Organic Macromolecules PDF

Preview

Summary

Organic Macromolecules...

Description

Organic Macromolecules The unique bonding of carbon allows for the creation of a variety of different molecules. The result... Carbon can arrange in orientations like THIS

or THIS

or THIS

Biological macromolecules are defined as large molecules made up of smaller organic building blocks. In carbohydrates, proteins, and nucleic acids, these building blocks are called monomers. While the structure of monomers varies between macromolecules, the process of putting them together is similar for all organic macromolecules.

Dehydration Synthesis (also known as condensation reactions) is the process of attaching monomers by removing hydrogen (-H) and a hydroxyl (-OH) group for the removal of a water molecule. When two monomers attach, the created molecule is called a dimer. When three or more monomers are attached, they are called polymers. Dehydration synthesis and similar processes in which simpler pieces are assembled into more complicated structures are also referred to as anabolism or constructive metabolism.

Hydrolysis is the reverse reaction of dehydration synthesis. In this process, a water molecule is introduced to macromolecules to split them into their respective monomers. Hydrolysis reactions happen when complicated structures are broken down into more simple building blocks. This process is also referred to as catabolism.

The four major types of organic macromolecules essential for biological life are:  carbohydrates  proteins  lipids  nucleic acids

Carbohydrates Carbohydrates are composed of monomers called monosaccharides. Two monosaccharides attached through dehydration synthesis are called disaccharides and the polymer of three or more monosaccharides is called a polysaccharide. Carbohydrates consist of carbon, hydrogen, and oxygen. They are usually found in the ratio of C H O (ex: C H O ) although there are some exceptions. n

2n

n

6

12

6

Carbohydrates may exist as cyclic ring formations (see figure 2.8) or as chain formations. In biological systems, carbohydrates usually are found in rings of five to seven carbons. Carbohydrates are named with the suffix “-ose” (i.e. glucose, fructose, lactose, dextrose ) Popularly, carbohydrates are classified as simple or complex. Typically, simple carbohydrates include monosaccharides and disaccharides while the complex carbohydrates are made up of mostly polysaccharides. Complex carbohydrates are also classified as starches.

Lipids Lipids, much like carbohydrates, are composed of carbon, hydrogen, and oxygen. The three varieties of lipids are fats, oils, and waxes. Fats, such as butter, are usually derived from animal origin and are solid at room temperature. Oils, such as vegetable oil, are typically derived from plants and are liquid at room temperature. Waxes can be of plant or animal origin and are solid at temperatures below 45˚C (113˚C). The monomers for fats and oils are called triglycerides. Triglycerides are composed of a glycerol molecule and three molecules of fatty acids that are attached through dehydration synthesis. Fatty acids are classified as chains of hydrocarbons with a carboxylic acid group (COOH) on one end.

Figure 2.10 - Reactants of a triglyceride

Fat molecules are composed of three fatty acids and a molecule of glycerol. The fatty acids attached to a glycerol molecule can vary in length and type / orientation of bonds.

Figure 2.11 Products of a triglyceride through a dehydration synthesis. The shaded regions maintain the same colors as found in Figure 2.10. t

Saturated, Unsaturated and Trans Fats Fatty acids can be classified by the types of bonds they contain. Fatty acids with single bonds between each carbon are considered saturated fatty acids. Fatty acids with at least one double or triple bond between carbons are considered an unsaturated fatty acid or partially hydrogenated due to having fewer hydrogens than saturated fats. In general, single bonds are less reactive than double bonds and double bonds are less reactive than triple bonds. The result of this is that saturated fats are more stable and don’t break down as easily as unsaturated fats. As double and triple bonds are added to molecules, rotation of the molecule becomes restricted and allows for less movement (compared to what is seen with single bonds). With limited rotation, hydrogen and functional groups can be added on the same side (cis) or opposite sides (trans) of double bonds. Since the Carbon - Hydrogen bonds are polar covalent due to the difference in electronegativity, this creates a slight positive charge near the hydrogens. The resulting intramolecular forces are greater in cis unsaturated fats as opposed to trans unsaturated fats. The result is that trans fats are harder to break apart.

Figure 2.12 - Types of Fatty Acids

Other uses of Lipids Phospholipids Much like wax on a car causes water to bead up on a car’s surface and how oils and water separate, lipids make an excellent moisture barrier. Phospholipids are structurally similar to triglycerides but in place of the third fatty acid, a phosphate group is present. The hydrocarbon tails of the fatty acids are still hydrophobic, but the phosphate group end of the molecule is water-soluble and hydrophilic. This means that phospholipids are soluble in both water and oil. Cell membranes are made mostly of phospholipids arranged in a double layer with the tails from both layers “inside” and the heads facing “out” (toward the watery environment) on both surfaces.

