Polymers are assembled and disassembly

Because macromolecules provide all of the important life functions in a cell, it is vital for the cell to be able to assemble these polymers so that they can perform the necessary functions, and disassemble the polymers if needed.

New bonds are created in dehydration reactions (a) when a water molecule is removed. Bonds are broken in hydrolysis reactions (b) when a water molecule is added.

New bonds are created in dehydration reactions (a) when a water molecule is removed. Bonds are broken in hydrolysis reactions (b) when a water molecule is added.

The process in which polymers are assembled and disassembled is basically the same regardless of the specific polymer or polymer class. The process in which polymers are built is assisted by specialized macromolecules called enzymes, which can speed up biochemical reactions. To build a polymer, a dehydration reaction occurs, linking monomers. A dehydration reaction is when the loss of a water from unlinked monomers, results in a covalent bond between the two. Each of the monomers contributes to the water molecule released; one will donate a hydroxyl group, while the other donates a hydrogen. This process is repeated over and over, until the desired polymer is completed. In contrast, hydrolysis is responsible for the break down of polymers. This is when a water breaks the bond between two monomers by attaching a hydroxyl group to one and a hydrogen to the other. The word hydrolysis, is derived from the Greek word "hydro," which means water, and the Greek word "lysis," which means "break".

Hydrolysis occurs when we digest our food. The food, which is made up primarily of polymers, is broken down to monomers by enzymes in the digestive tract. These monomers can then be taken up by the blood and deposited where they are needed. enzyme : A globular protein that catalyses a biological chemical reaction. hydrolysis : A chemical process of decomposition involving the splitting of a bond and the addition of the hydrogen cation and the hydroxide anion of water. dehydration reaction : An elimination reaction in which the small molecule removed is water

Many different types of polymers exist

The four main classes of macromolecules include carbohydrates, lipids, proteins, and nucleic acids.
The number of macromolecules types is large, but these polymers are built from a relatively small number of monomers (40 to 50). The diversity in polymers comes from the vast arrangement of monomers. Despite the vast amounts of macromolecules, they can still be grouped together by four major classes. nucleic acid : Any acidic, chainlike biological macromolecule consisting of multiply repeat units of phosphoric acid, sugar and purine and pyrimidine bases; they are involved in the preservation, replication and expression of hereditary information in every living cell protein : Any of numerous large, complex naturally-produced molecules composed of one or more long chains of amino acids, in which the amino acid groups are held together by peptide bonds. lipid : Any of a group of organic compounds including the fats, oils, waxes, sterols, and triglycerides. Lipids are characterized by being insoluble in water, and account for most of the fat present in the human body. They are, however, soluble in nonpolar organic solvents. carbohydrate : A sugar, starch, or cellulose that is a food source of energy for an animal or plant; a saccharide.

_+_+_+_+_+_+_+_+CARBOHYDRATES

The carbohydrate: sugar

Carbohydrates are a class of macromolecule that includes sugars and their polymers, and are responsible for the storage of energy and are structural components of cells.

A).

B).

C).

D).

E).

F).

G).

(a) glyceraldehyde: (triose, aldose) product of glucose metabolism (b) dihydroxyacetone: (triose, ketose) product of glucose metabolism (c) ribose: (pentose, aldose) RNA component (d) ribulose: (pentose, ketose) intermediate product of photosynthesis (e) glucose and (f) galactose: (hexose, aldehyde) energy storing molecules (g) fructose: (hexose, ketose) energy storing molecule

Sugar variation occurs due to different carbon skeleton lengths, carbonyl group location (C=O), and the spatial arrangement surrounding an asymmetric carbon (C-4 in ribulose and galactose). Three, five, and six carbon sugars are known as trioses (C3H6O3), pentoses (C5H10O5), and hexoses (C6H12O6), respectively. When the carbonyl group is located at the end of the carbon skeleton the sugar is an aldose (aldehyde sugar) and when the carbonyl group is within the carbon skeleton the sugar is a ketose (ketone sugar). Shown here are the structural formulas for 6 common monosaccharides:

(a)

Ring and linear forms of glucose: Between the linear and ring structure of glucose, chemical equilibrium greatly favors the formation of rings for glucose. The 1st carbon of glucose bonds to the oxygen attached to the 5th carbon to achieve the ring structure. (b) An animation showing the transition from linear to ring structure in glucose. (c) The full and abbreviated ring structure of glucose: Ring structures can be represented in multiple ways. In the abbreviated structure, each of the ring corners represents a carbon atom in glucose. The thicker ring edge indicates that you are viewing the glucose from the edge. The attached components are located above or below the ring plane.

