Carbohydrates are the most abundant biomolecule on Earth. Living organisms use carbohydrates as accessible energy to fuel cellular reactions and for structural support inside cell walls. Cells attach carbohydrate molecules to proteins and lipids, modifying structures to enhance functionality. For example, small carbohydrate molecules bonded to lipids in cell membranes improve cell identification, cell signaling, and complex immune system responses. The carbohydrate monomers deoxyribose and ribose are integral parts of DNA and RNA molecules.
To recognize how carbohydrates function in living cells, we must understand their chemical structure. The structure of carbohydrates determines how energy is stored in carbohydrate bonds during photosynthesis and how breaking these bonds releases energy during cellular respiration.
Biomolecules meet specific structural criteria to be classified as carbohydrates. Simple carbohydrates are modifications of short hydrocarbon chains. Several hydroxyls and one carbonyl functional group modify these hydrocarbon chains to create a monosaccharide, the base unit of all carbohydrates.
Monosaccharides consist of a carbon chain of three or more carbon atoms containing a hydroxyl group attached to every carbon except one. The lone carbon atom is double-bonded to an oxygen atom, and this carbonyl group may be in any position along the carbon chain. Therefore, one oxygen atom and two hydrogen atoms are present for every carbon atom in a monosaccharide. Consequently, we can define monosaccharides as possessing the molecular formula (CH2O)n, where n equals the number of carbon atoms and must be greater than or equal to three.
Monosaccharides (Greek, meaning “single sugar”) are simple sugars and are frequently named using the suffix –ose. Sugars with the carbonyl group attached to a carbon at the end of the chain are aldoses (“aldehyde sugar”) such as glucose. When the carbonyl group is located anywhere other than the end of the carbon chain, the monosaccharide is a ketose (“ketone sugar”) such as fructose.
Because the position of individual atoms within a sugar molecule varies, many monosaccharides are isomers of one another. For example, glucose and fructose share the molecular formula C6H12O6, but are structurally different. Differences between isomers are not always as readily apparent as in structural isomers like glucose and fructose. More subtle stereoisomers share the same order of covalent bonds between atoms, but differ in the three-dimensional positions of the atoms around one or more individual carbon atoms. For example, glucose and galactose are stereoisomers, and appear very similar in drawings. Small details such as whether an – OH extends from the right or left side of each carbon atom are extremely important to taste, chemical reactivity, and human health.
In crystalline form, the majority of monosaccharides are present in a “long chain” structure. In contrast, sugars dissolved in a solution, such as the fluid of a cell’s interior, frequently convert into a “ring” structure. The molecular formula of a sugar is not affected by conversions from a long chain to a ring structure. The ring forms of sugars are the structures that react to form carbohydrate dimers and polymers.
Some monosaccharides are modified by cellular enzymes to enhance or change their cellular function. Although modified sugars do not meet the formal definition for carbohydrates, they are formed through small modifications to common monosaccharides. Deoxyribose, a key sugar component of all DNA molecules, is a “deoxy sugar.” To form deoxyribose, the 5-carbon monosaccharide ribose is “deoxygenated,” removing one specific hydroxyl group and replacing it with a hydrogen atom. In contrast, “amino sugars” are modified by the addition of a new functional group. In an amino sugar, one or more hydroxyl groups are replaced by nitrogen-containing functional groups. Amino sugars play important roles in the immune system, neuronal processing, and structural support.
Functional Groups of Carbohydrates
This activity tests your ability to identify all of the functional groups of monosaccharides in carbohydrates.
Carbohydrate Structure and Function
Carbohydrate monomers, short chains, and polymers perform important cellular functions to maintain life. The number and type of monosaccharides used, as well as the position of the bond between them, determines the three-dimensional structure of each carbohydrate. By recognizing the structural and functional differences between common carbohydrate monomers and polymers, we can better understand the roles carbohydrates play inside cells and in the human diet.
Cells build carbohydrate polymers by using energy to form glycosidic linkages, the bonds between monosaccharides. A dehydration synthesis reaction forms a bond between carbon atoms in two monosaccharides, sandwiching an oxygen atom between them and releasing a water molecule. A disaccharide forms when two monomers are joined. Sucrose (table sugar) is made by joining two specific monomers, glucose and fructose. Different monosaccharide pairs produce many of the common disaccharide sugars we associate with food, including sucrose, maltose (malt sugar, two glucose monomers) and lactose (milk sugar, glucose and galactose monomers).
Carbohydrate chains are extended by additional dehydration synthesis reactions, adding one monomer at a time to a growing chain. Short chains called oligosaccharides are frequently attached to lipids and proteins. These carbohydrate “tags” support immune system functions, participate in cell communication, and help attach cells to extracellular surfaces and other cells.
