In this group the side chain is an imine . This amino acid is found in bends due to its structure. Proline, Pro, P. Now you will need to use your imagination a bit. Keep in mind that these are real molecules in the real world with a 3-dimensional shape, not the 2-dimensional shape as they are drawn on the page. Try to imagine a pyramid with the central carbon hidden from view at the center of this pyramid. But branching out from this central carbon producing the four corners of the pyramid are the four things attached to the central carbon. One corner of the pyramid is the amino group (NH2), another corner of this pyramid is the acid group (COOH), another corner is the single hydrogen atom (H), and the fourth corner is the variable side group (commonly designated 'R-group'). That is how the amino acids really look in your body. Since there are four different things attached to the central carbon, this molecule is asymmetric. Imagine looking at an amino acid in the mirror. There is the central carbon with a group attached to it to the right, to the left, to the top, and to the bottom.

The original amino acid and its mirror image are chemically the same, all the same pieces, but 3-dimensionally they are different, they have a different 3-dimensional arrangement of all the same atoms. It would be the same as looking at your left hand in the mirror. That image is just like your left hand, but if it were real it would not fit into a left hand glove. It is 3-dimensionally the opposite, even though it consists of all the same components. In nature, we will find both the 'right-hand' and 'left-hand' form of all these 20 amino acids. The term that is used to distinguish between whether we have the 'right-hand' form or the 'left-hand' form are the letters "D" and "L". For reasons that are not completely understood, all of the amino acids that are used by organisms to make proteins are of the "L" form. In other words, all the amino acids that you have making up all of your proteins are the "L" form, L-serine, L-proline, etc. It is also of interest to mention that there are several biologically important amino acids not found in human proteins.

For example, the amino acids L-homoserine, L-ornithine and sarcosine are never used as part of a protein, but are found in our bodies as intermediate amino acids when converting one kind into another. Another important amino acid used in the human body, but not used directly for proteins is the amino acid gamma-aminobutyric acid (GABA) which is used as a neurotransmitter between neurons. You will notice that the amino acid cysteine has a sulfur containing side group. Commonly if one cysteine becomes arranged across from another cysteine amino acid, the two cysteines will each lose a hydrogen atom from the sulfur and use these open bonds to covalently bond the two sulfur atoms and so covalently link the two cysteines together. In this form the amino acid is called cystine. So as a free amino acid it will be called cysteine since the sulfur will contain its hydrogen atom. However, when part of a protein chain, most likely the cysteine will link to another cysteine and now be called cystine. To be complete, we should also mention that there are four amino acids that can be found in proteins that are slightly modified from their original structure.

These are phosphoserine (serine plus a phosphate group), hydroxyproline (proline plus a hydroxy group (OH)), hydroxylysine (lysine plus a hydroxy group), and carboxyglutamic acid (glutamic acid plus an additional acid group (COOH)). Protein Structure: Now that we have discussed in good detail amino acids, we can now start to talk about linking them together, one by one, into a linear chain, similiar to the cars of a train, as we mentioned at the very beginning of this page. Joining Amino Acids Together: Individual amino acids may be linked together, one after another, like cars of a train. The covalent bond that is used to attach one amino acid to the next is called a 'peptide bond'. All that is done is that an -OH group is removed from the first amino acid and a -H is removed from the second amino acid being linked to the first. What is removed is -OH plus -H which can combine into H-O-H, or a water molecule. The exposed, broken bonds left on the two amino acids are then attached together, thus linking these two amino acids together, creating this peptide bond.

This can be repeated again to attach another amino acid to the chain. Since the by-product of this reaction is simple water, these types of reactions are also called 'dehydration reactions'. This is how our cells build proteins. In fact, for us to break apart a protein, to digest a protein in the meat we eat, the enzymes in our intestines break this very same 'peptide bond', then break apart a water molecule into a -OH and a -H, then add back the -OH onto the one exposed bond on the first amino acid and add back the -H onto the second exposed bond from the broken peptide bond. In other words, just the opposite direction as our creating the peptide bond. That's it. 3-D Structure of a Protein: Keep in mind that all proteins in the body are simply a linear chain of amino acids. This long chain of one amino acid after another and another however is not loose like an unwound piece of string. Instead, this long, linear string of amino acids is looped and coiled around into a three dimensional ball.

Because every protein has its unique three dimensional shape, and this three dimensional shape essentially determines what that protein will be and what it will do, we need a way to describe its three dimensional shape with all its loops and folds. In order to do this, so that you could talk to someone over the telephone 1000's of miles away and describe in exact detail what your protein looks like, a series of terms has been created to describe every protein's three dimensional shape. Review: Protein Structure Biochemistry of Metabolism Review: Basic Concepts of Protein Structure Note: It is assumed that students will be already familiar with basic concepts of protein and nucleic acid structure, as well as enzyme kinetics and mechanisms, before using the Biochemistry of Metabolism educational web. A review of some elementary concepts relating to protein structure is provided here. For a more complete discussion see, e.g., Biochemistry by D. Voet & J. G. Voet, 3rd Ed, chapters 4, 7 & 8. Key-words on this page: Protein Primary Structure Proteins are polymers of amino acids. Each amino acid has the same fundamental structure, differing only in the side-chain, designated the R-group.

The carbon atom to which the amino group, carboxyl group, and side chain (R-group) are attached is the alpha carbon (Ca). Structures of amino acids, with their R-groups in blue, are shown below with their three-letter and one-letter abbreviated names. Glycine has just a hydrogen atom in place of an R-group. At physiological pH, some amino acid R-groups are charged, because of dissociation or association of a proton by, e.g., a carboxyl or amino group. Note that histidine is shown charged, but its pK is close to the physiological range. Some side-chain groups that are uncharged at the near-neutral pH of the cytosol or extracellular space, may dissociate or gain a proton in the microenvironment of an enzyme active site. Peptide bonds link amino acid residues within proteins. The sequence of covalently linked amino acids is known as the primary structure of a protein. The reaction by which two amino acids are joined in a peptide bond, with elimination of H2O, is represented at right. For detail on the mechanism of peptide bond formation, see the section on protein synthesis .

A protein is a polypeptide, a linear polymer of many amino acids, linked by peptide bonds. The peptide linkages, along with the a-carbon atoms to which R-groups are attached, form the protein backbone, with sequence NCCNCCNCCNCC... Protein Secondary Structure. Segments of polypeptides often fold locally into stable structures that include a-helices and b-pleated sheets. a-Helix. In an a-helix (alpha helix), the polypeptide backbone follows a helical path. There are 3.6 amino acid residues per turn of the helix. Some protein domains assume other helical structures, but the a-helix is most common. An a-helix is stabilized by hydrogen bonds between backbone amino and carbonyl groups and those in the next turn of the helix, represented as N-Hï¿½ï¿½ï¿½ï¿½O=C. The hydrogen and oxygen atoms are attracted to one another because the H atom carries a partial positive charge and the O atom carries a partial negative charge, due to unequal sharing of electrons in N-H and O=C bonds. Diagram p. 224 of Voet & Voet text.