(a) Maltose in synthesized through a dehydration reaction: Two glucose molecules bond to form maltose through a glycosidic bond. The formation of the bond must be between the 1 carbon of the first glucose and the 4 carbon of the second glucose to form maltose (1-4 glycosidic linkage). If the glucose monomers were linked in a different way, a different disaccharide would be formed. (b) Sucrose is synthesized through a dehydration reaction: The formation of sucrose is similar to that of maltose except sucrose is composed of one molecule of glucose and one molecule of fructose linked by a 1-2 glycosidic linkage. Also, even though fructose is a hexose like glucose, it forms a five-sided ring, rather than a 6 sided ring. A carbohydrate is a class of macromolecule that encompasses both sugars and sugar polymers. The basic building block of a monosaccharide is CH2O. The molecular formulas of these sugars are usually some multiple of this base. An important example that displays this structure, with a carbonyl group (C = O), and numerous hydroxyl groups (-OH), is glucose, which has the formula C6H12O6. A sugar is described as either a ketose or an aldose on the basis of the structural placement of the carbonyl group. If the carbonyl group is within the sugar structure, it is a ketose; on the outside of the structure, it is an aldose. Another way sugars are often grouped is by the carbon number of their skeleton. The carbon number can range from 3 to 7, with 3, 5, and 6 carbons being the most common. A three-carbon sugar is called a triose; a six-carbon sugar, a hexose; and a five-carbon sugar, a pentose. Glucose and fructose are both hexose sugars. Sugars can also differ as a result of an asymmetric carbon (as mentioned in isomers chapter). For example, glucose and galactose are identical other than the structural arrangement around their asymmetric carbons. While this difference is small, it results in the sugars having different shapes and behaviors.

While sugars like glucose are often drawn as straight lines due to simplicity, this is not really accurate. In an aqueous solution, most pentoses and hexoses, including glucose, exist as a ringed structure. A major nutrient source for a cell comes from glucose and other monosaccharides. Energy is extracted using glucose as the starting material in a process called cellular respiration. In addition to being used for cellular respiration, the carbons of simple sugars are often used to build other small organic molecules, such as fatty or amino acids. When two monosaccharides are linked together, it is called a disaccharide. The two sugars of a disaccharide are linked together with a glycosidic linkage, which is a covalent bond between two monosaccarides formed through a dehydration reaction. Some examples of disaccharides include maltose, which has two glucose molecules; sucrose (table sugar), which has a glucose and fructose linked together; and lactose, which has the monosaccharides glucose and galactose covalently linked. glycosidic linkage : In chemistry, a glycosidic bond is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate. disaccharide : Any sugar, such as sucrose, maltose and lactose, consisting of two monosaccharides combined together. monosaccharide : A simple sugar such as glucose, fructose or deoxyribose that has a single ring. carbohydrate : A sugar, starch, or cellulose that is a food source of energy for an animal or plant; a saccharide. Example 1 : Figure 2 illustrates monosaccharide molecules with increasing numbers of building blocks Cm(H2O)m. These sugars are aldoses, they all have formyl group H(C=O)- at position 1. Each row of sugars with a given formula is represented by different isomers. Example 2 : Some examples of disaccharides include maltose, which has two glucose molecules; sucrose (table sugar), which has a glucose and fructose linked together; and lactose, which has the monosaccharides glucose and galactose covalently linked.

The polymer polysaccharide

Polysaccharides are polymers made from monosaccharides joined by glycosidic linkage that have different properties depending on their structure.

Glucose monomers link together in chains to form glycogen and starches. In unbranched regions of the polymers, they have a tendency to form helices because of the angle the 1-4 linkages create

The alpha and beta forms of glucose differ as a result of the position hydroxyl group bound to the 1st carbon. (b) Starch: Because of the 1-4 linkages between alpha glucoses, all of the monomers are oriented in the same way.(c) Cellulose: The beta glucose structures cause every monomer to be upside down in relation to its neighbor. Polymers, made up of a few hundred to several thousand monosaccharides, joined together by glycosidic linkages, are called polysaccharides. Polysaccharides can serve as a fuel source or the building material for structures designed to protect the cell or an entire organism. The make up and function of a polysaccharides are a result of its sugar monomers and glycosidic linkage positions. polysaccharide : A polymer made of many saccharide units linked by glycosidic bonds. Example 1 : Starch and glycogen are polysaccharides that serve as fuel sources, while cellulose and chitin are structuralpolysaccharides.

Polysaccarides as Energy

Storage polysaccharides, such as starch and glycogen, are utilized by a cell to save sugars for energy and biosynthesis.
In order to save sugars, plants and animals store them in the framework of storage polysaccharides. In plants, the polysaccharide used is starch, and in animals, the polysaccharide used is glycogen. Starch, which is a polymer of glucose monomers, is stored as granules in the plastids, which include chloroplasts of plants. Synthesizing starch from glucose monomers, most of which are joined together with linkages between carbon 1 and carbon 4, enables the plant to stash away glucose until it is needed. Starch is considered a stored energy, because it becomes glucose when hydrolyzed, which is a prominent fuel used by cells. Humans and other animals ingest starch from plant tissue, such as potato tubers, corn, and rice. Once ingested, enzymes can breakdown the starch into usable glucose. Amylose is a straight chain polysaccharide and is the simplest form of starch. Amylopectin, is also starch but unlike amylose, it is branched, with one to six linkages at its branches. Glycogen is the polysaccharide form that animals store. Animals have the abiity to break down glycogen into glucose when energy is needed. Glycogen is more branched than the polysaccharide amylopectin. Without replenishment,glycogen will become depleted in humans in about one day. This is why diet plans that restrict carbohydrates can be worrisome. glycogen : A polysaccharide that is the main form of carbohydrate storage in animals; converted to glucose as needed. starch : A widely diffused vegetable substance found especially in seeds, bulbs, and tubers, and extracted (as from potatoes, corn, rice, etc.) as a white, glistening, granular or powdery substance, without taste or smell, and giving a very peculiar creaking sound when rubbed between the fingers. It is used as a food, in the production of commercial grape sugar, for stiffening linen in laundries, in making paste, etc. storage polysaccharide : Any polysaccharide that serves to store energy in plants (typically starch) or animals (typically glycogen)

