Bio-Organic Game 1

Carbohydrates

The following show a small sampling of Nature’s choices for energy use, structural support and also serve as recognition targets in cells. Nature almost exclusively picks one enantiomer of a pair, though apparently some bacteria can make both enantiomers. When drawn as a the common stereoisomer has the second to the last OH on the right side. In Biochemistry, this is referred to as the “D” isomer. If the second to last OH were on the left side in a Fischer projection it would be referred to as the “L” isomer. There is no logical reason for these designations. They must be memorized, as do the positions of all of the other “OH” groups up the chain. “Reducing carbohydrates” have an aldehyde carbon at C1 and can be 2Cs, 3Cs, 4Cs, 5Cs, 6Cs or more in length. is probably the most famous of the carbohydrates. Some of these are shown below. How many chiral centers does each example have? Through tautomeric changes an aldehyde (glucose) can be converted into a keto carbohydrate (). How many stereoisomers are possible for each length of carbon? What are the absolute configurations of any chiral centers? What stereochemical relationship does the first stereoisomer as A (then B, C, etc.) have to the others? Are there any meso structures. (See problem below.)

A unique two carbon carbohydrate is possible, but not technically considered a carbohydrate, 2- hydroxyethanal

O H C

H OH achiral

H glycoaldehyde

Three carbon aldose carbohydrates – two possible (enantiomers), both are 2,3-dihydroxypropanal

O O H H R When the second to the last "OH" is on the C C top CO2H right side, biochemists refer to it as a "D" R H OH carbohydrate. Most carbohydrates in nature H OH H2N H HO H are "D". Most amino acids, on the other D L hand are "L" with a "NH " on the left side. CH2OH 2 R CH2OH CH2OH generic carbohydrate D- L-glyceraldehyde generic amino acid

Four carbon aldose carbohydrates– four possible, all are 2,3,4-trihydroxybutanal (enantiomers and )

O O O O H H H H C C C C Biochem names are all different. Organic names are easier. All of these are 2,3,4-trihydroxybutanal. R H OH HO H HO H H OH 1 = (2R,3R)-2,3,4-trihydroxybutanal R H OH HO H H OH HO H 2 = (2S,3S)-2,3,4-trihydroxybutanal 3 = (2S,3R)-2,3,4-trihydroxybutanal CH2OH CH2OH CH2OH CH2OH 4 = (2R,3S)-2,3,4-trihydroxybutanal D- L-erythrose D- L-threose

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Five carbon aldose carbohydrates – eight possible, all are 2,3,4,5-tetrahydroxypentanal (enantiomers and diastereomers)

O O O O O O O O H H H H H H H H C C C C C C C C R H OH HO H HO H H OH H OH HO H HO H H OH R H OH HO H H OH HO H HO H H OH HO H H OH R H OH HO H H OH HO H H OH HO H H OH HO H

CH2OH CH2OH CH2OH CH2OH CH2OH CH2OH CH2OH CH2OH D- L-riboseD- L-arabinose D- L-xylose D- L-lyxose

Six carbon aldose carbohydrates – 16 possible, all are 2,3,4,5,6-pentahydroxyhexanal (enantiomers and diastereomers)

O O O O O O O O H H H H H H H H C C C C C C C C R H OH HO H HO H H OH H OH HO H H OH HO H R H OH HO H H OH HO H HO H H OH H OH HO H R H OH HO H H OH HO H H OH HO H HO H H OH R H OH HO H H OH HO H H OH HO H H OH HO H

CH OH CH OH CH OH CH OH 2 2 2 2 CH2OH CH2OH CH2OH CH2OH D- L-allose D- L-altrose D-glucoseL-glucose D-gluose L-gluose

O O O O O O O O H H H H H H H H C C C C C C C C

HO H H OH H OH HO H HO H H OH HO H H OH

HO H H OH HO H H OH H OH HO H HO H H OH

H OH HO H HO H H OH HO H H OH HO H H OH

H OH HO H H OH HO H H OH HO H H OH HO H

CH OH CH OH CH OH CH OH 2 2 2 2 CH2OH CH2OH CH2OH CH2OH D- L-mannose D- L-galactose D-idoseL- D- L-talose

