in a 5'->3' direction while RNA synthesis is in a 3'->5' direction.falseDNA polymerases have an exonuclease domain that allows for corrective removal of mismatched bases while RNA polymerases do not have exonuclease activity.True (DNA polymerase needs exonuclease activity)The result of _____________ signaling is the trafficking of _____________ to the cell surface.insulin, glucose transportersInsulin receptor substrate proteins are adaptor proteins because their _____________ recognize receptor phospohtyrosines, but also serve a a substrate for the binding of _____________ through their own phosphotyrosines.SH2 domain, Phosphoinositide 3-kinaseMost of the transduction signaling pathway for EGF is amplified through activation of ____________ and turned off by the action of _________________.protein kinases, protein phosphatasesProtein kinases are recurring elements of signal transduction pathways since they move high-transfer-potential phosphoryl groups between inactive and active substrates. In the Beta-adrenergic pathway, the second messenger _____________ amplifies the adrenalin signal and ultimately activates _______________.Cyclic AMP, PKAInsulin and EGF are polypeptide signals of similar mas that are held in compact conformations through inter- and intrachain disulfide bonds. These similarities allow for cross-talk between the pathways so that each signal can initiate transduction of both pathways.FalseMeselson-Stahl showed that DNA replication is _____________________ (each parental DNA molecule serves as a template for replication) because over generations, the heavier nitrogenous isotope became ________________ in culture.Semiconservative, dilutedSome viruses, like the one responsible for HIV are called retroviruses b/c they use:viral-encoded reverse transcriptase to make DNA copy of their genomeGene expression is the transformation of DNA into functional molecules. Upon transcription in eukaryotes, a pre-mRNA is synthesized and must be processed before translation. Processing pre-mRNA molecules involves:addition of a 5'-CAP, Addition of a 3' polyA tail, and splicingTransfer RNA (tRNA) are the adaptor molecules of translation because of their structure. The 5'-end of tRNA's is phosphorylated. Indicate the functional components of structures A and B.-Structure A: the 3' end of tRNA is the site of amino acid attachment -Structure B: (the bottom of the middle loop) is the anticodonSignal transduction pathway must be able to turn off, and often the conditions to turn off the pathway are preset during pathway initiation. Four molecular mechanisms were discussed regarding shutting down the beta-adrenergic pathway after activation. One involves resetting the heterotrimeric G-protein, while three others involve the beta-adrenergic receptor itself. List the four mechanisms to reset the transduction pathway.1. GTPase activity hydrolyzing GTP to GDP (resetting G-protein) 2. Concentration of substrate falls (epinephrine decreases 3. Beta adrenergic receptor is phosphorylated 4. beta-arrestin binds and shuts down receptorGlycogen and starch are storage forms they have similar structure , but starch is more branched than glycogen .FalseMatch definitionAnomers and Epimers switchedSelectivity filters of ion channels-uncage water molecules from ions aqueous compartments -facilitate rapid diffusion across membranes by repulsionfusion of two phospholipid membranes is energetically unfavorable process that :-happens during receptor - mediated endocytosis -happens during vesicle fusion of neurotransmitter release -requires SNARE proteins______ and _______ contribute to membrane fluidity-fatty acid chain length -degree of unsaturation -types of phospholipids -cholesterol -protein content -membrane structureSecondary active transporters move ions across the membrane up their concentration gradientsPartly true and false, some ions are moved up and down gradientsOf fatty acid list , which saturated fatty acid have lowest melting tempMyristate , lower #carbons and least amt of double bonds = lowest melting pointDuring depolarization ______Na + into , becoming less negativeWhich AA most likely to be found in cytoplasm of membrane - bound proteinPhe (most positive Delta G) -in integral membrane protein, jumping from non-polar to polar environment -positive delta G because it wants to remain in environmentMembrane proteins and glycolipids flipping from the inner leaflet to outer leaflet of lipid bilayers causes membranes to be asymmetricFalse , not why asymmetric , flipping inner to outer is unfavorableISOMERSHave the same molecular formula but different structuresCONSTITUTIONAL ISOMERSDiffer in the order of attachment of atomsSTEREOISOMERSAtoms are connected in the same order but differ in spatial arrangementENANTIOMERSNonsuperimposable mirror imagesDIASTEREOISOMERSIsomers that are not mirror imagesEPIMERSDiffer at one of several asymmetric carbon atomsANOMERSIsomers that differ at a new asymmetric carbon atom formed on ring closure