Introduction to Biochemistry: Final

1,3-bis-phosphoglycerate
The product of the sixth step of glycolysis. A mixed anhydride of phosphote and carboxylic acid. Has a high-energy bond.
2,3-bis-phosphoglycerate
An intermediate of the eighthstep of glycolysis.
2-phosphoglycerate
The product of the eighth step of glycolysis.
3′ end
The end of a polynucleotide with a free carbon 3′ OH group (not phosphorylated). Sequences are written from 5′ end to 3′ end.
3-phosphoglycerate
The product of the seventh step of glycolysis.
5′ end
The end of a polynucleotide with a free carbon 5′ OH group (not phosphorylated). Sequences are written from 5′ end to 3′ end.
?-ketoglutarate
The product of the third step of the citric acid cycle. Easily converted into glutamate by transaminase.
?-ketoglutarate dehydrogenase
Catalyzes the oxidation of ?-ketoglutarate into succinyl CoA and CO2, the fourth step of the citric acid cycle.
? subunit
Part of F1 of ATP synthase. There are three identical versions. Part of the ?3?3 complex. Changes conformation as the ? unit rotates. Stationary.
?3?3 complex
The ? and ? subunits of F1 of ATP synthase. Stays stationary while the ? subunit rotates, changing the conformations of the ? and ? subunits. Stationary.
?-hydroxyacyl-CoA dehydrogenase
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.
?-ketoacyle-CoA
The product of the third step of beta oxidation. Breakage of the bond between the ? and ? carbons is made possible by its ?-dicarbonyl functionality.
? subunit
Part of F1 of ATP synthase. Changes conformation as the ? unit rotates. Stationary.
? subunit
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.
? subunit
Part of F1 of ATP synthase. Attaches the b2 subunit to the ?3?3 complex. Stationary.
? subunit
Part of F1 of ATP synthase. Attaches the ? subunit to Fo. Rotates.
Acetaldehyde
An intermediate of alcoholic fermentation.
Acetate
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.
Acetone
A common organic solvent. Has a similar structure to dihydroxyacetone.
Acetyle

R-C(=O)-CH3

A common functional group.

Acetyl CoA (CoASAc)
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.
Acetyl moiety
An acid with two carbons. Removed during each repetition of beta oxidation.
Acid anhydride
Two carboxylic acids linked together with an ester linkage. Created by a condensation region.
Acontinase
Catalyzes the formation of isocitrate through cis-aconitate, the second step of the citric acid cycle.
Acyl adenylate
An intermediate in converting fatty acids into fatty acyl-CoA thioester. The fatty acid attackes ATP, and replaces PPi, which floats away. The thiolate anion form of CoA attacks the group, replacing AMP.
Acyl CoA
Coenzyme A carrying any acid. Includes aceyl CoA and palmitoyl CoA. A product of beta oxidation.
Acyl-CoA dehydrogenase
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.
Acyl-CoA synthetase

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 PPi, which floats away. The thiolate anion form of CoA attacks the group, replacing AMP.

?G0′ = – 34 kJ/mol

Acyl group
Acids, including acetic acid.
Adenine (A)

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.

Adenosine (A)
The ribose nucleoside of adenine.
Adenosine diphosphate (ADP)
A nucleotide of adenine and ribose, plus two phosphategroups. Produced from the hydrolysis of the gamma linkage of ATP.
Adenosine monophosphate (AMP)
A nucleotide of adenine and ribose, plus one phosphate group. Produced from the complete hydrolysis of ATP.
Adenosine triphosphate (ATP)

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

Adenylate
A group that ATP can add to substrates or enzymes, driving reactions.
Adsorption chromatography
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.
Aerobic conditions
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.
Albert Szent-Gyorgyi

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.

Alcohol dehydrogenase
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.
Alcoholic fermentation

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+

Aldehyde

R-C(=O)H

A carbonyl group. A common functional group.

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

Polyhydroxy aldehyde

A monosaccharide where the carbonyl group is an aldehyde.

Alkaptonuria
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.
Allose
An aldo-hexose.
Alpha (?) anomer
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.
Alpha (?) carbon
In fatty acid nomenclature, the first carbon in the carbon chain. Subsequent carbons are labeled with the Greek alphabet.
Alpha (?) phosphate
The phosphate bonded to the nucleotide in ATP by a low-energy phosphate ester bond.
Altrose
An aldo-hexose.
Amido

R-C(=O)-NH2

A common functional group.

Amino

R – NH3+

A common functional group.

Anabolism
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.
Anaerobic conditions

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

Anhydride

R-C(=O)-O-C(=O)-R

Two carboxylic acid moieties bound. A common functional group.

Anomer
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.
Anomeric carbon
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.
Arabinose
An aldo-pentose.
Arachidate

20:0

“Peanut”

A saturated fatty acid with 20 carbons.