O OH OH O O H H OH OH O C C R R R R R R R H R H OH H OH R S H R OH OH OH S H OH HO H OH OH OH D-allose D-glucose R = R = H OH OH OH O H OH OH OH O R R H OH H OH H H CH2OH CH2OH OH OH OH D-allose D-glucose OH OH OH Without the dashes and wedges, these Without the dashes and wedges, these two carbohydrates look the same two carbohydrates look the same

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Problem – What would happen to the number of stereoisomers in each case above if the top aldehyde functionality were reduced to an alcohol functionality (a whole other set of carbohydrates!)? A generic structure is provided below to show the transformation. Nature makes some of these too. How many chiral centers does each example have? How many stereoisomers are possible for each length of carbon? What are the absolute configurations of any chiral centers? Specify the first stereoisomer as A (then B, C, etc.) and state what each relationship is to the others. Are there any meso structures.

O H Three carbon tri-ol carbohydrate = becomes only one structure (glycerol), CH OH which is achiral C 2 Reduce Four carbon tetra-ol carbohydrates = becomes three stereoisomers aldehyde (one meso pattern) to alcohol Five carbon penta-ol carbohydrates = becomes four stereoisomers (two meso patterns, one duplication)

CH2OH CH2OH Six carbon hexa-ol carbohydrates = becomes ten stereoisomers (two meso patterns, two duplications)

D-glucose is the most common choice of the 6 carbon examples above (can you think of a possible reason?). Even though it is a single , Nature can arrange glucose in many possible ways. Only a few are shown below.

open chain D-glucose ring of glucose (6 atoms), the aldehyde oxygen can be on the top = equatorial (< 1% in body) (called ) or on the bottom = axial (called ), both are observed in the body B OH OH H H H2C H H2C H H top O cyclization O H H O H B controlled O O by enzymes O O OH H B H H H H O O H H H H O H H H C rotation around -D-glucose (pyranose) the C1-C2 bond H OH B ( 66% in body) OH H HO H H2C H OH H H O H2C H OH H cyclization H O H B controlled O O H H H by enzymes O H O H H O H O H O H H B OH CH2OH H H OH bottom -D-glucose open chain D-glucose HO (pyranose) ( 33% in body) HO O O HO O Notice a similarity to Vit. C? HO O OH O (6 atom ring) (5 atom ring) HO  and  D-glucose 4 enzyme controlled () reactions, we are HO OH (< 1% in body) missing one of them Vit. C OH

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OH consists of long flat chains of glucose H OH H2C H  H C molecules (about 15,000) connected with the  etc. O OH 2 O  linkage, about 40 chains per fiber. It is said that O O HO HO O O cellulose accounts for about 1/2 of all the carbon in O HO 15 etc. the biosphere and about 10 kg of cellulose are OH H2C OH H H OH  synthesized and degraded every year. About 90% of cotton is cellulose. In our plant food it is referred to as or roughage. Ruminants and OH H OH termites can break down cellulose with the help of H2C H H2C microorganisms. etc. O O O HO H O OH HO (our glucose storage system) consists of helicies    of glucose molecules connected with the  linkage. We have OH OH H O HO O about 2000 Kcals of energy stored in this way in our liver. O When blood levels of glucose get low, our liver starts to release etc. glucose from our glycogen stores. When you start to run out H2C of glycogen your body switches over to fat metabolism to OH make glucose (gluconeogenisis). (1,4) linkages are shown but there are also some (1,6) linkages in glycogen.