Polysaccharides as Building Blocks

Structural polysaccharides, such as cellulose in plants and chitin in insects and arthropods, form structural components of cells.
Along with energy storage, polysaccharides can also be used as a structural component Cellulose is a structural polysaccharide found in plant cells. Worldwide, it is estimated that plants produce approximately 100 billion tons of cellulose, making it the most prevalent organic compound on earth. Cellulose is made up of glucose monomers, as is starch. However, cellulose has different glycosidic linkages than starch. The different linkages in starch and cellulose occurs because glucose has two different ring structures in each. In the ring of glucose, the hydroxyl group of the first carbon can either be above or below the plane of the ring. Depending the hydroxyl location, the glucose is either an alpha or beta glucose. Starch is made up of all alpha glucose monomers, where cellulose is made up the beta glucose monomers. Cellulose and starch have very different 3D structures as a result of linkages. Starch is often a helix, however, cellulose is always a straight chain. Because of the straight chains of cellulose, they have the ability to form hydrogen bonds with parallel cellulose chains. When a group of cellulose is grouped together by hydrogen bonds, they are called microfibrils. Most animals are not able to digest cellulose because of its B linkages. While it cannot be digested, cellulose is primarily the "fiber" we eat. The cellulose fiber moves through the digestive tract stimulates mucus in the intestine, assisting food movement through our body. Most people know that cows and termites eat grass and wood, both which are mainly cellulose. However, on their own cows and termites can not digest cellulose; they both contain gut microorganisms, which can break down the celluloseinto glucose. Chitin, which makes up the protective exoskeletons of insects and arthropods, is also a polysaccharide. Exoskeletons surrounds the animal for protection. Like cellulose, chitin has beta-linkages, however, unlike cellulose, its glucose monomer additionally contains a nitrogen-containing branch. Chitin is also used as a structural component of cell walls in fungi. On its own, pure chitin has a leathery texture, however, it becomes hardened when encrusted the salt calcium carbonate. chitin : A complex polysaccharide, a polymer of N-acetylglucosamine, found in the exoskeletons of arthropods and in the cell walls of fungi; thought to be responsible for some forms of asthma in humans. cellulose : A complex carbohydrate that forms the main constituent of the cell wall in most plants and is important in the manufacture of numerous products, such as paper, textiles, pharmaceuticals, and explosives. structural polysaccharide : Any polysaccharide that serves to supply stiffness to a plant (typically cellulose) or insect etc (typically chitin)

Introduction to Lipids
Lipids are a group of hydrophobic molecules that are used for energy storage, as a component of cell membranes, and as important signalling molecules.

Lipids are a very diverse and unique class of molecules. They are not true polymers and are not large enough to be macromolecules. The trait that lipids share is that they are all hydrophobic (do not mix well with water). triglyceride : A lipid, an ester of glycerol and three fatty acids (the same or different); the major constituent of animal and vegetable fats. hydrophobic : Lacking an affinity for water; unable to absorb, or be wetted by water. lipid : Any of a group of organic compounds including the fats, oils, waxes, sterols, and triglycerides. Lipids are characterized by being insoluble in water, and account for most of the fat present in the human body. They are, however, soluble in nonpolar organic solvents. Example 1 : Fats are a subgroup of lipids called triglycerides.

Glycerol and fatty acid molecule

Fats form a category of lipid that is distinguished from other lipids by their chemical structure and physical properties and are important for many forms of life, serving both structural and metabolic functions.

Fats are composed of a glycerol head group and 3 fatty acid tails. (a) shows the molecular strucutre and (b) shows the generic composition of a triglycerol.

Fats are composed of a glycerol head group and 3 fatty acid tails. (a) shows the molecular strucutre and (b) shows the generic composition of a triglycerol.

(a) Saturated fat, like the fat in butter, are solids at room temperature because the molecules can pack tightly together as a result of the long straight chains created by the single bonds in the fatty acid tails. (b) Unsaturated fats, like the fat in olive oil, are liquids at room temperature because the double bonds in the fatty acid tails create kinks that prevent the molecules from being tightly packed.
Fatty acids and the alcohol, glycerol, form a fat. Unlike sugars, fats are not polymers. A carboxylic acid with a long hydrocarbon chain (normally 16 to 18 carbons) form a fatty acid. The carboxyl group at the end of carbon skeleton is why it is called a fatty "acid". The hydrocarbon chain of a fatty acid is what causes its hydrophobic qualities. The hydrogen carbon bonds are non-polar, so when water molecules hydrogen bond with one another in an aqueous solution, fats are excluded. A triacylglycerol is three fatty acids joined to glycerol head group. The three fatty acids can be made up of the same or different fatty acid chains. On food packaging, fat is sometimes called a triglyceride. The structure of fatty acid will result in the fat being saturated or unsaturated. An unsaturated fat contains at least one double bond in its fatty acid chain, where a saturated fat contains only double bonds. The term saturated comes from the fact that the fatty acid is bonded to the maximum number of hydrogens or is saturated with hydrogens. Saturated fats can lead to atherosclerosis, which is the restriction of blood flow due to plaque build up in blood vessel walls. Normally, animal fats are saturated and are solid at room temperature. Plants usually produce unsaturated fats, which are generally liquid at room temperature. The solid and liquid forms at room temperature are a result of the double bonds (or lack thereof), which dictates how the fatty acids can associate with one another. Trans fats can be produced when unsaturated fatty acids are hydrogenated. It is thought that trans fats may be a greater health risk than even saturated fats. trans fat : An unsaturated fat with carbon-carbon double bonds in the trans configuration, especially one prepared by partial hydrogenation, associated with an elevated risk of coronary heart disease. unsaturated fatty acid : A fatty acid, such as oleic acid, that contains one carbon to carbon double bond. saturated fatty acid : a fatty acid, such as stearic acid, that contains no carbon to carbon double bonds triacylglycerol : A triglyceride (TG, triacylglycerol, TAG, or triacylglyceride) is an ester derived from glycerol and three fatty acids.

