Peter's Section 2 Final Study Guide

From Biolk483

Current revision as of 23:58, 17 November 2009

Cofactors

• Peridoxophophate (Vitamin B1) will make a schiff base.
• FAD = Vitamin B2
• Thymine (B1) connects glycolysis to the Kreb cycle by being a coenzyme for pyruvate dehydrogenase. It has an acidic carbon!
• Coenzyme A (Vitamin B3) has a sulphur group and lots of stuff on it. It is used to end chain with thioester.
• Biotin is involved in carboxylation reactions like pyruvate --CO2--> oxaloacetate.
• S-adenosyl methionine does methylation.
  • Phospholipids can be methylated in euks but not in proks.

Enzyme Regulation

• Allosteric regulation is very fast, often requires an oligomer to form, and therefore is highly affected by the environment and is very delicate.
  • Example: Thr->->->Ile where threonine dehydrogenase can be inhibited by Ile (end product inhibition).
  • Allosteric regulation is often found at branching points of pathways.
• Covalent regulation is modeled by phosphorylase A which is active only when the serine found on each of the four subunits is phosphorylated (by phosphorylase kinase which uses ATP). It can be turned back off by phosphorylase removing the 4 phosphates.
• An isozyme is multiple forms of the same enzyme. An example is lactate dehydrogenase which has 5 forms: A4, B4, A3B1, A2B2, and A1B3. Since each comes from a different type of cell, these can be used to track development.

Enzyme Kinetics

• The larger the Km, the poorer the binding.

Inhibition

• An inhibitor like di-isopropylfluorophosphate on chymotrypsin binds serine 195 and is irreversible. This can be used to identify the active site.
• Malate is considered a competitive inhibitor in the reaction succinate + FAD -> Fumarate + FADH2 because once malate settles into the active site, the succinate cannot react.
• m = Km / Vmax
• Km = how well the substrate binds.
• An example of a non-competitive inhibitor might be a heavy metal as it will attack any SH sites and generally stop the protein from working.
• Steps in the aspartate transaminase reaction: (as an example of a double displacement reaction)
  • Asp + alpha-ketogluterate -> glu + oxaloacetate

1. Bind aspartic acid, shift amine to pyridoxyl phosphate via schiff base formation.
2. Oxaloacetate leaves
3. Alpha ketogluterate binds, transfers amine from pyridoxyl phosphate to alpha keto gluterate to produce glu
4. Glu leaves

• Specific activity = number of enzyme units / milligram of protein.

Lipids

• Any lipid with its last double bond 9 carbons from the omega carbon is part of the omega 9 family.
• Omega 6 lipids encourage cancer and omega 3 lipids discourage cancer.
• We eat a 6:1 ratio of omega 6: omega 3 lipids when we used to eat a 1:1 ratio.
• Margerine is trans fat but butter is cis.
• Lipids with less than 10 carbons are liquid; lipids with 12 or more carbons are solid at room temperature.
• The shorter the chain of the lipid, the more water soluble.
• Any type of esterification can make a free fatty acid safe.
• Alkyl ethers are found in archael bacteria.
• Plasmalogens have ether at SN1 site and ester at SN2 site.
• Ester pKas are 10.1, 7.2, and 2.1.

Phospholipids

• PA is a precursor of the rest and gives a negative charge.
• PE gives a slight negative charge and is the major phospholipid in prokaryotes because the proks cannot change it to PC.
  • PE's small head makes it disrupt the lamelar phase causing a dry spot and a weak area.
• PC is just like PE only methylated 3 times via s-adenosyl methionine.
  • Most abundant phospholipid for humans. (45% PC, 30% PE)
• PS can be converted to PE which can then be methylated to PC.
  • PS provides a negative charge density in the membrane.
  • Makes up only 10% of our phospholipids.
  • All PS faces inside of cell.
• PI: can be an anchor of glycogens on proteins; GPI-anchored proteins.
  • PI can be used hormonally; one example it gives off two signal pathways transactors: diacylgycerol and inositol phosphate.
• PG: found in plants and proks. Found in mitochondrial inner membrane and does electron transport chain and oxidative phosphorylation stuff.
• Euks have SM, PC, PE while Proks have PE and PG.

Sphingolipids

• Ceramides have the alcohol of sphingosine as head group.
• Cerebrosides have sugar (either glucose or galactose) as head group.
• Gangliosides: have more than one sugar, one of which is sialic acid.

The Membrane

• 40% lipid, 60% protein by weight.
• 50 - 200 lipids / protein.
• Flipflop takes forever and hardly ever occurs.
• Lateral movement of lipids = 1Million movements per second.
• Proteins are 100% asymmetrical.
• Carbohydrates are 100% asymmetrical.
• Lipids are partially asymmetrical.
• Lectins hold two sugars together.
• FMMP binds to primary amines and was used to identify the location of PE and PS on the bilipid layer.
• Outside: PC, SM, Choleterol, Lipid rafts; Inside: PE, PS.

Diffusion

• Valinomycin is an example of facilitated passive diffusion. It is selective for K+ and is called an ionophore.
• Forces causing diffusion: dG = 2.3RTLog(10)([solute inside]/[solute outside]) + ZFdPsi
  • Where T = temp, R and F are constants, Z is the charge of the solute and dPsi is the transmembrane electrical gradient.
• -dG is favorable.
• Ouabainstops NaKATPase from working; death.
• Bonkrekate competes with ATP to bind in ATP ADP Exchange protein, thus causing death. Atricate competes with ADP causing death.

Bioenergetics

• Anarobic organisms only have substrate level phosphorylation available to make ATP (glycolysis).
• We consume 88 lbs of ATP / day; 1.1 lbs / min of hard exercids; 140 lbs of ATP used for one marathon.
• There are 4 resonance structures for ATP but 5 for ADP. The charge on ATP is distributed to ADP and Pi when cleaved. More H20 can form around ADP and Pi than just around ATP. These are reasons why ATP -> ADP + Pi is so favorable and so much energy is released.