Carbohydrate chains with hundreds or more monosaccharide units are polysaccharides. Unlike shorter chains, carbohydrate polymers are frequently composed of a single type of monosaccharide unit. Differences in the structure and function of these polymers arise mainly from differences in the glycosidic linkage, rather than the presence of different monosaccharides. Glycosidic linkages involve covalent bonds from one carbon atom in each monosaccharide to a single oxygen atom between them. However, which carbon atoms participate in this covalent bond may be different in each carbohydrate molecule.
The most common polysaccharides are built solely with glucose monomers, while significant structural differences between these polysaccharides arise mainly from the position and number of the glycosidic linkages in each glucose unit. Although these bond differences appear insignificant at first glance, the functional effect of minor structural differences in each glycosidic linkage is enormous.
Building and Breaking Carbohydrates
This activity tests your ability to identify the reactants and products in carbohydrate synthesis and hydrolysis.
Polysaccharides, the “complex carbohydrates,” play vital energy storage and structural roles in living organisms, making carbohydrates the most abundant biomolecules on Earth. Polysaccharides are excellent energy storage molecules because they are easily built and broken down by enzymes. Forming fairly compact structures, polysaccharides allow energy storage without the space required by a pool of free glucose monomers. Other polysaccharides form strong fibers that provide protection and structural support in both plants and animals.
With small differences in the bond between monomers, polymers can function as compact energy storage units in starch and glycogen or as strong, protective fibers in cellulose and chitin. Understanding the structure, synthesis, and breakdown of carbohydrate polymers provides a framework for understanding their function in living cells.
Animals, including humans, create glucose polymers called glycogen. The position of the glycosidic linkage between glucose monomers causes glycogen polymers to coil into spiral shapes. Glycogen polymers are significantly branched, with several monomers in the primary chain containing a second glycosidic linkage to a different glucose. The second attachment sites allow shorter glucose chains to branch away from the main chain, packing more glucose units into the compact coiled structure.
Although glycogen’s structure allows humans and other animals to store energy in a relatively compact form, the polymer can be degraded rapidly. Animals initiate enzyme-driven hydrolysis reactions to break down glycogen when energy is needed. For quick access to energy, glycogen is stored primarily in two locations in humans, the liver for easy delivery into the bloodstream and muscles for direct use as needed.
Plants synthesize two types of polysaccharides, starch and cellulose. The glycosidic bonds between glucose units in plant starch are similar to those in animal glycogen. Accordingly, starch molecules are structurally similar, forming compact coils, and play a similar role in energy storage for plants. Unlike glycogen, starch molecules vary widely in the level of branching. Most plants form a mixture of starch polymers with little to no branching and polymers with extensive branching.
In addition to providing energy for the plants that synthesize them, starches serve as the main food source for many animals. Humans and other animals produce enzymes that degrade starch molecules into small fragments during digestion. In humans, this digestion begins in the mouth by an enzyme called amylase, which degrades starch polymers into disaccharides (maltose). To experience starch digestion yourself, try chewing an unsalted cracker for a long time. After a while, did the cracker begin to taste sweet? This is the formation of maltose disaccharides in your mouth as the starch is digested. Salt may disguise many other tastes, so this mini-experiment works best with unsalted crackers.
Plants synthesize a structural polysaccharide called cellulose. Although cellulose is made with glucose, the glycosidic linkages between glucose monomers are different from the bonds in glycogen and starch. This unique bond structure causes cellulose chains to form linear flat strands instead of coils. The flat cellulose strands are able to form tightly packed bundles. Strong and rigid fibers result as hydrogen bonds form between polar hydroxyl groups in the bundled polymers. Cellulose fibers provide structural support to plants. Without cellulose, flower stems and tree trunks could not maintain their rigid, straight height.
Structural differences between the glycosidic linkages in starch and cellulose affect animals’ ability to digest plant foods. Enzymes such as amylase cannot break down cellulose polymers. Some animals, including cows and termites, digest cellulose by hosting special microorganisms in their digestive tracts that produce cellulose-degrading enzymes. However, humans and most animals do not make an enzyme capable of degrading cellulose, leaving cellulose fibers undigested as they pass through the body. Humans do exploit plant cellulose in non-dietary ways by processing trees, cotton, and other plants to make paper, clothing, and many other common materials. Humans also harvest large trees to build structures with the cellulose-rich lumber.
Some animals synthesize a special polysaccharide, chitin, which forms a protective exoskeleton shell. The glycosidic linkages in chitin are very similar to cellulose bonds, causing chitin to also form linear, well-packed sheets of strong fibers. Unlike cellulose, chitin is synthesized from a modified monosaccharide called an amino sugar. The chitin monomer is derived from glucose by replacing one hydroxyl group with a nitrogen-containing functional group. Interactions between the nitrogen-containing groups and the remaining hydroxyl groups in chitin’s polymer structure make it extremely strong and rigid. Chitin provides protection and structural support for many living organisms, including forming the exoskeletons of shellfish and insects and the cell walls of fungi.