fatty acid : Any of a class of aliphatic carboxylic acids, of general formula CnH2n+1COOH, that occur combined with glycerol as animal or vegetable oils and fats. Only those with an even number of carbon atoms are normally found in natural fats. fat : A specialized animal tissue with a high oil content, used for long-term storage of energy. triglyceride : A lipid, an ester of glycerol and three fatty acids (the same or different); the major constituent of animal and vegetable fats. Example 1 : Figure 2 illustrates a molecule of triglyceride with glycerol as a backbone and three different fatty acids attached via ester bond. Fatty acids from top to bottom: palmitic acid (saturated), oleic acid (unsaturated), alpha-linolenic acid (unsaturated).

Phospholipids
Phospholipids are molecules that consist of two fatty acids an a phosphate group joined on a glycerol backbone, and are major components of cell membranes.

A polar hydrophilic head and two hydrophobic tails make up a phospholipid. Different fatty acid tails and groups attached to the phosphate give rise to phospholipid diversity. The example shown is a phosphatidylcholine, which has a choline group attached to the phosphate. A kink is present because of the presence of a cis double bond. The second image shows the different components of phosphatidylcholine.

Biological membranes are primarily composed of phospholipid bilayers. The hydrophyllic and hydrophobic components of these molecules cause the phospholipid bilayer to automatically assemble so that the heads are oriented to interact with water and the hydrophobic tails are in contact with one another, shielded from water.
A phospholipid is made up of a glycerol linked to two fatty acids and a phosphate group. In addition, another group, such as choline, can then be joined to the phosphate group. Phospholipids are very important in cells, because they are a major component of cell membranes. The tails of the fatty acid are hydrophobic, however, the phosphate group and the group associated with the phosphate group are hydrophilic, so they interact with water. This is important because the hydrophobic and hydrophilic portions of the cell cause them to orient correctly. In an aqueous solution, the tails of the phospholipid move away from the water; the phosphate heads orient to interact with the water, forming a bilayer of tails interacting with other tails and heads interacting with water. Phosphoplids form a bilayer in cell membranes, with the heads positioned towards the aqueous solutions within and outside of the cell, and the tails oriented towards each other. phospholipid : Any lipid, such as lecithin or cephalin, consisting of a diglyceride combined with a phosphate group and a simple organic molecule such as choline or ethanolamine; they are important constituents of biological membranes hydrophilic : Having an affinity for water; able to absorb, or be wetted by water Example 1 : Figure 2 illustrates a lipid bilayer formed by phospholipids, where hydrophobic tails are facing each other, whilehydrophilic heads are facing outwards.

Steroids
Steroids are lipids that serve a wide range of functions, including the production of hormones and as a component of cell membranes.

Steroids are made up of four fused rings. Cholesterol is the steroid that serves as the precursor for all other steroids, including sex hormones. You can see the steroid foundation of this molecule as the typical fused four-ring structure.
A lipid composed of four fused rings is a steroid. Cholesterol is a steroid that is an integral part of animal membranes and also serves as the precursor for other steroids. Cholesterol is obtained from the diet and also made in the liver. Excess cholesterol levels in the blood can lead to atherosclerosis. cholesterol : A sterol lipid synthesized by the liver and transported in the bloodstream to the membranes of all animal cells; it plays a central role in many biochemical processes and, as a lipoprotein that coats the walls of blood vessels, is associated with cardiovascular disease. steroid : A class of organic compounds having a structure of 17 carbon atoms arranged in four rings; they are lipids, and occur naturally as sterols, bile acids, adrenal and sex hormones, and some vitamins; many drugs are synthetic steroids. Example 1 : Figure 1 illustrates cholesterol molecule. Cholesterol is synthesized by animals and is used to produce hormones and to establish proper cell membrane fluidity and permeability.

Introduction to Proteins
Proteins, a type of macromolecule that exists in all living things, often function as catalyzers of crucial biological reactions and are called enzymes.
Without proteins called enzymes, life could not occur. An enzyme acts as a catalyst. Catalysts are able to speed up a chemical reaction without being consumed. activation energy : The energy required to initiate a reaction. For example, the flame from the fuse of a firecracker provides a small initial amount of energy, after which the explosive reaction proceeds by itself, releasing a considerably larger quantity of energy. A small push given to a stable but top-heavy object may cause it to fall over; the potential energy released during the fall was present in the system all along but could not be realized as long as the object was upright and balanced. catalyst : A substance that increases the rate of a chemical reaction without being consumed in the process. enzyme : A globular protein that catalyses a biological chemical reaction. Example 1 : About 4,000 biochemical reactions that take place in a single cell are catalyzed by enzymes. These reactions proceed millions of times faster than un-catalyzed reactions.

