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323 Cards in this Set
- Front
- Back
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In serpentine receptors, the carboxyl terminmal undergoes what?
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Reverisible Ser/Thr phosphorylation
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Ligand binding causes a what?
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A confomational change which permits G-protein binding
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Activated G-proteins do what?
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• Activate or inhibit effector enzymes
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What is an example of a serpentine receptor? And what is it mediated by?
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β-Adrenergic Receptor Mechanism
• Mediated by epinephrine |
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What is an agonist and antagonist?
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• Agonist-structural analogs that bind to a receptor and mimic the normal ligand (activators)
• Antagonist-analogs that bind to a receptor and block its activity (inhibitors) |
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What are the 4 heterotrimeric G-proteins?
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Gs (stimulatory), Gi (inhibitory), Gr, Gq
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What is adenylate cyclase?
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An integral protein (not a signaling molecule)
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What are the steps to the β-Adrenergic Receptor Mechanism?
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1. Epinephrine binds to receptor causing a conformational change
2. The conformational change promotes binding of Gs to receptor 3. Gs-α GTP activates adenylate cyclase 4. Adenylate cyclase converts ATP to camp (second messenger) 5. G-proteins recycle, re-associate |
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What happens during desensitization of the β-Adrenergic Receptor Mechanism
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1. Receptor/ligand complex binds β-ARK
2. β-ARK phosphorylates a Ser on receptor 3. phosphorylation induces binding of β-Arrestin 4. receptor-arrestin complex enters the cell by endocytosis |
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What does arrestin do?
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• Prevents receptor interaction GTP-protein
• Recycles receptors • Signals for endocytosis |
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Describe the downstream effect.
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Conversion of glycogen to glucose through cAMP
• cAMP activates cAMP-dependent protein kinase (PKA) • PKA molecules activate other enzymes • Amplification |
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What is PKA and what does it do?
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• An Allosteric enzyme
• Regulates a number of enzymes via Ser/Thr phosphorylation |
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What are PKA and PKC?
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Antagonists
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What does phospholipase C do?
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Converts PIP2 to diacylglycerol and IP3 (2 important 2nd messengers)
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What happens in plasma hormone receptors with to intrinsic enzyme activity?
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1. hormone binds to receptor
2. GDP is exchanged for GTP on Gq 3. Activated Gq activates membrane phospolipase C 4. IP3 diffuses into endoplasmic reticulum and causes the release of intracellular Ca2+ 5. Ca2+ binds to PKA 6. PKA becomes insoluble and associates with membranes 7. Diacylglycerol binds to PKC as a cofactor-PKC is activated 8. PKC phosphorylates a number of substrates on Ser/Thr |
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What are some responses to increased intracellular calcium?
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• Exocytosis
• Muscle contraction • Cytoskeletal rearrangements • PKA and phosphatase activity increases • Activation of calcium channels • Calcium binding by intracellular proteins |
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What is Calmodulin?
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Ca2+ binding protein
• 4 binding sites • Ca2+ binding is cooperative (hill plot, similar to Hb) • A subunit of phosphorylase b and of Calmodulin-dependent Kinase |
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Effect or responses caused by extracellular signals depends on what?
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• The tissue or cells to which ligand binds
• The specific GTP-binding protein activated • The 2nd messenger species generated • The protein kinase activated |
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What is phosphorylation?
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Phosphoryl group transfer
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What is the feature of virtually all signal transduction mechanisms?
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Protein phosphorylation
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What are characteristics and tendencies of protein kinases?
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• Tend to remain in the cell location containing their activators and their substrates
• Tend to be cell and tissue specific • May be expressed as several isozymes (different form of same enzyme) |
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What important cell process is controlled by phosphorylation?
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Cell division
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What are modules?
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Binding site groups (often multivalent) and domains on signaling molecules the contribute to propagating signal and regulating them.
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What kind of binding domain does IRS-1 have?
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PhosphoTyrosine Binding Domain (PTB)
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When does signaling happen?
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When new binding sites are produced from groups of proteins
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IRS-1 can only bind to _______ after it is phosphorylated.
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Grb-2
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What are rafts?
What do they include? |
Regions of membranes “enriched” in certain proteins and lipis
• Some sphingolipids and sterols • Some GPI-linked proteins, Tyr-kinases |
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Rafts contain what?
And this does what? |
Contain tight concentrations of signaling molecules.
Makes responses more effective |
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What is the refractory period?
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In neuronal signaling, the time period during which receptors do not respond to ligand
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Why do steroid hormones need to be bound to a serum binding protein?
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Because they are hydrophobic
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How do steroid hormones pass throught the lipid membrane? What are they held together by?
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Carrier molecules
Held together by weak interactions |
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What do steroid hormones do at their target tissues?
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1. Pass through membrane by simple diffusion
2. Bind to specific receptor proteins in the nucleus with good affinity |
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Why does hormone binding trigger a conformational change?
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So they become capable of interacting with specific regulatory sequences in DNA called Hormone Response Elements (HRE).
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What effects do steroid hormones have on gene transcription?
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They enhance or inhibit it.
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How long does it take for a full response to occur?
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Hours to days
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What is Tamoxifen and what does it do?
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It is a breast cancer treatment.
It competes with estrogen binding (but does not enhance gene expression). |
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What important cell process is controlled via phosphorylation?
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Cell division
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What is Cyclin-dependent Kinase?
How many different CDKs do animals have? |
A heterodimer of Cylcin + Catalytic subunit
8 |
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What is cyclin and where is it synthesized?
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A regulatory subunit associated with the dimer (not required).
Synthesized in cells |
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How is cyclin an example of amplification and specificity?
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• Amplification- increases catalytic activity
• Specificity- animal cells have 10 different cyclins |
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What does CDK do?
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It phosphorylates specific proteins at timed intervals to orchestrate cell division.
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CDK activity is stimulated by what?
CDK activities occur with what? |
• Stimulated by cyclin
• Occur with regular oscillations |
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What is a destruction box and what does it do?
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It is a motif
Causes cyclin to bind several molecules of Ubiquitin Ubiquitin-tagged proteins are degraded by proteosomes. |
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What causes cyclin degradation?
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CDK phosphorylating DBRP (destruction box recognition protein)
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How is most energy in a system lost?
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As heat
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Biological energy flow requires what?