Arachidonate

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

Archibald Garrod
In 1904 he identified that human genetic diseases are deficiencies in specific enzymes.
Aspartate
Oxaloacetate is converted into it through a transamination process. Passes out of the mitochondrial matrix through transporter proteins. Part of the Malate-Aspartate shuttle.
ATP synthase

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 Fo.

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

“Help food”

Needing more than minimal medium.

Auxotrophic mutants
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.
Benzoic acid
Found in the urine of dogs fed fatty acids with an odd number of carbons in Franz Knoop’s experiment. Phenyl-labeled formic acid.
Beta (?) anomer
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.
Beriberi
A disease caused by a deficiency in thiamine, slowing the PDH complex. Higher than normal levels of pyruvate in blood and urine.
Beta (?)
THe second phosphate, bound to the alpha phosphate of ATP by a high-energy phosphoanhydride bond.
Beta oxidation
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.
Bilayer
A double layer of phospholipids that forms in aqueous solutions, with the polar heads to the outside. Folds over into itself to form liposomes.
Biochemical genetics
A method of elucidation. Includes genetic diseases, auxotrophic mutants, and transgenic organisms.
Biological membrane
A lipid bilayer containing hydrophobic proteins, oligosaccharides, and other structural and functional features.
Biphosphate
A molecule with two phosphates at different positions.
Caffeine

aka 1,3,7-trimethylxanthine

A purine.

Carbohydrate

aka Sugars

aka Saccharides

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

Carbon 1
In fatty acid nomenclature, the carbon in the carboxylic acid group. Subsequent carbons are counted numerically.
Carbon 14 (14C)
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.
Carbon dioxide (CO2)
The most oxidized form of carbon found in living systems.
Carboxylate

R-COOH

A common functional group.

Cardiolipin
A phospholipid found only in the IMM of a mitochondria.
Carl and Gerti Cori
Discovered the Cori cycle.
Carnitine transporter
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.
Carnitine acyl transferase
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.
Carotene
A lipid pigment.
Catabolism
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.
Cellular respiration
The complete oxidation of organic fuels into CO2 and H2O using O2.
Cellulose
A glucan. A structural element in plants.
Central Dogma of Molecular Biology

DNA > RNA > Protein

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

Chargaff’s Rules
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.
Chemical potential energy
A component of the proton motive force. Due to the difference in concetration of H+. One proton makes a ? pH of 0.75.
Chemiosmotic hypothesis
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.
Chirality

“Handedness”

aka Optical activity

A carbon with four different substituents has two possible configurations in space: “right-handed” and “left-handed”.

Chitin

A glucan

A strucutral element in animal exoskeletons.

Choline

OH-CH2-CH2-N(CH3)3+

The alcohol that is bound to PC.

Cis-aconitate
The intermediate of the second step of the citric acid cycle. An alkene.
Cis configuration
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.
Citrate synthase
Catalyzes the condensation of oxaloacetate with acetyl CoA, the first step of the citric acid cycle.
Citrate

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.

Citric acid cycle (TCA)

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.

Claisen condensation
Beta oxidation in reverse. The condensation of two beta-keto-esters. Named after Ludwig Claisen, 1851 – 1930.
Cleavage of fructose-1,6-biphosphate
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.
Cofactors
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.
Codon
Groups of three nucleotides in RNA that code for certain amino acids according to genetic code during translation.
Coenzyme
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.
Coenzyme A (CoASH)
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.
Coenzyme Q

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.

Complete hydrolysis of ATP
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. PPi is then catalyzed by pyrophosphatase, releasing two Pi.
Complex

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.

Complex I

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+

Complex II

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

Complex III

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+

Complex IV

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

Condensation of oxaloacetate with acetyl CoA
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.
Conformations
Three different stages that ? and ? subunits can be in. Changes as the ? rotates inside the ?3?3 complex. Loose, tight, and open.
Conjugated
An unsaturated carbon chain where the double bond pattern is double-single-double-single. Found in biomolecules. Uncommon in fatty acids.
Conversion of 3-phosphoglycerate to 2-phosphoglycerate
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.
Conversion of succinyl CoA to succinate
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.
Cori cycle
The exchange of metabolites in the body. Includes gluconeogenesis. Discovered by Carl and Gerti Gori.
Coupling
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.
Creatine phosphate
Stores energy in muscles. A super-high-energy phosphorylated chemical.
Cyanide
Inhibits complex IV in the electron transport chain.
Cyclization
When a hemiacetal or hemiketal is formed on the same molecule, making a ring-shaped molecule. Reaction happens more easily.
Cytidine (C)
The ribose nucleoside of cytosine.
Cytochrom

“Coloured stuff in the cell”

A class of hemeproteins that participate in redox reactions.