Amino acid polymers are called polypeptides

An amino acid is a monomer, or a building block of a protein polymer, and contains an amino and carboxyl group, a side chain (R-group), and a hydrogen atom, all of which are bonded to the alpha carbon at the center of the molecule.

Amino acids are shown here with their structural formulas and are grouped according to side chain properties. The structures are shown in their ionic form at pH 7.2, which is the pH within a cell. The commonly used three and one letter abbreviations for each amino acid are in parentheses.

Proteins function in a multitude of ways, including: enzymatic, defensive, storage, transport, hormonal, receptor, motor, and structural.

The carboxyl group of one amino acid is linked to the amino group of another amino acid through a dehydration reaction. The peptide bonds start at the amino end (N terminus) and are added one by one.

The backbone of a polypeptide is repetitive, the attached amino acid side chains are the cause of diversity in the polypeptide. An amino acid is a molecule that contains an amino and carboxyl group. The basic structure of an amino acid consists of these two groups, a hydrogen atom, and a side chain referred to as the R-group, which is different for each of the amino acids. All four of these groups are bonded to the alpha carbon, a centrally located asymmetric carbon atom. These two groups bond to a central carbon Amino acids are the building blocks of a protein. There are 20 amino acids that make up proteins. An amino acid polymer linked linearly is called a polypeptide. There are 20 amino acids that are used to construct polymers. Proteins are a macromolecule that consists of one or more polypeptides oriented in a specific 3D structure. A peptide bond can be formed between two amino acids. A peptide bond is covalent bond that results when the carboxyl group and amino group of two amino acids become joined through a dehydration reaction. Amino acids will form peptide bonds with one another multiple times to form a polypeptide. Polypeptides can range from a few amino acids to thousands, and each polypeptide is unique due to the sequence of the amino acids. peptide : A class of organic compounds consisting of various numbers of amino acids in which the amine of one is reacted with the carboxylic acid of the next to form an amide bond. polypeptide : A polypeptide is a long, continuous, and unbranched peptide. Proteins consist of one or more polypeptides arranged in a biologically functional way and are often bound to cofactors, or other proteins. R group : The R group is a side chain specific to each amino acid that confers particular chemical properties to that amino acid. alpha carbon : The first carbon atom of an aliphatic chain that is attached to a functional group amino acid : Any of the twenty naturally occurring -amino acids (having the amino, and carboxylic acid groups on the same carbon atom), and a variety of side chains, that combine, via peptide bonds, to form proteins. protein : Any of numerous large, complex naturally-produced molecules composed of one or more long chains of amino acids, in which the amino acid groups are held together by peptide bonds. Example 1 : Figure 2 illustrates structures of 21 amino acids that are found in eukaryotes, group by the properties of their side chains (R-groups). The R-groups can dictate function of a whole protein. For example, proteins that are found in cellular membranes have to have amino acids with hydrophobic side chains in order to integrate into a lipid bilayer of a membrane.

The structure and role of proteins

Proteins function is defined by its structure, which in turn is defined by the properties of its amino acid chains.
Proteins have a very specific 3D structure. This structure results in a protein's specific function. This 3D arrangement was first discovered by Fredrick Sanger.

A protein is made up of polypeptides, but they are not synonyms for one another. A protein must include one or more polypeptides folded or twisted in a very specific way. A polypeptide will generally fold on its own because of bonds created at different regions of the polypeptide chain. Proteins are often a round shape, called globular, or long and fiber like, called fibrous. A protein's structure dictates its function. Protein function is based primarily on its ability to identify and bind with other molecules. Antibodies are proteins specifically designed to bind to a foreign object and tag it for removal. fibrous protein : Scleroproteins, or fibrous proteins, constitute one of the three main classes of proteins, alongside globular proteins and conjugated proteins. Keratin, collagen, elastin, and fibroin are all scleroproteins. globular protein : Globular proteins, or spheroproteins are one of the three main protein classes, comprising "globe"-like proteins that are more or less soluble in aqueous solutions (where they form colloidal solutions). This characteristic distinguishes them from fibrous proteins (the other class), which are practically insoluble. membrane protein : A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle. More than half of all proteins interact with membranes. chaperone : A protein that assists the non-covalent folding/unfolding and the assembly/disassembly of other macromolecular structures, but does not occur in these structures when the latter are performing their normal biological functions. Example 1 : Antibodies are proteins that recognize foreign agents in the human body. Each antibody has specific structure that allows it to recognize a specific foreign object, such as one type of influenza virus. Therefore, survival of organism as a whole can depend on the proper three dimensional folding of a single protein.

Protein Structures
The way a protein is folded determines its function, and the folding of a protein depends on the properties of its amino acid sequence connected by peptide bonds in its primary structure, which is encoded in DNA.

The secondary structure of a protein is created by hydrogen bonding between atoms in the polypeptide backbone. (a) A pleated sheet. (b) An helix.

The secondary structure of a protein is created by hydrogen bonding between atoms in the polypeptide backbone. (a) A pleated sheet. (b) An helix.

The tertiary structure is a three dimensional shape that is maintained by interactions between side chains.