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• Conservation of energy
• Efficient utilization of free energy • A constant source of energy |
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Define bioenergetics
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• The quanititative study of biological energy transduction (movement of energy from one molecule to another one)
• The study of chemical processes that yield or use energy |
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Define: Gibb’s Free Energy, Enthalpy, Entropy
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• Gibb’s Free Energy (ΔG)- the amount of energy capable of doing work during a reaction.
• Enthalpy (ΔH)- how many bonds and what kind are made and broken during a reaction. o Exothermic=release of heat • Entropy (ΔS)- Quantity of randomness or order; increases with disorder |
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Relate free energy, enthalpy, and entropy in an equation.
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ΔG=ΔH-TΔS
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What are the symbols for standard transformed conditions?
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ΔG’° and K’eq
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How are ΔG’° and K’eq related?
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ΔG’° = -RTln K’eq
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What are ΔG’° and ΔG?
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The maximal free energies available under ideal conditions
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What lowers the activation energy?
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Catalysis
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If there is a common intermediate, what can you do with ΔG and Keq?
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ΔG-add
Keq-multiply |
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Reactions in which the terminal phosphoryl group of ATP is transferred to an acceptor molecule to produce a covalent bond is an example of what?
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Group tranfer (NOT simple ATP hydrolysis)
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What are the theoretical and actual energy values obtained from hydrolysis of ATP? Why are they Different?
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Theoretical: -30.5 kj/mol
Actual: -51.5 kj/mol ATP and ADP form a complex with MG2+ and free energy change is depended on that complex. |
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What is Phosphorylation Potential?
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Actual energy available for biochemical reactions.
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What class of reactions does ATP use to provide energy for biological processes?
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Group Transfer
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In hydrolysis reactions, why are the products more stable than the reactants?
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1. Bond strain due to electrostatic repulsion is relieved by charge separation
2. Products are stabilized by: a. Ionization b. Isomerization c. Resonance |
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A large and negative free energy (ΔG’°) results from coupling what?
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1. Hydrolysis of the P-O bond
2. Formation of a reactive intermediate 3. Summation of all free energies |
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What are the 3 different groups ATP can transfer to other molecules in reactions?
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1. ADP (phosphoryl) α
2. AMP (pyrophosphoryl) β 3. PPi (adenyl) γ |
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What is adenylylation and what is an example?
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When ATP transfers adenylate as an adenylyl group to the nucleofile
Ex) fatty acid activation before oxidation |
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What is a transphosphorylation?
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Transfer of a phosphoryl group
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What are phosphoryl group donors?
What is the primary one? |
All nucleoside triphosphates (NTPs) and deoxynucleoside triphosphates (dNTPs)
ATP |
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What are examples of enzymes that carry phosphoryl groups from ATP to the other nucleotides?
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• Nucleoside disphosphate kinase
• Adenylate kinase • Creatine kinase |
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What happens to the transfer of phosphoryl group with nucleoside diphosphate kinse?
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1. Phosphoryl group from ATP transfers to an active site on His
2. Phosphoryl group transferred from enzyme His to NDP or dNDP |
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What happens in transphosphorylation with adenylate kinase?
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• ADP accumulates under periods of high metabolic activity (interferes with muscle contraction)
• Adenylate kinase removes the ADP |
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What is oxidation and reduction?
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• Oxidation-electron loss
• Reduction-electron gain |
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The flow of electrons in an oxidation/reduction reaction is dependent upon what?
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The differences in affinity for electrons between 2 molecules
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What is the force generated as a result of differences in electron affinity is defined by what? Measured in what?
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Defined by Electromotive Force (EMF)
Measured in Volts |
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What is a dehydrogenation reaction and what enzyme catalyzes?
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Conversion of an alkane to an alkene
Catalyzed by dehydrogenases |
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What is a reducing and oxidizing agent?
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• Reducing- electron donor (reductant)
• Oxidizing- electron acceptor (oxidizer) |
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What is defined as a reducing equivalent in biological systems?
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One electron moving by any of the 4 mechanisms of electron transfer
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How many reducing agents do most biochemical enzymatic dehydrogenations transfer?
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2
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What are the 4 mechanisms of electron transfer?
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1. Direct transfer of the electron
2. Transfer of a hydrogen atom (acid base) 3. Hydride ion transfers 4. Direct combination with oxygen (hydrocarbon is the e- donor and oxygen is the e- acceptor) |
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What is the standard reduction potential?
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E°, Measure of the affinity of the electron acceptor for a pair of electrons
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What is the Nernst Equation?
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E=E° + [(RT)/(nF)]ln(e- acceptor)/(e- donor)
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What equation relates standard reduction potential to free energy?
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ΔG=-nFΔE
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What are water-soluble electron carriers that move between several enzymes?
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NAD+ and NADP+
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What are water-soluble electron carriers that do NOT move between several enzymes, but serve as prosthetic groups?
What do they bind to? |
FMN and FAD (flavonucleotides)
Bind to flavoproteins |
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NAD+ and NADP+ (names)
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Nicotinadmide Adenine Dinucleotide
Nicotinadmide Adenine Dinucleotide Phospohate |
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What are NADH and NADPH derived from?
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Niacin
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What does difficiency of NADH and NADPH cause?
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Pellagra, dermatitis, diarrhea, dementia, death
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When a substrate oxidizes, what happens to the 2 H+ it gives up?
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1. NAD+ or NADP+ accept a hydride ion
a. Both become reduced b. Both forms absorb light at 340 nm 2. The other proton is released into the environment and buffered. |
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What functions to NADH and NADPH have?
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• NAD+>>NADH, favors flow of electrons to carrier
o Catabolic oxidations • NADPH>>NADP+, favors transfer of electrons to substrate o Anabolic reductions |
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What are flavin nucleotides (FMN and FAD) derived from?
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Riboflavin
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FMN and FAD (names)
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Flavin Mononucleotide
Flavin Adenine Dinucleotide |
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Why do FMN and FAD participate in a wider range of reactions than NAD and NADP?
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They accept 1 or 2 electrons
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What bio molecules are membranes composed of?
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• Proteins
• Polar Lipids • Carbohydrates |
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Constituents of membrane lipids vary with what?
Not with what? |
• Vary with climate
o Nature of cell membrane is temp dependent • NOT with diet o Determines what is available, not how it is used |
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The fact that each membrane source has characteristic lipids implies that there are regulatory controls on what?
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The fact that each membrane source has characteristic lipids implies that there are regulatory controls on what?