Cytochrome C
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.
Cytosine (C)
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.
D-sugars
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.
Dehydration
Removal of water without breaking the molecule.
Dehydration of 2-phosphoglycerate
The ninth step of glycolysis. Enolase dehydrates 2-phosphoglycerate, forming PEP.
Dehydrogenation
Removal of a hydrogen ion.
Deoxyadenosine (dA)
The deoxyribose nucleoside of adenine.
Deoxycitidine (dC)
The deoxyribose nucleoside of cytosine.
Deoxyguanine (dG)
The deoxyribose nucleoside of guanine.
Deoxyribonucleic acid (DNA)
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.
Deoxyribose
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.
Diabetes
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”.
Diastereomers
Stereoisomers that differ in chirality around some carbons but not others. Have differing chemical properties. Includes epimers.
Diester
A phosphoric acid with two ester groups.
Digoxin

“Digitalis”

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

Dihydroxyacetone
A keto-triose. No chiral carbons.
Dihydroxyacetone phosphate (DHAP)
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.
Dinitrophenol (DNP)

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

Diphosphate
A molecule with two phosphates at the same position, or a pyrophosphate group.
Disaccharide
Two cyclic monosaccharides bonded by a glycosidic bond. Includes lactose, maltose, trehalose, and sucrose.
Disulfide

R-S-S-R

A common functional group.

DNA replication
DNA is used as a template for DNA synthesis. Occurs when the cell replicates.
Efrain Racker
With colleagues, first purified F1 of ATP synthase in the 1960s.
Electrical potential energy
A component of the proton motive force. Due to the separation of charges. One proton makes a ?? of 0.15 V.
Electron-transferring flavoproteins
Accepts reducing equivalents from FADH2 and passes them to coenzyme Q.
Electron transport chain
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.
Elucidation
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.
Emil Fischer

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.

Enantiomers
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.
Endergonic reaction
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.
Enol

R-CH(OH)=CH2

A common functional group.

Enolase

aka Phosphopyruvate hydratase

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

Enolpyruvate
The minor tautomer of pyruvate. Produced in glycolysis.
Enoyl-CoA hydratase
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.
Epimers
Diasteromers that differ in chirality around one carbon. Simple to convert epimers back and forth.
Erythrulose
A keto-tetrose. One chiral carbon. Two enantiomers: D and L.
Escherichia coli
A common bacteria lab subject. A phototroph.
Ester

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.

Ester linkage
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.
Ethanolamine

OH-CH2-CH2-NH2

The alcohol that is bound to PE.

Ether

R-O-R

A common functional group.

Ethyl

R-CH2-CH3

A common functional group.

Even fatty acid
A fatty acid with an even number of carbons. Common in the body.
Exergonic reaction
Catabolism of fuel molecules. Free energy is released, and is used to produce phosphorylated chemicals, such as ATP out of ADP.
F1
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.
Fo
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.
FAD

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

Faraday constant (F)
The charge of one mole of electrons. 96.5 e Coloumbs/mole.
Fat
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.
Fatty acid
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.
Fatty acyl carnitine
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.
Fatty acyl-CoA thioester
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.
Fischer projection
A standardized way of drawing linear monosaccharides. Carbons are numbered from top to bottom.
Fischer ring
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.
Flavin nucleotides
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.
Flavin ring
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.
Flavoproteins
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.
FMN

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

Franz Knoop
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.
Free energy (?G)

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 ; Pi

Friedrich Miescher

1844 – 1895

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

Fritz Lipmann
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.
Fructose
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.
Fructose-1,6-phosphate
The product of the third step of glycolysis.
Fructose-6-phosphate
The product of the second step of glycolysis.
Fumarase
Catalyzes the hydration of fumarate to malate, the seventh step of the citric acid cycle.
Fumarate
The product of the sixth step of the citric acid cycle. An alkene.
Furanose ring
A five-sided sugar ring. Size of the ring depends on thermodynamics and geometry of the molecule. Example: fructose.
G3P dehydrogenase
Catalyzes the oxidation of G3P, the sixth step of glycolysis.
Galactose
An aldo-hexose.
Gamma (?) phosphate
The third phosphate, bound to the beta phosphate in ATP by a high-energy phosphoanhydride bond.
Gas-liquid chromatography (GLC)
Separates transesterfied fatty acids by chain length and saturation. The mobile phase is a gas.
Genetic code
The “code” by which codons in RNA translate into amino acids during translation.
Genetic diseases
A biochemical genetics method of elucidation. Analysis of the effects of genetic diseases where there is a deficiency in a specific enzyme.
George Beadle and Edward Tatum
In 1940 they found that each enzyme ina cell is encoded by a specific gene.
Gibbs free energy (G)

The change in G is proportional to the difference in reduction potential of the half-reactions of a redox reaction.

?G0′ = – nF?E0′

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

aka Hexokinase IV

Found in the liver.