Proteins Of all the macromolecules, proteins have some of the most diverse functions in biology. Some uses are for skin pigment, carrying oxygen, assisting in the transport of materials in and out of cells and in assisting cells themselves move. Proteins are macromolecules of monomers called amino acids. Amino Acids are composed of a central carbon covalently bonded to hydrogen, a carboxylic acid, -(COOH) and its namesake, an amino group (-NH2). Amino acids share a word origin with that of ammonia, which has a similar chemical structure -NH3. Ammonia was named by the chemist Torbern Bergman when he obtained salts of ammonium chloride near a temple to Ammon in Libya. The salts were obtained "from the sands where the camels waited while their masters prayed for good omens." These sands smelled of ammonia which resulted from the bacterial breakdown of camel urea. The name for the smell became associated with the temple.

Amino acids share a word origin with that of ammonia, which has a similar chemical structure -NH3. Ammonia was named by the chemist Torbern Bergman when he obtained salts of ammonium chloride near a temple to Ammon in Libya. The salts were obtained "from the sands where the camels waited while their masters prayed for good omens." These sands smelled of ammonia which resulted from the bacterial breakdown of camel urea. The name for the smell became associated with the temple. Amino acids vary based on the R group attached to the central carbon. R-groups stand for side chains that vary in size and complexity. These R-groups can be polar, non-polar, charged or uncharged. The sheer variety of amino acid monomers coupled with their different chemical properties allows for a great deal of variety in the proteins that can be produced.

Like carbohydrates and lipids, amino acids form macromolecules through dehydration synthesis. Since each monomer has different chemical properties, this causes proteins to fold into a variety of shapes. The primary structure of a protein is determined by the sequence of amino acids joined together much like beads on a string.

The secondary structure of a protein is a product of the R group side chains. Some R groups form attractions through Van der Waals forces and hydrogen bonding. These minute pushes and pulls between amino acids affect the structure of the protein.

Secondary structures can result in the subunit shapes of  helical (or α-helix)  plated sheets (or β sheets)  random coils (usually the result of denaturation)

As a peptide sequence further folds and gains three-dimensional characteristics, the overall shape of a peptide sequence is called the tertiary structure of a protein. Finally, proteins are sometimes arranged with more than one peptide strand. The interaction between multiple secondary and tertiary structures is the quaternary structure of a protein. An example of this is the globular proteins (like hemoglobin) are the result of interactions between α-helices and pleated β sheets.

Since the structure and shape of a protein determine the function it performs, maintaining the structure is important. The Van der Waals forces and hydrogen bonding that causes protein folding are weaker attractions than covalent and hydrogen bonds - due to this, chemical factors can affect the bonding. Some factors that can change the shape (and in doing so change the function) are changes in pH and changes in temperature. The process by which proteins and nucleic acids change their shape is called denaturation. A common example of denaturation is in cooking an egg. In this process, the egg white protein albumin changes shape as the solvent it is in evaporates and the attractive forces between amino acids weaken. If egg whites were exposed to a strong base, a similar denaturation would be seen also causing the (now inedible) egg white to turn white.

ENZYMES One special class of proteins are enzymes. Enzymes act to catalyze, or speed up chemical reactions in organisms. Enzymes do this by lowering the activation energy required for specific reactions and do so without actually taking part in the reaction; the enzyme remains unchanged before and after the reaction. Enzymes are very selective. A single enzyme may catalyze only one specific reaction or a series of closely related reactions. Lactase, for example, breaks down the disaccharide lactose into the monosaccharides galactose and glucose. The suffix -ase generally identifies enzymes. The first explanation of enzyme action was developed in 1894 by organic chemist Emil Fischer. This mechanism called the lock and key model, describes that enzymes act at specific substrates - a place in a molecule where a reaction takes place. In this model, a substrate enters a rigid enzyme’s “active site” and the substrate is modified upon leaving. In 1958, a modification to the lock and key method was suggested, called the “induced fit” model. In the induced fit hypothesis, the enzyme may change shape and distort bonds making it more likely to break or induce a change of charge also making substrates more likely to break apart. Many enzymes also require the presence of a non-protein molecule in order to be involved in a reaction. These molecules are called co-factors. Two classes of cofactors include metal ions (Zn , Fe ) and organic groups ( nicotine, adenine, dinucleotide, phosphate, thiamine). 2+