In an a-helix, the amino acid R-groups protrude out from the helically coiled polypeptide backbone. The surface of an a-helix largely consists of the R-groups of amino acid residues. At right, an a-helix is shown end-on and from the side. In this image, H atoms are not visible. Colors: C N O R-group Some amino acids have a greater tendency to be found within an a-helix. The amino acid proline tends to interrupt an a-helix. Its fused ring, which includes the a-carbon and the peptide-forming amino N, prevents the polypeptide backbone from assuming a conformation compatible with an a-helix in the vicinity of a proline. Explore below the structure of an a-helix, using MDL's software plug-in Chime. Note that with this data file hydrogen atoms will not be visible. For a tutorial on the Chime software, see Chime: How to use it , a website maintained by Eric Martz. With the cursor on the image below, click down on the right mouse button to choose from menus. With Chime, usually one selects something, and then alters its display, color, etc.

Use the left mouse button to drag the image to view the a-helix from different perspectives. Using the right mouse button, choose display backbone. Drag to view the spiraling backbone from the side as well as down its axis. Now choose display ball & stick with color CPK (a color convention in which C is grey, O is red, N is blue, etc.) To distinguish the R-groups, select protein-sidechain, and then display as sticks. Identify atoms of the protein backbone with sequence NCCNCCNCCNCC... Hold down the shift key and left-drag to zoom in for a closer look. Question: Structures of individual amino acids are given above. Based on the R-group structures, identify each amino acid residue and specify the sequence of amino acids in this peptide. Now select protein - sidechain; then select - change color to and pick a color. This will give the R-groups a color distinct from the CPK-colored backbone atoms. Select protein - protein. Try other display options including spacefill-Van der Waals, and ribbons. Questions: What part of the polypeptide is mainly exposed to the surrounding medium. Is an a-helix a hollow structure? Beta pleated sheets.

Another common secondary structure is the b sheet (beta sheet). In a b sheet, strands of protein lie adjacent to one another, interacting laterally via H bonds between backbone carbonyl oxygen and amino H atoms. The strands may be parallel (N-termini of both strands at the same end) or antiparallel. See diagrams p. 228-229 of Voet & Voet. Because of the tetrahedral nature of carbon bonds, a b-sheet is puckered, leading to the designation pleated sheet. R groups of amino acids in a b-strand alternately point to one side or the other of a b-strand. Hence every other amino acid is exposed on one side or the other of a b-sheet. Explore at right two strands of a b-sheet (Data file derived from PDB 1ICM). Recommended displays: Display as cartoon. Question: Are the two b-strands parallel or antiparallel? Now change the display to ball & stick, with color CPK. Then select protein-sidechain, and select-change color to. Specify a color not already visible, such as green. View the 2-stranded b-sheet from the side.

Note the "pleated" appearance of each b-strand. Note how the protein side-chains (R-groups) alternate in extending above and below the b-sheet. Note how, within the plane of the sheet, backbone carbonyl oxygen atoms point toward backbone amino N atoms of the adjacent strand. (H atoms involved in interchain H-bonds are not visible in this structure, which is based on X-ray crystallographic analysis.) These two b-strands are actually part of a larger protein that you will explore below. A common structural motif, the b-barrel, is equivalent to a b-sheet that is rolled up to form a cylinder. An example of a protein that consists mainly of a b-barrel is the bacterial channel porin . In some cases, a b-barrel may be partly flattened, to form what is called a b-clam structure (see below). Other common folding motifs involve combinations of a-helices and b-strands. One example is the a,b-barrel, explored elsewhere in an exercise on Triose Phosphate Isomerase (TIM). Explore at right an intestinal fatty acid binding protein (Data file PDB 1ICM, structure solved by J. C. Eads, J. C.

Sacchettini, A. Kromminga, & J. I Gordon in 1993.) Recommended displays: Display as cartoon, and color structure. Different colors distinguish the b-strands, a-helices and sharp turns called hairpin loops. Question: Would you describe the predominant structure as a b-sheet, b-barrel, or b-clam? To view the fatty acid, select hetero-ligand and display as spacefill with color CPK. Now select protein-protein and display as spacefill with color chain. Is the fatty acid well enclosed by its binding protein? Tertiary protein structure refers to the complete three dimensional folding of a protein. Stabilization of a protein's tertiary structure may involve interactions between amino acids located far apart along the primary sequence. These may include: weak interactions such as hydrogen bonds and Van der Waals interactions. ionic bonds involving negatively charged and positively charged amino acid side-chain groups. disulfide bonds, covalent linkages that may form as the thiol groups of two cysteine residues are oxidized to a disulfide: 2 R-SH ï¿½ R-S-S-R.

Interactions with the aqueous solvent, known as the hydrophobic effect results in residues with non-polar side-chains typically being buried in the interior of a protein. Conversely, polar amino acid side-chains tend to on the surface of a protein where they are exposed to the aqueous milieu. There are, however, many exceptions in which polar residues are buried or non-polar residues exposed on the surface of a protein. Such atypical locations might be stabilized, e.g., by interaction of amino acid side-chains with enzyme prosthetic groups or other ligands, by interactions between amino acid side-chains, or by association of proteins with lipid membranes , etc. Many proteins have a modular design with multiple distinct domains resulting from gene fusion events during evolution. A domain with a particular structure and function may be part of the structure of several otherwise distinct proteins. For example, an enzyme's primary structure may include a segment that folds to produce an active site with particular catalytic activity, plus other segments that may mediate regulation of the enzyme or binding of the enzyme to a membrane. Quaternary protein structure refers to the regular association of two or more polypeptide chains to form a complex.

A multi-subunit protein may be composed of two or more identical polypeptides, or it may include different polypeptides. Quaternary structure tends to be stabilized mainly by weak interactions between residues exposed on surfaces polypeptides within a complex. A multimeric complex may be important to enzyme activity, e.g., in cases in which an active site is formed by residues from more than one polypeptide subunit, or when adjacent active sites may be involved sequentially in catalysis of a complex reaction. Regulation of functional activity may involve cooperative interactions among protein subunits in a complex. Examples of these are included throughout this web. Ribulose Bisphosphate Carboxylase, Copyright ï¿½ 2003 by Joyce J. Diwan. All rights reserved. CHEMISTRY II: WATER AND ORGANIC MOLECULES CHEMISTRY II: WATER AND ORGANIC MOLECULES Table of Contents Structure of Water | Back to Top It can be quite correctly argued that life exists on Earth because of the abundant liquid water. Other planets have water, but they either have it as a gas (Venus) or ice (Mars). This relationship is shown in Figure 1.