Carbohydrate Ring Toss
In this activity, you will classify characteristics of several major carbohydrates.
Glycobiology is the study of the structure, function and biology of carbohydrates, also called glycans, which are widely distributed in nature. It is a small but rapidly growing field, with relevance to biomedicine, biotechnology and basic research. Proteomics, the systematic study of proteins in biological systems, has expanded the knowledge of protein expression, modification, interaction and function. However, in eukaryotic cells the majority of proteins are post-translationally modified (1). A common post-translational modification essential for cell viability is the attachment of glycans, as shown in Figure 1. Glycosylation defines the adhesive properties of glycoconjugates and it is largely through glycan–protein interactions that cell– cell and cell–pathogen contacts occur, a fact that highlights the importance of glycobiology. Considering the central role that glycans play in molecular encounters, glycoprotein and carbohydrate-based drugs and therapeutics represent a greater than $20 billion market (2). Glycomics, the systematic study of all glycan structures in a biological system, relies on effective enzymatic and analytical techniques for correlation of glycan structure with function.
Classification of Glycans
Several classes of glycans exist, including N-linked glycans, O-linked glycans, glycolipids, O-GlcNAc, and glycosaminoglycans. N-linked glycosylation occurs when glycans are attached to asparagine residues on the protein. O-linked glycans are most commonly attached to serine or threonine residues through the N-Acetylgalactosamine residue. Removal of oligosaccharides from glycoproteins, termed deglycosylation, is often used in order to simplify analysis of the peptide and/ or glycan portion of a glycoprotein. Detailed knowledge of the glycan structures helps to correlate them to their respective function. To do this, tools are required for highly sensitive analysis of glycan chains. Both chemical and enzymatic methods exist for removing oligosaccharides from glycoproteins. Chemical methods such as β-elimination with mild alkali (3) or mild hydrazinolysis (4) result in the degradation of the protein; whereas enzymatic methods are much gentler and can provide complete sugar removal with no protein degradation.
For structural analysis of asparagine-linked carbohydrates, sugars are released from the protein backbone by enzymes such as PNGase F (NEB #P0704). PNGase F is the most effective enzyme for removing almost all N-linked oligosaccharides from glycoproteins. PNGase F cleaves between the innermost GlcNAc and asparagine residues of high mannose, hybrid and complex oligosaccharides from N-linked glycoproteins (5), as shown in Figure 2.
PNGase F digestion deaminates the asparagine residue to aspartic acid, leaving the oligosaccharide intact for further analysis. However, it is critical to note that oligosaccharides containing a fucose α(1-3)-linked to the glycan core often found in plant and insect glycoproteins are resistant to PNGase F, and would therefore require PNGase A treatment. Other commonly used endoglycosidases such as Endoglycosidase H (NEB #P0702) are not suitable for general deglycosylation of N-linked sugars, because it only deglycosylates glycoproteins containing primarily high mannose N-linked structures, as well as leaving one N-acetylglucosamine residue attached to the asparagine.
In order to achieve complete removal of N-linked glycans from a protein using PNGase F, it is recommended that the glycoprotein first be denatured by heating with SDS and DTT prior to PNGase F treatment. Denaturation of the glycoprotein will decrease the steric hindrances that can inhibit PNGase F activity. However, if denaturation of a glycoprotein is not desirable, native conditions may be used. Under native conditions PNGase F retains full activity; however more enzyme may be needed in order to achieve complete deglycosylation.
The study of N-glycosylation is related to many important pathways. Because N-glycans are added as polypeptides that are synthesized in the ER, these sugars control the correct conformation of glycoproteins. Once a correctly folded glycoprotein leaves the ER, its N-glycans are re-modeled in a protein- and cell-specific fashion. Differences in N-glycan structure result in different functions for the same polypeptide. This is well illustrated in the case of immunoglobulin G (IgG), in which the glycan composition affects complement binding, activation and other biological properties (Figure 3). Accordingly, the manufacturing of therapeutic antibodies demands assessment of a product’s microheterogeneity and its batch-to-batch consistency (6,7).
Removing O-linked glycan chains while rendering a protein intact for further examination is a more difficult task. Chemical methods, such as β-elimination, may result in incomplete sugar removal and degradation of the protein. On the other hand, enzymatic removal of O-linked glycans must be performed as a series of exoglycosidase digestions until only the Galβ1-3GalNAc (Core 1) and/or the GlcNAc β1-3GalNAc (Core 3) cores remains attached to the serine or threonine residue. NEB’s Enterococcus faecalis Endo-α-N-Acetylgalactosaminidase (NEB #P0733), also known as O-Glycosidase, catalyzes the removal of Core 1 and Core 3 disaccharide structures with no modification of the serine or threonine residues. Any modification of the core structures, including sialyation, will block the action of the O-Glycosidase. Sialic acid residues are easily removed by a general α2-3,6,8 Neuraminidase (NEB #P0720). In addition, exoglycosidases such as β(1-4) Galactosidase (NEB #P0730) and β-N-Acetylglucosaminidase (NEB #P0732) can be included in deglycosylation reactions to remove other complex modifications often known to be present on the core structures.
