Biochem Exam IV

Glycolysis

Occurs in the cytoplasm where ATP is produced by the oxidation of glucose. Requires investment of 2 ATP molecules, while a net gain of 2 ATP, 2 NADH, and 2 pyruvate are produced

Phosphorylated Intermediates

When transforming glucose in the steps of glycolysis, these items keep components in the cell through adding a phosphate group to them → cannot escape cell membrane this way

Hexokinase Reaction

First step that requires Mg2+ to bind the negative phosphates in ATP. Irreversible step that takes phosphate from ATP and attaches it to the 6th carbon on a glucose ring (makes glucose-6-phosphate)

Phosphoglucose Isomerase reaction

Second step reversible reaction that transforms glucose-6-phosphate into fructose-6-phosphate → makes the H on carbon 1 CH2OH

Phosphofructokinase Reaction

Third step irreversible reaction that adds a phosphate to carbon-1 from ATP on fructose-6-phosphate (generates fructose-1,6-biphosphate)

Fructose-2,6-biphosphate

Made by PFK-2 (NOT an enzyme of glycolysis) to regulate and turn on phosphofructokinase (PFK-1) → binds to PFK-1 to increase its affinity for fructose-6-phosphate. This is not generated when glucose levels are low and the cell wants to perform gluconeogenesis

Aldolase Reaction

Fourth step reversible pathway since reactants are low in the cell that severs fructose-1,6-biphosphate into two 3 carbon sugars → dihydroxyacetone (ketone), and glyceraldehyde-3-phosphate (aldehyde)

Triose Phosphate Isomerase Reaction

Fifth step reversible pathway that converts dihydroxyacetone phosphate into an additional glyceraldehyde-3-phosphate in order for it to proceed in glycolysis → it is an induced fit catalytically perfect enzyme that obtains a very high affinity for its substrate

Glyseraldehyde-3-phosphate (GAP) Dehydrogenase Reaction

Sixth step reversible pathway that oxidizes and phosphorylates carbon-1, creating 1,3-Biphosphoglycerate, and reduces NAD+ to NADH

Phosphoglycerate Kinase

Seventh step reversible pathway that transfers the phosphate on carbon-1 of 1,3-Biphosphoglycerate, and attaches it to an ADP (creating ATP) → creates 3-phosphoglycerate

Substrate Level Phosphorylation

The formation of ATP by phosphoric group transfer from a substrate

Phosphoglycerate Mutase Reaction

Eith step reversible pathway that transfers a phosphate group from carbon-3 to carbon-2 → 3-phosphoglycerate to 2-phosphoglycerate (isomerase reaction)

Enolase

Ninth step reversible dehydration pathway that removes an H from carbon-2 and an OH from carbon-3, and in turn generates a double C=C bond as well as yields a water molecule → 2-phosphoglycerate → phosphoenolpyruvate

Pyruvate Kinase Reaction

Tenth step irreversible pathway that removes the phosphate on carbon-3 and attaches it to an ADP molecule (creating ATP) → phosphoenolpyruvate → pyruvate

Fates of Pyruvate

Under aerobic conditions, it’s oxidized into acetyl-CoA and under anaerobic conditions, it is reduced to lactate or ethanol. If necessary, it can also be converted into oxalacetate that is used to synthesize amino acids

Lactate Dehydrogenase

During excercise, mammals utilize this enzyme to temporarily turn pyruvate into lactate by oxidizing NADH to NAD+ and therefore, reduces pyruvate

Regeneration of NAD+ in Yeast

Pyruvate generated into acetaldehyde and yields CO2 molecule by way of pyruvate decarboxylase, then utilizes alcohol dehydrogenase to oxidize NADH and in turn, reduce acetaldehyde into ethanol

Gluconeogenesis

The pathway that converts pyruvate and related three and four carbon compounds to glucose → mainly occurs in the liver of mammals, but also occurs in plants, fungi, and microorganisms as well

The First Bypass 1

Step one in glyconeogenesis where pyruvate is transferred from the cytosol into mitochondria. Here, pyruvate carboxylase converts pyruvate to oxaloacetate and requires the coenzyme biotin along with ATP

Phosphoenolpyruvate Carboxylkinase

Part of the first bypass in glyconeogeneis where oxaloacetate is converted into phosphoenolpyruvate → a phosphate is added, a CO2 is yielded, and the process oxidizes GTP to GDP (reversible under intracellular conditions)

Fructose 1,6-biphosphatase (FBPase-1)

The enzyme in step 7 of glyconeogenesis that performs fructose-1,6-biphosphate + H2O → fructose-6-phosphate + Pi. IS carried out by hydrolysis of the carbon-1 phosphate, requires Mg2+, and is essentially irreversible