Recent studies of Mars reveal the presence sometime in the past of running fluid, possibly water. The chemical nature of water is thus one we must examine as it permeates living systems: water is a universal solvent, and can be too much of a good thing for some cells to deal with. Figure 1. Water can exist in all three states of matter on Earth, while only in one state on our two nearest neighboring planets. The above graph is from . Water is polar covalently bonded within the molecule. This unequal sharing of the electrons results in a slightly positive and a slightly negative side of the molecule. Other molecules, such as Ethane, are nonpolar, having neither a positive nor a negative side, as shown in Figure 2. Figure 2. The difference between a polar (water) and nonpolar (ethane) molecule is due to the unequal sharing of electrons within the polar molecule. Nonpolar molecules have electrons equally shared within their covalent bonds. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. These link up by the hydrogen bond discussed earlier.

Consequently, water has a great interconnectivity of individual molecules, which is caused by the individually weak hydrogen bonds , shown in Figure 3, that can be quite strong when taken by the billions. Figure 3. Formation of a hydrogen bond between the hydrogen side of one water molecule and the oxygen side of another water molecule. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Water has been referred to as the universal solvent. Living things are composed of atoms and molecules within aqueous solutions (solutions that have materials dissolved in water). Solutions are uniform mixtures of the molecules of two or more substances. The solvent is usually the substance present in the greatest amount (and is usually also a liquid). The substances of lesser amounts are the solutes. The solubility of many molecules is determined by their molecular structure. You are familiar with the phrase "mixing like oil and water." The biochemical basis for this phrase is that the organic macromolecules known as lipids (of which fats are an important, although often troublesome, group) have areas that lack polar covalent bonds.

The polar covalently bonded water molecules act to exclude nonpolar molecules, causing the fats to clump together. The structure of many molecules can greatly influence their solubility. Sugars, such as glucose, have many hydroxyl (OH) groups, which tend to increase the solubility of the molecule. This aspect of water is illustrated in Figure 4. Figure 4. Dissolution of an ionically bonded compound, sodium chloride, by water molecules. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Water tends to disassociate into H+ and OH- ions. In this disassociation, the oxygen retains the electrons and only one of the hydrogens, becoming a negatively charged ion known as hydroxide. Pure water has the same number (or concentration) of H+ as OH- ions. Acidic solutions have more H+ ions than OH- ions. Basic solutions have the opposite.The pH of several common solutions is shown in Figure 5. An acid causes an increase in the numbers of H+ ions and a base causes an increase in the numbers of OH- ions. Figure 5.

pH of some common items. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. The pH scale is a logarithmic scale representing the concentration of H+ ions in a solution. Remember that as the H+ concentration increases the OH- concentration decreases and vice versa . If we have a solution with one in every ten molecules being H+, we refer to the concentration of H+ ions as 1/10. Remember from algebra that we can write a fraction as a negative exponent, thus 1/10 becomes 10-1. Conversely 1/100 becomes 10-2 , 1/1000 becomes 10-3, etc. Logarithms are exponents to which a number (usually 10) has been raised. For example log 10 (pronounced "the log of 10") = 1 (since 10 may be written as 101). The log 1/10 (or 10-1) = -1.

pH, a measure of the concentration of H+ ions, is the negative log of the H+ ion concentration. If the pH of water is 7, then the concentration of H+ ions is 10-7, or 1/10,000,000. In the case of strong acids, such as hydrochloric acid (HCl), an acid secreted by the lining of your stomach, [H+] (the concentration of H+ ions, written in a chemical shorthand) is 10-1; therefore the pH is 1. Organic molecules | Back to Top Organic molecules are those that: 1) formed by the actions of living things; and/or 2) have a carbon backbone. Methane (CH4) is an example of this. If we remove the H from one of the methane units below, and begin linking them up, while removing other H units, we begin to form an organic molecule. (NOTE: Not all methane is organically derived, methane is a major component of the atmosphere of Jupiter, which we think is devoid of life). When two methanes are combined, the resultant molecule is Ethane, which has a chemical formula C2H6.

Molecules made up of H and C are known as hydrocarbons. The formulas and structural representations of several simple organic molecules are shown in Figure 6. Figure 6. Types of hydrocarbon compounds and their structure. Images from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Scientists eventually realized that specific chemical properties were a result of the presence of particular functional groups. Functional groups are clusters of atoms with characteristic structure and functions. Polar molecules (with +/- charges) are attracted to water molecules and are hydrophilic. Nonpolar molecules are repelled by water and do not dissolve in water; are hydrophobic. Hydrocarbon is hydrophobic except when it has an attached ionized functional group such as carboxyl (acid) (COOH), then molecule is hydrophilic. Since cells are 70-90% water, the degree to which organic molecules interact with water affects their function. One of the most common groups is the -OH (hydroxyl) group. Its presence will enable a molecule to be water soluble.

Isomers are molecules with identical molecular formulas but differ in arrangement of their atoms (e.g., glyceraldehyde and dihydroxyacetone). Selected functional groups and related data are shown in Figure 7. Figure 7. Functional groups in organic molecules. Images from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Carbon has four electrons in outer shell, and can bond with up to four other atoms (usually H, O, N, or another C). Since carbon can make covalent bonds with another carbon atom, carbon chains and rings that serve as the backbones of organic molecules are possible. Chemical bonds store energy. The C-C covalent bond has 83.1 Kcal (kilocalories) per mole, while the C=C double covalent bond has 147 Kcal/mole. Energy is in two forms: kinetic, or energy in use/motion; and potential, or energy at rest or in storage. Chemical bonds are potential energy, until they are converted into another form of energy, kinetic energy (according to the two laws of thermodynamics).

Each organic molecule group has small molecules (monomers) that are linked to form a larger organic molecule (macromolecule). Monomers can be jouined together to form polymers that are the large macromolecules made of three to millions of monomer subunits. Macromolecules are constructed by covalently bonding monomers by condensation reactions where water is removed from functional groups on the monomers. Cellular enzymes carry out condensation (and the reversal of the reaction, hydrolysis of polymers). Condensation involves a dehydration synthesis because a water is removed (dehydration) and a bond is made (synthesis). When two monomers join, a hydroxyl (OH) group is removed from one monomer and a hydrogen (H) is removed from the other. This produces the water given off during a condensation reaction. Hydrolysis (hydration) reactions break down polymers in reverse of condensation; a hydroxyl (OH) group from water attaches to one monomer and hydrogen (H) attaches to the other. There are four classes of macromolecules (polysaccharides, triglycerides, polypeptides, nucleic acids). These classes perform a variety of functions in cells. 1.

Carbohydrates have the general formula [CH2O]n where n is a number between 3 and 6. Note the different CH2O units in Figure 8. Carbohydrates function in short-term energy storage (such as sugar); as intermediate-term energy storage (starch for plants and glycogen for animals); and as structural components in cells ( cellulose in the cell walls of plants and many protists), and chitin in the exoskeleton of insects and other arthropods. Sugars are structurally the simplest carbohydrates. They are the structural unit which makes up the other types of carbohydrates. Monosaccharides are single (mono=one) sugars. Important monosaccharides include ribose (C5H10O5), glucose (C6H12O6), and fructose (same formula but different structure than glucose). Figure 8. The chain (left) and ring (center and right) method of representing carbohydrates. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission.