Disaccharides are two linked together ( or ). Common carbohydrate possibilities have 3C, 4C, 5C and 6C structures and the carbonyl group can be an aldehyde or a ketone. As mentioned above, the 6C sugars can be six atom heterocycles (pyranoses such as glucose) or five atom heterocycles (furanoses such as fructose). and are two of the more famous disaccarides. O O "Glucose" in the general class of "Fructose" in the pyranoses. general class of furanoses.

sucrose - found in beets and sugar cane lactose - found in mother's milk OH H acetal  acetal  linkage hemi-acetal H linkage OH linkage O OH HO H OH  HO H H ketal O H H  H O OH linkage HO O H O HO H H O OH OH H H H OH H OH "galactose" "glucose" HO OH -D-galactopyranosyl-(1 4)--D-glucopyranose HO -D-glucopyranosyl-(1 2)--D-fructofuranoside The nomenclature of biochemistry often appears more complicated than the nomenclature of organic chemistry.

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There are approximately 60 amino sugars known, having many important functions. N- acetylglucosamine is part of a biopolymer in bacterial cell walls and a major component of the cell walls of most fungi. It is also the monomeric unit of the polymer , which forms the outer coverings of insects and crustaceans. When polymerized with glucoronic acid, it forms hyaluronic acid, which is a polymer with a molecular weight in the millions. A 150 pound body has about 15 grams of hyaluronic acid in it.

O OH OH H OH H OH H H H O O O HO HO HO OH HO O H H H n N OH hyluronan H H H H H N OH O H H glucoronic acid O

N-acetyl-D-glucosamine N-acetyl-D-glucosamine

Glycolipids can serve as markers for cellular recognition and are found on the outer surface of all eukaryotic cell membranes. They extend from the phospholipid bilayer into the aqueous environment outside the cell where it acts as a recognition site for specific chemicals as well as helping to maintain the stability of the membrane and attaching cells to one another to form tissues.

O OH OH H H R = fatty acid chain H H O O O R HO HO HO O HO O R O R H H OH OH H H H H O glycero glyco lipids O glycolipids

Blood types are based, in part, on carbohydrate coatings linked to lipid molecules on the outer cell membranes. There is also a soluble form linked to proteins in the blood. About 75% of type A individuals have a repeat of the 3 terminal sugars. Type AB (4% in the US) have both A and B patterns on their cell surfaces and are universal acceptors. There is some variation in the position number of the connections and the / linkage is not indicated. Science News (vol 151, p 24, 1-11-97) discusses enzymes from chicken livers (type A) and coffee beans (type B) that can cleave the single sugar at the end of the cell coatings. This would convert type A and type B to type O, which would allow for universal donation. The article discusses the possible commercial production for blood donations. There are over 7,000,000,000 (billion) people on the earth. Every one of us has a unique biochemical profile that is uniquely recognized by our immune system. The blood types give you a hint at how this is possible.

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gluc galac N-acet galac The linkages are unspecified here. type O (45% in US) universal donor H C 3 OH O HO cell membrane This sequence is the same HO OH in all blood types (type O) fucose OH OH

O gluc galac N-acet galac galac HO OH

type A (40% in US) galactose OH OH

O HO cell membrane The extra galactose HO OH makes this type A. fucose glucose OH OH OH gluc galac N-acet galac N-acet O HO OH type O (11% in US) N H The extra cell membrane O N-acetylgalactosamine N-acetylgalactosamine makes this type B. fucose

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Cycles

1. Glycolysis – simple version (not all steps are shown in the usual cycyle)

glucose CH2OH 2 NADPH + H+ glyceraldehyde-3-phosphate dehydrogenase (glycolysis) O H H H O H glucose H OH H -2 2 OH OH O3P O C C C 1,3-bisphosphoglycerate

-2 H OH OH OPO3

ATP glucokinase 2 ATP phosphoglycerate kinase -2 H O3P O CHOH O O H2 H -2 3-phosphoglycerate H H O3P O C C C glucose-6-phosphate OH H OH OH OH O phosphoglycerate mutase H OH H phosphoglucose O H -2 2 2-phosphoglycerate HO C C C O3P O CH2 O H2C OH fructose-6-phosphate -2 O H HO O3P O H OH enolase OH H O phosphofructokinase 1 -2 -2 H2C C C phosphoenol pyruvate (PEP) O3P O CH2 O H2C O-PO3 -2 O H HO fructose-1,6-bisphosphate O3P O H OH pyrovate kinase 2 ATP O O OH H aldolase H3CCC pyruvate (x2) O H S-CoA O -2 O O H2 acetyl Co-A -2 H2 phosphate H2C C C OPO3 O3P O C C C isomerase alanine H HO O H cysteine OH phosphate glycine ...or transported in blood to liver glyceraldehyde-3-phosphate (x2) (made into glyceraldehyde-3-phosphate) H3CCC and oxidized back to pyruvate and serine made back into glucose via 2 NADPH + H+ glyceraldehyde-3-phosphate dehydrogenase threonine H gluconeogenosis tryptophan lactate OH 1,3-bisphosphoglycerate

