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55 Cards in this Set
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Matter
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Organisms are composed of matter, which is defined as anything
that takes up space and has mass.* Matter exists in many diverse forms. Rocks, metals, oils, gases, and humans are just a few examples of what seems an endless assortment of matter. |
*Sometimes we substitute the term weight for mass, although the two are not identical. Mass is the amount of matter in an object, whereas the weight of an object is how strongly that mass is pulled by gravity. The weight of an astronaut walking on the moon is approximately 1/6 the astronaut’s weight on Earth, but his or her mass is the same. However, as long as we are earthbound, the weight of an object is a measure of its mass; in everyday language, therefore,
we tend to use the terms interchangeably. |
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Element
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An element is a substance that
cannot be broken down to other substances by chemical reactions. Today, chemists recognize 92 elements occurring in nature; gold, copper, carbon, and oxygen are examples. Each element has a symbol, usually the first letter or two of its name |
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Compound
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A compound is a substance consisting of two or more different
elements combined in a fixed ratio. Table salt, for example, is sodium chloride (NaCl), a compound composed of the elements sodium (Na) and chlorine (Cl) in a 1:1 ratio. Pure sodium is a metal, and pure chlorine is a poisonous gas. When chemically combined, however, sodium and chlorine form an edible compound. Water (H2O), another compound, consists of the elements hydrogen (H) and oxygen (O) in a 2:1 ratio. These are simple examples of organized matter having emergent properties: A compound has characteristics different from those of its elements (Figure 2.3). |
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Essential Elements
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Of the 92 natural elements, about 20–25% are essential
elements that an organism needs to live a healthy life and reproduce. The essential elements are similar among organisms, but there is some variation—for example, humans need 25 elements, but plants need only 17. Just four elements—oxygen (O), carbon (C), hydrogen (H), and nitrogen (N)—make up 96% of living matter. Calcium (Ca), phosphorus (P), potassium (K), sulfur (S), and a few other elements account for most of the remaining 4% of an organism’s mass. |
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Trace Elements
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Trace elements are required by an organism in
only minute quantities. Some trace elements, such as iron (Fe), are needed by all forms of life; others are required only by certain species. For example, in vertebrates (animals with backbones), the element iodine (I) is an essential ingredient of a hormone produced by the thyroid gland. A daily intake of only 0.15 milligram (mg) of iodine is adequate for normal activity of the human thyroid. An iodine deficiency in the diet causes the thyroid gland to grow to abnormal size, a condition called goiter. Where it is available, eating seafood or iodized salt reduces the incidence of goiter. All the elements needed by the human body are listed in Table 2.1. |
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Mass of Proton and Neutron
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The neutron and proton are almost identical in mass, each
about 1.7 10^-24 gram (g) |
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Dalton
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Thus, for atoms and subatomic particles (and for
molecules, too), we use a unit of measurement called the dalton, in honor of John Dalton, the British scientist who helped develop atomic theory around 1800. (The dalton is the same as the atomic mass unit, or amu, a unit you may have encountered elsewhere.) Neutrons and protons have masses close to 1 dalton. Because the mass of an electron is only about 1/2,000 that of a neutron or proton, we can ignore electrons when computing the total mass of an atom. |
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Atomic Number
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Atoms of the various elements differ in their number of subatomic
particles. All atoms of a particular element have the same number of protons in their nuclei. This number of protons, which is unique to that element, is called the atomic number and is written as a subscript to the left of the symbol for the element. The abbreviation 2He, for example, tells us that an atom of the element helium has 2 protons in its nucleus. Unless otherwise indicated, an atom is neutral in electrical charge, which means that its protons must be balanced by an equal number of electrons. Therefore, the atomic number tells us the number of protons and also the number of electrons in an electrically neutral atom. |