KM = 8 mM

Gluconeogenesis
The process in the liver that recycles lactate into glucose. Part of the Cori cycle.
Glucose
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.
Glucose-6-phosphate
The product of phosphorylation of glucose, the first step of glycolysis. It cannot leave the cell.
GLUTs

GLUcose Transporters

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

Glutamate
An amino acid which can be produced from ?-ketoglutarate, a product of the citric acid cycle, by transaminase.
Glutamine synthesis
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. Pi is displaced and leaves the group.
Glyceraldehyde
An aldo-triose. Has one chiral carbon.
Glyceraldehyde-3-phosphate (G3P)
One of the products of the fourth step of glycolysis. DHAP is converted into it in step five.
Glycerol

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.

Glycerol-3-phosphate
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.
Glycerol-3-phosphate dehydrogenase
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.
Glycerol-3-phosphate shuttle
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.
Glycogen
A glucan. Stores energy in animals. Carries 2,500 kJ of energy in an adult human.
Glycolipid
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.
Glycolysis

“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.

Glycolytic intermediate
Glycerol is converted into this during fat catabolism.
Glycoside
Two cyclic sugar molecules bonded by a glycosidi bond. Includes polysaccharides, nucleosides, and digoxin.
Glycosidic bond
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.
GTP
A high-energy compound which can exchange energy for ATP.
Guanidium

R-NH-C(=NH2+)-NH2

A common functional group.

 

Guanine (G)

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.

Guanosine (G)
The ribose nucleoside of guanine.
Gulose
An aldo-hexose.
Half-channels
Channels in subunit a of Fo 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.
Half-reaction
An oxidation and a reduction reaction. Their sum is the total overall reaction.
Hans Krebs

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.

Haworth structure
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.
Heme
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.
Hemeproteins
Proteins with a heme prosthetic group. Includes hemoglobin and cytochromes. Some have the heme ring covalently linked in and some do not.
Hemiacetal
An aldehyde that has had a condensation reaction with an alcohol. Forms a new chiral carbon. Includes aldose rings.
Hemiketal
A ketone that has had a condensation reacction with an alcohol. Forms a new chiral carbon. Includes ketose rings.
Heptose
Monosaccharides with 7 carbons.
Heteroatoms
Non-carbon atoms, such as nitrogen, oxygen, or sulfur.
Heterocycles
Cyclical molecules with heteroatoms. Includes nucleotide bases.
Heteropolysaccharides
Polysaccharides made up of two or more types of monosaccharides.
Hexokinase
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.
Hexose
Monosaccharides with 6 carbons. The most common monosaccharide in nature. Includes psicose, fructose, sorbose, and tagatose.
High energy bonds
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.
High-performance liquid chromatography (HPLC)
Separates transesterfied fatty acids by chain length and saturation.
Homocystein
Cystein with one extra CH2 group. An amino acid.
Homopolysaccharide
A polysaccharide made of one type of sugar. Includes glucans.
Hydration
Water is added to a molecule, but it does not break.
Hydration of fumarate to malate
The seventh step of the citri acid cycle. Fumarase adds water to fumarate, forming malate.
Hydride ion
Two electrons and one proton. Has a negative charge. A reducing equivalent. Has two electrons.
Hydrogen atoms
A reducing equivalent. Has one electron.
Hydrolysis
An energetically favourable reaction. Has a negative ?G. Water is added to a molecule, breaking it.
Hydrolysis of gamma linkage
Breaking of a high energy bond. One Pi 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.
Hydrolysis of mixed anhydride
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.
Hydrophobic
Molecules that partition into the organic solvent phase during two-phase extraction of a cell extract.
Hydroquinone
The fully reduced form of quinone. Both ketones are reduced.
Hydroxyl

R-OH

aka Alcohol

A common functional group. Acts as the nucleophile in glycosidic bonds.

Idose
An aldo-hexose.
Imidazole
A common functional group.
Imine

R-C(=N-R)-R

A common functional group.

Inner mitochondrial membrane (IMM)
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.
Inorganic ions
Can act as cofactors. Includes Fe2+, Mg2+, Mn2+, Zn2+, and Cu2+.
Insulin
Stimulates GLUT-mediated glucose uptake in skeletal muscle and adipose tissue. Diabetes is a lack of insulin or a reduced response to insulin.
Intermembrane space
Part of a mitochondria. A space similar to the cytosol.
Isocitrate
The product of the second step of the citric acid cycle. A secondary alcohol, which is more easily oxidized.
Isocitrate dehydrogenase
Catalyzes the oxidation of isocitrate into ?-ketoglutarate, the third step of the citric acid cycle.
Isomerase
Enzymes that change a molecule into an isomer of that same molecule; chemical formula stays the same. Includes mutases.
Isomerization of citrate
The second step of the citric acid cycle. Aconitase reversibly isomerizes citrate by first dehydrating it, forming cis-aconitate, then rehydrating it, forming isocitrate.
Isomerization of DHAP
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.
Isozyme
Different enzymes which catalyze the same reaction. Encoded by different genes.
John E. Walker
Won the Nobel Prize in Chemistry in 1997 for discovering the structure of F1 of ATP synthase.
Ketone

R-C(=O)-R

A carbonyl group. A common functional group.

