question

1,3-bis-phosphoglycerate

answer

The product of the sixth step of glycolysis. A mixed anhydride of phosphote and carboxylic acid. Has a high-energy bond.

question

2,3-bis-phosphoglycerate

answer

An intermediate of the eighthstep of glycolysis.

question

2-phosphoglycerate

answer

The product of the eighth step of glycolysis.

question

3' end

answer

The end of a polynucleotide with a free carbon 3' OH group (not phosphorylated). Sequences are written from 5' end to 3' end.

question

3-phosphoglycerate

answer

The product of the seventh step of glycolysis.

question

5' end

answer

The end of a polynucleotide with a free carbon 5' OH group (not phosphorylated). Sequences are written from 5' end to 3' end.

question

?-ketoglutarate

answer

The product of the third step of the citric acid cycle. Easily converted into glutamate by transaminase.

question

?-ketoglutarate dehydrogenase

answer

Catalyzes the oxidation of ?-ketoglutarate into succinyl CoA and CO₂, the fourth step of the citric acid cycle.

question

? subunit

answer

Part of F₁ of ATP synthase. There are three identical versions. Part of the ?3?3 complex. Changes conformation as the ? unit rotates. Stationary.

question

?3?3 complex

answer

The ? and ? subunits of F₁ of ATP synthase. Stays stationary while the ? subunit rotates, changing the conformations of the ? and ? subunits. Stationary.

question

?-hydroxyacyl-CoA dehydrogenase

answer

Catalyzes the third step of beta oxidation. The H in the alcohol group on the ? cardbon in L-?-hydroxy acyl-Coa is removed by NAD⁺, forming a ketogroup; ?-ketoacyl CoA is formed. Two electrons are transported.

question

?-ketoacyle-CoA

answer

The product of the third step of beta oxidation. Breakage of the bond between the ? and ? carbons is made possible by its ?-dicarbonyl functionality.

question

? subunit

answer

Part of F₁ of ATP synthase. Changes conformation as the ? unit rotates. Stationary.

question

? subunit

answer

Part of F₁ of ATP synthase. Interacts asymmetrically with the ?3?3 complex so that each of the ? and ? subunits has a different configuration. Rotates while the ?3?3 complex stays stationary. Rotation is driven by the subunit c ring. One full rotation produces 3 ATP.

question

? subunit

answer

Part of F₁ of ATP synthase. Attaches the b2 subunit to the ?3?3 complex. Stationary.

question

? subunit

answer

Part of F₁ of ATP synthase. Attaches the ? subunit to F_o. Rotates.

question

Acetaldehyde

answer

An intermediate of alcoholic fermentation.

question

Acetate

answer

An amino acid which can be produced from oxaloacetate, a product of the citric acid cycle, by replacing the keto group with an amino group.

question

Acetone

answer

A common organic solvent. Has a similar structure to dihydroxyacetone.

question

Acetyle

answer

R-C(=O)-CH₃
A common functional group.

question

Acetyl CoA (CoASAc)

answer

Coenzyme A carrying acetic acid. In catabolism it carries acetyl groups derived from fats, carbohydrates, and some amino acids. In anabolism it is converted into larger molecules. A product of beta oxidation, and aerobic condition pyruvate oxidation. Enters the citric acid cycle.

question

Acetyl moiety

answer

An acid with two carbons. Removed during each repetition of beta oxidation.

question

Acid anhydride

answer

Two carboxylic acids linked together with an ester linkage. Created by a condensation region.

question

Acontinase

answer

Catalyzes the formation of isocitrate through cis-aconitate, the second step of the citric acid cycle.

question

Acyl adenylate

answer

An intermediate in converting fatty acids into fatty acyl-CoA thioester. The fatty acid attackes ATP, and replaces PP_i, which floats away. The thiolate anion form of CoA attacks the group, replacing AMP.

question

Acyl CoA

answer

Coenzyme A carrying any acid. Includes aceyl CoA and palmitoyl CoA. A product of beta oxidation.

question

Acyl-CoA dehydrogenase

answer

Catalyzes the first step of beta oxidation. FAD dehydrogenates fatty acyl CoA, forming a double bond between the ? and ? carbons, forming trans-?2-enoyl-CoA. Two eletrons are transferred, forming FADH₂.

question

Acyl-CoA synthetase

answer

An enzyme that catalyzes the conversion of fatty acids into fatty acyl-CoA thioester in an ATP driven (complete hydrolysis) reaction in the outer mitochondrial membrane. The fatty acid attacks ATP, producing acyl adenylate and replaces PP_i, which floats away. The thiolate anion form of CoA attacks the group, replacing AMP.
?G^0' = - 34 kJ/mol

question

Acyl group

answer

Acids, including acetic acid.

question

Adenine (A)

answer

6-aminopurine
A purine. Found in DNA and RNA. In DNA it forms 2 H bonds with thymine. Its ribose nucleoside is adenosine. Its deoxyribuse nucleoside is deoxyadenosine.

question

Adenosine (A)

answer

The ribose nucleoside of adenine.

question

Adenosine diphosphate (ADP)

answer

A nucleotide of adenine and ribose, plus two phosphategroups. Produced from the hydrolysis of the gamma linkage of ATP.

question

Adenosine monophosphate (AMP)

answer

A nucleotide of adenine and ribose, plus one phosphate group. Produced from the complete hydrolysis of ATP.

question

Adenosine triphosphate (ATP)

answer

A nucleotide of adenine and ribose, plus three phosphate groups: ?, ?, and ?. The exergonic and endergonic reactions occur in the phosphate groups. ATP is metabolically available, kinetically stable, and chemically versatile. It is coupled with many reactions, driving them forward. It can also transfer pyrophosphoryl or adenylate moieties to substrates or enzymes, driving reacions. A 70 kg person uses about 40 kg of ATP in a restful day. Turnover is very fast: seconds to minutes. A carrier of phosphate.
?G = 50 kJ/mol
?G' = 30.5 kJ/mol

question

Adenylate

answer

A group that ATP can add to substrates or enzymes, driving reactions.

question

Adsorption chromatography

answer

A method of separating lipids based on their properties. Includes column chromatography and thin layer chromatography. More non-polar lipids elude from the silica gel first.

question

Aerobic conditions

answer

A pyruvate oxidation pathway that occurs in animals on a regular basis. Pyruvate is moved into the mitochondria. PDH reduces pyruvate into acetyl CoA, which enters the citric acid cycle, producint CO₂ and H₂O. The electron transport chain re-oxidizes NADH.

question

Albert Szent-Gyorgyi

answer

1893 - 1986
Hungarian biochemist who won the Nobel Prize in 1937 for the discovery of vitamin C. Studies lead to the concept of the citric acid cycle in the 1930s. Found that by adding certain organic acids such as succinic acid to preparations, use of O₂ is increased in a way that suggests acids act catalytically rather than stoichiometrically.

question

Alcohol dehydrogenase

answer

Catalyzes the second step of alcoholic fermentation. Acetaldehyde is converted into ethanol. Animals have this enzyme, but it is used for the reverse reaction in the metabolism of ethanol.

question

Alcoholic fermentation

answer

A pyruvate oxidation pathway that occurs in anaerobic conditions in some bacteria and yeast. Pyruvate decarboxylase is converted into acetaldehyde, releasing CO₂. Alcohol dehydrogenase reduces acetaldehyde into ethanol, producing NADH⁺. Alcoholic beverages are made using this pathway. The bubbles in champagne are CO₂ from the first step.
Pyruvate > CO₂ + Acetaldehyde
Acetaldehyde + NADH + H⁺ > Ethanol + NADH⁺

question

Aldehyde

answer

R-C(=O)H
A carbonyl group. A common functional group.

question

Aldolase

answer

Catalyzes the cleavage of fructose-1,6-biphosphate, the fourth step of glycolysis.

question

Aldose

answer

Polyhydroxy aldehyde
A monosaccharide where the carbonyl group is an aldehyde.

question

Alkaptonuria

answer

Agenetic disease where there is a deficiency in an enzyme in the phenylalanien catabolism pathway, causing a build-up of homogentisic acid, which turns the person's urine black.

question

Allose

answer

An aldo-hexose.

question

Alpha (?) anomer

answer

One of the possible orientations of the chiral carbon created during cyclization. The hydroxyl group of the anomeric carbon is drawn facing downwards in a Haworth structure.

question

Alpha (?) carbon

answer

In fatty acid nomenclature, the first carbon in the carbon chain. Subsequent carbons are labeled with the Greek alphabet.

question

Alpha (?) phosphate

answer

The phosphate bonded to the nucleotide in ATP by a low-energy phosphate ester bond.

question

Altrose

answer

An aldo-hexose.

question

Amido

answer

R-C(=O)-NH₂
A common functional group.

question

Amino

answer

R - NH₃⁺
A common functional group.

question

Anabolism

answer

The synthesis of larger, more complex molecules from simple precursors. Requires ATP. Anabolic pathways diverge. Acetyl CoA is converted into fatty acids, steroids, proteins, nucleic acids, and others.

question

Anaerobic conditions

answer

aka Hypoxia
A pathway of oxidation of pyruvate. Occurs in oxygen-starved mammals, such as during exercise, when electron transport cannot produce NAD⁺, which is necessary for glycolysis. Red blood cells can only use this pathway. Lactate dehydrogenase oxidizes pyruvate into lactate. Lactate is recycled into glucose in the gluconeogenesis pathway through the Cori cycle.
Pyruvate + NADH > Lactate + NAD⁺
?G₀' = - 25.1 kJ/mol

question

Anhydride

answer

R-C(=O)-O-C(=O)-R
Two carboxylic acid moieties bound. A common functional group.

question

Anomer

answer

An epimer that results from cyclization due to creation of a new chiral carbon. Can be in alpha (?) or beta (?) forms. In a Haworth structure, if a squiggly line is drawn to the side, it signifies either alpha or beta forms.

question

Anomeric carbon

answer

The carbonyl carbon in linear form. Becomes a chiral carbon in cyclization. The only carbon bound to 2 oxygens. Very reactive. May react with alcohols or amines. Acts as the electrophile in glycosidic bonds. If the anomeric carbon is not bound to alcohol or amine, the sugar is a reducing sugar.

question

Arabinose

answer

An aldo-pentose.

question

Arachidate

answer

20:0
"Peanut"
A saturated fatty acid with 20 carbons.

question

Arachidonate

answer

20:4(?^5,8,11,14)
aka Arachidonic acid
An unsaturated fatty acid with 20 carbons and 4 double bonds on carbons 5, 8, 11, and 14.
Melting point = -49.5?C

question

Archibald Garrod

answer

In 1904 he identified that human genetic diseases are deficiencies in specific enzymes.

question

Aspartate

answer

Oxaloacetate is converted into it through a transamination process. Passes out of the mitochondrial matrix through transporter proteins. Part of the Malate-Aspartate shuttle.

question

ATP synthase

answer

aka ATPase
aka Complex V
Catalyzes the synthesis of ATP using proton motive force as protons flow into the matrix, down their concentration gradient. Consists of F₁ and F_o.