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Energy & Potential Energy
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An atom’s electrons vary in the amount of energy they
possess. Energy is defined as the capacity to cause change— for instance, by doing work. Potential energy is the energy that matter possesses because of its location or structure. For example, water in a reservoir on a hill has potential energy because of its altitude. When the gates of the reservoir’s dam are opened and the water runs downhill, the energy can be used to do work, such as turning generators. Because energy has been expended, the water has less energy at the bottom of the hill than it did in the reservoir. Matter has a natural tendency to move to the lowest possible state of potential energy; in this example, the water runs downhill. To restore the potential energy of a reservoir, work must be done to elevate the water against gravity. |
The electrons of an atom have potential energy because of
how they are arranged in relation to the nucleus. The negatively charged electrons are attracted to the positively charged nucleus. It takes work to move a given electron farther away from the nucleus, so the more distant an electron is from the nucleus, the greater its potential energy. Unlike the continuous flow of water downhill, changes in the potential energy of electrons can occur only in steps of fixed amounts. An electron having a certain amount of energy is something like a ball on a staircase (Figure 2.8a). The ball can have different amounts of potential energy, depending on which step it is on, but it cannot spend much time between the steps. Similarly, an electron’s potential energy is determined by its energy level. An electron cannot exist between energy levels. |
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Inert (elements)
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At the far right of the periodic table are helium,
neon, and argon, the only three elements shown in Figure 2.9 that have full valence shells. These elements are said to be inert, meaning chemically unreactive. All the other atoms in Figure 2.9 are chemically reactive because they have incomplete valence shells. |
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Orbital
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atom. In reality, we can never know the exact location of
an electron. What we can do instead is describe the space in which an electron spends most of its time. The threedimensional space where an electron is found 90% of the time is called an orbital. |
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Covalent Bond:
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A covalent bond is the sharing of a pair of valence electrons
by two atoms. |
Two or more atoms held together
by covalent bonds constitute a molecule, in this case a hydrogen molecule. |
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Molecule:
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Two or more atoms held together
by covalent bonds constitute a molecule, in this case a hydrogen molecule. |
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Pure elements Vs. Compounds:
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The molecules H2 and O2 are pure elements rather than
compounds because a compound is a combination of two or more DIFFERENT elements. Water, with the molecular formula H2O, is a compound. |
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Nonpolar Covalent Bond:
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In a covalent bond between two atoms of the same element, the electrons are shared equally because the two atoms have the same electronegativity—the tug-of-war is at a standoff. Such a bond is called a nonpolar covalent bond. For example, the single bond of H2 is nonpolar,
as is the double bond of O2. |
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Polar Covalent Bond
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When one atom is bonded to a more electronegative atom, the electrons of the bond are not shared equally. This type of bond is called a polar covalent bond. Such bonds vary in their polarity, depending on the relative electronegativity
of the two atoms. For example, the bonds between the oxygen and hydrogen atoms of a water molecule are quite polar (Figure 2.13). |
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There are No Salt Molecules!
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A molecule is a compound that is covalently bonded. It's technically incorrect to refer to sodium chloride, which has ionic bonds, as a molecule, but lots of chemists do it anyway. It's kind of like using the wrong fork at a formal dinner. Some people may notice, but most don't notice or don't care. But just so you know, the correct term for ionic compounds is Formula Unit.
