Biochemistry: Nucleotides and Carbohydrates

Plane Electromagnetic Waves

• Plane electromagnetic waves are a wave consisting of oscillating electromagnetic fields radiating outward at the speed of light.
• The electric field (E) and magnetic field (B) oscillate perpendicular to each other and to the direction of wave propagation.

Polarization of Light Waves

• Normal light has electric field oscillations in all directions.
• A polarizing filter only allows light oscillating in one plane to pass through.
• The resulting light oscillating in a single direction is called plane-polarized light.
• Chiral molecules rotate the plane of polarization of plane-polarized light.
• Jean-Baptiste Biot discovered this phenomenon in 1815.
• Some naturally occurring organic substances, like camphor, rotate the plane clockwise (dextrorotatory).
• Other compounds rotate the plane counterclockwise (levorotatory).
• This rotation is due to the chirality of the substances.

Molecules that Rotate Plane-Polarized Light

• Molecules that rotate plane-polarized light clockwise are called dextrorotatory.
• Molecules that rotate plane-polarized light counterclockwise are called levorotatory.
• Enantiomers rotate light by the exact same amount but in opposite directions.

Chirality of Amino Acids, Proteins, Enzymes, and Receptors

• Amino acids are chiral.
• Proteins are chiral.
• Enzymes and receptors are chiral.
• Enzymes or receptors in the human body form a chiral environment that distinguishes between R and S enantiomers.

Carbohydrates

• Monosaccharides are simple sugars and cannot be hydrolyzed into simpler molecules.
• The relationship between monosaccharides and polysaccharides is analogous to that of amino acids and proteins, or nucleotides and nucleic acids.

Carbohydrates: Transformations of Light Energy

• Carbohydrates are mainly produced by photosynthesis.
• They are the most abundant class of molecules of biological origin.
• They are essential components for all living organisms.
• Carbohydrates account for more than 90% of the dry matter in plants.
• They contribute 55-70% of caloric intake in humans.
• The relationship between monosaccharides, polysaccharides, amino acids, and proteins is analogous to that between nucleotides and nucleic acids.

The Building Block

• Chiral tetrahedral carbon atoms are covalently linked to a hydroxyl group, a carbonyl group, and the remainder of the chain.
• These are aldehydes or ketones of aliphatic polyhydroxy alcohols.
• Molecules have carbon atoms between 3 and 7.
• In nature, D-stereoisomerism is prevalent.

Glyceraldehyde

• Glyceraldehyde is the simplest aldose displaying optical activity (C2 asymmetric).
• The two enantiomers are indicated by D (+) and L (-).
• Conventionally, the two stereoisomers of glyceraldehyde are used as a reference to classify all monosaccharides.

Monosaccharides

• Monosaccharides are aldehydes or ketones of aliphatic polyhydroxy alcohols with 3 to 7 carbon atoms.
• In all monosaccharides belonging to the D series, the hydroxyl group on the asymmetric carbon furthest from the carbonyl group is positioned on the right.

Classification of Monosaccharides

• Monosaccharides are classified according to the nature of the carbonyl group (aldehyde or ketone) and the number of carbon atoms (trioses, tetroses, pentoses, hexoses, heptoses).
• Aldoses are monosaccharides with an aldehyde group at carbon 1.
• Ketoses are monosaccharides with a ketone group at a carbon other than carbon 1.

Stereoisomerism

• Monosaccharides possess numerous chiral centers.
• The number of possible stereoisomers is 2n-2 for aldoses and 2n-3 for ketoses.
• Monosaccharides that differ only in the configuration of a carbon atom are called epimers.

Epimers

• Epimers are stereoisomers that differ in the configuration of a single carbon atom.
• In D-glucose, D-mannose, and D-galactose, differences in OH configuration at different carbon atoms create epimers.

Cyclic Conformations

• Hydroxyl and carbonyl groups in 5- or 6-carbon monosaccharides spontaneously react intramolecularly to form cyclic hemiacetals or hemiketals.

Haworth Projections

• A monosaccharide displaying a 6-carbon ring is called a pyranose.
• A monosaccharide displaying a 5-carbon ring is called a furanose.

D(+)-glucose

• D(+)-glucose is a reducing sugar with a sweetening power of 70% of sucrose.
• It exhibits a specific optical rotation of +52.7° at room temperature.
• It reacts frequently with amino acids, leading to Maillard reactions (browning reactions).