Glucose-6-phosphatase

The enzyme utilized in the last step (third bypass) of glyconeogenesis that utilizes simple hydrolysis to generate glucose + Pi → requires Mg2+, found in the ER, and is an irreversible pathway

Glycogenolysis

The breakdown of cellular glycogen beginning with glucose-6-phosphate and then broken down into glucose-1-phosphate via phosphoglutomase

Glycogen Synthesis

Consumes the free energy from UTP by transforming glucose-1-phosphate into UDP-glucose utilizing UDP-glucose-phosphorylase and inorganic pyrophosphatase

Glycogen Synthase

Adds glucose to extend the glycogen polymer

Glycogen Branching Enzyme

Catalyzes the formation of the alpha1-6 bonds found at the branch points of glycogen

Glycogen Phosphorylase

Enzyme that catalyzes phosphorolytic cleavages at the non reducing ends of glycogen chains → requires a phosphate and acts repetitively until it reaches a point four residues away from an alpha1-6 branch point (makes glucose-1-phosphate)

Debranching Enzyme

Transfers branches onto main chains and releases the residue at the alpha1-6 branch as free glucose

Phosphoglucomutase

Catalyzes the reversible conversion of glucose-1-phosphate to glucose-6-phosphate

Pentose Phosphate Pathway

Alternative pathway for glucose oxidation that occurs in the cytosol of most cells and produces pentoses for nucleotide synthesis and NADPH for the biosynthesis of fatty acids. Begisn with glucose-6-phosphate, then gets oxidized in order to reduce NADP+, then 6-phosphogluconate dehydrogenase that gets oxidized to reduce more NADP+, then produces ribulose-5-phosphate (irreversible pathway)

Ribulose-5-phosphate

Product of the pentose phosphate pathway that is utilized in nucleotide synthesis, and can be further converted into fructose-6-phosphate that can also proceed along the glycolysis pathway (reversible pathway)

Citrate Synthase

Catalyzes the first step in the citric acid cycle where water is required for oxaloacetate to receive an acetyl group from acetylCoA and becomes citrate → irreversible

Aconite Isomerase

Catalyzes second step in citric acid cycle that moves OH and H on citrate to make isocitrate

Aconitate

The intermediate product in between citrate and isocitrate in the aconitate isomerase reaction

Isocitrate Dehydrogenase

Catalyzes the third step in the citric acid cycle that generates NADH and CO2 → makes isocitrate into alpha-ketoglutarate

alpha-Ketoglutarate Dehydrogenase

catalyzes the fourth step in the citric acid cycle that yields NADH and CO2 and used coenzyme-A to transform alpha-ketoglutarate into succinyl-CoA

Succinylcholine-CoA Synthetase

Catalyzes the fifth step in the citric acid cycle that breaks off the CoA group, adds a phosphate to it, then gives that phosphate to a histidine residue and releases succinate. That phospho-his then give the phosphate to GDP and generates GTP (energy)

Succinyl Phosphate

The intermediate product formed inbetween succinyl-CoA and succinate by way of succinyl-CoA synthetase

Succinate Dehydrogenase

Embedded in the inner mitochondrial membrane that catalyzes the sixth step of the citric acid cycle. Turns succinate into fumarate → utilizes enz-FAD

Enz-FAD

Becomes enz-FADH2 in the sixth step of the citric acid cycle by oxidizing succinate. Then it re-oxidizes itself and donates its electrons to make QH2 (ubiquinol)

Fumarase

Catalyzes the seventh step of the citric acid cycle and utilizes water to turn fumarate into malate

Malate Dehydrogenase

Catalyzes the eighth step of the citric acid cycle and turns malate back into oxaloacetate to be able to restart the cycle → generates NADH

Intermediate for Glucose

Oxaloacetate → PEP

Intermediate for Pryimidines

Oxaloacetate

Intermediate for Porphyrins and Heme

Succinylcholine-CoA

Intermediate for Purines

alpha-Ketoglutarate

Intermediate for Fatty Acids and Sterols

Citrate

Anaplerotic Reactions

Chemical reactions that replenish intermediates

Tumor Causing

Mutations in succinate dehydrogenase and fumarate

Glial Cell Tumors

Mutant NADPH-dependent isocitrate dehydrogenase that loses nits ability to convert isocitrate to alpha-ketoglutarate and gain ability to convert alpha-ketoglutarate into 2hydroxyglutarate

Hydroxyethyl-TPP

Forms after pyruvate attaches to it and releases a molecule of CO2 in the process

Lipoamide

Receives the acetyl group from TPP

Coenzyme A

Takes the acetyl group off of lipoamide and becomes acetyl-CoA → lipoamide becomes reduced