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Electronegativity
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Atoms in a molecule attract shared electrons to varying degrees,
depending on the element. The attraction of a particular atom for the electrons of a covalent bond is called its electronegativity. The more electronegative an atom is, the more strongly it pulls shared electrons toward itself. In a covalent bond between two atoms of the same element, the electrons are shared equally because the two atoms have the same electronegativity—the tug-of-war is at a standoff. |
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Hydrogen Bond
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Among the various kinds of weak chemical bonds, hydrogen
bonds are so important in the chemistry of life that they deserve special attention. The partial positive charge on a hydrogen atom that is covalently bonded to an electronegative atom allows the hydrogen to be attracted to a different electronegative atom nearby. This noncovalent attraction between a hydrogen and an electronegative atom is called a hydrogen bond. In living cells, the electronegative partners are usually oxygen or nitrogen atoms. Refer to Figure 2.16 to examine the simple case of hydrogen bonding between water (H2O) and ammonia (NH3). |
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Chemical Reactions
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The making and breaking of chemical bonds, leading to
changes in the composition of matter, are called chemical reactions |
An example is the reaction between hydrogen
and oxygen molecules that forms water. The coefficients indicate the number of molecules involved; for example, the coefficient 2 in front of the H2 means that the reaction starts with two 'molecules' of hydrogen. Notice that all atoms of the reactants must be accounted for in the products. Matter is conserved in a chemical reaction: Reactions cannot create or destroy matter but can only rearrange it. |
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Chemical Equilibrium
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One of the factors affecting the rate of a reaction is the
concentration of reactants. The greater the concentration of reactant molecules, the more frequently they collide with one another and have an opportunity to react and form products. The same holds true for products. As products accumulate, collisions resulting in the reverse reaction become more frequent. Eventually, the forward and reverse reactions occur at the same rate, and the relative concentrations of products and reactants stop changing. The point at which the reactions offset one another exactly is called chemical equilibrium. |
This is a dynamic equilibrium; reactions are
still going on, but with no net effect on the concentrations of reactants and products. Equilibrium does not mean that the reactants and products are equal in concentration, but only that their concentrations have stabilized at a particular ratio. The reaction involving ammonia reaches equilibrium when ammonia decomposes as rapidly as it forms. In some chemical reactions, the equilibrium point may lie so far to the right that these reactions go essentially to completion; that is, virtually all the reactants are converted to products. |
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What are Functional Groups?
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Different chemical groups
contribute to function by affecting the molecule’s shape. In other cases, the chemical groups affect molecular function by being directly involved in chemical reactions; these important chemical groups are known as functional groups. Each functional group participates in chemical reactions in a characteristic way from one organic molecule to another. (chapter review gives: Chemical groups attached to the carbon skeletons of organic molecules participate in chemical reactions (functional groups) or contribute to function by affecting molecular shape). |
Yahoo best answers has a similar definition:
Such a huge number of organic compounds requires organization. They are sorted into organic families defined by functional groups. Functional groups are small structural units within molecules at which most of the compound's chemical reactions occur. |
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Referencing Functional Groups. What are the seven chemical groups most important in biological processes?
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The seven chemical groups most important in biological
processes are the hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups. The first six groups can act as functional groups; they are also hydrophilic and thus increase the solubility of organic compounds in water. The methyl group is not reactive, but instead often serves as a recognizable tag on biological molecules. |
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About Hydroxyl:
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In a hydroxyl group (¬OH), a
hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH-) |
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About Carbonyl:
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The carbonyl group ( > CO) consists
of a carbon atom joined to an oxygen atom by a double bond. |
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About Carboxyl:
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When an oxygen atom is doublebonded to a carbon atom that is also bonded to an ¬OH group, the entire assembly of atoms is called a carboxyl
group (¬¬¬COOH). |
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About Amino:
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The amino group (¬NH2)
consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. |
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About Sulfhydryl:
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The sulfhydryl group (¬¬¬SH)
consists of a sulfur atom bonded to an atom of hydrogen; it resembles a hydroxyl group in shape. |
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About Phosphate:
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In the phosphate group shown here, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges (¬OPO3 ^2-). In this text, P represents an attached phosphate group.
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About Methyl:
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A methyl group (¬CH3)
consists of a carbon bonded to three hydrogen atoms. The carbon of a methyl group may be attached to a carbon or to a different atom. |
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What is an Isomer?
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Variation in the architecture of organic molecules can be seen
in isomers, compounds that have the same numbers of atoms of the same elements but different structures and hence different properties. |
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What are the three types of Isomers?
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Three types of isomers are
structural isomers, cis-trans isomers, and enantiomers. |
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What are Structural Isomers?
