BIOC*2580 - 4

Previous Class Recap

  • Topics Discussed:

    • Formation of glycosides from sugars.

    • Sugars as reducing agents.

Reducing and Non-Reducing Sugars

  • Definition:

    • Reducing sugars: Sugars that can act as reducing agents due to their ability to open into the linear form.

  • Key Concepts:

    • Glycosidic Bond:

    • Formed when a sugar reacts with an alcohol or amino group.

    • Involves the anomeric carbon of the sugar.

    • The bond prevents the sugar from reverting to a linear form, thus categorizing it as a non-reducing sugar.

    • Identifying sugar types:

    • Free Anomeric Carbon: If the anomeric carbon has a free hydroxyl group, it is a reducing sugar; otherwise, it is a non-reducing sugar.

Example: Copper Reduction Test

  • Reducing Sugar Reaction:

    • When a reducing sugar is treated with copper (II), it forms a reddish-brown precipitate.

    • Example: Glucose and fructose are reducing sugars, while sucrose is a non-reducing sugar (remains blue in the test).

Disaccharides

  • Definition:

    • Formed from the combination of two monosaccharides via glycosidic bonds. Disaccharides are glycosides.

  • Formation:

    • Anomeric carbon acts as the electrophile, the alcohol as a nucleophile.

Example: Lactose

  • Components:

    • Formed from condensation reaction of galactose and glucose.

      • The glycosidic bond of lactose is formed by the anomeric carbon of galactose in the β configuration reacting with the hydroxyl of carbon 4 of glucose

    • Structures:

    • Beta-D-galactose (anomeric carbon hydroxyl pointing upwards).

    • Glucose (hydroxyl group on carbon 4 acts as the nucleophile).

  • Glycosidic Bond:

    • Described as (beta 1—>4)glc linkage between galactose and glucose, indicating their bond configuration.

  • Naming Convention:

    • GAL for galactose, GLC for glucose, and the numbers indicating the respective carbohydrate atoms involved in the bond formation.

Reducing Nature of Lactose

  • Identifying Reducing Sugars:

    • For a disaccharide to be a reducing sugar, at least one anomeric carbon must be free.

    • Lactose can act as a reducing sugar due to glucose's free hydroxyl. Galactose's anomeric carbon is involved in the bond, hence not free.

Structural Isomers of Disaccharides

  • Definition:

    • Different configurations of the same monosaccharide can lead to structurally different disaccharides.

Example Structures

  • Sucrose: non reducing

    • Comprised of glucose and fructose with glycosidic bond 

  • Maltose:

    • Two glucose units connected by an

  • Trehalose: non reducing

    • Glucose units connected by an

Polysaccharides

  • Definition:

    • Long chains of monosaccharide units connected through glycosidic bonds.

  • Features:

    • Can have highly branched structures due to multiple alcohol groups in sugars.

      • Branches can act as the nucleophile in forming a glycosidic bond, bonding a single subunit to two (or more) others.

    • Differentiation based on types of sugars involved and glycosidic bond types. (sugar units that are linked, in the length of the chains, in the type of bonds linking the units, and in the degree of branching)

Types of Polysaccharides

  • Homopolysaccharides:

    • Composed of the same monosaccharides (e.g., starch, glycogen, cellulose).

  • Heteropolysaccharides:

    • Composed of different monosaccharides.

Nucleic Acids

  • Types:

    • DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid)

      • RNA is rapidly hydrolyzed under alkaline conditions; DNA is much more stable

    • Function: Encodes genetic information.

Primary Structure of Nucleic Acids

  • Made of Nucleotides:

    • Each nucleotide consists of a base, sugar, and phosphate.

  • Connection:

    • Joined by phosphodiester bonds between the sugar and phosphate groups of adjacent nucleotides to form “sugar-phosphate backbone”.

Nucleotide Composition

  • Sugar Types: Both occur in their β-furanose form

    • D-Ribose in RNA.