question

Auto Brewery Syndrome

answer

A large amount of yeast in the intestines. Consumption of carbohydrates causes alcoholic fermentation to occur in the intestines, making the person inadvertently drunk.

question

Auxotroph

answer

"Help food"
Needing more than minimal medium.

question

Auxotrophic mutants

answer

A biochemical genetics method of elucidation. A phototroph, such as E. coli have a gene inactivated by mutagens and become an auxotroph. Analysis of the metabolite(s) required by the new auxotrophs.

question

Benzoic acid

answer

Found in the urine of dogs fed fatty acids with an odd number of carbons in Franz Knoop's experiment. Phenyl-labeled formic acid.

question

Beta (?) anomer

answer

One of the possible orientations of the chiral carbon created during cyclization. The hydroxyl group of the anomeric carbon is drawn facing upward in a Haworth structure.

question

Beriberi

answer

A disease caused by a deficiency in thiamine, slowing the PDH complex. Higher than normal levels of pyruvate in blood and urine.

question

Beta (?)

answer

THe second phosphate, bound to the alpha phosphate of ATP by a high-energy phosphoanhydride bond.

question

Beta oxidation

answer

The first step of fatty acid catabolism. Occurs in the mitochondrial matrix. Fatty acyl-CoA thioester is broken down into acetyl CoA and reduced cofactors. There are four steps which are repeated, removing an acetyl moiety each time as acetyl CoA, which enters the citric acid cycle. Produces one FADH₂, one NADH, and one H⁺ each round. Reduced cofactors enter the electron transport chain.

question

Bilayer

answer

A double layer of phospholipids that forms in aqueous solutions, with the polar heads to the outside. Folds over into itself to form liposomes.

question

Biochemical genetics

answer

A method of elucidation. Includes genetic diseases, auxotrophic mutants, and transgenic organisms.

question

Biological membrane

answer

A lipid bilayer containing hydrophobic proteins, oligosaccharides, and other structural and functional features.

question

Biphosphate

answer

A molecule with two phosphates at different positions.

question

Caffeine

answer

aka 1,3,7-trimethylxanthine
A purine.

question

Carbohydrate

answer

aka Sugars
aka Saccharides
A component of nucleotides and glycoproteins. The most abundant biomolecule on earth. Includes monosaccharides, disaccharides, trisacchardies, and polysaccharides.

question

Carbon 1

answer

In fatty acid nomenclature, the carbon in the carboxylic acid group. Subsequent carbons are counted numerically.

question

Carbon 14 (¹⁴C)

answer

A radioisotope of carbon created by bombarding carbon with neutrons. Behaves like normal carbon (¹²C), but is easy to trace because it releases energy as it decays.

question

Carbon dioxide (CO₂)

answer

The most oxidized form of carbon found in living systems.

question

Carboxylate

answer

R-COOH
A common functional group.

question

Cardiolipin

answer

A phospholipid found only in the IMM of a mitochondria.

question

Carl and Gerti Cori

answer

Discovered the Cori cycle.

question

Carnitine transporter

answer

An aclohol derivative of lysine. Transports fatty acids with more than 12 carbons across the outer and inner mitochondrial membranes. Carnitine acyl transferase catalyzes the conversion of fatty acyl CoA thioester into fatty acyl carnitine.

question

Carnitine acyl transferase

answer

Catalyzes the conversion of fatty acyl CoA thioester into fatty acyl carnitine (an ester bond) which can transport across both mitochondrial membranes through transport proteins, and the same reaction in reverse on the other side of the membrane.

question

Carotene

answer

A lipid pigment.

question

Catabolism

answer

The breakdown of large molecules into simpler products. Produces ATP. Catabolic pathways converge. Sugars, fats, and amino acids are converted into acetate which is carried by acetyl CoA. The convergence phenomenon allows cells to have a limited number of high-flux, carefully regulated reactions while maintaining the flexibility of using a wide variety of fuels.

question

Cellular respiration

answer

The complete oxidation of organic fuels into CO₂ and H₂O using O₂.

question

Cellulose

answer

A glucan. A structural element in plants.

question

Central Dogma of Molecular Biology

answer

DNA > RNA > Protein
The flow of information. Includes DNA replication, transcription, and translation. One exception is reverse transcription.

question

Chargaff's Rules

answer

Discovered by Erwin Chargaff. In DNA, the amount of G is always nearly equal to the amount of C, and the amount of A is always nearly equal to the amount of T. The percent of the DNA that was A/T and G/C varies from organism to organism.

question

Chemical potential energy

answer

A component of the proton motive force. Due to the difference in concetration of H⁺. One proton makes a ? pH of 0.75.

question

Chemiosmotic hypothesis

answer

Proposed by Peter Mitchell. Explains the connection between the electron transport chain and ATP synthesis, and the coupling between them. Dependenton a generation of a proton gradient across the inner mitochondrial membrane. Free energy liberated by redox reactions in the electron transport chain is used to pump protons from the matrix into the inter-membrane space. Energy is stored as the proton motive force. As protons flow back into the matrix, down their concentration gradient, the energy is used for the generation of ATP, using ATP synthase.

question

Chirality

answer

"Handedness"
aka Optical activity
A carbon with four different substituents has two possible configurations in space: "right-handed" and "left-handed".

question

Chitin

answer

A glucan
A strucutral element in animal exoskeletons.

question

Choline

answer

OH-CH₂-CH₂-N(CH₃)₃⁺
The alcohol that is bound to PC.

question

Cis-aconitate

answer

The intermediate of the second step of the citric acid cycle. An alkene.

question

Cis configuration

answer

A double bond where the chains both go in the same direction. Causes a kink in the chain, drastically reducing the melting point of a fatty acid.

question

Citrate synthase

answer

Catalyzes the condensation of oxaloacetate with acetyl CoA, the first step of the citric acid cycle.

question

Citrate

answer

aka Citric acid
Abundant in citrus fruits such as lemons and oranges. Knoop discovered that citric acid is oxidized into ?-ketoglutarate. The product of the first step of the citric acid cycle. A tricarboxylic acid and tertiary alcohol. A poor substrate for oxidation.

question

Citric acid cycle (TCA)

answer

aka Kreb's cycle
The second stage of cellular respiration. Acetyl CoA enters this cycle and is oxidized into CO₂ and H₂O, using O₂, making GTP, NADH, and FADH₂. Energy is released as reduced cofactors. Allows for easier oxidation of the alpha carbon in acetate. Derived from an ancient non-oxidative metabolic process. Intermediates provide multiple opportunities for interface with other pathways. Has 8 steps. Produces 2 CO₂, 3 NADH, 1 FADH₂, 1 ATP/GTP, 1 CoA, and 3 H⁺ each round.

question

Claisen condensation

answer

Beta oxidation in reverse. The condensation of two beta-keto-esters. Named after Ludwig Claisen, 1851 - 1930.

question

Cleavage of fructose-1,6-biphosphate

answer

The fourth step of glycolysis. Aldolase splits the linear form of fructose-1,6-biphosphate between carbons 3 and 4, forming two pieces: G3P and DHAP.

question

Cofactors

answer

Chemical compounds that help enzyme carry out their functions, especially redox reactions. Includes inorganic ions and coenzymes. Reduce cofactors from beta oxidation enter the electron transport chain.

question

Codon

answer

Groups of three nucleotides in RNA that code for certain amino acids according to genetic code during translation.

question

Coenzyme

answer

Complex organic or metaolorganic compounds that act as transient carriers of specific functional groups. Many are adenosine derivatives, including ATP, coenzyme A, NADH, NDPH, FMN, FAD, PAPS, SAM, and THF.

question

Coenzyme A (CoASH)

answer

A carrier of acyl groups. Discovered by Fritz Lipmann. Forms thioester derivatives with organic acids. The most central and important molecule in metabolism. The source of carbon atoms entering the citricacid cycle. Synthesizes fatty acids and steroids. An adenosine with a phosphate group bound to ?-mercaptoethylamine and pantothenic acid by a pyrophosphate linkage. Derived from pantothenic acid, vitamin B5.

question

Coenzyme Q

answer

aka Ubiquinone
Q stands for Quinone. A lipid enzyme cofactor in the mitochondrial electron transport chain. Has a hydrophobic tail of isoprene units that allows it to stay inside the inner mitochondrial membrane. Acceps reducing equivalents from mitochondrial glycerol-3-phosphate dehydrogenase in the glycerol-3-phosphate shuttle mechanism. Accepts reducing equivalents from complexes I and II. Accepts reducing equivalents from electron-transferring flavoproteins. Passes reducing equivalents to complex III.

question

Complete hydrolysis of ATP

answer

Breaking of two high-energy bonds. Twice as much energy is released as in hydrolysis of the gamma linkage. First the beta linkage is hydrolyzed, releasing PPi and AMP. PP_i is then catalyzed by pyrophosphatase, releasing two P_i.

question

Complex

answer

A large enzyme
An assembly of proteins and other molecules that catalyze individual electron-transfer steps it the electron transfer chain. Integral membrane proteins in the inner mitochondrial membrane. Includes complexes I, II, III, andIV.

question

Complex I

answer

aka NADH dehydrogenase
Part of the mitochondrial electron transport chain. Accepts reducing equivalents from NADH and passes them to coenzyme Q. Catalyzes two coupled reactions. Pumps 4 protons into the intermembrane space.
Transfer of a hydride ion from NADH and H⁺ from the matrix into coenzyme Q is exergonic.
NADH + H⁺ +Q > NAD⁺ + QH₂
Transfer of four protons from the matrix into the intermembrane space is endergonic.
NADH + 5H⁺ + Q > NADH⁺ + QH₂ + 4H⁺

question

Complex II

answer

aka Succinate dehydrogenase (from the citric acid cycle). Part of the mitochondrial electron transport chain. Accepts reducing equivalents from FADH₂ and passes them to coenzyme Q. No protons are pumped into the intermembranespace.
FADH₂ + Q > FAD + QH₂

question

Complex III

answer

aka Cytochrome C reductase
Part of the mitochondrial electron transport chain. Accepts reducing equivalents from coenzyme Q and passes them to cytochrome C. Pumps 4 electrons into the intermembrane space.
QH₂ + 2 cytochrome C (oxidized) + 2H⁺ > Q + 2 cytochrome C (reduced) + 4H⁺

question

Complex IV

answer

aka Cytochrome oxidase
Part of the mitochondrial electron transport chain. Accepts 2 reducing equivalents from cytochrome C and passes them to oxygen. Inhibited by cyanide.
2 cytochrome C (reduced) + 4H⁺ + ?O₂ > 2 cytochrome C (oxidized) + 2 H⁺ + H₂O

question

Condensation of oxaloacetate with acetyl CoA

answer

The first step of the citric acid cycle. Citrate synthase condensaes acetyl CoA with oxaloacetate, forming citric acid and coenzyme A. The methyl carbon of acetyl CoA attacks the electrophilic carbonyl carbon of oxaloacetate. The only step where a C-C bond is formed.

question

Conformations

answer

Three different stages that ? and ? subunits can be in. Changes as the ? rotates inside the ?3?3 complex. Loose, tight, and open.

question

Conjugated

answer

An unsaturated carbon chain where the double bond pattern is double-single-double-single. Found in biomolecules. Uncommon in fatty acids.