Ketopyruvate
The major tautomer of pyruvate.
Ketose

Polyhydroxy hetone

A monosaccharide where the carbonyl group is a ketone.

Kinase
An enzyme which catalyzes phosphorylation reactions.
L-?-hydroxy-acyl-CoA
The product of the second step of beta oxidation. The beta carbon is chiral, but only the L stereoisomer can be made.
L-sugars
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.
Lactate
The product of anaerobic conditions oxidation of pyruvate. Recycled into glucose in the gluconeogenesis pathway.
Lactate dehydrogenase
Catalyzes the oxidation of pyruvate in anaerobic conditions.
Lactose

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.

Laurate

12:0

aka Lauric acid

aka Dodecanoic acid

“Bay”

“Laurel”

A saturated fatty acid with 12 carbons.

Melting point: 44.2?C.

Lingoceric acid

24:0

aka Tetracosanoic acid

“Wood”

“Wax”

A saturated fatty acid with 24 cabrons.

Melting point: 86.0?C.

Linoleate

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.

Linolenate

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

Lipase
Catabolyzes the hydrolysis of triglycerides into three fatty acids and a glycerol.
Lipid
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.
Lipid peroxidation
Uncontrolled oxidation. Occurs if you leave butter out for too long and it goes rancid.
Lipoic acid
Used in the synthesis of lipomide.
Lipomide
A cofactor used in PDH complex. Derived from lipoic acid.
Lipoproteins
Molecules containing both protein and lipid portions. Associated with cardiovascular health and diseases. Includes VLDL, LDL, and HDL.
Liposome

aka Vesicle

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

Loose
A conformation of the ? and ? subunits in F1 of ATP synthase. Binds ADP and Pi.
Low-energy phosphorylated chemicals
Simple phosphate esters, alcohols, sugar phosphates, esters, amids, and glucose 6- phosphate.
Lyxose
An aldo-pentose.
Major groove
The larger gap in a DNA strand. The edges of bases are more exposed through this gap.
Malate
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.
Malate-Aspartate shuttle
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.
Malonate
A competitive inhibitor of succinate dehydrogenase.
Maltose

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.

Mannans
Homopolysaccharides made of mannose.
Mannose
An aldo-hexose.
Matrix
The inside of a mitochondria. Very different composition from the cytosol.
Metabolic inhibitors
A method of elucidation. Inhibitors block the metabolic pathway at certain points, leading to a build-up of the preceding metabolite.
Metabolic pathway
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.
Metabolism
Complex metabolic reactions occurring in cells. Involves compounds, reactions, genes, cellular physiology, and energy. Has two halves: anabolism and catabolism.
Metabolites
Intermediate products formed during a metabolic pathway.
Methyl

R-CH3

A common functional group.

Methylene-bridged
An unsaturated carbon chain where the double bond pattern is double-single-single-double-single-single.
Micelle
The smallest, simplest lipid aggregate in aqueous solution. Round clusters of lipid.
Minimal medium
Water, sugar, nitrogen, and mineral salts. This is all E. coli, and other phototrophs need to survive.
Minor groove
The smaller gap in a DNA strand.
Mitochondria
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.
Mitochondrial electron transport chain
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.
Mixed anhydride
R-C(=O)-O-PO(=O)-OH
Mixed tryglyceride
A triglyceride with 2 or 3 different kinds of fatty acids linked to it.
Monoester
A phosphoric aid that has one ester group.
Monosaccharide

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.

Monosaturated fatty acid
A fatty acid with one double bond.
Mutarotation
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.
Mutase
An isomerase that moves a functional group from one position to another.
Myristate

14:0

aka Myristic acid

aka Tetradecanoic acid

“Myrtle”

“Nutmeg”

A saturated fatty acid with 14 carbons.

Melting point: 53.9°C 

NADH

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

?E0′ = +1.14 V

?G0′ = -220 kJ/mol

NADPH

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

Naming fatty acids

Example:

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

Niacin

aka Vitamin B3

Nicotinamide rings are derived from it.

Nicotinamide ring
A group found in pyridine nucleotides. Derived from niacin.
Non-reducing sugar
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.
Nucleic acids
RNA and DNA. Encode genetic information. Polynucleotides.
Nucleic base
A component of nucleotides. Heterocycles. Includes purines (adenine and guanine), and pyrimidines (cytosine, thymine, and uracil). Hydrophobic.
Nucleoside
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.
Nucleotide
A phsophorylated nucleoside. Phosphoric acid attaches to the carbon 5′ hydroxyl group (on the sugar).
Odd fatty acid
A fatty acid with an odd number of carbons. Uncommon in the body.
Oil
A lipid that functions in energy storage in plants. Mostly triglycerides. Less saturated than fats and has a lower melting point.
Oleate