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Structural isomers differ in the covalent arrangements
of their atoms. Compare, for example, the two five-carbon compounds in Figure 4.7a. Both have the molecular formula C5H12, but they differ in the covalent arrangement of their carbon skeletons. The skeleton is straight in one compound but branched in the other. The number of possible isomers increases tremendously as carbon skeletons increase in size. There are only three forms of C5H12 (two of which are shown in Figure 4.7a), but there are 18 variations of C8H18 and 366,319 possible structural isomers of C20H42. Structural isomers may also differ in the location of double bonds. |
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What are Cis-Trans Isomers?
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In cis-trans isomers (formerly called geometric isomers),
carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds. Single bonds allow the atoms they join to rotate freely about the bond axis without changing the compound. In contrast, double bonds do not permit such rotation. If a double bond joins two carbon atoms, and each C also has two different atoms (or groups of atoms) attached to it, then two distinct cis-trans isomers are possible. Consider a simple molecule with two double-bonded carbons, each of which has an H and an X attached to it (Figure 4.7b). The arrangement with both Xs on the same side of the double bond is called a cis isomer, and that with the Xs on opposite sides is called a trans isomer. The subtle difference in shape between such isomers can dramatically affect the biological activities of organic molecules. For example, the biochemistry of vision involves a light-induced change of retinal, a chemical compound in the eye, from the cis isomer to the trans isomer (see Figure 50.17). Another example involves trans fats, which are discussed in chapter 5. |
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What are Enantiomers?
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Enantiomers are isomers that are mirror images of each
other and that differ in shape due to the presence of an asymmetric carbon, one that is attached to four different atoms or groups of atoms. (See the middle carbon in the ball-and-stick models shown in Figure 4.7c.) The four groups can be arranged in space around the asymmetric carbon in two different ways that are mirror images. Enantiomers are, in a way, left-handed and right-handed versions of the molecule. Just as your right hand won’t fit into a left-handed glove, a “right-handed” molecule won’t fit into the same space as the “left-handed” version. Usually, only one isomer is biologically active because only that form can bind to specific molecules in an organism. The concept of enantiomers is important in the pharmaceutical industry because the two enantiomers of a drug may not be equally effective, as is the case for both ibuprofen and the asthma medication albuterol (Figure 4.8). Methamphetamine also occurs in two enantiomers that have very different effects. One enantiomer is the highly addictive stimulant drug known as “crank,” sold illegally in the street drug trade. The other has a much weaker effect and is even found as an ingredient in an over-the-counter vapor inhaler for treatment of nasal congestion! The differing effects of enantiomers in the body demonstrate that organisms are sensitive to even the most subtle variations in molecular architecture. Once again, we see that molecules have emergent properties that depend on the specific arrangement of their atoms. |
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What are Macromolecules?
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Given the rich complexity of life on Earth, we might expect
organisms to have an enormous diversity of molecules. Remarkably, however, the critically important large molecules of all living things—from bacteria to elephants—fall into just four main classes: carbohydrates, lipids, proteins, and nucleic acids. On the molecular scale, members of three of these classes—carbohydrates, proteins, and nucleic acids—are huge and are therefore called Macromolecules. For example, a protein may consist of thousands of atoms that form a molecular colossus with a mass well over 100,000 daltons. Considering the size and complexity of macromolecules, it is noteworthy that biochemists have determined the detailed structure of so many of them. |
Dalton: a unit used in expressing the molecular weight of proteins, equivalent to atomic mass unit.
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Polymers & Monomers
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The macromolecules in three of the four classes of life’s organic
compounds—carbohydrates, proteins, and nucleic acids—are chain-like molecules called polymers (from the Greek polys, many, and meros, part). A polymer is a long molecule consisting of many similar or identical building blocks linked by covalent bonds, much as a train consists of a chain of cars. The repeating units that serve as the building blocks of a polymer are smaller molecules called monomers (from the Greek monos, single). Some of the molecules that serve as monomers also have other functions of their own. |
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What are enzymes?
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Specialized macromolecules that speed up chemical reactions.
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What is a Dehydration Reaction?