We classify monosaccharides by the number of carbon atoms and the types of functional groups present in the sugar. For example, glucose and fructose, illustrated in Figure 9, have the same chemical formula (C6H12O6), but a different structure: glucose having an aldehyde (internal hydroxyl shown as: -OH) and fructose having a keto group (internal double-bond O, shown as: =O). This functional group difference, as small as it seems, accounts for the greater sweetness of fructose as compared to glucose. Figure 9. Models of glucose and fructose. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. In an aqueous solution, glucose tends to have two structures, a (alpha) and b (beta), with an intermediate straight-chain form (shown in Figure 10). The a form and b form differ in the location of one -OH group, as shown in Figure 9. Glucose is a common hexose, six carbon sugar, in plants. The products of photosynthesis are assembled to form glucose.

Energy from sunlight is converted into and stored as C-C covalent bond energy. This energy is released in living organisms in such a way that not enough heat is generated at once to incinerate the organisms. One mole of glucose yields 673 Kcal of energy. (A calorie is the amount of heat needed to raise one gram of water one degree C. A Kcal has 1000 times as much energy as a cal.). Glucose is also the form of sugar measured in the human bloodstream. Figure 10. D-Glucose in various views (stick and space-filling) from the web. Right image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Disaccharides are formed when two monosaccharides are chemically bonded together. Sucrose, a common plant disaccharide is composed of the monosaccharides glucose and fructose. Lactose, milk sugar, is a disaccharide composed of glucose and the monosaccharide galactose.

The maltose that flavors a malted milkshake (and other items) is also a disaccharide made of two glose molecules bonded together as shown in Figure 11. Figure 11. Formation of a disaccharide (top) by condensation and structure of two common disaccharides. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Polysaccharides are large molecules composed of individual monosaccharide units. A common plant polysaccharide is starch (shown in Figure 12), which is made up of many glucoses (in a polypeptide these are referred to as glucans). Two forms of polysaccharide, amylose and amylopectin makeup what we commonly call starch. The formation of the ester bond by condensation (the removal of water from a molecule) allows the linking of monosaccharides into disaccharides and polysaccharides. Glycogen (see Figure 12) is an animal storage product that accumulates in the vertebrate liver. Figure 12.

Images of starch (top), glycogen (middle), and cellulose (bottom). Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Cellulose, illustrated in Figure 13 and 14, is a polysaccharide found in plant cell walls. Cellulose forms the fibrous part of the plant cell wall. In terms of human diets, cellulose is indigestible, and thus forms an important, easily obtained part of dietary fiber. As compared to starch and glycogen, which are each made up of mixtures of a and b glucoses, cellulose (and the animal structural polysaccharide chitin) are made up of only b glucoses. The three-dimensional structure of these polysaccharides is thus constrained into straight microfibrils by the uniform nature of the glucoses, which resist the actions of enzymes (such as amylase) that breakdown storage polysaccharides (such a starch). Figure 13. Structure of cellulose as it occurs in a plant cell wall.

Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Figure 14. Cellulose Fibers from Print Paper (SEM x1,080). This image is copyright Dennis Kunkel at , used with permission. 2. Lipids are involved mainly with long-term energy storage. They are generally insoluble in polar substances such as water. Secondary functions of lipids include structural components (as in the case of phospholipids that are the major building block in cell membranes) and "messengers" (hormones) that play roles in communications within and between cells. Lipids are composed of three fatty acids (usually) covalently bonded to a 3-carbon glycerol. The fatty acids are composed of CH2 units, and are hydrophobic/not water soluble. Some examples of fatty acids are shown in Figure 15. Fatty acids can be saturated (meaning they have as many hydrogens bonded to their carbons as possible) or unsaturated (with one or more double bonds connecting their carbons, hence fewer hydrogens).

A fat is solid at room temperature, while an oil is a liquid under the same conditions. The fatty acids in oils are mostly unsaturated, while those in fats are mostly saturated. Figure 15. Saturated (top and middle) and unsaturated (bottom) fatty acids. The term staurated refers to the "saturation" of the molecule by hydrogen atoms. The presence of a double C=C covalent bond reduces the number of hydrogens that can bond to the carbon chain, hence the application of therm "unsaturated". Images from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Fats and oils function in long-term energy storage. Animals convert excess sugars (beyond their glycogen storage capacities) into fats. Most plants store excess sugars as starch, although some seeds and fruits have energy stored as oils (e.g. corn oil, peanut oil, palm oil, canola oil, and sunflower oil). Fats yield 9.3 Kcal/gm, while carbohydrates yield 3.79 Kcal/gm. Fats thus store six times as much energy as glycogen.

Diets are attempts to reduce the amount of fats present in specialized cells known as adipose cells that accumulate in certain areas of the human body. By restricting the intakes of carbohydrates and fats, the body is forced to draw on its own stores to makeup the energy debt. The body responds to this by lowering its metabolic rate, often resulting in a drop of "energy level." Successful diets usually involve three things: decreasing the amounts of carbohydrates and fats; exercise; and behavior modification. Another use of fats is as insulators and cushions. The human body naturally accumulates some fats in the "posterior" area. Subdermal ("under the skin") fat plays a role in insulation. Phospholipids and glycolipids are important structural components of cell membranes. Phospholipids, shown in Figure 16, are modified so that a phosphate group (PO4-) is added to one of the fatty acids. The addition of this group makes a polar "head" and two nonpolar "tails". Waxes are an important structural component for many organisms, such as the cuticle, a waxy layer covering the leaves and stems of many land plants; and protective coverings on skin and fur of animals. Figure 16.

Structure of a phospholipid, space-filling model (left) and chain model (right). Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Cholesterol and steroids: Most mention of these two types of lipids in the news is usually negative. Cholesterol, illustrated in Figure 17, has many biological uses, it occurs in cell membranes, and its forms the sheath of some types of nerve cells. However, excess cholesterol in the blood has been linked to atherosclerosis, hardening of the arteries. Recent studies suggest a link between arterial plaque deposits of cholesterol, antibodies to the pneumonia-causing form of Chlamydia, and heart attacks. The plaque increases blood pressure, much the way blockages in plumbing cause burst pipes in old houses. Figure 17. Structure of four steroids. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. 3. Proteins are very important in biological systems as control and structural elements.

Control functions of proteins are carried out by enzymes and proteinaceous hormones . Enzymes are chemicals that act as organic catalysts (a catalyst is a chemical that promotes but is not changed by a chemical reaction). Click here for an illustrated page about enzymes. Structural proteins function in the cell membrane, muscle tissue, etc. The building block of any protein is the amino acid , which has an amino end (NH2) and a carboxyl end (COOH). The struucture of a generalized aminio acid as well as the specific structures of the 20 biological amino acids are shown in Figure 18 and 19 respectively. The R indicates the variable component (R-group) of each amino acid. Alanine and Valine, for example, are both nonpolar amino acids, but they differ, as do all amino acids, by the composition of their R-groups. All living things (and even viruses) use various combinations of the same twenty amino acids. A very powerful bit of evidence for the phylogenetic connection of all living things. Figure 18. Structure of an amino acid.

Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Figure 19. Structures in the R-groups of the twenty amino acids found in all living things. Images from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Amino acids are linked together by joining the amino end of one molecule to the carboxyl end of another. Removal of water allows formation of a type of covalent bond known as a peptide bond . This process is illustrated in Figure 20. Figure 20. Formation of a peptide bond between two amino acids by the condensation (dehydration) of the amino end of one amino acid and the acid end of the other amino acid. The above image is from . Amino acids are linked together into a polypeptide, the primary structure in the organization of proteins. The primary structure of a protein is the sequence of amino acids, which is directly related to the sequence of information in the RNA molecule, which in turn is a copy of the information in the DNA molecule.

Changes in the primary structure can alter the proper functioning of the protein. Protein function is usually tied to their three-dimensional structure. The primary structure is the sequence of amino acids in a polypeptide.. The secondary structure is the tendency of the polypeptide to coil or pleat due to H-bonding between R-groups. The tertiary structure is controlled by bonding (or in some cases repulsion) between R-groups. Tertiary structure of an HIV protein and its similarity to gamma interferon are shown in Figure 22. Many proteins, such as hemoglobin , are formed from one or more polypeptides. Such structure is termed quaternary structure . Structural proteins, such as collagen, have regular repeated primary structures. Like the structural carbohydrates, the components determine the final shape and ultimately function. Collagens have a variety of functions in living things, such as the tendons, hide, and corneas of a cow. Keratin is another structural protein. It is found in fingernails, feathers, hair, and rhinoceros horns. Microtubules, important in cell division and structures of flagella and cilia (among other things), are composed of globular structural proteins. Figure 21.

HIV p17 protein and similarities of its structure to gamma interferon. Image is from . 4. Nucleic acids are polymers composed of monomer units known as nucleotides . There are a very few different types of nucleotides. The main functions of nucleotides are information storage (DNA), protein synthesis (RNA), and energy transfers (ATP and NAD). Nucleotides, shown in Figure 22, consist of a sugar, a nitrogenous base, and a phosphate. The sugars are either ribose or deoxyribose. They differ by the lack of one oxygen in deoxyribose. Both are pentoses usually in a ring form. There are five nitrogenous bases. Purines (Adenine and Guanine) are double-ring structures, while pyrimidines (Cytosine, Thymine and Uracil) are single-ringed. Figure 22. Structure of two types of nucleotide. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission.

Deoxyribonucleic acid (better known as DNA) is the physical carrier of inheritance for 99% of living organisms. The bases in DNA are C, G, A and T, as shown in Figure 23. We will learn more about the DNA structure and function later in the course (click here for a quick look [actually take all the time you want!] ;)). Figure 23. Structure of a segment of a DNA double helix. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. DNA functions in information storage. The English alphabet has 26 letters that can be variously combined to form over 50,000 words. DNA has four letters (C, G, A, and T, the nitrogenous bases) that code for twenty words (the twenty amino acids found in all living things) that can make an infinite variety of sentences (polypeptides). Changes in the sequences of these basesinformation can alter the meaning of a sentence. For example take the sentence: I saw Elvis.

This implies certain knowledge (that I've been out in the sun too long without a hat, etc.). If we alter the sentence by inverting the middle word, we get: I was Elvis (thank you, thank you very much). Now we have greatly altered the information. A third alteration will change the meaning: I was Levis. Clearly the original sentence's meaning is now greatly changed. Changes in DNA information will be translated into changes in the primary structure of a polypeptide, and from there to the secondary and tertiary structures. A mutation is any change in the DNA base sequence. Most mutations are harmful, few are neutral, and a very few are beneficial and contribute the organism's reproductive success. Mutations are the wellspring of variation, variation is central to Darwin and Wallace's theory of evolution by natural selection . Ribonucleic acid (RNA) , shown in Figure 24 was discovered after DNA. DNA, with exceptions in chloroplasts and mitochondria, is restricted to the nucleus (in eukaryotes, the nucleoid region in prokaryotes).

RNA occurs in the nucleus as well as in the cytoplasm (also remember that it occurs as part of the ribosomes that line the rough endoplasmic reticulum). There are three types of RNA: Messenger RNA (mRNA) is the blueprint for construction of a protein. Ribosomal RNA (rRNA) is the construction site where the protein is made. Transfer RNA (tRNA) is the truck delivering the proper amino acid to the site at the right time. Details of RNA and its role in protein synthesis are available by clicking here . Figure 24. Structure of the RNA molecule. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Adenosine triphosphate, better known as ATP (Figure 25), the energy currency or coin of the cell, transfers energy from chemical bonds to endergonic (energy absorbing) reactions within the cell. Structurally, ATP consists of the adenine nucleotide (ribose sugar, adenine base, and phosphate group, PO4-2) plus two other phosphate groups.

Energy is stored in the covalent bonds between phosphates, with the greatest amount of energy (approximately 7 kcal/mole) in the bond between the second and third phosphate groups. This covalent bond is known as a pyrophosphate bond. Figure 25. A cartoon and space-filling view of ATP. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates ( ) and WH Freeman ( ), used with permission. Dissolved substances are called solutes; a fluid in which one or more substances can dissolve is called a solvent. Describe several solutions that you use everyday in terms of what is the solvent and what is the solute. Define acid and base and be able to cite an example of each. The concentration of free hydrogen ions in solutions is measured by the pH scale.. Nearly all large biological molecules have theor organization influenced by interactions with water. Describe this interaction as it exists with carbohydrate molecules. Be able to list the three most abundant elements in living things. Each carbon atom can form as many as four covalent bonds with other carbon atoms as well as with other elements. Be able to explain why this is so.

Be able to list the four main groups of organic molecules and their functions in living things. Enzymes are a special class of proteins that speed up chemical reactions in cells. What about the structure of proteins allows for the reaction specificity that occurs with most enzymes. Condensation reactions result in the formation of covalent bonds between small molecules to form larger organic molecules. Be able to describe a condensation reaction in words. Be able to describe what occurs during a hydrolysis reaction. Be able to define carbohydrates and list their functions. The simplest carbohydrates are sugar monomers, the monosaccharides. Be able to give examples and their functions. A polysaccharide is a straight or branched chain of hundreds or thousands of sugar monomers, of the same or different kinds. Be able to give common examples and their functions. Be able to define lipids and to list their functions. Distinguish betwen a saturated fat and an unsaturated fat. Why is such a distinction a life and death matter for many people? A phospholipid has two fatty acid tails attached to a glycerol backbone. What is the importance of these molecules. Define steroids and describe their chemical structure.