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

Oligomycin
Inhibits the ATP synthase enzyme by binding to Fo.
Oligosaccharides
Short chains of 4 – 20 cyclic sugars connected by glycosidic bonds. Includes starch and cellulose.
Omega (?) carbon
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.
Open
A conformation of the ? and ? subunits in F1 of ATP synthase. Releases ATP. No bound nucleotides.
Organic solvents
Dissolve lipids. Includes chloroform, acetone, ether, and hexane.
Oswald Avery
With colleages, first identified DNA as the genetic material in the 1940’s.
Outer membrane
Part of a mitochondria. Freely permeable to small molecules and ions.
Oxaloacetate
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.
Oxidation of G3P
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 Pi, is oxidized with 2 electrons, using NAD+, and is phosphorylated, forming 1,3-bis-phosphoglycerate.
Oxidation of malate to oxaloacetate
The eigth step of the citric acid cycle. Malate dehydrogenase uses NAD+ to oxidize malate into oxaloacetate.
Oxidation of succinate to fumarate
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.
Oxidation reaction
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.
Oxidative decarboxylation of ?-ketoglutarate
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.
Oxidative decarboxylation of isocitrate
The third step of the citric acid cycle. Isocitrate dehydrogenase uses NAD+ to oxidize isocitrate into ?-ketoglutarate, producing CO2.
Oxidative phosphorylation
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.
Oxidizing agent

aka Oxidant

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

Oxygen

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.

P/O ratio

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

Palmitate

16:0

aka Palmitic acid

aka Hexadecanoic acid

“Palm”

A saturated fatty acid with 16 carbons.

Melting point: 63.1?C

Palmitoleic acid

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

Palmitoyl CoA
Coenzyme A carrying palmitate.
Pantothenic acid

aka Vitamin B5

Coenzyme A is derived from pantothenic acid.

 

PAPS
A carrier of sulfate groups. An adenosine derivative coenzyme.
Paracrine hormone
A lipid that functions as a signalling molecule. Includes prostaglandins and diaclyglycerols.
Partial dehydrogenation
Used in manufacturing margarine. Isomerizes the double bonds, creating trans fats.
Paul Boyer

Studied the kinetics of ATP synthase using isotopes of oxygen to measure the exchange of phosphategroups among ADP, ATP, and Pi. 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 + Pi > ATP + H2O

Payoff phase
The last five steps of glycolysis. ATP is produced.
Pentose
Monosaccharides with 5 carbons. Two chiral carbons. Includes ribulose, xylulose, ribose, arabinose, xylose, and lyxose.
Pentose phosphate pathway
An alternative catabolic pathway for glucose, other than glycolysis.
Perspective formula
A standardized way of drawing linear monosaccharides. Wedges and dashed lines illustrate the 3D nature of the sugar.
Peter Michell
In the 1960’s, proposed the chemiosmotic hypothesis to explain the connection between the electron transport chain and ATP synthesis.
Phenol
An alcohol.
Phenylacetic acid
Found in the urine of dogs fed fatty acids with an even number of carbons in Franz Knoop’s experiment. Phenyl-labeled acetic acid.
Phosphate ester
An alohol and phosphoric acid linked by a phosphodiester linkage.
Phosphatidylcholine (PC)

aka Lecithin

A phospholipid with a choline group. A major class of membrane lipids.

Net charge at pH 7: 0

Phosphatidylethanolamine (PE)

A phospholipid with an ethanolamine group. A major class of membrane lipids.

Net charge at pH 7: 0

Phosphatidylglycerol (PG)

A phospholipid with a glycerol group.

Net charge at pH 7: -1

Phosphatidylserine (PS)

A phospholipid with a serine group.

Net charge at pH 7: -1

Phosphoanhydride

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.

Phospho-enol-pyruate (PEP)
The product of the ninth step of glycolysis. A high-energy phosphorylated compound.
Phosphodiester linkage
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.
Phosphoenzyme intermediate
The intermediate of the fifth step of the citric acid cycle. Succinyl CoA and Pi bound to succinyl CoA synthetase.
Phosphoester bond
The bond between a phosphoric acid and a sugar. The low-energy alpha phosphate in ATP.
Phosphofructokinase
Catalyzes the phosphorylation of fructose-6-phosphate, the third step of glycolysis.
Phosphoglycerate kinase
Catalyzes the hydrolysis of mixed anhydride, the seventh step of glycolysis.
Phosphoglycerate mutase

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

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

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.

Phosphoric acid

H3PO4

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

Phosphoryl

R-O-POO-O-POO-O

A common functional group.