    • Deoxyribose in DNA (missing hydroxyl at carbon 2 (replaced by -H)).

  • Nitrogenous Bases:

    • Classified as purines (Adenine, Guanine) or pyrimidines (Cytosine, Uracil in RNA, Thymine in DNA).

      • Pyrimidines- Both DNA and RNA contain two major pyrimidine
        bases (both contain Cytosine)

      • Purines- The purine ring is a fused (joined together),
        bicyclic (two rings) heterocycle. 

  • Tautomerism:

    • Bases can exist in tautomeric forms (i.e., shift in hydrogen position affecting double bonds).

    • OH goes under keto/enol tauterism

    • The NH2 group undergoes amino/ imino tautomerism.

    • The form shown in the middle (amino + keto) predominates

Nucleosides and Nucleotides

  • Nucleoside Formation: Base + Sugar → Nucleoside

    • Base linked to sugar via a glycosidic bond (specifically, a nitrogen-sugar connection makes it a nucleoside).

    • Nucleosides is glycoside found in nucleic acids

    • glycosidic bond is sometimes called a “glycosylic” bond to designate
      the C-N linkage

  • Naming:

    • Adenosine (A), Cytidine (C), Guanosine (G), and Thymidine (T) for DNA (do not indicate deoxy).

  • Nucleotide Formation: Base + Sugar + Phosphate → Nucleotide

    • Nucleoside + phosphate forms nucleotide.

  • phosphorylated nucleosides

    Primary Structure of Nucleic Acids

    • Made of Nucleotides:

      • Each nucleotide consists of a base, sugar, and phosphate.

    • Connection:

      • Joined by phosphodiester bonds between the sugar and phosphate groups of adjacent nucleotides to form “sugar-phosphate backbone”.

    Phosphodiester Linkages and Strand Directionality

    • Phosphodiester Linkage:

      • A phosphate group connects the 5′5′ hydroxyl (OH) of one nucleotide unit to the 3′3′ hydroxyl (OH) of an adjacent nucleotide.

      • This linkage forms the sugar-phosphate backbone and is structurally identical in both DNA and RNA.

    • Strand Directionality:

      • Each linear nucleic acid strand has a defined 5′5′ end (lacking a nucleotide at the 5′5′ position) and a 3′3′ end (lacking a nucleotide at the 3′3′ position).

      • Nucleotide sequences are conventionally written from the 5′5′ end to the 3′3′ end (e.g., 5′extATG3′5′extATG3′).

    • Phosphate Groups:

      • At physiological pH (pH 7), the phosphate groups are completely ionized, imparting a negative charge to the nucleic acid backbone.

Secondary Structure of DNA

  • Discovery History:

    • Key figures: Erwin Chargaff (Chargaff's rules: A=T, G=C), Rosalind Franklin (X-ray crystallography, Photo 51), James Watson and Francis Crick (model building).

  • Double Helix Structure:

    • Features two right-handed helices with sugar-phosphate backbones on the outside and bases on the inside (antiparallel strands).

    • The hydrophobic bases are stacked inside the double
      helix perpendicular to helix axis.

    • Base pairing rules: A pairs with T; G pairs with C.

Structural Details

  • Spacing:

    • Base pairs are 3.4 angstroms apart; 10 base pairs make one complete turn of the helix (34 angstroms).

    • The two strands of DNA are antiparallel to each other: the 3′,5′-phosphodiester bonds run in opposite directions.

    • each turn of the helix contained ~10 base pairs (34 Å) Å (2 nm)

  • Functional Implications:

    • Stability of DNA due to lack of hydroxyl group, contrasting with RNA which is less stable and prone to hydrolysis.

Quiz Preparation

  • Concepts Covered:

    • Be prepared to discuss reducing vs non-reducing sugars, disaccharide formation, polysaccharide structures, nucleotide composition, and DNA/RNA structures.