Be able to discuss the importance of the steroids known as cholesterol and hormones. Be able to describe proteins and cite their general functions. Be prepared to make a sketch and name the three parts of every amino acid. Describe the complex structure of a protein through its primary, secondary, tertiary, and quaternary structure. How does this relate to the three-dimensional structure of proteins? Describe the three parts of every nucleotide.. Be able to give the general functions of DNA and RNA molecules. Review Questions | Back to Top The chemical reaction where water is removed during the formation of a covalent bond linking two monomers is known as ___. a) dehydration; b) hydrolysis; c) photosynthesis; d) protein synthesis The monomer that makes up polysaccharides is ____. a) amino acids; b) glucose; c) fatty acids; d) nucleotides; e) glycerol Proteins are composed of which of these monomers? a) amino acids; b) glucose; c) fatty acids; d) nucleotides; e) glycerol Which of these is not a function of lipids?

a) long term energy storage; b) structures in cells; c) hormones; d) enzymes; e) sex hormones All living things use the same ___ amino acids. a) 4; b) 20; c) 100; d) 64 The sequence of ___ bases determines the ___ structure of a protein. a) RNA, secondary; b) DNA, quaternary; c) DNA, primary; d) RNA, primary Which of these is not a nucleotide base found in DNA? a) uracil; b) adenine; c) guanine; d) thymine; e) cytosine Which of these carbohydrates constitutes the bulk of dietary fiber? a) starch; b) cellulose; c) glucose; d) fructose; e) chitin A diet high in _____ is considered unhealthy, since this type of material is largely found in animal tissues. a) saturated fats; b) testosterone; c) unsaturated fats; d) plant oils The form of RNA that delivers information from DNA to be used in making a protein is ____.

a) messenger RNA; b) ribosomal RNA; c) transfer RNA; d) heterogeneous nuclear RNA The energy locked inside an organic molecule is most readily accessible in a ___ molecule. a) fat; b) DNA; c) glucose; d) chitin; e) enzyme Phospholipids are important components in ____. a) cell walls; b) cytoplasm; c) DNA; d) cell membranes; e) cholesterol Links | Back to Top Chemicool A colorful and easy to use Periodic Table. More information about elements than most of us would want. WebElements Much more detailed Periodic Table. Even more information about those pesky elements! If this site is busy there are a series of mirror sites . James K. Hardy's Chemistry Site (U of Akron). Powerpoint slides (that run over the web) and a series of animations...a must see! Ch 3: The Chemical Building Blocks of Life - Biology 151 with Ladonski at University of South Dakota - StudyBlue Good to have you back! If you've signed in to StudyBlue with Facebook in the past, please do that again.

Ch 3: The Chemical Building Blocks of Life Ch 3: The Chemical Building Blocks of Life Joseph D. Last Modified: 2013-05-16 Size: 115 Views: 137 a compound of hydrogen and carbon, such as any of those that are the chief components of petroleum and natural gas. Functional Groups Distinctive arrangements of groups of atoms that impart characteristic chemical properties to the molecules that contain them. Advertisement ) OH bonded to carbon skeleton found in carbohydrates, proteins, nucleic acids, lipids properties polar/hydrophillic due to strongly electronegative oxygen atom increases water solubility by forming H-bonds w/ water Isomers Organic molecules that have the same molecular or empirical formula but have a different structure. a sub definition of isomers, where molecules with the same molecular formula have atoms bonded together in different orders, as opposed to stereoisomerism. mirror image isomers. react the same except for the direction they polarize light. Chiral A molecule that has mirror-image versions.

chiral compounds Not superimposable on their images lack a plane of symmetry exist as pair of non-superimposable mirror images (enantiomers), a "right-handed" D form and a "left-handed" L form. Polymer A molecule chain of repeating units of the same monomer. Dehydration reaction A reaction in which two molecules are covalently bonded to each other, with the loss of a water molecule. Hydrolysis Reaction Splitting of a compound be the addition of water with the H+ being incorporated in one fragment and the OH- in the other. Carbohydrates Compounds made up of carbon, hydrogen, and oxygen atoms, usually in the ration 1:2:1. Monosaccharides generally have molecular formulas that are some multiple of the unit CH2O. Plays the central role in energy storage disaccharide a carbohydrate compound consisting of two monosaccharide molecules joined together polysaccharides Longer polymers of monosaccharides joined through dehydration synthesis Advertisement Starch a complex plant carb made of linked chains of glucose molecules; a source of stored energy Cellulose Structural polysaccharide consisting of glucose molecules linked in chains. Makes up the walls in plant cells.

Glycogen Animal starch; a complex branched polysaccharride that serves as food reserve in animals, bacteria, and fungi. Information is stored in DNA by varying the sequence of the 4 types of ____ that make up each strand. Nucleotides Phospholipids have distinct polar and nonpolar regions lipids have small polar regions but are mostly nonpolar steroids are composed of interlocking carbon rings while fats are composed of glycerol and fatty acids fats are more similar in structure to phospholipids than they are to steroids Amylose common form of starch, with a relatively linear structure Chitin Carbohydrate material present in the exoskeletons of arthropods and insects and also in the cell walls of some fungi. Deoxyribonucleic acid (DNA) Macromolecule consisting of nucleotides which contain genetic information for making proteins necessary for the cell to function properly.

Capable of self-replication and synthesis of RNA ribonucleic acid (RNA) A type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U); usually single-stranded; functions in protein synthesis, gene regulation, and as the genome of some viruses. BASES (DNA) Like in DNA, the purine bases are the same:Adenine = A Guanine = G But the pyramiding bases have now changed to: Cytosine = C Urasyl = U.

(instead of thymine) Polynucleotide chains Each consists of a sequence of nucleotides linked together by phosphodiester bonds (located btw the phosphate group of one nucleotide and the deoxyribose of an adjacent nucleotide) joining adjacent moieties Double Helix Two strands of DNA polymer that wind around each other and is composed of two chains complementary the bases that participate in base-pairing adenine can only pair with thymine (in DNA) or with uracil (in RNA) cytosine can pair only with guanine Adenosine Triphosphate (ATP) An organic molecule that acts as the main energy source for cell processes; composed of a nitrogenous base, a sugar, and three phosphate groups. NAD+ - nicotinamide adenine dinucleotide an electron carrier and co-enzyme that can easily cycle between its oxidized form NAD+ and its reduced form NADH -functions as an oxidizing agent during cellular respiration FAD (Flavin adenine dinucleotide) important vitamin- derived electron carrier molecule.