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Which membrane lipids are found on the outer monolayer of the plasma membrane?
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• Phosphatidylcholine
• Sphingomyelin |
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Which membrane lipids are found on the innermonolayer of the plasma membranes?
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• Phosphatidylethanolamine
• Phosphatidylserine • Phosphatidylinositol • Phosphatidylinolsitol 4-phosphate • Phosphatidylinositol 4,5-bisphosphate |
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Prosthetic group of Lipoproteins and example
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• Lipids
• Ex) B-lipoprotein of blood |
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Prosthetic group of Glycoproteins and example
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• Carbohydrates
• Ex) Immunoglobulin G |
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Prosthetic group of Phosphoproteins and example
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• Phosphate groups
• Ex) Casein of milk |
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Prosthetic group of Hemoproteins and example
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• Heme (iron pophyrin)
• Ex) Hemoglobin |
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Prosthetic group of Flavoproteins and example
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• Flavin nucleotides
• Ex) Succinate dehydogenase |
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Prosthetic group of Metalloproteins and examples
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• Iron- Ferritin
• Zinc- Alcohole dehydrogenase • Calcium- Calmodulin • Molybdenum- Dinitrogenase • Copper- Plastocyanin |
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What is meant by the term “functional asymmetry” in membrane proteins?
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Protein domains exposed on one side of the bilayer are different from those exposed on the other side.
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What does “semi-permeable” mean in reference to the lipid bilayer?
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It is permeable to nonpolar compounds.
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Which way do nonpolar and polar (head groups) face on the lipid bilayer?
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• Nonpolar-internally
• Polar-outward |
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Why is the term “fluid mosaic” used to describe the lipid bilayer?
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It is constantly moving due to weak (noncovalent) interactions
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What does the term “sidedness” mean in reference to the lipid bilayer?
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The way the proteins are distributed causes the membrane to be asymmetric.
• Carbohydrate is always on outside, it is normally attached to a protein/glycoprotein. |
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Proteins interspersed through the lipid bilayer are stabilized by what?
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Hydrophobic interactions
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What are the 3 classes of membrane lipids that biological membranes are composed of?
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1. Glycerophospholipids
2. Sphingolipids 3. Sterols |
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What are the 3 structures that membrane lipids form and which is the most stable?
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1. Micelle
2. Bilayer 3. Liposome Liposome is most stable |
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What are the individual subunits of micelles and bilayers?
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What are the individual subunits of micelles and bilayers?
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Micelles form easily from what?
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1. Free fatty acids
2. Lysophospholipids 3. Detergents |
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What 2 factors affect the degree of mobility in a membrane?
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1. Temperature
2. Lipid composition |
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What state do lower/higher temperatures favor and what state is preferred by cells?
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• Low-paracrystal
• High-fluid state (liquid disordered) • Gel is preferred by cells (liquid ordered) |
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What is phase change defined as?
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Transition Temperature
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What does adding more unsaturated fatty acids do to a membrane lipid?
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It lowers the transition temperature
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What do sterols do to the transition temperature of a membrane lipid and why?
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Increase transition temperature
• Prevent ordering of acyl chains • Favors liquid-ordered state |
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What are the 3 levels of membrane lipid mobility? (example of the rare one)
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1. Lipid acyl chains move freely, but whole lipid does not move
2. Lipid acyl chains move freely and rapidly through the plane of the membrane 3. Mobility from one side of the bilayer to another (rare, requires enzyme: flipase) Ex) phospolipid biosynthesis in bacteria |
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What feature about the primary structure of a protein is considered evidence of a trans-membrane domain?
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The presence of unbroken sequences of more than 20 hydrophobic residues in a membrane
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How can the “sidedness” of a protein be checked?
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Hydropathy Plot- Used to predict trans-membrane domains of proteins (not absolute). Amino sequence often indicates secondary structure (α-helixes, β-sheets).
When secondary structure of proteins is known, hydrophobicity is revealed. |
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Hydropathy Index
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A scale that expresses the relative hydrophobic and hydrophilic tendency of a chemical group
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What are the 4 functions of metabolic pathways?
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1. Obtain chemical energy from capturing solar energy or from degradation of energy rich nutrients.
2. Conversion of nutrient molecules into cellular precursors. 3. Polymeration of monomeric precursors into macromolecules. 4. Synthesis and degradation of specialized cellular biomolecules. |
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What is catabolism?
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the degradative phase of metabolism where organic nutrient molecules (carbs, fats, proteins) are converted into smaller, simpler end products (lactic acid, CO2, NH3)
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What happens in a catabolic pathway?
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It releases energy, some is conserved in the form of ATP and NADH, NADPH, FADH2, the rest is lost as heat
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What is anabolism?
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small, simple precursers are built into larger and more complex molecules (lipids, polysaccharides, proteins, nucleic acids)
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What does anabolism require?
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an input of energy, usually in the form of phosphoryl group transfer of ATP and reducing power of NADH, NADPH, FADH2.
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How were the metabolic pathways elucidated?
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1. Metabolic inhibitors, growth studies, and biochemical genetics
2. Isotopes-atoms with same number of protons but different number of neutrons-specific labeling wihtout changing the chemical properties of the metablites |
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What Precurser of Heme was figured out by an isotope?
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Glycerine
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What can you use to detect isotopes?
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NMR
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What does the P-NMR do?
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monitors levels of ATP, ADP, and Pi; it is useful to study energy metabolism in muscle.
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What are the 5 general principles of Metabolic Pathways?
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1. Metabolic Pathways are irreversible
2. Catabolic and Anabolic Process must differ 3. Every metabolic pathway has a committed step (usually the rate determining step) 4. All metabolic pathways are heavily regulated 5. Metabolic pathways in eukaryotic cells occur in specific compartments |
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What are metabolic pathways irreversible?
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It is a highly exergonic reaction-it goes to completion
If a highly exergonic reaction is part of a multistep pathway the entire pathway is irreversible |
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Why does every metabolic pathway have a committed step?
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early in each pathway, there is an irreversible reaction which "commits" the intermediate that is produces to continue down the pathways.
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What are metabolic pathways regulated by?
What is usually regulated? |
Regulated by the law of supply and demand.
The rate limiting step (usually the committed step) is usually regulated |
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Why do metabolic pathways in eukarytic cells occur in specific compartments?
Example? |
different metabolites can operate in different locations and in different pathways.