question

Conversion of 3-phosphoglycerate to 2-phosphoglycerate

answer

The eighthstep of glycolysis. Phosphoglycerate mutase adds a phosphate to carbon 2 of 3-phosphoglycerate, briefly forming the intermediate 2,3-bis-phosphoglycerate, then removes the phosphate from carbon 3, forming 2-phosphoglycerate. A reversible reaction.

question

Conversion of succinyl CoA to succinate

answer

The fifth step of the citric acid cycle. A substrate level phosphorylation. Succinyl CoA synthetase converts succinyl CoA into succinate, producing ATP or GTP and releasing CoASH. Form a phosphoenzyme intermediate.

question

Cori cycle

answer

The exchange of metabolites in the body. Includes gluconeogenesis. Discovered by Carl and Gerti Gori.

question

Coupling

answer

The phenomenon of the electron transport chain and ATP synthesis being coupled. If the electron transport chain is blocked, ATP synthesis stops because there is no more proton motive force being generated. If ATP synthesis is blocked, the electron transport chain stops because the proton motive force becomes too large. This relationship can be undone by uncouplers such as DNP.

question

Creatine phosphate

answer

Stores energy in muscles. A super-high-energy phosphorylated chemical.

question

Cyanide

answer

Inhibits complex IV in the electron transport chain.

question

Cyclization

answer

When a hemiacetal or hemiketal is formed on the same molecule, making a ring-shaped molecule. Reaction happens more easily.

question

Cytidine (C)

answer

The ribose nucleoside of cytosine.

question

Cytochrom

answer

"Coloured stuff in the cell"
A class of hemeproteins that participate in redox reactions.

question

Cytochrome C

answer

A hemeprotein. Its heme ring is covalently linked in. Part of the mitochondrial electron transport chain. Soluble in the intermembrane space. Accepts reducing equivalents from compelx III and passes them to complex IV. When reduced, it has a peak at wavelength 410 nm, the Soret band. Observed with a spectrophotometer to elucidate the electron transport chain.

question

Cytosine (C)

answer

A pyrimidine. Found in RNA and DNA. In DNA it forms 3 H bonds with guanine. The keto-amino tautimer is predominant. Its ribose nucleoside is cytidine and its deoxyribose nucleoside is deoxycytidine.

question

D-sugars

answer

The chiral carbon furthest from the carbonyl group has the same configuration of D-glyceraldehyde. In a Fischer projection the hydroxyl group is drawn to the right. Most common sugars in biochemistry are D-sugars.

question

Dehydration

answer

Removal of water without breaking the molecule.

question

Dehydration of 2-phosphoglycerate

answer

The ninth step of glycolysis. Enolase dehydrates 2-phosphoglycerate, forming PEP.

question

Dehydrogenation

answer

Removal of a hydrogen ion.

question

Deoxyadenosine (dA)

answer

The deoxyribose nucleoside of adenine.

question

Deoxycitidine (dC)

answer

The deoxyribose nucleoside of cytosine.

question

Deoxyguanine (dG)

answer

The deoxyribose nucleoside of guanine.

question

Deoxyribonucleic acid (DNA)

answer

A nucleid acid. The sugar deoxyribose in beta form. Not as easily hydrolyzed as RNA. Deoxyribose doesn't have a free OH group on carbon 2', so it doesn't act as a nucleophile, hydrolyzing the phosphodiester linkage as it does in RNA. Secondary structure is unaffected by base sequence. Two complementary, antiparallel polynucleotide strands plectonemically coiled in a right-handed double helix. A and T form 2 H bonds together, and C and G form 3 H bonds together. A higher C/G portion makes DNA harder to separate. Extends 3.4 A per base pair, and 34.0 A per each full turn of 10 base pairs. Due to the angle formed by base pairs, there is a major groove and a minor groove. DNA is held together by H bonds, hydrophobic effect, and Van der Waals forces.

question

Deoxyribose

answer

The sugar in DNA. It has a missing hydroxyl group on carbon 2. Its structure is so peculiar it wasn't figured out until 1930.

question

Diabetes

answer

A condition where blood glucose is not adequately taken up into cells. Blood glucose rises and can cause major problems in blood and organs. Glucose is excreted in urine. Type 1 is where the person lacks insulin. Type 2 is where the body has developed a reduced response to insulin. The body "starves in the midst of plenty".

question

Diastereomers

answer

Stereoisomers that differ in chirality around some carbons but not others. Have differing chemical properties. Includes epimers.

question

Diester

answer

A phosphoric acid with two ester groups.

question

Digoxin

answer

"Digitalis"
A glycoside. A medicine for heart problems. Found in foxglove. During digestion, the glycosidic bond is broken, releasing the active drug.

question

Dihydroxyacetone

answer

A keto-triose. No chiral carbons.

question

Dihydroxyacetone phosphate (DHAP)

answer

One of the products of the fourth stage of glycolysis. Converted into G3P in step five. Oxidized into glycerol 3-phosphate by mitochondrial glycerol-3-phosphate dehydrogenase, and reduced from glycerol-3-phosphate by cytosolic glycerol-3-phosphate dehydrogenase in the glycerol 3-phosphate shuttle mechanism.

question

Dinitrophenol (DNP)

answer

An uncoupler. A hydrophobic, strong weak acid. Acts as a proton ionophore. Freely carries protons over the inner mitochondrial membrane by becoming protonated, diffusing into the matrix, becoming deprotonated, then diffusing back into the intermembrane space. Destroys the proton motive force.
pKa = 4

question

Diphosphate

answer

A molecule with two phosphates at the same position, or a pyrophosphate group.

question

Disaccharide

answer

Two cyclic monosaccharides bonded by a glycosidic bond. Includes lactose, maltose, trehalose, and sucrose.

question

Disulfide

answer

R-S-S-R
A common functional group.

question

DNA replication

answer

DNA is used as a template for DNA synthesis. Occurs when the cell replicates.

question

Efrain Racker

answer

With colleagues, first purified F₁ of ATP synthase in the 1960s.

question

Electrical potential energy

answer

A component of the proton motive force. Due to the separation of charges. One proton makes a ?? of 0.15 V.

question

Electron-transferring flavoproteins

answer

Accepts reducing equivalents from FADH₂ and passes them to coenzyme Q.

question

Electron transport chain

answer

Reduces cofactors from beta oxidation and pyruvate oxidation enter this process. Cofactors are oxidized by O₂. Generates ATP. Reducing equivalents are passed from molecule to molecule in order of higher reducing potential, until oxygen. Indirectly passes energy step by step, rather than all at once, which would be energetically wasteful. Different organisms have different electron transport chains. Humans have a mitochondrial electron transport chain.

question

Elucidation

answer

Determining the precursor-product relationships, stoichiometry, cofactors, enzymes, and regulation of each step in a metabolic pathway. Cells are complex; metabolic pathways have tiny flux and there are thousands of metabolites together in the cell. Elucidation methods include metabolic inhibitors, biochemical genetics, and radioactively labeled substrates.

question

Emil Fischer

answer

1852 - 1911
Won the Nobel Prize in Chemistry in 1902. Studied the analysis, synthesis, and stereochemistry of simple sugars. Introduced the terminology we use today.

question

Enantiomers

answer

Stereoisomers with completely opposite chirality. Perfect mirror images. Identical chemical properties, but polarize light in opposite directions. This fact was discovered by Louis Pasteur. They are the D and L forms of a sugar.

question

Endergonic reaction

answer

Consumes phosphorylated chemicals, such as ATP, which donate their energy to processes that require energy, such as synthesis of metabolites, macromolecules, active transport, and mechanical motion.

question

Enol

answer

R-CH(OH)=CH₂
A common functional group.

question

Enolase

answer

aka Phosphopyruvate hydratase
Catalyzes the dehydration of 2-phosphoglycerate, the ninth step of glycolysis. Named after its reverse reaction.

question

Enolpyruvate

answer

The minor tautomer of pyruvate. Produced in glycolysis.

question

Enoyl-CoA hydratase

answer

Catalyzes the second step of beta oxidation. Water is added to trans-?2-enoyl-CoA, breaking the double bond between the ? and ? carbons and adding an alcohol group to the ? carbon, forming L-?-hydroxy-acyl-CoA.

question

Epimers

answer

Diasteromers that differ in chirality around one carbon. Simple to convert epimers back and forth.

question

Erythrulose

answer

A keto-tetrose. One chiral carbon. Two enantiomers: D and L.

question

Escherichia coli

answer

A common bacteria lab subject. A phototroph.

question

Ester

answer

R-C(=O)-O-R
A common functional group. A carboxylic acid bound to an alcohol with an ester linkage. Created by a condensation reaction.

question

Ester linkage

answer

The link formed by a condensation reaction between two carboxylic acids (such as fatty acids), or a carboxylic acid and an alcohol. Forms an ester or acid anhydride.

question

Ethanolamine

answer

OH-CH₂-CH₂-NH₂
The alcohol that is bound to PE.

question

Ether

answer

R-O-R
A common functional group.

question

Ethyl

answer

R-CH₂-CH₃
A common functional group.

question

Even fatty acid

answer

A fatty acid with an even number of carbons. Common in the body.

question

Exergonic reaction

answer

Catabolism of fuel molecules. Free energy is released, and is used to produce phosphorylated chemicals, such as ATP out of ADP.

question

F₁

answer

One of the components of ATP synthase. A peripheral membrane protein. First purified by Efraim Racker and colleages in the 1960s. Consists of 9 subunits: 3 ?, 3 ?, 1 ?, 1 ?, and 1 ?. The ? and ? subunits together form the ?3?3 complex.

question

F_o

answer

One of the components of ATP synthase. An integral membrane protein. The sight where oligomycin binds. A transmembrane protein. Includs multiple subunit c's that aggregate into a ring, and the stator arm which consists of subunits a and b2. The number of subunit c's depends on the species: 8, 10, 11, or 14.

question

FAD

answer

Fully reduced form: FADH₂
Semiquinone radical form: FADH
A flavin nucleotide. Carrier of single electrons or electron pairs. A flavin ring and a ribitol bound to an adenosine by a pyrophosphate linkage. In the electron transport chain FADH₂ results in 6 protons pumped into the intermembrane space.
FAD + 2e^- + 2H⁺ > FADH₂
FADH₂ + ?O₂ > FAD + H₂O
?E₀' = +1.04 V
?G₀' = -200 kJ/mol

question

Faraday constant (F)

answer

The charge of one mole of electrons. 96.5 e Coloumbs/mole.

question

Fat

answer

A lipid that functions in energy storage in animals. Mostly triglycerides. Insultes from the environment. More saturated than oils and has higher melting point. The most concentrated form of metabolic energy. Very reduced; a lot of free energy when oxidized. Very hydrophobic; can be stored in the cell without water. 10 kg of fat carries 500,000 kJ of energy. Its only purpose is energy storage.