Enzyme catalysis proteins Biological organisms use a class of highly specific and efficient protein catalysts called ENZYMES Defense proteins Globular proteins use their shapes to shapes to recognize foreign microbes and cancer cells. This forms the bodies endocrine and immune systems. Transport Proteins Ex. hemoglobin. Membrane transport proteins help move ions and molecules across the membrane. Support (proteins) structural roles such as keratin in hair, fibrin in blood clots, and collagen ( which forms the matrix of skin, ligaments tendons, and bones and is the most abundant protein in a vertebrate body). Motion (proteins) muscles contract through sliding motion of two types of protein filaments: actin and myosin proteins - regulation small proteins are inercellular messengers hormones: deliver messages through out body storage proteins stores calcium and iron by binding them as ions amino acids make up a protein. 20 different amino acids found in living things. Each amino acid has an amine (-NH2) and a carboxylic acid (-COOH) functional group.

Peptide Bond the resulting covalent bond between two amino acids polypeptide A peptide which on hydrolysis yields more than two amino acids called tripeptides, tetrapeptides, etc, according to the number of amino acids contained. In cells,____ directs the synthesis of mRNA which directs the synthesis of ___ DNA, proteins The 4 main groups of biological macromolecules are: Proteins, Lipids Nucleic acids Carbohydrates Changes in a protein's environment can cause the protein to unfold and lose its shape in a process called: Denaturation A group of biomolecules most efficient for storing energy. fats and oils the main component of cell membranes terpenes (primary function) some are components of important biological pigments steroids (primary function) some function as hormones in animals what determines the function of a protein molecule shape of the protein long polymers of repeating subunits called nucleotides.

The functions of proteins are Catalyze chemical reaction they transport oxygen in the blood of vertebrates They help the body recognize and destroy foreign microbes any cancer cells They play a key role in moving materials within cells They play a key role in the contraction of muscles Transport ions and molecules across the cell membranes provide structural support for many animal tissues Type of bond that forms between two amino acids during dehydration synthesis peptide bonds The major functional groups found in amino acids carboxyl group and amino group Relationship between temperature and enzyme activity Each enzyme has an optimum temperature where it functions best 3 components of an amino acid Carboxyl (acid), Amino & R-group are used for long-term energy storage The simplest carbohydrates are Transport forms of sugars are commonly made by linking 2 monosaccharides together to form a ______. Disaccharide one double bond between carbons Polysaturated fatty acids have more than one double bond Saturated Fatty acids All the bonds between the carbon atoms in the hydrocarbon chain are single bonds. There are no double bonds. How are DNA and RNA molecules similar?

both have nitrogenous base both use phosphodiester bonds to link the nucleotides in a single strand together both are composed of nucleotides Lipid Examples steroids, fats, prostaglandins if the 4 subunits that make up a hemoglobin molecule separate without losing their individual tertiary structure, the process is called _____. Dissociation Carbon-oxygen and carbon-nitrogen bonds are: Polar covalent.Formed by an unequal sharing of electrons. Hydrophobic exclusion Repulsion of nonpolar amino acid side chains Disulfide bridge formation of a covalent bond between 2 different amino acid side chains van der Waals attraction Type of (individually weak) noncovalent bond that is formed at close range between nonpolar atoms. ionic bonding attraction between 2 charged amino acid side chains hydrogen bonding attraction between atoms in 2 polar amino acid side chains Phosphodiester bond bond that connects adjacent nucleotides in a single strand of a nucleic acid five-carbon sugars that are components of nucleic acids ribose and deoxyribose same amount of carbon atoms but they are arranged differently to make carbon skeletons A protein's secondary structure is maintained primarily by ____ ____ Hydrogen bonds.

Forms the core of all biological membranes Phospholipids ____ ____ are long polymers of repeating subunits called nucleotides. Nucleic acids arrangement of 2 or more polypeptides to form a functional protein quarternary structure alpha helices and beta sheets the secondary structural level of a protein consists of __________. The folding of a single polypeptide helix into a complex globular three-dimensional structure is referred to as what level of protein structure? tertiary Biological polymers are often made using dehydration (or condensation) reactions. During these dehydration reactions 2 separate molecules are joined together by a covalent bond a molecule of water is formed an H atom is removed from one molecule and an -OH group is removed from another molecule single sugar 5=pentose 6=hexose small groups if atoms that are attached to larger molecules, giving them specific chemical properties, are called ______ _____. Functional groups Which molecules are composed of 1 or more nucleotides? RNA, ATP, NAD+, DNA a sub definition of isomers, where molecules with the same molecular formula have atoms bonded together in different orders, as opposed to stereoisomerism.

Stereoisomers isomers that have the same molecular and structural formulas, but different spatial arrangements of their atoms. Information is stored in DNA by varying the sequence of the 4 types of ___ that make up each strand. bases These interactions determine a proteins tertiary structure Ionic bonds In nucleic acids, adjacent nucleotides are covalently linked by ____ bonds. phosphodiester regular and repeated patterns of coiling or folding within a polypeptide chain makes up a proteins secondary structure In water, phospholipid molecules spontaneously form bilayers with the _____ located in the interior. hydrophobic regions, hydrocarbon tails, and nonpolar regions The structure of proteins is usually discussed in terms of a hierarchy of how many levels? 4 2 basic types of secondary structures Alpha helix and beta sheet Where are the peptide bonds located in a polypeptide? Between the amino group of one amino acid and the carboxyl group of another glycogen & starch Introduction to Biology - Molecules and Cells - Organic Molecules Introduction to Biology What makes a Molecule "Organic"? As the science of chemistry was developing, there was an understandable fascination with chemistry that was unique to living things.

As more and more was learned about the elements that could be found in living things, it was realized that carbon was a major component, found in any type of organism that was analyzed, and even in every compound that was extracted. Molecules with carbon in them were assumed to be associated with organisms, and so were called organic molecules. We know that carbon, with its ability to bond to four other atoms, can form very complex molecular structures, making it the perfect candidate for building such molecules around. But this is science, and no terms or ideas seem to last without some modification. There did seem to be carbon compounds in minerals that were not derived from living things, so carbon alone wasn't enough; organic molecules came to need both carbon and hydrogen. We have since found methane, CH4, and other such materials, in the dust of space and on other planets and moons, but the old definition hasn't been changed. It is now thought that when the Earth first formed, the oceans were full of the small organic molecules of space dust, forming primordial soup, from which truly living systems formed. More on organic molecules. Major Types of Organic Molecules The organic molecules found in living things fall into four major classes.

Each class of molecule has features that determine its use in living systems. The first class of molecules are called carbohydrates. The simplest type of these, monosaccharide simple sugars, have a basic formula: for every carbon atom, there are two hydrogens and one oxygen, or one water for each carbon. Carbo - hydrate. Glucose is a common carbohydrate that will show up again and again as we discuss cell chemistry: its formula is C6H12O6. Table sugar, sucrose, is two single sugars bound together: a disaccharide simple sugar. Sugars can be anything from a single sugar molecule up to several bound together. When organic molecules are bound together, a bonding site must be freed up on each participant. This happens by clipping a single hydrogen from one participant, and an oxygen-hydrogen piece (hydroxide) off of the other. Where each bit used to be become the new bond, and the two freed pieces stick together as H2O. This building process where water comes out is called dehydration synthesis, and is used whenever we build molecule from components.