Example: ATP is synthesized in mitochondria but used in cytosol Acetyl-CoA is produced in mitochondrion but utilized in cytosol |
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What metabolic pathways occur in the mitochondria?
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*citric acid cycle
*electron transport *oxidative phosphorylatioins *fatty acid oxidation *amino acid breakdown |
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What is caveolin and what does it do?
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It is an integral membrane proteins with 2 globular domains connected by a hairpin-shaped hydrophobic domain.
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Where does caveolin bind?
What does it bind? |
To the cytoplasmic leaflet of the plasma membrane.
It binds cholesterol in the membrane. |
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Caveolae involve what?
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Both leaflets of the bilayer
Cytoplasmic-where the caveolin globular domains project Endoplasmic-typical sphingolipid/cholestrol raft with associated GPI-linked proteins |
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What cellular functions is caveolae implicated in?
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What cellular functions is caveolae implicated in?
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Describe the movement of Glucose across the intestinal epithelial cells
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1. glucose enters cells on the apical (luminal side)
Na+ gets in at the same time (Na+/glucose symporter) 2. glucose moves through the cell and passes into the blood via GLUT2 3. Na+/K+ transporter continues to pump Na+ outward to maintain the Na+ gradient that drives glucose uptake |
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What are examples of a Gated Ion Channel?
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Na+/K+ ATPase
Nicotinic Acetylcholine Receptor Neuronal Signaling |
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What are examples of Receptor enzymes?
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Insulin Receptor
Guanylyl Cyclase |
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What are examples of Steroid Hormones?
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Regulation of Transcription
Tamoxifen Regulation of the cell cycle by protein kinases |
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What are the main points of the Insulin Receptor Signal Transduction?
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1. Autophosphorylation
2. Tyr-Kinase activity 3. IRS-1 is phosphorylated 4. Sequential formation of complexes 5. Low Mr G-proteins are activated 6. Protein phosphorylation cascade 7. Nuclear event |
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What are the responses of the insulin signal transduction pathway?
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*inducing the expression of proteins
*glycogen synthesis |
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What is the Scatchard analysis used for?
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Estimation of the dissociation constant (Kd)
Number of receptor-binding sites in a given preparation |
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What can we find with the Scatchard analysis?
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Kd
Bmax-then number of unoccupied sites |
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What are SH2 domains and what do they do?
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(insulin receptor signal transduction)
Bind phosphotyrosine residues with high affinity Present on many signaling proteins |
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What do G-proteins do? What is it stimulated by?
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Stimulated by activated receptor
Exchanges bound GDP for GTP |
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What are the 5 Main Classes of Reactions that cells use in Metabolic Pathways?
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1. Oxidation-reduction
2. Reactions that make or break C-C bonds 3. Internal rearrangements, isomerizations, and eliminations 4. Group Transfer Reactions 5. Free radical Reactions |
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Phosphoryl groups yield energy as what?
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Group transfer reactions
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The PPi product of adenylylation is hydrolyzed by what?
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Inorganic pyrophosphatase
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Reaction that Nucleoside diphosphate kinase catalyzes
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ATP + NDP (or dNDP) ←→ADP + NTP (or dNTP) G’°= 0
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Reaction that adenylate kinase catalyzes
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2ADP←→ATP + AMP G’°= 0
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Reaction that creatine kinase catalyzes
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ADP + PCr←→ATP + Cr G’°= -12.5
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Reaction that polyphosphate kinase-1 catalyzes
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ATP + polyPn ←→ ADP + polyPn+1 G’°= -20
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Reaction that polyphosphate kinase-2 catalyzes
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GDP + polyPn+1 ←→ GTP + polyPn
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What metabolic pathways occur in the cytosol?
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Glycolysis, pentose phosphate pathway, fatty acid biosynthesis, gluconeogenesis,
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What metabolic pathways occur in the ER (rough)?
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Protein synthesis
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What metabolic pathways occur in the ER (smooth)?
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Lipid and steroid biosynthesis
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Where does gluconeogenisis and storage of fats take place?
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Gluconeogensis-liver
Storage of fats-adipose tissue |
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What are the 3 pathways of glucose utilization?
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1.glycogen, starch, sucrose (storage)
2. pyruvate→citric acid cycle (energy) 3. Ribose 5-phosphate→nucleotide biosynthesis |
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What are the 3 fates of pyruvate? What conditions allow them to happen?
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1. Aerobic conditions: 2 Acetyl CoA oxidized via citric acid cycle to 4CO2 + 4H2O
Animal, plant, and many microbial cells 2. Anaerobic conditions: 2 ethanol + 2 CO2 Fermentation to alcohol in yeast 3. Anaerobic conditions: 2 lactate Fermentation to lactate in vigorously contracting muscle, erythrocytes, some other cells, and in some microorganisms |
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What is the main goal of glycolysis?
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To convert energy from glucose into ATP
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What are 2 ways energy is stored in the form of ATP?
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Substrate-level phosphorylation
S-P + ADP → S + ATP Oxidative phosphorylation NADH → NAD+ + H+ |
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What drives ATP-synthesis?
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Proton gradient across the mitochondrial membrane
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What processes of glycolysis liberate energy? What happens?
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Oxidation processes. Glucose is oxidized and NAD+ is reduced to NADH
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Phosphate is ionized what what pH? What does this do?
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7 (net negative charge)
prevents glucose to diffuse across the membranes |
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Phosphoryl groups do what to help make ATP?
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They conserve energy used for ATP
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What does binding of Mg2+ -phosphate group to active site do?
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Provides additional binding energy that lowers activation energy
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What is a kinase?
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Enzymes that catalyze the transfer of the terminal phosphoryl group from ATP to an acceptor nucleophile
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Glycolysis: 1st step of the preporatory phase + enzyme
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Phosphorylation of Glucose:
Glucose is phosporylated by ATP at C-6 to yield glucose 6-phosphate Catalyzed by hexokinase |
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Which kinase requires Mg2+ for its activity?