The quaternary structure is created by the association of several polypeptides (each colored differently here). The result is a fully functional protein.

Collagen is a fibrous protein composed of three identical alpha helices wound into a larger helix. This gives the protein strength. 40% of the protein in the human body is collagen, mainly in connective tissues.

quaternary structure: hemoglobin Hemoglobin is a globular protein composed of four polypeptide subunits (two alpha chains, in blue, and two beta pleated sheets, in red). The heme groups are the green structures.

All proteins are made up a primary, secondary, and tertiary structures. Most proteins also have a quaternary structure when the protein is made up of two or more polypeptides. Proteins with primary structure are made up of the amino acids and the sequence they are linked together. The primary structure is dictated by the DNA sequence. The next structure levels, secondary and tertiary, are determined by the primary structure. Folds and coils within the polypeptide chain create a protein's secondary structure. Secondary structure takes place because of hydrogen bonding between the repeating members of a polypeptide (not the side chains). Examples of secondary structures are beta-pleated sheets and alpha helix. The alpha helix is a coil held together by hydrogen bonds linking every fourth amino acid in the primary linear chain. A beta-pleated sheet is created by two or more beta strands lined up side by side with hydrogen bonds linking them. Beta-pleated sheets often compose globular proteins and provide strength and stretch. Tertiary structures are similar to secondary structure; however, a tertiary structure is based on interactions between the side chains of polypeptides, rather than the repeating constituents. Tertiarys structure can occur because of hydrophobic interactions, which are a result of non-polar side chains clustering together away from water. They are held in place by van der Waals interactions. Also, disulfide bridges occur when the sulfurs on the side chains of cysteines bond to one another. When two polypeptides aggregate to form one protein, they give rise to quaternary structure. quaternary structure : The arrangement of multiple folded or coiled proteins to form a multi-subunit complex disulfide bridge : In chemistry, a disulfide bond (Br.E. disulphide bond) is a covalent bond, usually derived by the coupling of two thiol groups. hydrophobic interaction : In chemistry, hydrophobicity (from the Attic Greek hydro, meaning water, and phobos, meaning fear) is the physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water. tertiary structure : The manner in which the helices or sheets of a protein are folded to give a threedimensional structure secondary structure : The general three-dimensional structure of a biopolymer such as DNA or a protein. primary structure : the linear sequence of amino acids covalently linked by peptide bonds to form a single polypeptide chain beta pleated sheet : The sheet (also -pleated sheet) is the second form of regular secondary structure in proteins, only somewhat less common than the alpha helix. alpha helix : A secondary structure found in many proteins, where the amino acids are arranged in a coil, or helix, with almost no free space on the inside and all side chains being pointed towards the outside. Example 1 : Figure 1 illustrates different levels of protein folding, from primary to quaternary structure. DNA polymerase, an enzyme that synthesizes DNA in a cell, without which cell cannot divide and propagate its genetic material into daughter cells, can function properly only in its quaternary structure.

Protein Folding
In order to properly fold into their functional forms, many proteins require assistance of chaperonins or chaperone proteins, and misfolded proteins that did not achieve their native conformation are targeted for degradation.
Chaperonins (aka chaperone proteins) within the cell assist protein folding. The chaperonins do not influence the final protein shape, rather they shield the protein from outside influences in the cytoplasm that may disrupt or change the folding process. A chaperonin consists of multiple proteins and contains an hollow cylinder. Within this cylinder, proteins can undergo the folding process unimpeded. In addition, other molecules double check the protein folding process. If a protein is not folded properly, it is either refolded or disposed of. Mis-folded proteins are observed in many diseases, including Alzheimer's and Parkinson's. One of the first methods developed to identify the 3D structure of proteins was X-ray crystallography. chaperonin : Chaperonins are proteins that provide favourable conditions for the correct folding of other proteins, thus preventing aggregation. Chaperonins belong to a large class of molecules that assist protein folding, called molecular chaperones. X-ray crystallography : A technique in which the patterns formed by the diffraction of X-rays on passing through a crystalline substance yield information on the lattice structure of the crystal, and the molecular structure of the substance. Example 1 : Alzheimer's disease is thought to be caused by an accumulation of abnormally folded amyloid beta protein in the brains of Alzheimer's patients

Protein Denaturation
Denaturation is the process in which proteins loose their native conformations, which can be caused by the change in protein's environments, such as change in pH or substantial increase in temperature.
Denatured and properly folded protein A protein's function can be lost if it is denatured. Denaturation can occur as a result of chemical treatments or high heat. Often, if the protein remains in solution, it can reform if its normal environment returns.

If the conditions of a protein's environment change, the bonds within protein may be disrupted and denaturation can occur. Denaturation is when a protein "unfolds" or loses its native shape. If proteins are moved to non-aqueous environment, a pH change occurs, or substantial heat is added, denaturation often occurs. denaturation : The change of folding structure of a protein (and thus of physical properties) caused by heating, changes in pH, or exposure to certain chemicals. Example 1 : Egg whites consist of a protein called albumin. When eggs are boiled, albumin denatures and egg whites turn from translucent to white.

Abnormalities in Protein Shape

Sickle cell disease or sickle-cell anemia is a genetic disorder that results in an abnormal shape of red blood cells and is due to the misfolding of the -globin chain of hemoglobin.