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Although each class of polymer is made up of a different type
of monomer, the chemical mechanisms by which cells make and break down polymers are basically the same in all cases. In cells, these processes are facilitated by enzymes, specialized macromolecules that speed up chemical reactions. Monomers are connected by a reaction in which two molecules are covalently bonded to each other, with the loss of a water molecule; this is known as a dehydration reaction (Figure 5.2a). When a bond forms between two monomers, each monomer contributes part of the water molecule that is released during the reaction: One monomer provides a hydroxyl group (—OH), while the other provides a hydrogen (—H). This reaction is repeated as monomers are added to the chain one by one, making a polymer. |
Wikipedia Defines it as:
In chemistry and the biological sciences, a dehydration reaction is usually defined as a chemical reaction that involves the loss of a water molecule from the reacting molecule. |
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What is Hydrolysis?
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Polymers are disassembled to monomers by hydrolysis, a
process that is essentially the reverse of the dehydration reaction (Figure 5.2b). Hydrolysis means to break using water (from the Greek hydro, water, and lysis, break). The bond between the monomers is broken by the addition of a water molecule, with the hydrogen from the water attaching to one monomer and the hydroxyl group attaching to the adjacent monomer. An example of hydrolysis working within our bodies is the process of digestion. The bulk of the organic material in our food is in the form of polymers that are much too large to enter our cells. Within the digestive tract, various enzymes attack the polymers, speeding up hydrolysis. The released monomers are then absorbed into the bloodstream for distribution to all body cells. Those cells can then use dehydration reactions to assemble the monomers into new, different polymers that can perform specific functions required by the cell. |
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What is an Asymmetric Carbon?
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An asymmetric carbon is a carbon attached to four
different atoms or groups of atoms. Glucose and galactose, for example, differ only in the placement of parts around one asymmetric carbon (see the purple boxes in Figure 5.3). What seems like a small difference is significant enough to give the two sugars distinctive shapes and behaviors. |
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Most names of sugars end in?
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ose
Ie. Fructose, sucrose, galactose, etc. |
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What does the Greek word Monos stand for?
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Single
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What does the Greek word Sacchar stand for?
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Sugar
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What is a Monosaccharide?
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Monosaccharides (from the Greek monos, single, and
sacchar, sugar) generally have molecular formulas that are some multiple of the unit CH2O. Glucose (C6H12O6), the most common monosaccharide, is of central importance in the chemistry of life. |
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What does the prefix di- stand for?
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two
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Disaccharide & Glycosidic Linkage
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A disaccharide consists of two monosaccharides joined
by a glycosidic linkage, a covalent bond formed between two monosaccharides by a dehydration reaction. For example, maltose is a disaccharide formed by the linking of two molecules of glucose (Figure 5.5a). Also known as malt sugar, maltose is an ingredient used in brewing beer. The most prevalent disaccharide is sucrose, which is table sugar. Its two monomers are glucose and fructose (Figure 5.5b). Plants generally transport carbohydrates from leaves to roots and other nonphotosynthetic organs in the form of sucrose. Lactose, the sugar present in milk, is another disaccharide, in this case a glucose molecule joined to a galactose molecule. |
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What does Poly stand for?
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Many
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Polysaccharide
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Polysaccharides are macromolecules, polymers with a few
hundred to a few thousand monosaccharides joined by glycosidic linkages. Some polysaccharides serve as storage material, hydrolyzed as needed to provide sugar for cells. Other polysaccharides serve as building material for structures that protect the cell or the whole organism. The architecture and function of a polysaccharide are determined by its sugar monomers and by the positions of its glycosidic linkages. |
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Starch
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Plants store starch, a polymer of
glucose monomers, as granules within cellular structures known as plastids, which include chloroplasts. Synthesizing starch enables the plant to stockpile surplus glucose. Because glucose is a major cellular fuel, starch represents stored energy. The sugar can later be withdrawn from this carbohydrate “bank” by hydrolysis, which breaks the bonds between the glucose monomers. Most animals, including humans, also have enzymes that can hydrolyze plant starch, making glucose available as a nutrient for cells. Potato tubers and grains—the fruits of wheat, maize (corn), rice, and other grasses—are the major sources of starch in the human diet. |
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Glycogen
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Animals store a polysaccharide called glycogen, a polymer
of glucose that is like amylopectin but more extensively branched (Figure 5.6b). Humans and other vertebrates store glycogen mainly in liver and muscle cells. Hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases. This stored fuel cannot sustain an animal for long, however. In humans, for example, glycogen stores are depleted in about a day unless they are replenished by consumption of food. This is an issue of concern in low-carbohydrate diets. |
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Cellulose
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the polysaccharide called cellulose is a major component of the tough walls that enclose plant cells.