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Hexokinase
|
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What are isozymes?
|
2 enzymes that catalyze the same reaction but are encoded in different genes
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Glycolysis: 2nd step of the preporatory phase + enzyme
|
Isomerization
Conversion of glucose 6-phosphate to fructose 6-phosphate (an aldose to a ketose) Catalyzed by phosphohexose isomerase |
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Glycolysis: 3rd step of the preporatory phase + enzyme
|
Phosphorylation (1st committed step)
Fructose 6-phosphate is phosphorylated by ATP to yield fructose 1,6-bisphosphate Catalyzed by phosphofructokinase-1 (PFK-1) |
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Glycolysis: 4th step of the preporatory phase + enzyme
|
Cleavage of 6-C sugar into 3-C units
Fructose 1,6-bisphosphate is cleaved into glyceraldehydes 3-phosphate (aldose) and dihydroxyacetone phosphate (ketose) Catalyzed by aldolase |
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Glycolysis: 5th step of the preporatory phase + enzyme
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Interconversion of the triose phosphates
Dihydroxyacetone phosphate is converted to glyceraldehydes 3-phosphate Catalyzed by triose phosphate isomerase |
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Glycolysis: 1st step of the payoff phase + enzyme
|
Oxidation of glyceraldehyde 3-phosphate and formation of NADH
Glyceraldehydes 3-phosphate is oxidized to yield 1,3-bisphosphoglycerate Catalyzed by glyceraldehydes 3-phosphate dehydrogenase 1st energy-conserving reaction of glycolysis |
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Energy of the oxidation of glyceraldehyde 3-phosphate is conserved how? Why?
|
In the formation of acyl phosphate.
It has very high phosphoryl group transfer potential |
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Glycolysis: 2nd step of the payoff phase + enzyme
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Substrate level phosphorylation: formation of the 1st 2 ATP molecules
Phosphoryl transfer from 1,3-bisphosphate to ADP yields 3-phosphoglycerate and ATP Catalyzed by phosphoglycerate kinase |
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Glycolysis: 3rd step of the payoff phase + enzyme
|
Conversion to form a 2nd molecule with high phosphoryl group transfer potential
Enzyme is initially phosphorylated on a His residue. Phosphoryl group transfers to 3-phosphoglycerate, forming 2,3-BPG. Phosphoryl group is transferred to same His residue, producing 2-phosphoglycerate. Catalyzed by phosphoglycerate mutase |
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Glycolysis: 4th step of the payoff phase + enzyme
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Conversion to form PEP
A molecule of water is removed from 2-phosphoglycerate to yield phosphoenolpyruvate (PEP) Catalyzed by enolase |
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Glycolysis: 5th step of the payoff phase + enzyme
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Substrate level phosphorylation: formation of the 2nd 2 molecules of ATP
Phosphoryl group is transferred from phosphoenolpyruvate to ADP, yielding pyruvate Catalyzed by pyruvate kinase |
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Which step of glycolysis is most heavily controlled?
|
The 3rd: phosphorylation
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Anaerobic and aerobic glucose consumption deliver how many molecules of ATP?
|
Anaerobic-2
Aerobic-32 |
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Equation for anaerobic glucose consumption
|
Glucose + 2 ADP + 2 Pi + 2 NAD+ → 2 pyruvate + 2 ATP + 2 NADH + H+ + 2 H2O
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Equation for aerobic glucose consumption
|
Glucose → 6 CO2 + 2 ATP + 2 GTP + 10 NADH + 2 FADH2
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What is the main purpose of pyruvate’s 3 fates?
|
To regenerate NAD+
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Cancer cells depend on what for energy production?
|
Glycolysis
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What is fermentation?
|
Process in which energy is extracted without the consumption of oxygen
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What ferments milk to yogurt?
|
Lactobacillus bulgaris
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What ferments milk to propionic acid and CO2?
|
Propionibacterium freudenrechii
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The reduction of pyruvate to lactate is catalyzed by what?
|
Lactate dehydrogenase
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What is the 1st step of converting pyruvate to ethanol + enzyme
|
Pyruvate is decarboxylated in an irreversible reaction yielding acetaldehyde
Catalyzed by pyruvate decarboxylase. (enzyme our body doesn't have) |
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What is the 2nd step of converting pyruvate to enthanol + enzyme
|
Acetaldehyde is reduced to enthanol
Catalyzed by alcohol dyhydrogenase |
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What does pyruvate decarboxylate require? And what is its tightly bound coenzyme?
|
Mg2+
Thiamine pyrophosphate (TPP) |
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What happens when your body digests carbohydrates? (steps)
|
Starch, glycogen, sucrose→oligosaccharides, di- and trisaccharides→oligosaccharides, di- and trisaccharides (chyme)→lactose→glucose/galactose
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What enzymes catalyze the digestion of carbohydrates?
|
Salivary amylase in mouth/esophagus (degrades and hydrolyzes sugar)
Acid hydrolysis in stomach (degrades further) α-amylase in small intestine lactase |
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What does glycogen phosphorylase do? What kind of reaction does it take place in?
|
Catalyze an attack by Pi on the cose residues at the nonreducing end, generatings glucose 1-phosphate and a polymer one glucose unit shorter
Phosphorolysis |
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What removes the branches (α1→6) for glycogen phophorylase?
|
Debranching enzyme
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What is a mutase?
|
An enzyme that catalyzes the transfer of a functional group from one position to another in the same molecule
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What must happen to disaccharides before they enter cells?
|
They must be hydrolyzed to monosaccharides
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Conversion of galactose 1-phosphate to glucose 1-phosphate involves with 2 nucleotide derivatives?
|
UDP-galactose and UDP-glucose
|
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What is glycogenolysis?
|
Catabolic Conversion of glycogen to glucose 6-phosphate
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What is glycolysis?
|
Catabolic Conversion of glucose 6-phosphate to pyruvate
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What is gluconeogenisis?
|
Anabolic Conversion of pyruvate to glycogen
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What is glycogenesis?
|
Anabolic conversion of glucose to glycogen
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What is glycogen?
What is the structure? Where is it located? |
It is a Major storage form of glucose in animals
α1→4 glycocidic bonds and every 8-10 glucose molecules is α1→6 glycolytic branch Mainly in the liver and muscle |
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What amount of glucose is stored as individual glucose and glycogen in hepatocyte?
|
Individual glucose: .4M
Glycogen: .01 μM |
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What does the brain rely on for fuel?
|
Glucose, not fatty acid
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How long is liver glycogen around for?
|
1 day
|
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Where is glycogen stored?
|
Large cytosolic β-granules, 20-40 granules form rosettes
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What does glycogen phosphorylase do?
|
Attacks α1→4 glycosidic bond at the non reducing end
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What enzyme is used in glycogenolysis?
|
Phosphoglucomutase
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What does a debranching enzyme do?
|
Shifts 3 glucose molecules to nearby non reducing end. Single glucose is released.