question

Fatty acid

answer

The simplest lipid. A carboxylic acid with an unbranched hydrocarbon chain ranging from 4 to 36 carbons. Intermediates in metabolism. Free fatty acids are rare. Carbons are numbered numerically, with the Greek alphabet, or with the omega system. The longer and more saturated a fatty acid chain, the lower its solubility and higher its melting point. The building blocks of TAGs and phospholipids. In fat catabolism they are converted into acyl adenylate then fatty acyl-CoA thioester in a reaction catalyzed by acyl-CoA synthetase that completely hydrolyzes ATP.

question

Fatty acyl carnitine

answer

Fatty acyl-CoA thioester is converted into this catalyzed by carnitine acyl transferase. Can enter both mitochondrial membranes through transport proteins. It is converted back into fatty acyl CoA thioester in the mitochondrial matrix.

question

Fatty acyl-CoA thioester

answer

In fat catabolism fatty acids are converted into this after being converted into acyl adenylate. An ATP driven (full hydrolysis) reaction catalyzed by acyl-CoA synthetase in the outer mitochondrial membrane. Enter the mitochondria in the form of fatty acyl carnitine, a conversioncatalyzed by carnitine acyl transferase, are recoverted back into fatty acyl-CoA thioester inside the membrane by the same enzyme, and enter beta oxidation.

question

Fischer projection

answer

A standardized way of drawing linear monosaccharides. Carbons are numbered from top to bottom.

question

Fischer ring

answer

A standardized way of drawing cyclic sugars. A Fischer projection with a line connecting the carbons where cyclization takes place. An old-fashioned style from times when manual typsetters were used.

question

Flavin nucleotides

answer

Important redox reaction cofactors. Redox reactions occur on the Flavin rings. Carriers of single electrons or electron pairs. Often act as prosthetic groups, tighlty bound to enzymes. Includes FMN and FAD.

question

Flavin ring

answer

Dimethyl-isoalloxazine. A group on Flavin nucleotides and flavoproteins. It is yellow in colour. Flavins and flavoproteins are bright orange or yellow coloured. Obtained from vitamin B2, riboflavin.

question

Flavoproteins

answer

Contain Flavin rings. Enzymes that catalyze redox reactions with the help of Flavin nucleotides. Have a great diversity of reactions due to their ability to participate in one as well as two electron transfers.

question

FMN

answer

Fully reduced form: FMNH₂
Semiquinone radical form: FMNH
A Flavin nucleotide. Carrier of single electrons or electron pairs. A Flavin ring and ribitol bound to one phosphate.
FMN + 2e^- + 2H⁺ > FMNH₂

question

Franz Knoop

answer

In 1904 he labelled the omega carbons of fatty acids with phenyl groups, and fed the fats to dogs and collected their urine. Dogs fed fatty acids with even numbers of carbons had uring containing phenlacetic acid. Dogs fed fatty acids with odd numbers of carbons had urine containing benzoic acid. This proved that the carbons in fatty acids are metabolized two at a time, and that oxidation occurs at the beta carbon, not the alpha carbon. Discovered that citric acid is oxidized into ?-ketoglutarate.

question

Free energy (?G)

answer

Energy released by hydrolysis. Depends on the nature of the bond being hydrolyzed. Amides, esters, and phosphoesters have ?G values around 15 - 20 kJ/mol, and ATP has a ?G of 50 kJ/mol. The energy is passed onto drive other reactions such as biosynthesis
Phosphoenolpyruvate ; 1,3-biphosphoglycerate ; creatine phosphate ; ATP ; glucose 6-phosphate ; P_i

question

Friedrich Miescher

answer

1844 - 1895
First isolated DNA from the nuclei of white blood cells in 1869.

question

Fritz Lipmann

answer

Discovered coenzyme A, and first recognized the significance of phosphorylated compounds in bioenergetics. Shared the Nobel Prize in Physiology and Medicine with Hans Krebs in 1953.

question

Fructose

answer

A keto-hexose. Can form a pyranose ring or furanose ring, but more commonly forms a furanose ring. The carbonyl group bonds with the hydroxyl group on carbon 5.

question

Fructose-1,6-phosphate

answer

The product of the third step of glycolysis.

question

Fructose-6-phosphate

answer

The product of the second step of glycolysis.

question

Fumarase

answer

Catalyzes the hydration of fumarate to malate, the seventh step of the citric acid cycle.

question

Fumarate

answer

The product of the sixth step of the citric acid cycle. An alkene.

question

Furanose ring

answer

A five-sided sugar ring. Size of the ring depends on thermodynamics and geometry of the molecule. Example: fructose.

question

G3P dehydrogenase

answer

Catalyzes the oxidation of G3P, the sixth step of glycolysis.

question

Galactose

answer

An aldo-hexose.

question

Gamma (?) phosphate

answer

The third phosphate, bound to the beta phosphate in ATP by a high-energy phosphoanhydride bond.

question

Gas-liquid chromatography (GLC)

answer

Separates transesterfied fatty acids by chain length and saturation. The mobile phase is a gas.

question

Genetic code

answer

The "code" by which codons in RNA translate into amino acids during translation.

question

Genetic diseases

answer

A biochemical genetics method of elucidation. Analysis of the effects of genetic diseases where there is a deficiency in a specific enzyme.

question

George Beadle and Edward Tatum

answer

In 1940 they found that each enzyme ina cell is encoded by a specific gene.

question

Gibbs free energy (G)

answer

The change in G is proportional to the difference in reduction potential of the half-reactions of a redox reaction.
?G^0' = - nF?E^0'

question

Glucans

answer

Homopolysaccharides made from glucose. Includes starch, glycogen, cellulose, and chitin.

question

Glucokinase

answer

aka Hexokinase IV
Found in the liver.
KM = 8 mM

question

Gluconeogenesis

answer

The process in the liver that recycles lactate into glucose. Part of the Cori cycle.

question

Glucose

answer

A common aldo-hexose. Forms a pyranose. The carbonyl group binds to the hydroxyl group on carbon 5. Linear and cyclic forms have different chemical properties. The most common monosaccharide. Found in fructose, glycogen, cellulose, and starch. Breaks into monosaccharide form before entering glycolysis or the pentose phosphate pathway. Carries 150 kJ of energy in an adult human. The only possible fuel for many cells including red blood cells, renal medulla, brain, and sperm cells. The brain consumes 100 g daily. Blood gluose levels are normally 5 mM. Highly polar. Cannot enter cells by passive diffusion.

question

Glucose-6-phosphate

answer

The product of phosphorylation of glucose, the first step of glycolysis. It cannot leave the cell.

question

GLUTs

answer

GLUcose Transporters
Transport glucose across cell membranes. Stimulated by insulin in skeletal muscle and adipose tissue.

question

Glutamate

answer

An amino acid which can be produced from ?-ketoglutarate, a product of the citric acid cycle, by transaminase.

question

Glutamine synthesis

answer

Conersion of glutamate into glutamine by the enzyme-catalyzed condensation of ammonia with the gamma-carboxylic acid moiety of glutamate. The reaction is coupled to ATP hydrolysis. ATP reacts with glutamate, producing a mixed anhydride covalent intermediate, then ammonia acts as a nucleophile, reacting with the electrophilic carbonyl carbon. P_i is displaced and leaves the group.

question

Glyceraldehyde

answer

An aldo-triose. Has one chiral carbon.

question

Glyceraldehyde-3-phosphate (G3P)

answer

One of the products of the fourth step of glycolysis. DHAP is converted into it in step five.

question

Glycerol

answer

OH-CH₂-CH(OH)-CH₂-OH
Found in triglycerates and phosphoglycerides. Has a similar structure to glyceraldehyde. In fat catabolism it is converted into glycolytic intermediate.

question

Glycerol-3-phosphate

answer

Reduced from DHAP by cytosolic glycerol-3-phosphate dehydrogenase, and oxidized into DHAP by mitochondrial glycerol-3-phosphate dehydrogenase in the glycerol-3-phosphate shuttle mechanism.

question

Glycerol-3-phosphate dehydrogenase

answer

The enzyme in the glycerol-3-phosphate mechanism. Has a cytosolic version that catalyzes the reduction of DHAP into glycerol-3-phosphate, and a mitochondrial membrane protein version that catalyzes the oxidation of glycerol-3-phosphate into DHAP, producing an FADH₂ in the membrane, which passes H₂ to coenzyme Q.

question

Glycerol-3-phosphate shuttle

answer

A mechanism for transporting NADH and NAD⁺ across membranes. Found int he brain and muscles. Cytosolic glycerol-3-phosphate dehydrogenase reduces DHAP, using NADH, in the cytosol, forming glycerol-3-phosphate. Mitochondrial glycerol-3-phosphate oxidizes glycerol-3-phosphate into DHAP, producing FADH₂ on the matrix side which passes H₂ to coenzyme Q. NADH doesn't physically cross the membrane, but its charge does.

question

Glycogen

answer

A glucan. Stores energy in animals. Carries 2,500 kJ of energy in an adult human.

question

Glycolipid

answer

Molecules containing both sugar and lipid portions. Important constituents of cell membranes. Blood groups are defined by glycolipids on the outer surface of blood cells. Includes sphingolipids and gangliosides.

question

Glycolysis

answer

"Sugar breakdown"
The central pathway in carbohydrate metabolism. Occurs in the cytosol. Glucose is converted into pyruvate in ten steps divided into the preparatory and payoff phases. The only pathway which can provide energy under anaerobic conditions; anaerobic organisms are dependent on glycolysis.
Net yield: 2 ATP and 2 NADH.

question

Glycolytic intermediate

answer

Glycerol is converted into this during fat catabolism.

question

Glycoside

answer

Two cyclic sugar molecules bonded by a glycosidi bond. Includes polysaccharides, nucleosides, and digoxin.

question

Glycosidic bond

answer

An ether bond between the anomeric carbon of one cyclic sugar and a hydroxyl group of another cyclic sugar. Either "up" (?) or "down" (?) oriented, based on the anomeric carbon. The most important formation in sugars.

question

GTP

answer

A high-energy compound which can exchange energy for ATP.

question

Guanidium

answer

R-NH-C(=NH₂⁺)-NH₂
A common functional group.

question

Guanine (G)

answer

6-oxo-2-aminopurine
A purine. Found in DNA and RNA. Discovered in guano (bird manure). In DNA it forms 3 H bonds with cytosine. Its ribose nucleoside is guanosine. Its deoxyribose nucleoside is deoxyguanosine.

question

Guanosine (G)

answer

The ribose nucleoside of guanine.

question

Gulose

answer

An aldo-hexose.

question

Half-channels

answer

Channels in subunit a of F_o of ATP synthase. One allows protons to pass from the inter-membrane space to an aspartate residue on an adjacent subunit c, breaking the bond to arginine on a subunit a. The subunit c ring is free to rotate. The other allows protons to pass from another subunit c into the matrix. This mechanism drives the spinning of the subunit c ring.

question

Half-reaction

answer

An oxidation and a reduction reaction. Their sum is the total overall reaction.

question

Hans Krebs

answer

1900 - 1981
Won the Nobel Prize in 1953 with Fritz Lipmann. Found that malonate blocks respiration leading to the accumulation of succinate. Malonate acts as a competitive inhibitor to succinate dehydrogenase that catalyzes the oxidation of succinate. Krebs realized the metabolism of organic acids is cyclical, not linear. By 1937 he had the citric acid cycle worked out. Involvement of acetyl CoA was not appreciated until 1945 when Lipmann discovered it was the feedstock to the cycle, rather than pyruvate.