FAD

Becomes FADH2 and oxidizes lipoamide

NAD+ in Pyruvate Dehydrogenase Complex

Receives electrons from FAD and becomes NADH

Standard Reduction Potential (E’)

Tendency of the oxidized form of a compound to accept electrons → the higher this value, the more susceptible a compound is to getting reduced

Nernst Equation

Entails the actual reduction potential → E = E’ - (0.026/n)ln[Areduced]/[Aoxidized]

Difference in Reduction Potential (deltaE’)

The larger the number, the greater the tendency of electrons to flow from one substance to the other and the greater the change between the system → E’(e- acceptor) - E’(e- donor)

Cytosolic Malate Dehydrogenase

Takes electrons from ocaloacetate and puts them on malate in order to transport it into the mitochondrial matrix

Matrix Malate Dehydrogenase

Regenerates NADH by stripping electrons off of malate and converts it back into oxaloacetate (then back into asparate) so it can re enter the cytosol and start the shuttle system over again

Mitochondrial transport Systems

Moves ADP through its own channel from the inter membrane space into the matrix along with Pi and H+ through another symport protein. In the matrix it is generated into ATP and then sent back down its own channel into the inter membrane space

ETC Complex I

NADH can carry 2 electrons and drops them off to Q at this site → 4H+ get pumped from matrix to inter membrane space

Flavin Mononucleotide

Found in complex I of ETC and accepts electrons from NADH → becomes FNMH2

Iron Sulfur Clusters

Part of complex I in the ETC and can accept one electron at a time from FMNH2

The Q Cycle

QH2 arrives at complex III and gives ONE electron to the ISP and then to cytochrome C while releasing 2H+ into the inter membrane space. The second electron goes to cytochrome B, and then back to Q to make Q-. A second QH2 enters and performs the same process. Total of 4H+ released to create proton gradient

Complex IV

Electrons arrive via 2cytochromeC, they join with oxygen to form water, and in turn 2H+ are pumped into inter membrane space

F0

Bottom component of ATP synthase that rotates protons and pumps them back into the matrix

F1

Upper component of ATP synthase that catalyzes the reaction of ADP +Pi → ATP + H2O

C Subunits

Part of the F0 complex that rotates and contains highly conserved aspartate or glutamate residues that serve as binding sites for protons in the inter membrane space (gamma unit spins with is)

Beta Subunits

Part of F1 complex responsible for that catalytic activity in generating ATP

Open Conformation 1 to Loose Conformation

Binds with ADP + Pi

Loose Conformation to Tight Conformation

Makes ATP

Tight Conformation to Open Conformation 2

Releases ATP

Liver Fed State

Most abundant storage of glycogen. Gluose can also be converted into acetyl-CoA and triacylglycerols

Liver Fasted State

Glycogen and/or amino acids broken down into glucose and triacylglycerols are broken down into acetyl-CoA into Ketone bodies sent out to the blood

Kidney

Rare process, but glutamine is converted to alpha-ketoglutarate to glucose

Adipose Tissue Fed State

Picks up glucose and fatty acids, turns glucose into glycerol and then triacylglycerol

Adipose Tissue Fasted State

Breaks down triacyl glycerols into fatty acids

Muscle Fed State

Converts glucose to glycogen (not main holder of glycogen though)

Muscle Active State

Glycogen converted to glucose, then pyruvate, then alanine or lactate. Or incoming fatty acids and ketone bodies can be converted to acetyl-CoA

Muscle Starved State

Proteins are broken down into amino acids

The Glucose-Alanine Cycle

Glucose in muscle cell broken down into pyruvate. Then an amino acid comes in to add on a nitrogen and creates alanine. Alanine is released to the blood and taken up by the liver. Here the nitrogen group is stripped off to undergo the urea cycle, and the re-generated pyruvate gets converted back into glucose to be put back in the blood and repeat the cycle

The Cori Cycle

Glycogen in the muscle is broken down into glucose, then pyruvate, and then lactate. The lactate goes into the blood, gets picked up by the liver, re-generates into pyruvate, and then undergoes gluconeogenesis to put glucose back in the blood to repeat the cycle

Pancreatic Islet Cells

Generates glucagon from alpha-cells, and generates insulin from beta-cells

GLUT4

A glucose transporter that gets put on the surface of the cell in the presence of high insulin activity

Glucagon

Signs to STOP making glycogen and release energy by adding phosphates to glycogen synthase to make it less active and to glycogen phosphorylase to make it more active

Insulin

When glucose levels are high, it removes phosphates from glycogen synthase to make it more active, and removes them from glycogen phosphorylase to make it less active

cAMP

A chemical messenger that activates and deactivates a number of proteins. Its presence is increased when glucagon and epinephrine are active to signal a need for releasing energy in a cell (either fight or flight or low glucose response)