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What happens with glycogen mobilization in the muscle?
|
Glycogen is converted to gluc-6-P, which directly enters glycolysis
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What happens with glycogen mobilization in the liver?
|
Glycogen is converted to gluc-6-P to glucose, which is released into the blood stream to supply brain with glucose during meals
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What is our body’s daily demand for glucose? What is our supply?
|
Demand: ~160 g (120 g for brain)
Supply: ~20 g body fluids, ~190 g glycogen |
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What does gluconeogenesis do? Occurs where? What does it usually start with?
|
Maintains steady glucose level in the blood for muscles and brain
Occurs mainly in liver and kidney Starts usually with pyruvate and lactate |
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What 3 enzymes in glycolysis are not in gluconeogenesis?
|
Hexokinase
Phosphofructokinase-1 Pyruvate kinase |
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What does the first bypass in gluconeogenesis involve? + enzyme
|
Conversion of pyruvate to oxaloacetate, catalyzed by pyruvate carboxylate
Pyruvate is reduced to malate, catalyzed by malate dehydrogenase Oxaloacetate is converted to PEP, catalyzed by phosphoenolpyruvate carboxykinase |
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What does the 2nd bypass in gluconeogenesis involve? +enzyme
|
Conversion of fructose 1,6-bisphosphate to fructose 6-phosphate
Catalyzed by fructose 1,6-bisphosphatase |
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What is the 3rd bypass in gluconeogenesis involve? +enzyme
|
dephosphorylation of glucose 6-phosphate to glucose
Catalyzed by glucose 6-phosphatase |
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|
What does pyruvate carboxylate require?
|
Acetyl-CoA as a positive effector
|
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What are precursors to gluconeogenisis. In animals, plants, and both.
|
Animals-lactate
Plants-CO2 fixation Both-triacylglycerols |
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|
What is the formula for gluconeogenesis?
|
2 pyruvate + 4 ATP + 2 GTP + 2 NADH + 6H2O → glucose + 4 ADP + 2 GDP + 6Pi + 2 NAD+ + 2 H+
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What are the intermediates of the citrate acid cycle? What is special about these?
|
Citrate
Isocitrate α-ketoglutarate succinyl-CoA succinate fumarate malate they can all undergo oxidation to oxaloacetate |
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|
What are glucogenic intermediates?
|
1. citric acid cycle intermediates
2. glucogenic amino acids |
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|
Do mammals have a net conversion of fatty acid into glucose? Why?
|
No. there is no pathway that converts acetyl-CoA into pyruvate
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Where does glycogen synthesis mainly happen? What is its starting point?
|
Mainly in the liver and muscle
Starting point is gluc-6-P |
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|
What enzyme converts glucose-6-P to Gluc-1-P?
|
Phosphoglucomutase
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|
What enzyme converts gluc-1-P to UDP glucose?
|
UDP-glucose pyrophosphorylase
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|
UDP glucose are key intermediates for what?
|
Polymeration reactions
Vit. C synthesis |
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|
What is an excellent leaving group on UDP-glucose?
|
Nucleotidyl group
|
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|
Formation of what is irreversible?
|
UDP-glucose
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What enzyme is used in the reaction converting UDP-glucose and glycogen to glycogen and UDP?
|
Glycogen synthase
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|
What is glycogenin?
|
The primer on which new chains are assembled during glycogen synthesis and the enzyme that catalysizes their assembly
|
|
|
What is the main goal of metabolic pathways?
|
To maintain homeostasis
|
|
|
Why do metabolic pathways want to maintain AMP?
|
AMP changes very dramatically because AMP starts out so low to begin with
|
|
|
What enzyme catalyzes the conversion of 2 ADP to AMP and ATP?
|
Adenylate kinase
|
|
|
What does the regulation of carbohydrate catabolism do?
|
• Prevent futile cycles (glycolysis-gluconeogenisis)
• Partition metabolites appropriately between alternative pathways • Shut down pathways when products accumulate • Use pathways best suited for the organism |
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|
What characteristics do the most heavily controlled (usually irreversible) steps of carbohydrate catabolism have?
|
• Equilibrium is far on the side of the product
• Regulated by the enzyme activity • Become the rate limiting steps of the pathway (valve) • Sit on branching points of a pathway (committed step) |
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|
What are the 4 isozymes of hexokinase?
|
• Muscle hexokinase I-III
• Liver hexokinase IV (glucokinase) |
|
|
What inhibits muscle hexokinases I and II?
|
Their product: glucose-6-phosphate
|
|
|
What inhibits hexokinase IV?
|
The reversible binding of a regulatory protein specific to liver.
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|
|
What is the most important control element in mammalian glycolysis?
|
Phosphofructokinase-1
|
|
|
What is Phosphofructokinase-1?
|
Most heavily regulated protein of glycolysis
Tetrameric protein with catalytic sites and regulatory sites in the same subunit |
|
|
What happens when PFK is active and inactive?
|
Active-glycolysis
Inactive-pentose phosphate pathway (ribose biosynthesis) |
|
|
What regulates PFK-1?
|
ATP-ATP binds to allosteric site and lowers the affinity for fruc-6-P
|
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|
What is a very potent activator of PFK? What does it do?
|
Fructose-2,6 bisphosphate
It is an allosteric activator that shifts the conformation from the T-state to the R-state It increases the affinity for fruc-6-P and dimishes the inhibitor effect of ATP |
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|
What does pyruvate kinase do?
|
Controls the outflow from glycolysis
|
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|
Describe allosteric regulation of pyruvate kinase
|
• ATP inhibits
• Fruc 1,6-bisphosphate activates |
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|
Describe the covalent regulation of pyruvate kinase
|
• L-type pyruvate kinase (liver isozyme) is reversibly phosphrylated when glucose level is low-inactivates enzyme
|
|
|
What inhibit all isozymes of pyruvate kinase?
|
• High concentrations of ATP
• Acetyl-CoA • Long-chain fatty acids |
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|
What is the decision point of gluconeogenesis vs. glycolysis?
|
Fruc-1,6 BP/Fruc-6-P
|
|
|
What are the 3 key enzymes of glycolysis?
|
1. hexokinase
2. phosphofructokinase-1 3. pyruvate kinase |
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|
What sugars enter the glucose feeder pathway?