question

Haworth structure

answer

A standardized way of drawing cyclic sugars. The anomeric carbon is drawn on the right, with the ester bond drawn in the top right area. Hydroxyl groups drawn to the left in Fischer projections are drawn above the ring, and hydroxyl groups drawn to the right are drawn below the ring.

question

Heme

answer

A prosthetic group present in hemeproteins. A porphyrin with four pyrrole rings forming a tetra pyrrole ring. Its four N atoms are positioned perfectly for binding to iron ions.

question

Hemeproteins

answer

Proteins with a heme prosthetic group. Includes hemoglobin and cytochromes. Some have the heme ring covalently linked in and some do not.

question

Hemiacetal

answer

An aldehyde that has had a condensation reaction with an alcohol. Forms a new chiral carbon. Includes aldose rings.

question

Hemiketal

answer

A ketone that has had a condensation reacction with an alcohol. Forms a new chiral carbon. Includes ketose rings.

question

Heptose

answer

Monosaccharides with 7 carbons.

question

Heteroatoms

answer

Non-carbon atoms, such as nitrogen, oxygen, or sulfur.

question

Heterocycles

answer

Cyclical molecules with heteroatoms. Includes nucleotide bases.

question

Heteropolysaccharides

answer

Polysaccharides made up of two or more types of monosaccharides.

question

Hexokinase

answer

An enzyme that phosphorylates glucose. There are four wchih can catalyze the first step of glycolysis: I, II, III, and IV (glucokinase). The type used is physiologically important. All have a KM value of 0.1 mM except IV which is 8 mM.

question

Hexose

answer

Monosaccharides with 6 carbons. The most common monosaccharide in nature. Includes psicose, fructose, sorbose, and tagatose.

question

High energy bonds

answer

Sometimes drawn as squiggles "~". The phosphoanhydride bonds between beta and gamma phosphates are high energy, but not the phosphate ester bond of the alpha phosphate.

question

High-performance liquid chromatography (HPLC)

answer

Separates transesterfied fatty acids by chain length and saturation.

question

Homocystein

answer

Cystein with one extra CH₂ group. An amino acid.

question

Homopolysaccharide

answer

A polysaccharide made of one type of sugar. Includes glucans.

question

Hydration

answer

Water is added to a molecule, but it does not break.

question

Hydration of fumarate to malate

answer

The seventh step of the citri acid cycle. Fumarase adds water to fumarate, forming malate.

question

Hydride ion

answer

Two electrons and one proton. Has a negative charge. A reducing equivalent. Has two electrons.

question

Hydrogen atoms

answer

A reducing equivalent. Has one electron.

question

Hydrolysis

answer

An energetically favourable reaction. Has a negative ?G. Water is added to a molecule, breaking it.

question

Hydrolysis of gamma linkage

answer

Breaking of a high energy bond. One P_i and one ATP is released. The ADP is immediately ionized, releasing a proton (this can drive the reaction in low pH). Electrostatic repulsion of the negative phosphates is released. The product is lower in energy and has greater resonance stabilization.

question

Hydrolysis of mixed anhydride

answer

The seventh step of glycolysis. The first substrate level phosphorylation. Phosphoglycerate kinase breaks the high energy bond of 1,3-bis-phosphoglycerate, forming 4-phosphoglycerate, and generating one ATP (two ATP per glucose). Mg²⁺ is a catalyst.

question

Hydrophobic

answer

Molecules that partition into the organic solvent phase during two-phase extraction of a cell extract.

question

Hydroquinone

answer

The fully reduced form of quinone. Both ketones are reduced.

question

Hydroxyl

answer

R-OH
aka Alcohol
A common functional group. Acts as the nucleophile in glycosidic bonds.

question

Idose

answer

An aldo-hexose.

question

Imidazole

answer

A common functional group.

question

Imine

answer

R-C(=N-R)-R
A common functional group.

question

Inner mitochondrial membrane (IMM)

answer

Part of a mitochondria. Highly folded, with high surface area. Rich in proteins; about 65% its mass is protein. Contains cardiolipin. Highly impermeable to most solutes.

question

Inorganic ions

answer

Can act as cofactors. Includes Fe²⁺, Mg²⁺, Mn²⁺, Zn²⁺, and Cu²⁺.

question

Insulin

answer

Stimulates GLUT-mediated glucose uptake in skeletal muscle and adipose tissue. Diabetes is a lack of insulin or a reduced response to insulin.

question

Intermembrane space

answer

Part of a mitochondria. A space similar to the cytosol.

question

Isocitrate

answer

The product of the second step of the citric acid cycle. A secondary alcohol, which is more easily oxidized.

question

Isocitrate dehydrogenase

answer

Catalyzes the oxidation of isocitrate into ?-ketoglutarate, the third step of the citric acid cycle.

question

Isomerase

answer

Enzymes that change a molecule into an isomer of that same molecule; chemical formula stays the same. Includes mutases.

question

Isomerization of citrate

answer

The second step of the citric acid cycle. Aconitase reversibly isomerizes citrate by first dehydrating it, forming cis-aconitate, then rehydrating it, forming isocitrate.

question

Isomerization of DHAP

answer

The fifth step of glycolysis. End of the preparatory phase and beginning of the payoff phase. Triose phosphate interchanges the keto group on DHAP for a hydroxyl group, forming G3P.

question

Isozyme

answer

Different enzymes which catalyze the same reaction. Encoded by different genes.

question

John E. Walker

answer

Won the Nobel Prize in Chemistry in 1997 for discovering the structure of F₁ of ATP synthase.

question

Ketone

answer

R-C(=O)-R
A carbonyl group. A common functional group.

question

Ketopyruvate

answer

The major tautomer of pyruvate.

question

Ketose

answer

Polyhydroxy hetone
A monosaccharide where the carbonyl group is a ketone.

question

Kinase

answer

An enzyme which catalyzes phosphorylation reactions.

question

L-?-hydroxy-acyl-CoA

answer

The product of the second step of beta oxidation. The beta carbon is chiral, but only the L stereoisomer can be made.

question

L-sugars

answer

The chiral carbon furthest from the carbonyl group has the same configuration as L-glyceraldehyde. In a Fischer projection the hydroxyl group is drawn to the left. Uncommon in biochemistry.

question

Lactate

answer

The product of anaerobic conditions oxidation of pyruvate. Recycled into glucose in the gluconeogenesis pathway.

question

Lactate dehydrogenase

answer

Catalyzes the oxidation of pyruvate in anaerobic conditions.

question

Lactose

answer

gal(?1 > 4)glc
A disaccharide formed between the anomeric carbon of galactose in ? formation, and carbon 4 of glucose. Forms an equilibrium between ? and ? anomers of the free anomeric carbon in glucose. A reducing sugar. Found in dairy products.

question

Laurate

answer

12:0
aka Lauric acid
aka Dodecanoic acid
"Bay"
"Laurel"
A saturated fatty acid with 12 carbons.
Melting point: 44.2?C.

question

Lingoceric acid

answer

24:0
aka Tetracosanoic acid
"Wood"
"Wax"
A saturated fatty acid with 24 cabrons.
Melting point: 86.0?C.

question

Linoleate

answer

18:2(?9,12)
aka Linoleic acid
aka Octadecadienoic acid
An unsaturated fatty acid with 18 carbons and 2 double bonds on carbons 9 and 12. Linoleic aid.
Melting point: 1 - 5°C.

question

Linolenate

answer

18:3(?9,12,15)
aka Linolenic acid
aka Octadecatrienoic acid
An unsaturated fatty acid with 18 carbons, and 3 double bonds on carbons 9, 12, and 15.
Melting point: - 11°C

question

Lipase

answer

Catabolyzes the hydrolysis of triglycerides into three fatty acids and a glycerol.

question

Lipid

answer

A class of molecules defined by their hyrophobicity. Aggregate into complexes such as micelles and bilayers in aqueous environments. Includes fats, oils, phospholipids, sterols, coenzyme Q, paracrine hormones, steroides, vitamins A, D, E, and K, and waxes.

question

Lipid peroxidation

answer

Uncontrolled oxidation. Occurs if you leave butter out for too long and it goes rancid.

question

Lipoic acid

answer

Used in the synthesis of lipomide.

question

Lipomide

answer

A cofactor used in PDH complex. Derived from lipoic acid.

question

Lipoproteins

answer

Molecules containing both protein and lipid portions. Associated with cardiovascular health and diseases. Includes VLDL, LDL, and HDL.

question

Liposome

answer

aka Vesicle
A bilayer that has folded into itself, forming a "proto-cell". Synthetic lipososmes can be used to deliver drugs.

question

Loose

answer

A conformation of the ? and ? subunits in F₁ of ATP synthase. Binds ADP and P_i.

question

Low-energy phosphorylated chemicals

answer

Simple phosphate esters, alcohols, sugar phosphates, esters, amids, and glucose 6- phosphate.

question

Lyxose

answer

An aldo-pentose.

question

Major groove

answer

The larger gap in a DNA strand. The edges of bases are more exposed through this gap.

question

Malate

answer

The reduced form of oxaloacetate. Passes into the mitochondrial matrix through specific transporter protein. Part of hte Malate-Aspartate shuttle. The product of the seventh step of the citric acid cycle. An alcohol.

question

Malate-Aspartate shuttle

answer

A mechanism for transporting NADH and NAD+ across membranes. Found in the liver, kidneys, and heart. In the cytosol, NADH reduces oxaloacetate into malate, which passes over the membrane into the mitochondrial matrix through a specific transporter protein. In the matrix, NAD+ reduces malate back into oxaloacetate, wchih is converted into aspartate through a transamination process. Aspartate crosses the membrane through a trasnporter protein and undergoes a reverse transamination into oxaloacetate. NAD doesn't physically cross the membrane, but its charge does.

question

Malonate

answer

A competitive inhibitor of succinate dehydrogenase.

question

Maltose

answer

glc(?1 > 4)glc
A disaccharide formed between the anomeric carbon of glucose in ? formation, and carbon 4 of glucose. A reducing sugar. Found in malted grain by the breakdown of starch.

question

Mannans

answer

Homopolysaccharides made of mannose.

question

Mannose

answer

An aldo-hexose.

question

Matrix

answer

The inside of a mitochondria. Very different composition from the cytosol.

question

Metabolic inhibitors

answer

A method of elucidation. Inhibitors block the metabolic pathway at certain points, leading to a build-up of the preceding metabolite.

question

Metabolic pathway

answer

Each step is enzyme-catalyzed. Many steps stick to central "themes". One-way. Well regulated by transcriptional control of enzymes, inhibition/actiation via reversible phosphorylation, and/or feedback inhibition. Regulation takes place near the beginning of the pathway.

question

Metabolism

answer

Complex metabolic reactions occurring in cells. Involves compounds, reactions, genes, cellular physiology, and energy. Has two halves: anabolism and catabolism.

question

Metabolites

answer

Intermediate products formed during a metabolic pathway.

question

Methyl

answer

R-CH₃
A common functional group.