Sickle cell anemia is caused by a change in hemoglobin's primary structure (a) Hemoglobin in sickle cells is altered because of a single amino acid change: valine for glutamine at position 6. This change in the primary protein structure causes the protein to fold improperly. (b) As a result, sickled hemoglobins crystallize and cluster together into fibers. (c) This impedes the cell's ability to carry oxygen and can create blockages to blood flow. In a normal red blood cell, the hemoglobin molecules carry oxygen an do not associate with each other. The micrograph (d) shows both healthy and sickled red blood cells.

Sickle cell anemia is a blood disorder that results in abnormal hemoglobin shapes. This abnormality can sometimes clog tiny blood vessels and prevent blood flow. Sickle cell anemia arises from a simple change in the primary structure of the hemoglobin protein. A valine is substituted for a glutamic acid. hemoglobin : The iron-containing substance in red blood cells that transports oxygen from the lungs to the rest of the body; it consists of a protein (globulin), and haem (a porphyrin ring with an atom of iron at its centre). sickle cell anemia : Sickle-cell disease (SCD), or sickle-cell anaemia (or anemia, SCA) or drepanocytosis, is an autosomal recessive genetic blood disorder with overdominance, characterized by red blood cells that assume an abnormal, rigid, sickle shape. Sickling decreases the cells' flexibility and results in a risk of various complications. hemolysis : The destruction of red blood cells, and subsequent release of hemoglobin, at the normal end of the cell's life. Example 1 : Figure 2 shows location of the glutamic acid to valine mutation on the beta-globin chain of hemoglobin.

Introduction to nucleic acids

Nucleic acids are biological molecules that are essential for life and include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).Nucleic acids are linear polymers (chains) of nucleotides.

A comparison of the two principal nucleic acids: RNA (left) and DNA (right), showing the helices and nucleobases each employs. Nucleotide monomers are the building blocks of nucleic acids, resulting in DNA and RNA. A specific nucleotide sequence can contain heritable information, referred to as a gene. gene : A unit of heredity; a segment of DNA or RNA that is transmitted from one generation to the next, and that carries genetic information such as the sequence of amino acids for a protein. nucleic acid : Any acidic, chainlike biological macromolecule consisting of multiply repeat units of phosphoric acid, sugar and purine and pyrimidine bases; they are involved in the preservation, replication and expression of hereditary information in every living cell

Example 1 : Although viruses are not alive, they carry their own genetic information in the form of RNA or DNA. Theirgenes encode for all of the processes necessary for the successful virus life cycle to occur, from the point when a single virus enters a cell and until millions of progeny viruses are released.

Purpose of nucleic acids

Genetic information in every plant and animal cell is encoded in the form of DNA, which encodes genes that serve as a template for the synthesis of mRNA (messenger RNA) that will be translated into the amino acid sequence of a protein.

mRNA is transcribed from DNA in the nucleus of a cell. The mRNA is then transported into the cytoplasm where it is translated into a protein. The growing polypeptide chain can be seen as a chain of circles extending from the attached molecule of tRNA. Plants and animals are made up of chromosomes, which contain extremely long strands of DNA. An organism inherits its DNA from its parents. DNA is responsible for the production of RNA, which then dictates the synthesis of proteins. DNA also dictates its own replication within the cell. DNA controls RNA synthesis. A specific type of RNA is called mRNA, the "m" standing for messenger. This mRNA contains the code for the polypeptides, which make up proteins. Most DNA resides inside the nucleus; however, protein synthesis occurs on ribosomes, which reside in the cytoplasm. The mRNA, which is synthesized by the nuclear DNA, moves from the nucleus to the ribosomes to carry out protein synthesis. messenger RNA : Messenger RNA (mRNA) is a molecule of RNA that encodes a chemical "blueprint" for a protein product. ribonucleic acid : A derivative of DNA having ribose in place of deoxyribose, and uracil in place of thymine; its primary function is in the transcription of genetic material and subsequent synthesis of protein.

deoxyribonucleic acid : A nucleic acid found in all living things (and some non-living, see virus); consists of a polymer formed from nucleotides which are shaped into a double helix; it is associated with the transmission of genetic information. Example 1 : Figure 1 shows how information encoded in DNA is transcribed into mRNA and then translated into proteins. This process is tightly regulated by various enzymes (proteins). Therefore, one of the puzzling questions in biology is what came first: nucleic acids or proteins.

Nucleotide structure
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA and are composed of three parts: a nucleobase (nitrogenous base), a five-carbon sugar (either ribose or 2'-deoxyribose), and one to three phosphate groups.

What forms a nucleic acid structure? (a) A polynucleotide chain is made up of a backbone that is comprised of sugars and phosphate groups, with different nitrogenous bases attached to the backbone. A nucleotide consists of a phosphate group, pentose sugar and nitrogenous base. The nitrogenous base and sugar, without the phosphate, are called a nucleoside. (b) The nitrogenous bases of a nucleic acid can be divided into two groups: purines and pyrimidines.

Pyrimidines have single rings and include: cytosine, thymine, and uracil (in RNA). Purines have two rings and include: adenine and guanine.(c) The sugar of a nucleic acid is a pentose: deoxyribose in DNA and ribose in RNA. These two molecules differ only in the atoms attached to the 2-carbon. Deoxyribose has an H where ribose has an OH.

