Carbohydrates, Nucleosides, and Nucleotides: Structure and Function in Biological Chemistry

Carbohydrates

General Formula and Main Types

Carbohydrates are essential biomolecules that serve critical functions in energy provision, structural support, and cell recognition. Their general formula is $C_n(H_2O)_n$.

• Functional Groups: Carbohydrates contain hydroxyl and carbonyl groups.

• Oxidation: Carbohydrates can be oxidized to $CO_2$ and release energy during cellular respiration.

• Main Types:

  • Monosaccharides: Single sugar units.

  • Disaccharides: Two monosaccharide units joined by glycosidic bonds.

  • Polysaccharides: Long chains of monosaccharide units, often branched, serving as energy storage or structural molecules.

Types of Monosaccharides According to Functional Group

Monosaccharides are classified based on the type of carbonyl group present:

• Aldoses: Contain an aldehyde group (e.g., Glucose is an aldohexose).

• Ketoses: Contain a ketone group (e.g., Fructose is a ketohexose).

Fischer Projection for 3D Structures

The Fischer projection is a method to represent the 3D structure of sugars:

• The aldehyde or ketone is at the top (1-position).

• Horizontal bonds project out of the plane; vertical bonds go into the plane.

• Still widely used for depicting sugar stereochemistry.

Naming by Number of Carbon Atoms

Monosaccharides are named according to the number of carbon atoms:

• Triose: 3 carbons (e.g., Glyceraldehyde)

• Tetrose: 4 carbons

• Pentose: 5 carbons (e.g., Ribose)

• Hexose: 6 carbons (e.g., Glucose)

Cyclic Forms of Monosaccharides

Monosaccharides cyclize in solution, forming rings:

• The carbonyl group reacts with a hydroxyl group to form a ring.

• 5-membered (furanose) and 6-membered (pyranose) rings are most common.

• This creates a new chiral center called the anomeric carbon.

Anomers: Stereoisomers of Cyclic Monosaccharides

Anomers are stereoisomers that differ at the anomeric carbon:

• In cyclic sugars, the carbonyl oxygen can be oriented up or down.

• Alpha (α) anomer: OH group on C1 is down.

• Beta (β) anomer: OH group on C1 is up.

Examples of Monosaccharides

• Glucose: Most important monosaccharide in human metabolism; building block for complex carbohydrates.

• Galactose: Isomer of glucose at the 4-position; monomer in lactose; found in peas.

• Fructose: Most important keto-monosaccharide; found in honey and fruit juices.

Disaccharides ($C_{12}H_{22}O_{11}$)

Disaccharides are formed by condensation (dehydration synthesis) between two monosaccharides:

• Glycosidic Bond: Covalent bond between the anomeric carbon of one sugar and a hydroxyl group of another.

• Nomenclature: Bonds are named by the carbon atoms involved and the anomeric configuration (e.g., α-1,4 bond).

Formation and Breakdown

• Condensation: Formation of glycosidic bond with loss of water.

• Hydrolysis: Breaking of glycosidic bond with addition of water.

Common Disaccharides

Name	Constituent Sugars	Bond Type
Sucrose	Glucose + Fructose	α-1,4
Lactose	Galactose + Glucose	β-1,4
Maltose	Glucose + Glucose	α-1,4

Polysaccharides

Polysaccharides are polymers of monosaccharides formed by condensation reactions:

• Starch: Storage carbohydrate in plants; mixture of amylose (straight chain, α-1,4 bonds) and amylopectin (branched, α-1,4 and α-1,6 bonds).

• Glycogen: Storage carbohydrate in animals, fungi, and bacteria; highly branched (α-1,4 and α-1,6 bonds).

• Cellulose: Structural carbohydrate in plants; straight chains of β-glucose (β-1,4 bonds); provides dietary fiber.

Nucleosides and Nucleotides

Nucleosides and Nucleotides: Structure

• Nucleoside: Composed of a pentose sugar and a nitrogenous base (purine or pyrimidine) at the 1' position.

• Nucleotide: Nucleoside with a phosphate group attached at the 5' position.

• Example: Adenosine (nucleoside), Adenosine Monophosphate (AMP, nucleotide).

Pentoses: Ribose and 2-Deoxyribose

• Ribose: Found in RNA; has an OH group at the 2' position.

• 2-Deoxyribose: Found in DNA; has an H at the 2' position.

Nitrogenous Bases

Pyrimidines

• Cytosine (C)

• Thymine (T) (DNA only)

• Uracil (U) (RNA only)

• Distinct properties arise from C=O, NH2, and R2N groups.

Purines

• Adenine (A)

• Guanine (G)

• Distinct properties arise from C=O, NH2, and R2N groups.