When molecule chains need to be broken apart, such as happens in digestion, the opposite reaction happens: the bond breaks, and one spot gets a hydrogen while the other gets hydroxide. A water molecule breaks apart - in Latin, that's hydrolysis, and that's what this process is called. Sugars can be bound together in long chains, which may form branches and even networks: these huge carbohydrates are called starches. Both sugars and starches are commonly used as sources of energy in cells: sugars are broken apart for the bond energy, and starches are a way to store lots of sugars in a fairly inactive form. Large, stiff starches can also be used as structural molecules: cellulose is what hold most plants up. That "-ose" ending is a giveaway that something is a carbohydrate, although they don't all end that way. When the same type of molecule component is used over and over in a much bigger molecule, the bigger molecules are called polymers. Starches, proteins, and nucleic acids are all different types of polymers. There are other uses for carbohydrates in living systems, but energy and structure are by far the most common ones. The second class of organic molecules are called lipids.

Fats and oils are included in this class of molecules. These have a fairly simple structure, starting with the 3-carbon glycerol molecule. Each carbon picks up a bit called a fatty acid, which can be short or fairly long, and then it's a lipid molecule. A pair of terms that can applied to other types of molecules often shows up in descriptions of lipids: a saturated molecule has all of the atoms its carbons could possibly hold, and has only single bonds in the fatty acid chains; an unsaturated molecule has at least one double bond between carbons, and so could hold at least one more hydrogen. Not surprisingly, this alters the chemistry of the molecules. Lipid molecules are usually hydrophobic: they won't dissolve in water and tend to separate out from it (materials that will dissolve in water are hydrophilic). Vegetable oil is a lipid - what happens when you mix them? This makes them useful as water barriers, and they are found in cell membranes as well as such things as waxes and waterproofing oils.

Not mixing with water also reduces their chemistry, and lipid molecules can be a nice, nonreactive place to store extra energy: the lipids in fat are constructed for longterm energy storage. When energy is really needed, the fat molecules are broken apart and "fed" into the middle of the same process that gets energy from sugar molecules. Some lipid molecules can dissolve well enough in water to move around, but also can dissolve through other lipids like those in cell membranes; this makes lipids good signaling molecules. Included in this group are steroid hormones. Lipids also has other, varied uses, including insulation in organisms that need to hold onto heat in unusual conditions, like deep underwater. Lipids are also commonly a holding point for lipid-soluble toxins, which can accumulate there to dangerous levels. Many manufactured toxins, like pesticides, are lipid soluble: it helps get them into the target organisms, but gets them into others as well. Article on how pesticides may disrupt female reproductive function. The last two classes of molecules are huge polymers. Proteins are long chains of components called amino acids and have three to four levels of structure. The first level of structure, called primary structure, is just the order of amino acids in each chain.

At the secondary structure level, amino acids in a particular region connect to each other and produce local formations, like pleated sheets of coils. At the tertiary structure level, the entire molecule is pulled together into a particular three-dimensional shape, often through hydrogen bonds but sometimes through cross-connecting covalent bonds. Only some proteins have a quaternary structure, where the molecule has more than a single chain of amino acids, but again the overall three-dimensional structure is critical, because the function of proteins is connected to their shapes. When these shapes are changed, the functions may change or disappear; this can happen when other molecules attach to them, when the proportion of ions around them changes (such as in pH shifts), or when a change in temperature shakes or compresses the shape. The possible shapes that proteins can take is virtually infinite, so they have a broad array of possible functions. What follows is just a partial list, some of the major things that proteins do in living systems. Structure . Most cells have particular shapes, and those shapes are commonly held together by proteins that connect to the outer membrane and often to each other. Cells are often held together with protein-based structures.

Protein is an important component to structure in fungi, in animals in exoskeletons, and in things like tendons, ligaments, and cartilage. Movement. A single cell moves, or swims, using a protein-based movement system. Animal muscle depends upon two proteins, actin and myosin, contracting cells. Membranes have proteins that help move things through the barrier. Communication. Cells often send signals to each other using various types of proteins. Many hormones are proteins, as well as pheromones (signals-by-scent) and alarmones (signals that alert other individuals). Protein neurotransmitters carry signals between nerve cells. Receptors may be at the target cell that will attach to the signal molecule, and there are receptors that pick up other things, such as the light receptors in visual systems. Antibodies are proteins made specifically to attach to "foreign" molecules (the foreign molecules are called antigens); once attached, the molecule changes to a shape that attaches to receptors on immune cells and activates them to attack whatever the antibody is attached to (in an autoimmune disease, a system makes antibodies to molecules on its own cells and calls attacks on them). Chemistry.

The reactions that happen in cells often need a boost to get going, and that boost is supplied by enzymes, most of which are proteins. Enzymes are catalysts, chemicals that activate and speed along reactions. They typically are named to give some indication of the reaction they aid, and commonly have the ending -ase on their names. Almost every bit of chemistry done in cells is aided by enzymes. How enzymes work. The last class of organic molecules are the nucleic acids. There are two varieties: ribonucleic acid, or RNA, and deoxyribonucleic acid, or DNA. These polymers are long chains of components called bases, of which there are only five types. RNA is a single-strand molecule; DNA is a spiral of two cross-connected strands. DNA carries information. Part of the DNA in a cell is genes, which code for protein molecules. Each type of receptor, or enzyme, or neurotransmitter, has a stretch of DNA in which its sequence of amino acids is coded. The code-to-primary-structure ratio is three-to-one: three bases (called a codon) per amino acid. The codes proteins can vary, and code variations for a single type of protein are called alleles.

Different alleles can produce proteins that have the exact same amino acid sequence, have different sequences but no difference in activity, have different sequences that produce different levels of activity (including no activity at all), or produce a new type of activity. These will be returned to in the chapter on genetics. DNA is the code from which living things are made, since the DNA codes for proteins and the proteins are the foundation of cellular chemistry. Carbohydrates, lipids, and nucleic acids are made by enzyme-driven systems. A huge proportion of the DNA on many chromosomes is not used for protein production. This non-coding DNA is made up of many different types of DNA stretches: some are critical to interacting with the proteins that hold chromosomes together; some are codes that aren't used, either old sequences or dangerously mutated sequences or foreign sequences (invaders from disease organisms); some are non-gene codes that work to get genes processed; some produce functional stretches of RNA (see below); some are short stretches that exists to propagate themselves, a kind of molecular parasite; and a lot of what's there, no one knows what the origin or possible purpose is. All of this used to be called junk DNA, but that term is going away as functions are discovered for these bits.

The other nucleic acid form, RNA, is used in getting DNA code to protein sequence. RNA moves the code from where it is stored to where it is executed. RNA is a critical component of the cell parts that takes the codes and makes the protein. Small RNA molecules do all sorts of things in and around the genes; some are ribozymes, having similar activity to enzymes.

Question: What term is used for chains of repeated groups of atoms e.g. DNA, proteins?
Answer: Polymers