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Glycolysis – long version Glycolysis HO H HO HO O OH O make hemi-acetal O glycogen O O H HO OH O O O H 1a cleave glucose 2 O OH OH HO OH H HO OH HO OH 1b open acetal open chain glucose cyclic glucose glycogen - glucose polymer

O ATP 3 OH OH O OH OH OH O P O

O O H tautomerization H open acetal HO O O OH O O OH O -2 H 5 H 4 -2 H O P O3P ene-diol 3 open chain glucose-6-phosphate HO OH cyclic glucose-6-phosphate 6 tautomerization -2 -2 O P O3P 3 H O O O OH OH make hemi-ketal ATP O O O OH H 8 O OH O 7 -2 HO HO -2 O P O OPO3 3 OH OH open chain fructose-6-phosphate H cyclic fructose-6-phosphate cyclic fructose-1,6-bisphosphate reverse hemi-ketal H 9 -2 -2 -2 H PO H O PO3 3 PO3 OH O O OH O R reverse S O O H via make hemi- ene-diol aldol thioacetal H 10 H O O 10b 11 O O O -2 O O3P -2 H O O3P H glyceraldehyde-3-phosphate dihydroxyacetone phosphate open chain fructose-1,6-bisphosphate -2 -2 PO 12 NAD+ -2 -2 3 PO3 PO3 make PO3 O O O O O O O mixed O O imidazole, anhydride make ATP phosphate on R P HO S O O HO 13 14 15 O O -2 O O O PO3 H H H 2,3-bisphosphoglycerate 1,3-bisphosphoglycerate 3-phosphoglycerate imidazole, O phosphate off 16 NADH O H pyruvate O make O O ATP elimination HO 19 of water H HO 18 HO (Mg+2 helps) lactate O NAD+ 22 HO H O O H 20 O -2 17 OH O O NADH PO3 -2 PO3 H CoA phosphoenol pyruvate (PEP) 2-phosphoglycerate 21 H S H ethanal acetyl Co-A ethanol

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Glycolysis step by step

Mechanism steps without arrows. B: = base and B+-H = acid. Add in necessary arrows to show electron movement. Stereochemistry is omitted. Each step is under enzyme control. Possible answers are shown below. HO 1 H H B H B O glycogen O H HO HO O O glycogen O O H HO

O O O O H 1a HO OH glycogen - 1 HO O cleave HO OH HO OH glucose H B glycogen B HO OH cyclic glucose

H B 1b 6 HO H O OH O B 5 O H B

HO O 1b 6 4 2 4 1 5 3 1 H 2 open 3 acetal O OH OH HO OH H H B cyclic glucose open chain glucose

H HO 2 O OH O H B 6 5 O H 2 6 4 2 HO O 5 3 1 H 1 B make 4 hemi-acetal 2 O OH OH 3 H HO OH cyclic glucose open chain glucose

B H 3 BH O O make -2 6 6 O3P 5 O H inorganic 5 O H ester O HO O HO O 1 4 1 4 ATP OPO 2 ADP O 2 3 3 HO OH O HO OH cyclic glucose cyclic glucose-6-phosphate

O 4 H B H O P O O OH O

O O open acetal HO O H

H O OH O -2 B H O P H B HO OH 3 open chain glucose-6-phosphate cyclic glucose-6-phosphate

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5 H B H B OH OH O OH OH O

tautomerization H H H O OH O -2 O OH O H B O P -2 H 3 O3P ene-diol open chain glucose-6-phosphate H B