The nitrogenous bases that make up DNA and RNA are purines and pyrimidines; a purine is made up of a six-ring, carbon-nitrogen structure fused to a five carbon-nitrogen ring, a pyrimidine is a six-ring structure made up of carbons and nitrogens. The sugars that make up a nucleotide are pentoses: deoxyribose in DNA and ribose in RNA. The only difference between the two structures is the lack of an oxygen in the deoxyribose sugar. When individual nucleotides are linked together, it is called a polynucleotide. ribose : A naturally occurring pentose sugar, which is a component of the nucleosides and nucleotides that comprise the nucleic acid biopolymer, RNA. It is also found in riboflavin. deoxyribose : A derivative of the pentose sugar ribose in which the 2' hydroxyl (-OH) is reduced to a hydrogen (H); it is a constituent of the nucleotides that comprise the biopolymer, deoxyribonucleic acid, or DNA. purine : Any of a class of organic heterocyclic base containing fused pyrimidine and imidazole rings; they are components of nucleic acids pyrimidine : A diazine in which the two nitrogen atoms are in the meta- positions; it is the basis of three of the bases found in DNA and RNA, thymine, uracil and cytosine nitrogenous base : A nitrogenous (nitrogen-containing) base is a nitrogen-containing molecule having the chemical properties of a base. It is an organic compound that owes its property as a base to the lone pair of electrons of a nitrogen atom. nucleotide : the monomer comprising DNA or RNA biopolymer molecules. Each nucleotide consists of a nitrogenous heterocyclic base (or nucleobase), which can be either a double-ringed purine or a singleringed pyrimidine; a five-carbon pentose sugar (deoxyribose in DNA or ribose in RNA); and a phosphate group. polynucleotide : A polymeric macromolecule composed of many nucleotides; examples include DNA and RNA Example 1 : Figure 3 shows the structure of sugar-phosphate backbone of RNA oligonucleotide. If U were replaced with T in this structure, it would create a DNA oligonucleotide.

Structural Differences between DNA and RNA

DNA is structured as a double helix, with the backbone of DNA on the outside of the double helix created by two strands of deoxyribose sugars and phosphate groups, and nucleotide bases oriented towards each other at the center of the helix.

(a) The typical structure of DNA is nitrogenous bases of the two DNA strands oriented towards one another and joined by hydrogen bonding. The sugarphosphate backbone of each strand is facing outwards. The DNA structure is that of a double-helix, meaning both strands form a spiral shape. For DNA, the A and T bases pair with one another, as do the G and C bases. (b) Transfer RNA structure is a result of binding between the bases in the antiparallel regions of the molecule. The structure of tRNA is shaped similarly to an L. For RNA a uracil base is present rather than a thymine.

The sugar phosphate backbone of DNA is located on the outside, while the bases of two polynucleotide chains are oriented towards each other. The bases are designed to interact with one another: adenine with thymine and cytosine with guanine. In RNA, thymine is not present, and is substituted with uracil. If we know the structure of one strand, we can

determine the other strand structure because the bases of a DNA strand must pair with the correct corresponding base. This quality means that DNA structure is complementary. The two polynucleotide chains of a DNA molecule are said to be antiparallel, because the two polynucleotides chains are oriented in opposite 5'-3' directions. DNA is oriented as a double helix, meaning that the polynucleotides form a spiral shape. RNA can also have stretches of complementary base pairing, and often has pairing between bases within the same RNA strand. This type of pairing leads to the different shapes of RNA. Transfer RNA is responsible for moving amino acids and bringing them to ribosomes during the process of polypeptide synthesis. This molecule is 80 nucleotides long. transfer RNA : Transfer RNA (tRNA) is an adaptor molecule composed of RNA, typically 73 to 93 nucleotides in length, that is used in biology to bridge the four-letter genetic code (ACGU) in messenger RNA (mRNA) with the twenty-letter code of amino acids in proteins. double helix : Refers to the structure formed by double-stranded molecules of nucleic acids such as DNA and RNA. complementary : Complementarity is a property shared between two nucleic acid sequences, such that when they are aligned antiparallel to each other, the nucleotide bases at each position will be complementary. antiparallel : The nature of the opposite orientations of the two strands of DNA Example 1 : Figure 1 shows tRNA structure, where loops, bulges, and hairpins create a t-shape. [[fig:3]] shows the structure of DNA double helix, where hydrogen bonds between nucleotide bases form a ladder.

Nucleotides are linked together by phosphodiester linkages

The DNA double helix sugar-phosphate backbone is created by stretches of deoxyribose sugars - attached to each other by phosphodiester bonds - which link nucleotides in a DNA molecule.

Two complementary regions of nucleic acid molecules will bind and form a double helical structure held together by base pairs.

A polynucleotide consists of a sugar-phosphate backbone. The nitrogenous bases are not part of this backbone. The ends of a polynucleotide are referred as the 3' and 5' ends and are different from one another. The 3'end has a free hydroxyl group, and the 5' end consists of a 5'-carbon attached to a phosphate. The amino acid sequence of the protein is dictated by the order of the nitrogenous bases codon : A sequence of three adjacent nucleotides, which encode for a specific amino acid during protein synthesis, or translation. Three special codons, called "stop codons," signal protein synthesis to terminate. Example 1 : Cancer can be caused by a single mutation of a single nucleotide in a single gene of a single cell in the entire human body.