D(-)-fructose

• D(-)-fructose, also known as levulose, has a sweetening power of 140% compared to sucrose.
• It exhibits a specific optical rotation of -92.4° at room temperature.

Glucose Cyclization

• The cyclization of a monosaccharide induces asymmetry in the anomeric carbon, leading to the formation of two diastereoisomers called anomers.
• The anomer with the anomeric hydroxyl on the opposite side of the ring to the CH2OH group is called the α-anomer.
• The anomer with the anomeric hydroxyl on the same side of the ring as the CH2OH group is called the β-anomer.

Mutarotation

• D-glucose anomers have different specific optical rotations: α-anomer: + 112.2°; β-anomer: + 18.7°.
• At room temperature, a D-glucose solution has a specific optical rotation of +52.7°.
• The two anomers rapidly interconvert.
• In water, the β-anomer is 63.6% and the α-anomer is 36.4%.

Conformation of Monosaccharides

• The stability of pyranose and furanose rings depends on stereochemical interactions between substituents.

Derivatives of Monosaccharides

• Deoxy-sugars: One or more hydroxyl groups are replaced by hydrogen.
• Amino-sugars: One or more hydroxyl groups are replaced by amino groups (often acetylated).

Glucose Family

• Monosaccharides can act as structural backbones for producing new biological entities.
• They exhibit novel chemical properties when substituted by other functional groups.

Redox Reactions

• Carbohydrates show typical reactivity of aldehydes and ketones.
• Mild oxidation of the carbonyl group (C1) of an aldose generates an aldonic acid.
• Oxidation of the last alcohol group (C6) produces uronic acids.
• Oxidation of both the last alcohol and aldehyde groups generates aldaric acids.

Lactonization

• Aldonic and uronic acids are prone to intramolecular esterification, forming 5- or 6-membered lactones.

Ascorbic Acid

• Vitamin C is a γ-lactone of a hexonic acid, exhibiting an enediol structure at carbon atoms 2 and 3.

Reduction Reactions

• Aldoses and ketoses can be reduced to alditols under mild conditions.
• Alditols don't have carbonyl groups and are common in nature.
• They generate similar caloric intake but slower absorption than monosaccharides.

D(-)-sorbitol

• Sorbitol is a sugar alcohol produced from the reduction of glucose.
• It's prevalent in plants and used in food industries.
• It's metabolized slower than glucose, doesn't significantly increase blood sugar.
• It's not easily fermented by yeasts, thus useful in products like jams and honey.

Xylitol

• Xylitol is a sugar alcohol found in small amounts in some fruits and vegetables.
• It has similar sweetness and caloric intake to sucrose.
• It is not cariogenic, and useful in diabetic products.

Glycosidic Bond

• Glycosidic bonds form when a monosaccharide reacts with an alcohol.
• The product is stable in alkaline and oxidizing conditions but can be hydrolyzed in acidic conditions.
• Glycosides are important in nature, forming components like polysaccharides and analogues of peptide bonds in polypeptides.

Glycosides

• Glycosides are derivatives formed from the reaction between a monosaccharide and an alcohol.
• They are stable in alkaline and oxidizing conditions, albeit reversible, and hydrolyze in acid.
• Glycosides are ubiquitous in nature, typically distinguishable into a glyconic and aglyconic component.
• These are utilized as pro-drugs.

Amylose

• Amylose is a linear polymer of α-(1,4)-linked glucose units.
• It forms a helical conformation.
• The average molecular weight is approximately 10^5-10^6.

Amylopectin

• Amylopectin is a branched polymer of a-(1,4)-linked glucose units with α-(1,6) branch points.
• Branches occur approximately every 24-30 glucose units.
• This molecule has a large molecular weight, about 10^8.

Starch Granules

• Starch granules display a concentric lamellar structure with alternating crystalline and amorphous phases.
• Crystalline phases arise from the regular packing of amylopectin terminal chains.

Starch Gelatinization

• Starch gelatinization occurs upon heating starch in water.
• The crystalline phase disintegrates, leading to granule swelling and subsequent hydration.
• Gelatinization allows amylose and amylopectin hydrolysis.

Starch Retrogradation

• Upon cooling, starch granules absorb water and amylose and amylopectin chains regroup, forming inter-chain H-bonds, crystallizing together.
• This process is called starch retrogradation and leads to a gel formation.