question

Methylene-bridged

answer

An unsaturated carbon chain where the double bond pattern is double-single-single-double-single-single.

question

Micelle

answer

The smallest, simplest lipid aggregate in aqueous solution. Round clusters of lipid.

question

Minimal medium

answer

Water, sugar, nitrogen, and mineral salts. This is all E. coli, and other phototrophs need to survive.

question

Minor groove

answer

The smaller gap in a DNA strand.

question

Mitochondria

answer

Probably started off as a free-living cell that was engulfed by a larger cell and began a symbiotic existence. Carry their own DNA and reproduce independently of the cell. Has a double membrane. Has an outer membrane, intermembrane spae, inner mitochondrial membrane, and mitochondrial matrix. Beta oxidation occurs here.

question

Mitochondrial electron transport chain

answer

The electron transport chain found in humans. NADH2 passes reducing equivalents to complex I. FADH2 passes reducing equivalents to complex II. Complexes I and II both pass reducing equivalents to coenzyme Q, which passes reducing equivalents to complex III, which passes reducing equivalents to cytochrome C, which passes reducing equivalents to complex IV, which passes reducing equivalents to oxygen.

question

Mixed anhydride

answer

R-C(=O)-O-PO^-(=O)-OH

question

Mixed tryglyceride

answer

A triglyceride with 2 or 3 different kinds of fatty acids linked to it.

question

Monoester

answer

A phosphoric aid that has one ester group.

question

Monosaccharide

answer

aka Simple sugar
One sugar unit. Water-soluble. Poorly soluble in organic solvents. Colourless. Sweet to the taste. Has a carbonyl group and at least two hydroxyl groups.

question

Monosaturated fatty acid

answer

A fatty acid with one double bond.

question

Mutarotation

answer

In solutions, glucose forms an equilibrium between its linear (trace amounts), cyclical ? (about 1/3), and cyclical ? (about 2/3) forms. The name comes from the phenomenon of polarity appearing to rotate as equilibrium is reached.

question

Mutase

answer

An isomerase that moves a functional group from one position to another.

question

Myristate

answer

14:0
aka Myristic acid
aka Tetradecanoic acid
"Myrtle"
"Nutmeg"
A saturated fatty acid with 14 carbons.
Melting point: 53.9°C

question

NADH

answer

Oxidized form: NAD⁺
Nicotinamide adenine dinucleotide
A pyridine nucleotide. A carrier of electron pairs. Used as an oxidizing agent in catabolic processes such as fatty aid oxidation and the citric acid cycle. The resulting NADH is re-oxidized in the electron transport chain. A nicotinamide ring bound to a pentase sugar by a pyrophosphate linkage. Its overall charge is actually -1, but this is ignored. In the electron transport chain it results in 10 protons being pumped into the intermembrane space.
NAD⁺ + 2e^- + H⁺ > NADH
NADH + H⁺ + ?O₂ > NADH⁺ + H₂O
?E^0' = +1.14 V
?G^0' = -220 kJ/mol

question

NADPH

answer

Oxidized form: NADP⁺
Nicotinamide adenine dinucleotide phosphate
A pyridine nucleotide. A carrier of electron pairs. Its only difference from NADH is that it has a phosphate group at the 2' position of the adenosine moiety. Used as a reducing agent in biosynthesis. Its overall charge is actually -3, but this is ignored.
NADHP⁺ + 2e^- + H⁺ > NADPH

question

Naming fatty acids

answer

Example:
Linoleic acid 18:2(?^9,12) means it has 18 carbons and 2 double bonds on carbons 9 and 12.

question

Niacin

answer

aka Vitamin B₃
Nicotinamide rings are derived from it.

question

Nicotinamide ring

answer

A group found in pyridine nucleotides. Derived from niacin.

question

Non-reducing sugar

answer

A sugar that does not have a free anomeric carbon, such as a glycoside where the anomeric carbon of two monosaccharides have a glycosidic bond with each other. Cannot open to its linear form.

question

Nucleic acids

answer

RNA and DNA. Encode genetic information. Polynucleotides.

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Nucleic base

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A component of nucleotides. Heterocycles. Includes purines (adenine and guanine), and pyrimidines (cytosine, thymine, and uracil). Hydrophobic.

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Nucleoside

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A nucleic base with a glycosidic bond to a sugar, ribose or deoxyribose. Sugar carbons are numbered with a prime ('), and base carbons are numbered normally.

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Nucleotide

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A phsophorylated nucleoside. Phosphoric acid attaches to the carbon 5' hydroxyl group (on the sugar).

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Odd fatty acid

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A fatty acid with an odd number of carbons. Uncommon in the body.

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Oil

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A lipid that functions in energy storage in plants. Mostly triglycerides. Less saturated than fats and has a lower melting point.

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Oleate

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18:1(?⁹)
aka Oleic acid
aka Octadecenoic acid
"Oil'
An unsaturated fatty acid with 18 carbons and one double bond on carbon 9.
Melting point: 13.4?C

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Oligomycin

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Inhibits the ATP synthase enzyme by binding to F_o.

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Oligosaccharides

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Short chains of 4 - 20 cyclic sugars connected by glycosidic bonds. Includes starch and cellulose.

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Omega (?) carbon

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In fatty acid nomenclature, the terminal carbon on a fatty acid chain. Subsequent carbons are numbered numerically (eg. omega 2, omega 3). Omega 3 and omega 6 acids (with double bonds on carbons omega 3 and 6) are important in human nutrition. Method used for naming PUFAs.

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Open

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A conformation of the ? and ? subunits in F₁ of ATP synthase. Releases ATP. No bound nucleotides.

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Organic solvents

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Dissolve lipids. Includes chloroform, acetone, ether, and hexane.

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Oswald Avery

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With colleages, first identified DNA as the genetic material in the 1940's.

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Outer membrane

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Part of a mitochondria. Freely permeable to small molecules and ions.

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Oxaloacetate

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The oxidized form of malate. Part of the Malate-Aspartate shuttle mechanism. The product of the eigth and last step of the citric acid cycle. It is fed back into the beginning of the cycle. Can be converted into acetate by replacing the keto group with an amino group.

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Oxidation of G3P

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The sixth step of glycolysis. The energy key to glycolysis. G3P binds to a cysteine residue on G3P dehydrogenase, reacts with an enzyme-bound thioester that is attacked by P_i, is oxidized with 2 electrons, using NAD⁺, and is phosphorylated, forming 1,3-bis-phosphoglycerate.

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Oxidation of malate to oxaloacetate

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The eigth step of the citric acid cycle. Malate dehydrogenase uses NAD⁺ to oxidize malate into oxaloacetate.

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Oxidation of succinate to fumarate

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The sixth step of the citric acid cycle. Succinate dehydrogenase uses FAD to oxidize succinate into fumarate. The beta carbon is oxidized, similar to beta oxidation.

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Oxidation reaction

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An oxidized universal electron carrier takes away two hydrogens. Always occurs along with a reduction reaction. NAD(P)⁺ accepts a hydride ion, becoming NAD(P)H, and the remaining proton is released into the environment.

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Oxidative decarboxylation of ?-ketoglutarate

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The fourth step of the citric acid cycle. ?-ketoglutarate dehydrogenase uses NAD⁺ and CoASH to form succinyl CoA and CO₂. Similar to the reaction catalyzed by PDH in pyruvate oxidation.

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Oxidative decarboxylation of isocitrate

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The third step of the citric acid cycle. Isocitrate dehydrogenase uses NAD⁺ to oxidize isocitrate into ?-ketoglutarate, producing CO₂.

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Oxidative phosphorylation

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Captures energy of the electron transport chain, making ATP. The final stage of oxidation of carbohydrates, lipids, and amino acids. Oxidation of reduced cofactors, NADH and FADH₂. Occurs in the mitochondria.

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Oxidizing agent

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aka Oxidant
Accepts an electron from the reducing agent in a redox reaction. Has the higher reduction potential.

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Oxygen

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O₂
The strongest oxidizing agent. When it first began to accumulate in the atmosphere it was a vast new energy source, but also a danger. Can cause uncontrolled oxidation such as fires, and lipid peroxidation. The terminal electron acceptor of electron transport chains. In the mitochondrial electron transport chain it accepts reducing equiavlents from complex IV.

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P/O ratio

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The number of ATP synthesized per mole of oxygen atoms reduced to water. Non-integral numbers are due to chemoismotic coupling.
NADH = 2.5
FADH₂ = 1.5
Fats = 7(nuber of carbons) - 6
Glucose (using glycerol-3-phosphate shuttle) = 30
Glucose (using malate-aspartate shuttle) = 32

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Palmitate

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16:0
aka Palmitic acid
aka Hexadecanoic acid
"Palm"
A saturated fatty acid with 16 carbons.
Melting point: 63.1?C

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Palmitoleic acid

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16:1(?⁹)
aka Hexadecenoic acid
An unsaturated fatty acid with 16 carbons and one double bond on carbon 9.
Melting point: -0.5 - +1?C

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Palmitoyl CoA

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Coenzyme A carrying palmitate.

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Pantothenic acid

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aka Vitamin B₅
Coenzyme A is derived from pantothenic acid.

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PAPS

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A carrier of sulfate groups. An adenosine derivative coenzyme.

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Paracrine hormone

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A lipid that functions as a signalling molecule. Includes prostaglandins and diaclyglycerols.

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Partial dehydrogenation

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Used in manufacturing margarine. Isomerizes the double bonds, creating trans fats.

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Paul Boyer

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Studied the kinetics of ATP synthase using isotopes of oxygen to measure the exchange of phosphategroups among ADP, ATP, and P_i. Found that, on the active site of ATP synthase, the equilibrium constant is almost 1. This means that ATP binds to the active site very tightly, and releasing it is the energy-consuming process. Released using rotational catlysis.
ADP + P_i > ATP + H₂O

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Payoff phase

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The last five steps of glycolysis. ATP is produced.

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Pentose

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Monosaccharides with 5 carbons. Two chiral carbons. Includes ribulose, xylulose, ribose, arabinose, xylose, and lyxose.

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Pentose phosphate pathway

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An alternative catabolic pathway for glucose, other than glycolysis.

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Perspective formula

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A standardized way of drawing linear monosaccharides. Wedges and dashed lines illustrate the 3D nature of the sugar.

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Peter Michell

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In the 1960's, proposed the chemiosmotic hypothesis to explain the connection between the electron transport chain and ATP synthesis.

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Phenol

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An alcohol.

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Phenylacetic acid

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Found in the urine of dogs fed fatty acids with an even number of carbons in Franz Knoop's experiment. Phenyl-labeled acetic acid.

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Phosphate ester

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An alohol and phosphoric acid linked by a phosphodiester linkage.

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Phosphatidylcholine (PC)

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aka Lecithin
A phospholipid with a choline group. A major class of membrane lipids.
Net charge at pH 7: 0

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Phosphatidylethanolamine (PE)

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A phospholipid with an ethanolamine group. A major class of membrane lipids.
Net charge at pH 7: 0

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Phosphatidylglycerol (PG)

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A phospholipid with a glycerol group.
Net charge at pH 7: -1

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Phosphatidylserine (PS)

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A phospholipid with a serine group.
Net charge at pH 7: -1

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Phosphoanhydride

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R-C(=O)-O-POO^--OH
A common functional group. A carboxylic acid and a phosphoric acid linked by a phosphodiester linkage. The high-energy links between the beta and gamma phosphates in ATP.