2+

Enzymes, like other proteins, are also sensitive to changes in pH and temperature. Most enzymes have an optimal temperature and pH around that of the human body (pH of 7.2, temperature of 98.6 F or 37 C). As temperatures and pH go beyond the optimal range, the tertiary and quaternary structure of the enzyme begins to break apart and enzymes lose their ability to catalyze their specific reaction. o

o

Nucleic Acids Nucleic acids are molecules that store genetic information for living organisms and assist in making proteins. Nucleic Acids contain phosphorus, nitrogen, carbon, hydrogen, and oxygen and are found in the body as DNA or RNA. Nucleic acids are composed of monomers called nucleotides. Each nucleotide is made of three distinct parts:  A five-carbon sugar (deoxyribose or ribose)  A phosphate group (-PO )  A nitrogenous base (adenine, thymine, guanine, cytosine or uracil) 4

NITROGENOUS BASE Like our other organic macromolecules, nucleic acids are formed when their monomers, the nucleotides, are joined together. Instead of dehydration synthesis, nucleotides connect by making linkages called phosphodiester bonds between the sugar and phosphates of neighboring nucleotides.

DNA and RNA differ in the following respects:  DNA is whereas RNA is single-stranded* (in most cases)  DNA’s sugar is deoxyribose, RNA’s sugar is ribose  DNA utilizes the nitrogenous bases of adenine, thymine, guanine and cytosine while RNA has the bases adenine, uracil, guanine and cytosine ATP Like nucleic acids, adenine triphosphate (ATP) is a nucleotide. ATP consists of the sugar ribose, the nitrogenous base adenine and three phosphates. ATP serves many roles in biological systems but is best known as the energy currency for cells.

Organic Reactions and Chirality Many compounds, specifically those associated with biology, are considered to be chiral. Chiral compounds are molecules with the same ratios of atoms but arranged as mirror images of each other. Chirality, discovered by Louis Pasteur, comes from the Greek word meaning ‘handedness.‘ Hands are a very good example for understanding the three dimensionality of chirality. While two hands, palms down are mirror images, they are non-superimposable and therefore asymmetric. No matter how you orient the right hand, it will never be arranged the same way as your left. If both thumbs are pointing to the right, you see one palm and the back of the other hand. In a similar way, three-dimensional chemical structures can also be arranged as chiral mirror images. Just as a right hand cannot shake hands in the normal way with a left hand, chemical reactions with enzymes designed for a ‘right-handed’ version of a compound cannot interact the same way with the ‘left-handed’ version of a compound. These different arrangements of molecules are called enantiomers. In fact, the right-handed (R-enantiomer) and left-handed (S enantiomer the Latin word for left is sinister) versions of compounds can have very different reactions. For example, often only one enantiomer of a pharmaceutical drug is responsible for the desired effects, while the other enantiomer can be inactive, less active, or sometimes cause undesired effects.

S-Aspartame (C H N O ) is an artificial sweetening agent that is more than one hundred times sweeter than sucrose. And yet, the R-aspertame enantiomer of the molecule tastes bitter. 14

18

2

5

In the late 1950s, thalidomide (C H N O ,), an anti-nausea drug, began production and sometimes was prescribed to pregnant women in Europe exhibiting morning sickness. While the R version of thalidomide acted as a sedative, the S version of thalidomide acted as a teratogen (a drug that is harmful to a fetus) and caused fetuses to develop with hands or feet directly attached to the torso. An individual employee of the United States Federal Drug Administration (FDA) named Frances Oldham Kelsey is attributed to refusing thalidomides approval due to concerns surrounding the lack of data on the drug’s application. (See more FDA.gov) 13

10

2

4

Organic Macromolecules in Diet Carbohydrates, proteins and lipids are used in the body as energy sources of energy. One chemical measurement of measuring energy within a substance is the calorie. A calorie, (note the lowercase) is the amount of energy required to raise 1 milliliter of water by 1 degree Celsius. Foods often measure the Calorie (again, the case is important) the amount of energy required to raise 1 liter of water 1 degree Celsius. By chemists, the Calorie is more commonly known as the kilocalorie.

Carbohydrates (as it will be discussed in chapter 4.4) are used as a quick energy source. Nutritionists recommend that 45-65% of a daily diet is composed of carbohydrates. Per gram consumed, carbohydrates contain an average of 4 Calories of energy.l Of the 22 amino acids, only 13 can be synthesized within the body. The other nine need to be consumed as part of the diet and are considered ‘essential’ amino acids. On average, proteins contain roughly 4 Calories of energy per gram consumed. Based on a recommended diet of 2,000 Calories per day, it is recommended that women consume 46g of protein per day and men consume 52 grams per day.

Lipids are useful as long term stores of energy. Per gram consumed, lipids contain roughly 9 calories. Since they are less reactive, saturated hydrocarbons accumulate more than nonsaturated hydrocarbons. Saturated hydrocarbons are associated with health risks including arterial plaques which can cause atherosclerosis, a hardening of the arteries which can lead to heart attacks and strokes....