Cellulose

• Cellulose is a linear polymer of β-(1,4)-linked glucose units.
• It's the most abundant organic polymer on Earth.
• Cellulose cannot be hydrolyzed by human enzymes.

Chitin

• Chitin is a linear polymer of N-acetyl-D-glucosamine linked by β-(1, 4)-glycosidic bonds.
• It's a significant component of insect/crustacean exoskeletons and fungal cell walls.
• Hydrophobic due to numerous intra and inter-chain hydrogen bonds.

Nucleosides and Nucleotides

• Nucleosides are formed by a nitrogenous base linked to a sugar (ribose or deoxyribose).
• Nucleotides are formed by a nucleoside linked to one or more phosphate groups.
• The nitrogenous bases are either purines (adenine, guanine) or pyrimidines (cytosine, thymine, uracil).

Phosphodiester Bond

• Nucleotides form a polymer chain through phosphodiester bonds.
• These bonds link the 3' hydroxyl group of one nucleotide to the 5' phosphate group of the next.

Complementary Base Pairing

• Adenine always forms two hydrogen bonds with thymine/uracil.
• Guanine always forms three hydrogen bonds with cytosine.

DNA Structure

• DNA is a double helix of two polynucleotide chains running antiparallel.
• The sugar-phosphate backbone is on the outside, and the nitrogenous bases are on the inside, paired via hydrogen bonds.
• Complementary base pairing (A-T and G-C) is fundamental to DNA structure.

Nucleotides and Energy: Phosphoanhydride Bonds

• Nucleotides are involved in energy storage and transfer, primarily through high-energy phosphoanhydride bonds.
• Adenosine triphosphate (ATP) is the universal energy currency in cells.

Phosphoric Anhydrides

• ATP's high-energy phosphoanhydride bonds store chemical energy that powers cellular processes.

Reaction Coupling

• Cells couple energetically unfavorable reactions to favorable ones using chemical energy releases from the high-energy phosphate bonds, like ATP hydrolysis.

Glycogen and Glucose Regulation

• Glycogen is the animal storage form of carbohydrates.
• It's more extensively branched than amylopectin.
• Two hormones control glycogen concentration in blood (insulin and glucagon).

Glycogen Synthase vs. Glycogen Phosphorylase

• Glycogen synthase catalyzes glycogen synthesis.
• Glycogen phosphorylase catalyzes glycogen breakdown.
• Both are regulated by allosteric effectors (like ATP, AMP, and glucose-6-phosphate).

Glucose Transformations Before Glycogen Synthesis

• Glucose is transformed into glucose-6-phosphate, then glucose-1-phosphate, then UDP-glucose.
• These steps are crucial for glycogen synthesis and use specific enzymes for each reaction.

Glycogen Synthesis Strategy

• The anomeric carbon of glucose is not reactive, thus needs UDP-glucose.

Conversion of Glucose-1-Phosphate into UDP-Glucose

• Glucose-1-phosphate is activated to UDP-glucose through the action of UDP-glucose pyrophosphorylase.
• This activation process is essential for glycogen synthesis because UDP-glucose is a reactive form of glucose.

Glycogen Synthesis

• Glycogen synthesis is catalyzed by glycogen synthase.
• Glycogenin acts as a primer, initiating the formation of the glycogen chain.
• Chain branching enzyme is necessary for creating the branched structure of glycogen.

Glycogen Synthesis Regulation

• Glycogen synthase and phosphorylase are regulated by allosteric effectors, such as ATP, AMP, and glucose-6-phosphate.
• Hormones like epinephrine can regulate glycogen synthesis and degradation through signaling cascades.

Regulation of Glycogen Hydrolysis

• The degradation of glycogen is catalyzed by glycogen phosphorylase using pyridoxal phosphate as a cofactor.
• The enzyme generates glucose-1-phosphate.
• Glycogen phosphorylase activity is also modulated by phosphorylation.

Glycogen Phosphorylase Mechanism

• The mechanism involves the formation of a ternary complex (E-phosphate-glycogen), including a carbocationic intermediate.
• The release of glucose-1-phosphate follows the reaction between the intermediate and the phosphate present in the active site.

Test your knowledge on the chemistry of nucleotides and carbohydrates with this quiz. Explore concepts related to ATP, glycosidic bonds, and the structural properties of polysaccharides. Perfect for students studying biochemistry or related fields.