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Phospho-enol-pyruate (PEP)

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The product of the ninth step of glycolysis. A high-energy phosphorylated compound.

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Phosphodiester linkage

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The link formed between an alcohol or carboxylic acid and a phosphoric acid. Forms a phosphate ester or phosphoanhydride. Joins sugars and phosphates in the sugar-backbone of polynucleotides by binding the 5' carbon of one sugar to the 3' carbon of another.

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Phosphoenzyme intermediate

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The intermediate of the fifth step of the citric acid cycle. Succinyl CoA and P_i bound to succinyl CoA synthetase.

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Phosphoester bond

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The bond between a phosphoric acid and a sugar. The low-energy alpha phosphate in ATP.

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Phosphofructokinase

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Catalyzes the phosphorylation of fructose-6-phosphate, the third step of glycolysis.

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Phosphoglycerate kinase

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Catalyzes the hydrolysis of mixed anhydride, the seventh step of glycolysis.

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Phosphoglycerate mutase

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Catalyzes the conversion of 3-phosphoglycerate to 2-phosphoglycerate, the eighth step of glycolysis. A mutase. Mg²⁺ is a catalyst.

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Phosphohexose isomerase

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Catalyzes the isomerization of glucose-6-phosphate, the second step of glycolysis. Has the same mechanism as triose phosphate.

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Phosphohexose isomerisation

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The second step of glycolysis. Phosphohexose isomerase isomerizes glucose-6-phosphate into fructose-6-phosphate. Mg²⁺ is a catalyst. The ring is opened, the keto group on carbon 1 is interchanged with the hydroxyl group on carbon 2, and the ring recloses as a pyranose ring.

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Phospholipid

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aka Phosphoglyceride
aka Glycerophospholipid
Glycerol with ester linkages to fatty acids on carbons 1 and 2 (the "tails"), and a phosphodiester linkagesto a phosphoric acid, which is also bound to an alcohol, on carbon 3 (the "head"). Due to the hydrophobic effect, it forms bilayers. Functions as a structural element of biological membranes. Includse PC, PE, PS, and PG.

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Phosphoric acid

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H₃PO₄
A strong acid. At neutral pH it is in an equilibrium between its -1 and -2 charged forms, which is denoted by P_i. Can form monoesters, diesters, and triesters. A component of phospholipids and nucleotides.

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Phosphoryl

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R-O-POO^--O-POO^--O
A common functional group.

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Phoshphorylation

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The addition of a phosphoric acid group to a molecule. Adds negative charge. Increases solubility. Creates phospholipids, sugar-phosphates, proteins, and nucleotides.

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Phosphorylation of fructose-6-phosphate

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The third step of glycolysis. Phosphofructokinase irreversibly phosphorylates carbon 1 of fructose-6-phosphate, forming fructose-1,6-biphosphate. Mg²⁺ is a catalyst. Uses ATP.

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Phosphorylation of glucose

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The first step of glycolysis. Glucose is irreversibly phosphorylated on carbon 6. Forms glucose-6-phosphate. Mg²⁺ is a catalyst. Uses ATP. Catalyzed by one of four hexokinases: I, II, III, or IV; the type used is physiologically important.

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Photo 51

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A famous X-ray crystallography image taken by Rosalind Franklin. Tells us that DNA is a helix shape with two periodicities: one 3.4 A and the other 34.0 A. Watson and Crick used this photograph to help them determine the structure of DNA.

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Phototroph

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"First food". Needing only minimal medium.

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Pigment

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A lipid that colours organisms. Includes carotene.

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Plectonemically coiled

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Wrapped around one another so that you cannot pull them apart unless you start at one end and unwind the whole strand. The two polynucleotide strands in DNA are plectonemically coiled.

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Polynucleotide

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Polymers of nucleotides connected by the sugar-phosphate backbone which is held together with phosphodiester links. Has a 5' end and a 3' end.

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Polysaccharide

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Polymers of 20+ monosaccharide units. Often branched. Sugar chains can have multiple hydroxyl groups bound to anomeric carbons. Includes homopolysaccharides and heteropolysaccharides.

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Polyunsaturated fatty acid (PUFA)

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An unsaturated fatty acid with double bonds separated by methylene carbons. Includes conjugated and methylene-bridged carbon chains. Named using the omega carbon counting method.

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Porphyrin

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A particular ring structure that binds to metal ions. Includes heme.

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Potentiometer

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Measures the reduction potential between two half reactions separated by a salt ridge. For biochemicals such as proteins, redox-active dye is added to ease the passage of electrons from proteins to the metal wire.

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Precursor-product relationship

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The product of each step in a metabolic pathway is the precursor of the next step. Each step does not produce much change, but the whole pathway together can have a larger change.

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Preparatory phase

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The first five stages of glycolysis. ATP is used to phosphorylate and activate glucose.

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Protein

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Carries 100,000 kJ of energy in an adult human.

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Proton gradient

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A reservoir of energy created by the electron transport chcain.

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Proton ionophore

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Ion carrier. Includes DNP.

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Proton motive force

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The energy stored in the proton gradient. Has two components: chemical potential energy and electrical potential energy. One proton produces a ?G of 20 kJ/mol. Used for bacterial flagellum rotation, phosphate translocase symporter, and ATP synthesis. Other uses cause the P/O ratio to be non-integral.

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Psicose

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A keto-hexose.

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Purines

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A class of nucleotide bases. Bicyclic. A pyrimidine ring fused with an imidazole ring. Bigger than pyrimidines. Has 4 nitrogens, and 5 carbons. Forms a glycosidic bond from the NH at position 1 in nucleosides. Includes adenine and guanine.

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Pyranose

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A six-sided sugar ring. Size of the ring depends on thermodynamics and geometry of the molecule. Example: glucose.

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Pyridine nucleotides

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The most important biological reducing and oxidizing agents. The positive charge is on the N atom of the oxidized nicotinamide rings. Includes NADH, and NADPH. Carriers of electoron pairs.

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Purimidines

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A class of nucleotide bases. A six-sided ring. Forms a glycosidic bond from the NH at position 9 in nucleosides. Includes cytosine, thymine, and uracil.

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Pyrophosphatase

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An enzyme that catalyzes the hydrolysis of the phosphoanhydride bond in PP_i, releasing two P_i.

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Pyrophoshpate (PP_i)

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A dimer of phosphoric acid moieties linked by a high energy phosphoanhydride bond. In the complete hydrolysis of ATP it is released from the hydrolysis of the beta linkage, and then its phosphoanhydride bond is broken, releasing two P_i, catalyzed by pyrophosphatase.

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Pryophosphate linkage

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Two phosphate groups connecting two groups. Found in pyridine nucleotides, FAD, and coenzyme A.

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Pyrophosphoryl

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A group which ATP can add to substrates or enzymes, driving reactions.

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Pyrrole ring

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Five-membered ring with one N atom.

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Pyruvate

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A three-carbon compound. The product of glycolysis. Tautomerizes into enolpyruvate and ketopyruvate. Ketopyruvate is the predominant form. This tautomerization drives glycolysis. Pyruvate is oxidized in anaerobic conditions, alcoholic fermentation, or aerobic conditions.

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Pyruvate decarboxylase

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Catalyzes the first step of alcoholic fermentation. Pyruvate is converted into acetaldehyde. Animals lack this enzyme, so cannot perform alcoholic fermentation.

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Pyruvate dehydrogenase complex (PDH)

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The link between glycolysis and the citric acid cycle. In the mitochondrial matrix. A series of three enzymes that catalyze the irreversible reduction of pyruvate into acetyl CoA. Five cofactors are used: TPP, lipomide, NAD⁺, FAD, and coenzyme A.

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Pyruvate kinase

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Catalyzes the transfer of a phosphoryl group from PEP to ADP. Named for its reverse reaction.

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Quinone

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An organic functional group with two ketone oxygens in a conjugated six-membered ring. Oxidizing agent. Reduced forms are semiquinone and hydroquinone.

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Radioactively labeled substances

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Radioisotopes such as carbon 14 are made by bombarding a target with neutrons. Carbon 14 is then tracked using scintillation counting or autoradiography. Compounds are identified by chromatography such as HPLC as it goes through the metbaolic pathway like normal, forming labelled peaks.

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Red blood cells

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Lack mitochondria. Can only oxidize pyruvate in the anaerobic conditions pathway.

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Redox couple

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The oxidized and reduced form of a compound.

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Redox reaction

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An oxidation reaction and a reduction reaction. May be written separately as half-reactions.

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Reduced cofactors

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NADH and FADH₂. Oxidized in the electron transport chain using O₂ as the ultimate oxidant. Energy is captured to form ATP in oxidative phosphorylation.

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Reducing agent

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aka Reductant
Donates an electron to the oxidizing agent in a redox reaction. Has the lower reduction potential.

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Reducing end

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The end of a disaccharide or polysaccharide with a free anomeric carbon.

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Reducing equivalents

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Passed from molecule to molecule in the direction of higher reducing potential in the electron transport chain, until taken by oxygen. Transfer of Fe³⁺ to Fe²⁺, hydrogen atoms, or hydride ions.

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Reducing sugar

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Sugars that reduce Cu2+ to Cu+, forming a red precipitate. Only occurs with the linear form of a sugar. A cyclical sugar with a free anomeric carbon is a reducing sugar sine it forms an equilibrium with its linear form.

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Reduction potential (E)

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A measure of the tendency to accept electrons. Measured with a potentiometer. Electron flow to the half reaction with a higher reduction potential. When changing the direction of electron flow, the sign of reduction potential is flipped. If E is positive, the reaction occurs spontaneously.

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Reduction reaction

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A reduced universal electron carrier adds an electron. Always occurs along with an oxidation reaction.

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Respiratory inhibitors

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Used to elucidate the electron transport chain. Blocks parts of oxidative phosphorylation. Include rotenone, barbiturates, and cyanide. Cofactors before the block are reduced, and cofactors after the block are oxidized.

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Reverse transcription

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An exception to the Central Dogma of Molecular Biology. Sometimes RNA can be a template for DNA.

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Ribitol

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A sugar-alcohol. Attached to flavin in riboflavin. Found in FAD and FMN.

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Riboflavin

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aka Vitamin B₂
A flavin ring and ribitol. Flavin rings are obtained from this, making flavin nucleotides and flavoproteins.

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Ribonucleic acid (RNA)

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A nucleic acid. Contains ribose sugar in beta form. Hydrolyzes quickly under alkaline conditions. The free 2' group acts as a nucleophile, hydrolyzing phosphodiester linkage by displacement. Has many functions, including mRNA, ribozymes, and RNA interference that regulates gene expression.

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Ribose

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An aldo-pentose. Forms a furanose ring. The sugar in RNA.

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Ribulose

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A keto-pentose. Epimer of xylulose.

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Rosalind Franklin

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In the 1950's, with Maurice Wilkins, used X-ray crystallography to study DNA. The first person to successfully create a useful X-ray diffraction image of DNA: photo 51.