|
• Trehalose
• Lactose • Sucrose • Fructose • Galactose |
|
|
What does fructose 6-phosphate do?
|
Activates glycolysis
Inactivates gluconeogenisis |
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|
High glucose level:
What is released? What happens? What enzyme? |
Insulin is released=raised levels of Fruc-2,6-BP=activates PFK-1=glycolysis
Causes glycogen formation Enzyme is glycogen synthase |
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|
Low glucose level:
What is released? What happens? What enzyme? |
Glucogon is released=raised levels of cAMP=raised levels of PKA=lower levels of F-2,6-BP=gluconeogenesis
Causes glycogen mobilization Enzyme is glycogen phosphorylase |
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|
Glycogen phosphorylase is regulated alssosterically by what? Covalently by what?
|
Allosterically by glucose (negative regulator)
Covalently by hormone-controlled phosphorylation (postive regulator) |
|
|
What are the 3 major hormones that regulate fuel metabolism?
|
Epinephrine
Insulin Glucogon |
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|
Epinephrine:
Secreted from what? Produced when? Increases what? Results in what? |
Secreted from adrenal medulla
Produced at moments of stress Increases strength of heart beat, raises BP, increases flow of oxygen and nutrients to tissue Results in Increase in blood glucose |
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|
Glucogon:
Released by what? Prime target is what? Results in what? |
Released by pancreas
Prime target is liver Results in increase in blood glucose |
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|
Insulin:
Produces where? Stimulates what? Results in what? |
Produced in the pancreatic β-cells
Stimulates glucose uptake in muscle Stimulates fatty acid synthesis Results in decreased blood glucose level, glycogen formation in muscle, fatty acid synthesis in adipose tissue |
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|
What happens in diabetes?
|
Cells do not have enough glucose (starving)
Triacylglycerol hydolysis, gluconeogenesis and ketone body formation is accelerated High blood glucose level, glucose spills into urine Ketone bodies are acidic, kidneys try to maintain blood pH and secret H+ and other ions=dehydration. |
|
|
What happens in Type 1 diabetes?
|
Autoimmune disease where antibodies destroy β cells of pancreas=no more insulin
Degenerative disease: Blindness (high glucose levels) Kidney failure |
|
|
What happens in Type 2 Diabetes? Multi-step process:
|
1. Insulin resistance-cells are unable to use insulin efficiently normal or elevated levels
2. Hyperglycemia-stimulates additional insulin secretion; glucose is fairly constant but insulin is highter 3. Pre-Diabetes-β-cells become exhausted and can no longer produce enough insulin=blood glucose is higher 4. Diabetes-untreated pre-diabetes |
|
|
What are 3 hormones that fat cells secrete? Which one is related to diabetes?
|
1.leptin (low in diabetes)-after each mean, fat cells signal appetite
2. resistin-too much causes insulin resistance 3. adiponectin-to little causes insulin resistance |
|
|
What molecules can be transformed into acetyl-CoA?
|
• Carbohydrates
• Fatty acids • Amino acids |
|
|
What are the 3 stages of cellular respiration?
|
1. pyruvate, fatty acids, and a.a. are oxidized to 2-C fragments (acetyl-CoA)
2. Acetyl groups are fed into citric acid cycle and oxidized to CO2; energy is conserved as reduced NADH and FADH2 3. Reduced NADH and FADH are oxidized and e- are transferred to oxygen via a chain of e- carrying molecules (respiratory chain), this induces the formation of a proton gradient across the mitochondrial membrane which drives ATP synthesis (oxidative phosphorylation) |
|
|
What is the decarboxylation of pyruvate to acetyl-CoA catalyzed by?
|
Pyruvate dehydrogenase complex (PDC)
|
|
|
What does Pyruvate dehydrogenase complex (PDC) consist of?
|
Dihydrolipoyl DH
Pyruvate DH Dihydrolipoyl transacetylase |
|
|
Pyruvate dehydrogenase:
Number of chains Prosthetic group Reaction catalyzed |
12
TPP Oxidative decarboxylation of pyruvate |
|
|
Dihydrolipoyl transeacetlyase:
Number of chains Prosthetic group Reaction catalyzed |
24
lipoamide transfer of the acetyl group to CoA |
|
|
Dihydrolipoyl dehydrogenase
Number of chains Prosthetic group Reaction catalyzed |
24
FAD Regeneration of the oxidized form of lipoamide |
|
|
What are 2 stoichiometric cofactors of PDC?
|
Coenzyme A
NAD+ |
|
|
Oxidative decarboxylation of pyruvate to acetyl-CoA by the PDH complex:
Step 1 + enzyme |
Decarboxylation of pyruvate
Catalyzed by pyruvate dehydrogenase component |
|
|
Oxidative decarboxylation of pyruvate to acetyl-CoA by the PDH complex:
Step 2 + enzyme |
Oxidaton of hydroxyethyl-TPP and transer onto dihydrolipoyl transacetylase
Catalyzed by pyruvate dehydrogenase component |
|
|
Oxidative decarboxylation of pyruvate to acetyl-CoA by the PDH complex:
Step 3 + enzyme |
Oxidation of hydroxyethyl-TPP and transfer onto dihydrolipoyl transacetylase
Catalyzed by dihydrolipoyl transacetylase |
|
|
Oxidative decarboxylation of pyruvate to acetyl-CoA by the PDH complex:
Step 4 + enzyme |
Oxidation of hihdrolipoamide
Catalyzed by dihydrolipoyl dehydrogenase |
|
|
What is Beriberi?