The study of O-glycosylated proteins is essential to understand the underlying mechanisms of several cellular processes. For instance, in many cancers of the mucosa (such as colon, ovary, uterus and bladder), tumor progression strongly correlates with alterations in the patterns of mucin (a surface protein) O-glycosylation (Figure 4). The enzyme responsible for Core 3 O-glycan synthesis, β3Gn-T6, is abundant in normal colon tissue while its expression is strongly downregulated in adenocarcinoma (8,9,10). As a result, mucin glycosylation switches from common Core 3 O-glycan structures to short Core 1 structures. These Core 1 structures, T and Tn, are hallmark epitopes of cell malignancy (11).
Through the use of endoglycosidase and exoglycosidase enzymes, researchers are able to obtain highly sensitive analysis of both protein and glycan components in a wide range of healthy and diseased glycoproteins.
Glycobiology Related Terms
Glycobiology – the study of the structure, function and biology of carbohydrates.
Glycomics – the systematic study of all glycan structures in a biological system.
Carbohydrate – A generic term used interchangeably with sugar and glycan. This term includes monosaccharides, oligosaccharides, and polysaccharides.
Glycan – A generic term for any sugar, in free form or attached to another molecule, used interchangeably with carbohydrate.
Complex glycan – A glycan containing more than one type of monosaccharide.
β-elimination – The cleavage of a C-O or C-N bond positioned on the β-carbon with respect to a carbonyl group. The process is used to cleave O-glycans from serine or threonine residues.
Endoglycosidase – An enzyme that catalyzes the cleavage of an internal glycosidic linkage in an oligosaccharide or polysaccharide.
Exoglycosidase – An enzyme that cleaves a monosaccharide from the non-reducing end of an oligosaccharide, polysaccharide or glycoconjugate.
Glycoconjugate – A molecule in which one or more glycan units are covalently linked to a non-carbohydrate entity.
Glycoforms – Different molecular forms of a glycoprotein, resulting from variable glycan structure and/or glycan attachment site occupancy.
Glycoforms – Different molecular forms of a glycoprotein, resulting from variable glycan structure and/or glycan attachment site occupancy.
Glycopeptide – A peptide having one or more covalently attached glycans.
Glycoprotein – A protein with one or more covalently attached glycans.
Glycoproteomics – The systems-level analysis of glycoproteins, including their protein identities, sites of glycosylation and glycan structures.
Glycosaminoglycans – Polysaccharide side chains of proteoglycans or free complex polysaccharides composed of linear disaccharide repeating units each composed of a hexosamine and a hexose or a hexuronic acid.
Glycosylation – The enzyme-catalyzed covalent attachment of a carbohydrate to a polypeptide, lipid, polynucleotide or another carbohydrate, generally catalyzed by glycosyltransferases.
Hexosamine – Hexose with an amino group in place of the hydroxyl group at the C-2 position. Common examples are the N-acetylated sugars, N-acetylglucosamine and N-acetylgalactosamine.
Hexose – A six-carbon monosaccharide typically with an aldehyde at the C-1 position and hydroxyl groups at all other positions. Common examples are mannose, glucose and galactose.
Hydrazinolysis – A chemical method that uses hydrazine to cleave amide bonds (e.g., the glycosylamine linkage between a glycan residue and asparagine or the acetamide bond in N-acetylhexosamines).
Lectin – A protein that specifically recognizes and binds to glycans without catalyzing a modification of the glycan.
Monosaccharide – A carbohydrate that cannot be hydrolyzed into a simpler carbohydrate. It is the building block of oligosaccharides and polysaccharides.
N-linked Glycan – Glycan covalently linked to an asparagine residue of a polypeptide chain in the consensus sequence: -Asn-X-Ser/Thr.
Non-reducing terminus – Outermost end of an oligosaccharide or polysaccharide chain, which is opposite to that of the reducing end.
O-linked Glycans – A glycan glycosidically linked to the hydroxyl group of the amino acids serine or threonine in the consensus GalNAcα1- O-Ser/Thr.
Oligosaccharide – Linear or branched chain of monosaccharides attached to one another via glycosidic linkages. The number of monosaccharide units can vary.
Polysaccharide – Glycan composed of repeating monosaccharides, generally greater than ten monosaccharide units in length.
Proteoglycan – Any protein with one or more covalently attached glycosaminoglycan chains.
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