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Rotational catalysis

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The mechanism by which ATP synthase releases ATP due to the rotation of the ? subunit.

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Rotor

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The rotating part of any engine.

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SAM

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A carrier of methyl groups. An adenosine derivative coenzyme.

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Saturated

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A fatty acid with no double bonds. Fully extended chain. Packs together tightly with other fatty acid chains with Van der Waals forces. Gives them a higher melting point. More solid.

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Semiquinone

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The partially reduced form of quinone. One of the two ketones is reduced. An intermediate to hydroquinone.

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Semiquinone radical

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Partially reduced forms of FAD and FMN; FADH and FMNH, or the partially reduced form of cytochrome Q. Only one electron is accepted.

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Serine

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OH-CH₂-CH(NH₂)-COOH
The alcohol bound to PS.

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Simple triglyceride

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A triglyceride with 3 of the same fatty acids linked to it.

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Sorbose

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A keto-hexose.

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Soret band

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The peak at wavelength 410 nm in cytochrome C. Named after the scientist who studied it.

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Spectrophotometer

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Measures the wavelengths of absorbances of substances. Can be used to elucidate metabolisms involving cytochromes.

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Standard hydrogen electrode (SHE)

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The arbitrarily defined reference point for reduciton potential. All other reduction potentials are measured as compared to this reaction.
E₀' = 0
pH 7, temperature 25?C
H₂ > 2H⁺ + 2e^-

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Standard reduction potential (E₀)

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The reduction potential measured in standard state.

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Standard state

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pH 7

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Starch

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A glucan. Stores energy in plants.

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Stator

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The static part of any engine.

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Stator arm

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The stationary portion of F_o of ATP synthase. Includes subunits a and b2. Stationary.

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Stearate

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18:0
aka Stearic acid
aka Octadecanoic acid
"Tallow"
A saturated fatty acid with 18 carbons.
Melting point: 76.5°C

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Stereoisomers

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Molecules with the same chemical formula, but different structures in space. The number of stereoisomers = 2ⁿ, where n is the number of chiral carbons. Includes enantiomers and diastereomers.

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Steroid

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A lipid that functions as a signalling molecule.

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Sterol

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A lipid that functions as a structural element of biological membranes.

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Substrate level phosphorylation

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The direct formation of a high-energy phosphate.

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Subunit a

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Part of the stator arm of F_o of ATP synthase. Attaches the ring of subunit c's to subunit b2. Has two half-channels through which protons must flow, spinning the subunit c ring.

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Subunit b2

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Part of the stator arm of F_o of ATP synthase. Attaches subunit a to the outside of the ?3?3 complex.

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Subunit c

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Part of F_o of ATP synthase. A hairpin of hydrophobic ? helices. 8, 10, 11, or 14 aggregate in a ring, forming the rotor portion of F_o. Has an aspartate residue which is protonate at the first half-channel of subunit a, and deprotonated at teh second half-channel, after it spins once around the ring. As it spins, it also spins the ? and ? subunits.

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Succinate

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The product of the fifth step of the citric acid cycle.

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Succinate dehydrogenase

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aka Complex II (in the electron transport chain).
Catalyzes the oxidation of succinate to fumarate, the sixth step of the citric acid cycle.

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Succinyl CoA

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The product of the fourth step of the citric acid cycle. A high energy thioester.

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Succinyl CoA synthetase

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Catalyzes the conversion of succinyl CoA into succinate, the fifth step of the citric acid cycle. Named for the reverse reaction. Some forms produce ATP and some produce GTP. Succinyl CoA and P_i bind together, releasing CoASH, and then bind to a histidine residue on the enzyme. Succinate falls off, leaving P_i behind, which is then attached to an ATP or GTP.

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Sucrose

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glc(?1 - ?2)fru
A disaccharide formed between the anomeric carbons of glucose in ? formation and fructose in ? formation. A non-reducing sugar. Common table sugar.

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Sugar-phosphate backbone

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The backbone of nucleic acids. Sugars and phosphates alternating, connected by phosphodiester bonds. Hydrophilic. OH groups form H bonds with water. Phosphates are ionized, giving a negative charge.

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Sulfhydryl

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R-SH
A common functional group.

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Super-high-energy phosphorylated chemicals

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Phosphate compounds, phoshpoenolpyruvate, creatine phosphate. Can generate ATP by transferring phosphate groups to ADP.

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Supercoiling

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DNA coils are further coiled into very dense supercoils that can fit inside the tiny nucleus.

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Synthetase

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Enzymes that are ATP dependent and join two moleucles into one.

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Tagatose

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A keto-hexose.

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Talose

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An aldo-hexose

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Tautomers

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Isomers that differ only in the positions of protons and double bonds. Forms an equilibrium in aqueous solution. Nucleoside bases form keto/enol tautomers and amino/imino tautomers. Pyruvate has keto/enol tautomers.

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Tetrapyrrole ring

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Four pyrrole rings together, forming a conjugated aromatic system.

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Tetrose

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Monosaccharides with 4 carbons. Have one chiral carbon. Includes erythrulose.

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Theobromine

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3,5-dimethylxanthine
A purine. Found in chocolate, which is made from the plant theobroma cacao, "food of the gods".

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THF

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A carrier of methyl groups and methylene groups. An adenosine derivative coenzyme.

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Thiamine

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aka Vitamin B₁
Used in the synthesis of TPP. Beriberi is a deficiency in thiamine.

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Thioester

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R-C(=O)-S-R
A common functional group. The sulfur analog of esters. Formed from a condensation of an acid and an alcohol. Coenzyme A forms thioesters with organic acids.

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Thiolase

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aka Acyl-CoA acetyltransferase
Catalyzes the fourth step of beta oxidation. CoAS^-breaks the bond between the ? and ? carbons of ?-ketoacyl-CoA. The ? and ? carbons become acetyl CoA. The rest of the fatty acid is a fatty acyl CoA which can then go through beta oxidation another time. A thiolysis reaction.

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Thiolysis reaction

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The sulfur equivalent of hydrolysis. The fourth step of beta oxidation is a thiolysis reaction.

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Threose

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An aldo-tetrose.

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Thymidine (T)

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The nucleoside of thymine. Only deoxyribose nucleosides are possible with thymine.

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Thymine (T)

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aka 5-methyluracil
A pyrimidine. Found in DNA only. Uracil with a methyl group on carbon 5. Discovered in thymus tissue. In DNA it forms 2 H bonds with adenine. Its nucleoside (only deoxyribose nucleosides possible) is thymidine.

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Tight

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A conformation of the ? and ? subunits in F₁of ATP synthase. Brings about the ready equilibrium of ADP + P_i with ATP. ATP remains tighly bound.

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TPP

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A coenzyme used in the PDH complex. Derived from thiamine

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Trans-?2-enoyl-CoA

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The product of the first step of beta oxidation.

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Trans configuration

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A double bond with the chains going in opposite directions. Uncommon in nature. Doesn't create a kink in the chain as a cis bond does.

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Trans fats

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Fats containing trans double bonds. Created during the partial hydrogenation of oils when manufacturing margarine. Has serious negative effects on cardiovascular health.

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Transaminase

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Catalyzes the conversion of ?-ketoglutarate, a product of the citric acid cycle, into glutamate, an amino acid. The keto group is replaced with an amino group.

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Transamination

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The process by which oxaloacetate is converted into asparate in the mitochondrial matrix in the malate-asparate shuttle mechanism. The reverse process occurs in the cytosol.

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Transcription

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DNA is used as a template for RNA synthesis.

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Transesterfication

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Fatty acids are mixed with NaOH and methanol, so that TAG and phospholipids form ester linkages with methanol, making them more volatile. They are then separated and identified using GLC, HPLC, and mass spectrometry.

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Transfer of phosphoryl group from PEP to ADP

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The tenth step of glycolysis. The second substrate-level phosphorylation. Pyruvate kinase removes the phosphategroup from PEP, generating one ATP (two per glucose), forming enolpyruvate, a tautomer of pyruvate. Mg²⁺ and K⁺ are catalysts.

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Transgenic organisms

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A biochemical genetics method of elucidation. Genetically engineering organisms to have metabolic blocks, or expressing enzymes in tissues that do not normally express them.

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Translation

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RNA is used as a template for protein synthesis. Codons code for certain amino acids according to genetic code.

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Trehalose

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glc(?1 - ?1)glc
A disaccharide formed between the anomeric carbons of two glucoses both in ? formation. A non-reducing sugar. Found in mushrooms.

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Triester

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A phosphoric acid with three ester groups. Possible, but doesn't occur in nature.

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Triglyceride (TAG)

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Triacylglycerol. Three fatty acids linked to one glycerol. Includes simple and mixed TAGs. The major constituent of fats and oils. THe most important storage form of fatty acids. Doesn't increase the osmotic potential of cells, and doesn't need to be stored with water. Very hydrophobic.

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Triose

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A monosaccharide with 3 carbons. The simplest sugars. Glyceraldehyde and dihydroxyacetone.

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Triose phosphate

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Catalyzes the fifth step of glycolysis. Has the same mechanism as phosphohexose isomerase.

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Trisaccharide

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Three sugar units.

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Two-phase extraction

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A method of extracting lipids from cells. Commonly a mixture of chloroform, methanol, and water is used. Polar molecules separate into the methanol/water phase. Lipids separate into the chloroform phase. Lipids are then separated by adsorption chromatography.

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Uncouplers

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Chemicals that disrupt the integrity of the inner mitochondrial membrane so that the proton gradient is eliminated. Uncouples the electron transport chain from ATP synthesis. Includes DNP.

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Universal electron carriers

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NADH, NADPH, FMN, and FAD. Act as electron acceptors or donors in redox reactions.

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Unsaturated

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A fatty acid chain with one or more double bonds. Triple bonds are possible but uncommon. Has kinks and doesn't pack tightly with other fatty acids. Gives them a lower melting point. More liquid. Includes monounsaturated and polyunsaturated.

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Uracil (U)

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Apyrimidine. Found in RNA only. Its nucleoside (only ribose nucleosides possible) is uridine.

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Uric acid

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A purine. A major form of nitrogenous waste eliminated by birds and reptiles.

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Uridine (U)

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The nucleoside of uracil. Only ribose nucleosides are possible with uracil.

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Vitamin A

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A lipid hormone precursor.

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Vitamin D

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A lipid hormone precursor.

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Vitamin E

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A lipid antioxidant.

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Vitamin K

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A lipid blood clotting agent.

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Watson ; Crick

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James Watson was a young American scientist, and Francis Crick was a biophysics professor at Cambridge. Used photo 51, taken by Rosalind Franklin, to make a theoretical model of the secondary structure of DNA. Won the Nobel Prize.

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Wax

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A lipid in waterproof coatings.

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Wire-frame

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A standardized way of drawing cyclic sugars. The most accurate way to draw cyclic sugars, but it is harder to draw.

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Wolfgang Jung

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Discovered the mechanism of the half-channels in subunit F_o of ATP synthase.

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Xylose

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An aldo-pentose.

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Xylulose

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A keto-pentose. Epimer of ribulose.

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