On a global scale, plants produce almost 1014 kg (100 billion tons) of cellulose per year; it is the most abundant organic compound on Earth. Like starch, cellulose is a polymer of glucose, but the glycosidic linkages in these two polymers differ. |
An example of Cellulose is Insoluble Fiber.
Enzymes that digest starch by hydrolyzing its α linkages are unable to hydrolyze the β linkages of cellulose because of the distinctly different shapes of these two molecules. In fact, few organisms possess enzymes that can digest cellulose. Animals, including humans, do not; the cellulose in our food passes through the digestive tract and is eliminated with the feces. Along the way, the cellulose abrades the wall of the digestive tract and stimulates the lining to secrete mucus, which aids in the smooth passage of food through the tract. Thus, although cellulose is not a nutrient for humans, it is an important part of a healthful diet. Most fresh fruits, vegetables, and whole grains are rich in cellulose. On food packages, “insoluble fiber” refers mainly to cellulose. Some microorganisms can digest cellulose, breaking it down into glucose monomers. A cow harbors cellulosedigesting prokaryotes and protists in its stomach. These microbes hydrolyze the cellulose of hay and grass and convert the glucose to other compounds that nourish the cow. Similarly, a termite, which is unable to digest cellulose by itself, has prokaryotes or protists living in its gut that can make a meal of wood. Some fungi can also digest cellulose, thereby helping recycle chemical elements within Earth’s ecosystems. |
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Chitin
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Another important structural polysaccharide is chitin,
the carbohydrate used by arthropods (insects, spiders, crustaceans, and related animals) to build their exoskeletons (Figure 5.9). An exoskeleton is a hard case that surrounds the soft parts of an animal. Pure chitin is leathery and flexible, but it becomes hardened when encrusted with calcium carbonate, a salt. Chitin is also found in many fungi, which use this polysaccharide rather than cellulose as the building material for their cell walls. Chitin is similar to cellulose, with β linkages, except that the glucose monomer of chitin has a nitrogen-containing appendage (see Figure 5.9, top right). |
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Lipids
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Lipids are the one class of large biological molecules that
does not include true polymers, and they are generally not big enough to be considered macromolecules. The compounds called lipids are grouped together because they share one important trait: They mix poorly, if at all, with water. The hydrophobic behavior of lipids is based on their molecular structure. Although they may have some polar bonds associated with oxygen, lipids consist mostly of hydrocarbon regions. Lipids are varied in form and function. They include waxes and certain pigments, but we will focus on the most biologically important types of lipids: fats, phospholipids, and steroids. |
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Fat & Fatty Acid
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Although fats are not polymers, they are large molecules assembled
from smaller molecules by dehydration reactions. A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids (Figure 5.10a). Glycerol is an alcohol; each of its three carbons bears a hydroxyl group. A fatty acid has a long carbon skeleton, usually 16 or 18 carbon atoms in length. The carbon at one end of the skeleton is part of a carboxyl group, the functional group that gives these molecules the name fatty acid. The rest of the skeleton consists of a hydrocarbon chain. The relatively nonpolar C¬H bonds in the hydrocarbon chains of fatty acids are the reason fats are hydrophobic. Fats separate from water because the water molecules hydrogenbond to one another and exclude the fats. This is the reason that vegetable oil (a liquid fat) separates from the aqueous vinegar solution in a bottle of salad dressing. |
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