Based on what? What is dry/wet beriberi? |
Neurological and cardiovascular disorder
Based on thiamine (Vit. B1) deficiency Dry beriberi- damage to peripheral nervous system-pain in limbs, weakness of muscles, distorted skin sensation Wet beriberi- damage to cardiovascular system-enlarged heart, increased cardiac output |
|
|
Thiamine deficiency:
Affects what? Increases in what? |
Affects the multienzyme complexes that contain enzymes with TPP cofactor:
1. Pyruvate dehydrogenase complex 2. α-ketoglutarate dehydrogenase complex 3. transketolase Increases in pyruvate and α-ketoglutarate dehydrogenase concentration |
|
|
What happens with arsenic and mercury poisoning?
|
What happens with arsenic and mercury poisoning?
|
|
|
Krebs cycle
1st step + enzyme |
Condensation of acetyl-CoA with oxaloacetate to for citrate
Catalyzed by citrate synthase |
|
|
Krebs cycle
2nd step + enzyme |
Transformation of citrate (to cis-aconitate) to isocitrate
Catalyzed by aconitase |
|
|
Krebs cycle
3rd step + enzyme |
Oxidation of isocitrate to α-Ketoglutarate, formation of NADH
Catalyzed by isocitrate dehydrogenase |
|
|
Krebs cycle
4th step + enzyme |
Oxidation of α-Ketoglutarate to Succinyl-CoA + CO2, formation of NADH
Catalyzed by α-ketoglutarate dehydrogenase complex |
|
|
Krebs cycle
5th step + enzyme |
Conversion of Succinyl-CoA to Succinate
Catalyzed by succinyl-CoA synthaetase |
|
|
Krebs cycle
6th step + enzyme |
Oxidation of Succinate to Fumarate, formation of FADH2
Catalyzed by Succinate Dehdrogenase |
|
|
Krebs cycle
7th step + enzyme |
Hydration of Fumarate to L-Malate
Catalyzed by fumarase |
|
|
Krebs cycle
8th step + enzyme |
Oxidation of L-Malate to Oxaloacetate, formation of NADH
Catalyzed by malate dehydrogenase |
|
|
How many ATP does one turn of the citric acid cycle produce?
|
10
|
|
|
What does 1 glucose yield?
|
2 pyruvate + 2 ATP
|
|
|
What does 1 pyruvate yield?
|
2 acetyl CoA + 2 CO2 + 2 NADH
|
|
|
What does 1 acetyl CoA yield?
|
4 CO2 + 6 NADH + 2 FADH2 + 2 GTP
|
|
|
What does 1 glucose ultimately yield?
|
6 CO2 + 2 ATP + 2 GTP + 10 NADH + 2 FADH2
|
|
|
What are 3 ways you can regenerate oxaloacetate?
|
Pyruvate (gluconeogenesis)
Phosphoenolpyruvate Malate |
|
|
What is biotin?
|
Cofactor of pyruvate carboxylase
Carrier or CO2 |
|
|
What is the 1st level of regulation of the citric acid cycle?
|
Control: Entry
Amount of acetyl-CoA that enters cell cycle is strictly regulated (Pyruvate dehydrogenase complex) |
|
|
What is the 2nd level of regulation of the citric acid cycle?
|
Control
The irreversible reactions of the citric acid cycle: • citrate synthase • isocitrate dehydrogenase • α-ketoglutarate dehydrogenase |
|
|
How are different levels of the citric acid cycle inhibited?
|
• Product inhibition
• Allosteric feedback inhibition • Inhibition by intermediates that reflect high energy state. |
|
|
What is the pyruvate dehydrogenase activated and inactivated by?
|
• Activated by molecules that signal high energy level (ATP, NADH, fatty acids)
• Inactivated by molecules that signal low energy level (AMP, CoA, NAD+, Ca2+) |
|
|
What is glyoxylate cycle and where does it take place?
|
Converstion of acetate to succinate (→ glucose)
Takes place in certain plants and microorganisms |
|
|
Why doesn’t glyoxylate take place in animals?
|
Formation of acetyl-CoA is too exergonic to e reversible
|
|
|
Glyoxylate Cycle: Bacteria and bacteria/plants
|
Bacteria: grow on acetate as only carbon sourse
Bacteria and plants: convert acetyl-CoA to succinate |
|
|
What are the 2 unique enzymes in the glyoxylate cycle?
|
Isocitrate lyase
Malate synthase |
|
|
Acetyl Co-A in glyoxylate cycle vs. citric acid cycle
|
Glyoxylate: 2
Citric acid: 1 |
|
|
What is the 1st step of the glyoxylate cycle + enzyme?
|
Conversion of Acetyl-CoA to Citrate
Catalyzed by citrate synthase |
|
|
What is the 2nd step of the glyoxylate cycle + enzyme?
|
Conversion of citrate into isocitrate
Catalyzed by aconitase |
|
|
What is the 3rd step of the glyoxylate cycle + enzyme?
|
Conversion of isocitrate into glyoxylate, release of succinate
Catalyzed by isocitrate lyase |
|
|
What is the 4th step of the glyoxylate cycle + enzyme?
|
Conversion of glyoxylate into malate, addition of Acetyl CoA
Catalyzed by malate synthase |
|
|
What is the 5th step of the glyoxylate cycle + enzyme?
|
Oxidation of malate into oxaloacetate, releases 1 NADH
Catalyzed by malate dehydrogenase |
|
|
Why is isocitrate a crucial intermediate?
|
Isocitrate dehydrogenase acts as a covalent modifier
• Phosphorylation inactivates • Dephosphorylation activates • Reduced cellular energy supply activates phosphatase |
|
|
Where does the glyoxylate cycle take place?
|
In plants in the glyoxysomes (specialized peroxisomes)
|
|
|
What does glyoxylate cycle allow plants and some microorganisms to do?
|
Use fat to make carbohydrates
|
|
|
What happens to succinate after it leaves the glyoxylate cycle?
|
It is exported to the mitochondria, where it is transformed to malate.
|
|
|
What are the 3 stages of the Calvin cycle?
|
1. CO2 fixation into 3-phosphoglycerate
2. Reduction: Converstion of 3-phosphoglycerate to glyceraldehyde 3-phosphate 3. Regeration: regeneration of ribulose 1,5-bisphosphate from triolose phosphates |
|
|
Calvin cycle: 1st step
|
3 CO2 + H2O combine with ribulose 1,5-bisphosphate to form phosphoglycerate
|
|
|
Calvin cycle: 2nd step
|
Phosphoglycerate to 1,3-bisphosphoglycerate
6 ATP to 6 ADP |
|
|
Calvin cycle: 3rd step
|
1,3-bisphosphoglycerate to glyceraldehyde 3-phosphate/dihydroxyacetone phosphate
6 NADPH + 6 H+ to 6 NADP+ + 6 Pi |
|
|
Calvin cycle: 4th step
|
release glyceraldehyde 3-phosphate
|
|
|
Calvin cycle: 5th step
|
glyceraldehyde 3-phosphate/dihydroxyacetone phosphate to ribulose 5-phosphate
release 2 Pi |
|
|
Calvin cycle: 6th step
|
ribulose 5-phosphate to ribulose 1,5-bisphosphate
3 ATP to 3 ADP |