BH 6 B H H O OH OH OH OH O

tautomerization H O OH O -2 H B O OH O O3P -2 H O P B 3 ene-diol open chain fructose-6-phosphate

-2 O3P 7 B H O O OH OH BH O make O hemi-ketal H

O OH O HO B -2 H B O O3P OH H open chain fructose-6-phosphate cyclic fructose-6-phosphate

-2 O P -2 8 3 O3P B O O H B OADP

O O O O O H ATP H O P OATP H B HO HO O O -2 OH OPO3 H OH cyclic fructose-6-phosphate B cyclic fructose-1,6-bisphosphate

9 -2 O P 3 BH B -2 O H PO3 O OH O B O O H reverse hemi-ketal

O O O H B HO -2 OPO3 -2 H OH O3P cyclic fructose-1,6-bisphosphate open chain fructose-1,6-bisphosphate

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10 H B -2 B H PO H 3 PO -2 O OH O O 3 via OH O H ene-diol reverse aldol H 10b O O O O O O -2 H B -2 O P H B O3P 3 open chain fructose-1,6-bisphosphate glyceraldehyde-3-phosphate dihydroxyacetone phosphate

-2 B -2 10b PO3 -2 BH PO3 OH O H PO3 O O O O B tautomerization H tautomerization H H B O O B O dihydroxyacetone phosphate BH H H ene-diol glyceraldehyde-3-phosphate

10 imine alternative to keto retroaldol (actually protonated iminium ion) -2 -2 H PO 3 H PO3 O OH O O OH O

H H H N B O O O N O O O -2 H -2 H O3P O P 3 H B R R BH BH

-2 H H PO3 -2 O PO3 O OH O OH O H

H O O O O N -2 N -2 H R O3P O P R 3 B H B hydrolyze imine via ene-diol -2 PO3 OH O

H

O

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11 BH -2 -2 H PO3 B PO3 R O O S O O S R H H make hemi- H thioacetal O B O H H glyceraldehyde-3-phosphate BHhemi-thioacetal

-2 B H -2 12 PO3 BH H PO3 R R N S O O O O R N H

oxidation NADH R NAD+ H S

O O H H

-2 13 -2 R H PO3 PO BH 3 S O O O O O B B O make P R mixed O O H P S anhydride O O O O O O BH H thioester H 1,3-bisphosphoglycerate

BH 14 -2 -2 PO3 PO3 B O O O O O

P O ADP O O O make HO O ATP ATP O P O O O H O H 1,3-bisphosphoglycerate 3-phosphoglycerate

-2 -2 15 PO PO3 3 R R O O O O N H O imidazole N O P N phosphate HO HO N O O O H -2 H PO3 H B 3-phosphoglycerate B 2,3-bisphosphoglycerate

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16 BH O O H P R B R O O O O O O N imidazole HO O P N HO N H H N O -2 O O -2 PO3 H PO3 2,3-bisphosphoglycerate 2-phosphoglycerate

H 17 H B O O O H H elimination O of water HO HO B (Mg+2 helps) B H O O -2 -2 PO3 PO3 H B 2-phosphoglycerate phosphoenol pyruvate (PEP)

O H B 18 B O HO make O ATP O HO O O ADP P O O O P OATP O phosphoenol pyruvate (PEP) pyruvate O

O reaction goes in both directions 19 a O

H HO reduction N R HO N R H H O BH O NADH NAD+ pyruvate B lactate H

19 b O O H N R N R H HO oxidation HO H NAD+ NADH O O pyruvate lactate H B H B

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O 20 BH O R O C N O R H R HO addition O N N O O S B O -CO2 BHpyruvate TPP ylid H S H S

R H O N R elimination N BH O H S ethanal TPP ylid B H S

21 B BH O H H NADH O N R N R H H H H ethanal NADH ethanol NAD+

B H 22 S R R S S N R O N S N O O H S R S H S elimination R H S R S H B B BH from step 20 H

R O B B H H O N S S H S R S ethanal R S TPP ylid H H H N H H N H

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