Phoshphorylation
The addition of a phosphoric acid group to a molecule. Adds negative charge. Increases solubility. Creates phospholipids, sugar-phosphates, proteins, and nucleotides.
Phosphorylation of fructose-6-phosphate
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.
Phosphorylation of glucose
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.
Photo 51
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.
Phototroph
“First food”. Needing only minimal medium.
Pigment
A lipid that colours organisms. Includes carotene.
Plectonemically coiled
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.
Polynucleotide
Polymers of nucleotides connected by the sugar-phosphate backbone which is held together with phosphodiester links. Has a 5′ end and a 3′ end.
Polysaccharide
Polymers of 20+ monosaccharide units. Often branched. Sugar chains can have multiple hydroxyl groups bound to anomeric carbons. Includes homopolysaccharides and heteropolysaccharides.
Polyunsaturated fatty acid (PUFA)
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.
Porphyrin
A particular ring structure that binds to metal ions. Includes heme.
Potentiometer
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.
Precursor-product relationship
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.
Preparatory phase
The first five stages of glycolysis. ATP is used to phosphorylate and activate glucose.
Protein
Carries 100,000 kJ of energy in an adult human.
Proton gradient
A reservoir of energy created by the electron transport chcain.
Proton ionophore
Ion carrier. Includes DNP.
Proton motive force
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.
Psicose
A keto-hexose.
Purines
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.
Pyranose
A six-sided sugar ring. Size of the ring depends on thermodynamics and geometry of the molecule. Example: glucose.
Pyridine nucleotides
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.
Purimidines
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.
Pyrophosphatase
An enzyme that catalyzes the hydrolysis of the phosphoanhydride bond in PPi, releasing two Pi.
Pyrophoshpate (PPi)
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 Pi, catalyzed by pyrophosphatase.
Pryophosphate linkage
Two phosphate groups connecting two groups. Found in pyridine nucleotides, FAD, and coenzyme A.
Pyrophosphoryl
A group which ATP can add to substrates or enzymes, driving reactions.
Pyrrole ring
Five-membered ring with one N atom.
Pyruvate
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.
Pyruvate decarboxylase
Catalyzes the first step of alcoholic fermentation. Pyruvate is converted into acetaldehyde. Animals lack this enzyme, so cannot perform alcoholic fermentation.
Pyruvate dehydrogenase complex (PDH)
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.
Pyruvate kinase
Catalyzes the transfer of a phosphoryl group from PEP to ADP. Named for its reverse reaction.
Quinone
An organic functional group with two ketone oxygens in a conjugated six-membered ring. Oxidizing agent. Reduced forms are semiquinone and hydroquinone.
Radioactively labeled substances
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.
Red blood cells
Lack mitochondria. Can only oxidize pyruvate in the anaerobic conditions pathway.
Redox couple
The oxidized and reduced form of a compound.
Redox reaction
An oxidation reaction and a reduction reaction. May be written separately as half-reactions.
Reduced cofactors
NADH and FADH2. Oxidized in the electron transport chain using O2 as the ultimate oxidant. Energy is captured to form ATP in oxidative phosphorylation.
Reducing agent

aka Reductant

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

Reducing end
The end of a disaccharide or polysaccharide with a free anomeric carbon.
Reducing  equivalents
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.
Reducing sugar
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.
Reduction potential (E)
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.
Reduction reaction
A reduced universal electron carrier adds an electron. Always occurs along with an oxidation reaction.
Respiratory inhibitors
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.
Reverse transcription
An exception to the Central Dogma of Molecular Biology. Sometimes RNA can be a template for DNA.
Ribitol
A sugar-alcohol. Attached to flavin in riboflavin. Found in FAD and FMN.
Riboflavin

aka Vitamin B2

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

Ribonucleic acid (RNA)
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.
Ribose
An aldo-pentose. Forms a furanose ring. The sugar in RNA.
Ribulose
A keto-pentose. Epimer of xylulose.
Rosalind Franklin
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.
Rotational catalysis
The mechanism by which ATP synthase releases ATP due to the rotation of the ? subunit.
Rotor
The rotating part of any engine.
SAM
A carrier of methyl groups. An adenosine derivative coenzyme.
Saturated
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.
Semiquinone
The partially reduced form of quinone. One of the two ketones is reduced. An intermediate to hydroquinone.
Semiquinone radical
Partially reduced forms of FAD and FMN; FADH and FMNH, or the partially reduced form of cytochrome Q. Only one electron is accepted.
Serine

OH-CH2-CH(NH2)-COOH

The alcohol bound to PS.

Simple triglyceride
A triglyceride with 3 of the same fatty acids linked to it.
Sorbose
A keto-hexose.
Soret band
The peak at wavelength 410 nm in cytochrome C. Named after the scientist who studied it.
Spectrophotometer
Measures the wavelengths of absorbances of substances. Can be used to elucidate metabolisms involving cytochromes.
Standard hydrogen electrode (SHE)

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

Standard reduction potential (E0)
The reduction potential measured in standard state.
Standard state
pH 7
Starch
A glucan. Stores energy in plants.
Stator
The static part of any engine.
Stator arm
The stationary portion of Fo of ATP synthase. Includes subunits a and b2. Stationary.
Stearate

18:0

aka Stearic acid

aka Octadecanoic acid

“Tallow”

A saturated fatty acid with 18 carbons.