DNA and RNA Nucleosides

DNA Nucleoside	Abbreviation
Deoxyadenosine	dA
Deoxyguanosine	dG
Deoxythymidine	dT
Deoxycytidine	dC

RNA Nucleoside	Abbreviation
Adenosine	A
Guanosine	G
Uridine	U
Cytidine	C

Nucleotide Polymers

• Phosphodiester Bond: Formed between the phosphate on C5' of one nucleotide and C3' of the next.

• This forms the backbone of DNA or RNA, catalyzed by enzymes such as DNA polymerase and DNA ligase.

DNA Strand Ends

• 5' End: Characterized by a free phosphate group attached to C5'.

• 3' End: Characterized by a free OH group attached to C3'.

History of DNA Structure

• Chargaff's Rule: For every mole of purine, there is a mole of pyrimidine; for every mole of adenine, there is a mole of thymine; for every mole of guanine, there is a mole of cytosine.

• Explained by the Watson-Crick model of base pairing.

Watson and Crick Double Helix

• 1953: James Watson and Francis Crick proposed the double helix model, using X-ray diffraction evidence from Rosalind Franklin and Maurice Wilkins.

A-T and G-C Base Pairing

• Adenine (A) hydrogen bonds with Thymine (T) (2 H-bonds).

• Guanine (G) hydrogen bonds with Cytosine (C) (3 H-bonds).

• In RNA, thymine is replaced by uracil.

DNA Double Helix Structure

• Two nucleotide polymers run antiparallel (one 5'→3', the other 3'→5').

• Hydrophilic phosphate groups are exposed to the aqueous environment.

• Bases form tight bonds with each other; water is expelled from the inside of the helix.

Major and Minor Grooves

• Major Groove: Wider and deeper; more base pairs exposed and accessible; DNA-binding proteins interact here.

• Minor Groove: Narrower and shallower; less information about base sequences accessible; some proteins and small molecules bind here.

Functions of DNA

• Stores instructions for building and maintaining an organism.

• Contains genes coding for proteins and functional RNA molecules.

• Passes genetic information from parents to offspring.

Replication

• Transcription: DNA is copied into messenger RNA (mRNA).

• Translation: mRNA directs assembly of amino acids into proteins.

• Proteins perform most cellular functions; DNA controls cellular activity.

Ribonucleic Acid (RNA)

• Messenger RNA (mRNA): Template for protein assembly; carries working copy of DNA code.

• Transfer RNA (tRNA): Short sequences; specific tRNAs for each amino acid; adaptor molecule linking amino acids to codons.

• Ribosomal RNA (rRNA): Major component of ribosomes (50–60% of weight).

Differences Between DNA and RNA

Feature	DNA	RNA
Pentose Sugar	Deoxyribose (H at 2')	Ribose (OH at 2')
Base	Thymine	Uracil
Strands	Double stranded, antiparallel	Single stranded
Base Sum	G + A = C + T	Sum not equal
Modification	Bases not modified	Bases modified
Hydrolysis	Resistant (deoxyribose)	Susceptible (ribose)
Location	Nucleus, mitochondria	Nucleus, cytoplasm

Transcription of DNA to mRNA

• DNA is partially unwound.

• The anti-sense strand is transcribed into mRNA.

• mRNA is released and DNA is rewound.

Codons

• There are 64 possible codons, encoding 20 amino acids.

• Several codons can encode the same amino acid.

• AUG: Start codon (Methionine).

• UAA, UAG, UGA: Stop codons.

Structure of tRNA

• Short nucleotide chains (73–93 nucleotides).

• Each tRNA picks up a specific amino acid and recognizes the appropriate codon on mRNA.

• Loops in the structure are due to unusual bases that do not form hydrogen bonds.

Translation of tRNA to Protein

• Two tRNA molecules bind to two binding sites of the ribosome (mRNA).

• A peptide bond forms between the two amino acids.

• The used tRNA leaves the ribosome; another tRNA binds, continuing the process.

Summary Table: Key Carbohydrates and Nucleic Acid Features

Biomolecule	Monomer	Bond Type	Main Function
Starch	α-glucose	α-1,4 and α-1,6 glycosidic	Energy storage (plants)
Glycogen	α-glucose	α-1,4 and α-1,6 glycosidic	Energy storage (animals)
Cellulose	β-glucose	β-1,4 glycosidic	Structural (plants)
DNA	Deoxyribonucleotide	Phosphodiester	Genetic information
RNA	Ribonucleotide	Phosphodiester	Protein synthesis, regulation

Additional info: These notes expand on the original slides by providing definitions, examples, and tables for comparison, ensuring a comprehensive and self-contained study guide for biochemistry students.