Melting point: 76.5°C

Stereoisomers
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.
Steroid
A lipid that functions as a signalling molecule.
Sterol
A lipid that functions as a structural element of biological membranes.
Substrate level phosphorylation
The direct formation of a high-energy phosphate.
Subunit a
Part of the stator arm of Fo 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.
Subunit b2
Part of the stator arm of Fo of ATP synthase. Attaches subunit a to the outside of the ?3?3 complex.
Subunit c
Part of Fo of ATP synthase. A hairpin of hydrophobic ? helices. 8, 10, 11, or 14 aggregate in a ring, forming the rotor portion of Fo. 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.
Succinate
The product of the fifth step of the citric acid cycle.
Succinate dehydrogenase

aka Complex II (in the electron transport chain).

Catalyzes the oxidation of succinate to fumarate, the sixth step of the citric acid cycle.

Succinyl CoA
The product of the fourth step of the citric acid cycle. A high energy thioester.
Succinyl CoA synthetase
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 Pi bind together, releasing CoASH, and then bind to a histidine residue on the enzyme. Succinate falls off, leaving Pi behind, which is then attached to an ATP or GTP.
Sucrose

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.

Sugar-phosphate backbone
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.
Sulfhydryl

R-SH

A common functional group.

Super-high-energy phosphorylated chemicals
Phosphate compounds, phoshpoenolpyruvate, creatine phosphate. Can generate ATP by transferring phosphate groups to ADP.
Supercoiling
DNA coils are further coiled into very dense supercoils that can fit inside the tiny nucleus.
Synthetase
Enzymes that are ATP dependent and join two moleucles into one.
Tagatose
A keto-hexose.
Talose
An aldo-hexose
Tautomers
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.
Tetrapyrrole ring
Four pyrrole rings together, forming a conjugated aromatic system.
Tetrose
Monosaccharides with 4 carbons. Have one chiral carbon. Includes erythrulose.
Theobromine

3,5-dimethylxanthine

A purine. Found in chocolate, which is made from the plant theobroma cacao, “food of the gods”.

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

aka Vitamin B1

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

Thioester

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.

Thiolase

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.

Thiolysis reaction
The sulfur equivalent of hydrolysis. The fourth step of beta oxidation is a thiolysis reaction.
Threose
An aldo-tetrose.
Thymidine (T)
The nucleoside of thymine. Only deoxyribose nucleosides are possible with thymine.
Thymine (T)

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.

Tight
A conformation of the ? and ? subunits in Fof ATP synthase. Brings about the ready equilibrium of ADP + Pi with ATP. ATP remains tighly bound.
TPP
A coenzyme used in the PDH complex. Derived from thiamine
Trans-?2-enoyl-CoA
The product of the first step of beta oxidation.
Trans configuration
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.
Trans fats
Fats containing trans double bonds. Created during the partial hydrogenation of oils when manufacturing margarine. Has serious negative effects on cardiovascular health.
Transaminase
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.
Transamination
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.
Transcription
DNA is used as a template for RNA synthesis.
Transesterfication
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.
Transfer of phosphoryl group from PEP to ADP
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.
Transgenic organisms
A biochemical genetics method of elucidation. Genetically engineering organisms to have metabolic blocks, or expressing enzymes in tissues that do not normally express them.
Translation
RNA is used as a template for protein synthesis. Codons code for certain amino acids according to genetic code.
Trehalose

glc(?1 – ?1)glc

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

Triester
A phosphoric acid with three ester groups. Possible, but doesn’t occur in nature.
Triglyceride (TAG)
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.
Triose
A monosaccharide with 3 carbons. The simplest sugars. Glyceraldehyde and dihydroxyacetone.
Triose phosphate
Catalyzes the fifth step of glycolysis. Has the same mechanism as phosphohexose isomerase.
Trisaccharide
Three sugar units.
Two-phase extraction
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.
Uncouplers
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.
Universal electron carriers
NADH, NADPH, FMN, and FAD. Act as electron acceptors or donors in redox reactions.
Unsaturated
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.
Uracil (U)
Apyrimidine. Found in RNA only. Its nucleoside (only ribose nucleosides possible) is uridine.
Uric acid
A purine. A major form of nitrogenous waste eliminated by birds and reptiles.
Uridine (U)
The nucleoside of uracil. Only ribose nucleosides are possible with uracil.
Vitamin A
A lipid hormone precursor.
Vitamin D
A lipid hormone  precursor.
Vitamin E
A lipid antioxidant.
Vitamin K
A lipid blood clotting agent.
Watson ; Crick
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.
Wax
A lipid in waterproof coatings.
Wire-frame
A standardized way of drawing cyclic sugars. The most accurate way to draw cyclic sugars, but it is harder to draw.
Wolfgang Jung
Discovered the mechanism of the half-channels in subunit Fo of ATP synthase.
Xylose
An aldo-pentose.
Xylulose
A keto-pentose. Epimer of ribulose.
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