Unit 2: BiochemistryBiochemistry can be translated as literally "the chemistry of life." Chemistry in the study of matter and its properties and so in many ways, biology can really be be thought of as a subset of chemistry. The fundamental unit of biology may be the cell, but cells could not exist without molecules which form from atoms, the fundamental unit of chemistry. In this unit we will study the basic characteristics of atoms and how they combine together through various types chemical bonds to form molecules. We will examine how polar form from certain chemical bonds and how polarity results in the various and unique properties of water We will define what it means to be organic and examine the four major types of organic macromolecules which serve as the building blocks for cells. And finally, we will take a look at enzymes, a special subclass of organic macromolecules that are particularly important to organisms in their ability to catalyze essential chemical reactions.
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Basic Chemistry
The Structure of Matter
Matter is anything that takes up space and has mass including stars, planets, trees, people even gases like oxygen. All of these material structures can be broken down into smaller parts; a person can be divided into organ systems, organ systems into individual organs, organs into tissues and tissues into cells. Cells may be the most basic unit of life, by they are by no means the most basic unit of matter. To find the smallest unit of matter, we have to think smaller. Atoms are the most basic unit of matter, meaning they are smallest structure that can retain its chemical properties. Ironically, atoms themselves are even smaller components- protons, neutrons and electrons. Protons are subatomic particles with a positive charge; neutrons have a neutral charge and electrons have a negative charge. In an individual atom, protons and neutrons are located in the nucleus, the small, dense region at the core of an atom. Electrons do not occupy the nucleus but instead orbit around the nucleus at high speeds (about 1% the speed of light) forming an electron cloud with a diameter many, many times larger than the nucleus. |
Atoms and Molecules; Elements and Compounds
As you already know, the most basic unit of matter is the atom because this is the smallest structure that can retain its chemical properties. But what exactly determines the chemical properties of an atom, what is it that makes each atom unique? It turns out that the answer to this question is protons- each type of atom has a different number of protons. For example, hydrogen atoms always have 1 proton, helium atoms always have two protons and carbon atoms always have 4 protons. Any substance that is composed of a single atom that cannot be broken down anymore is known as an element. This is the foundation of the periodic table of elements, which organizes elements according to a number of features including their atomic numbers and atomic mass. An element's atomic number always refers to the number of protons located in an atom of that element. As you can see in the periodic table of elements below, oxygen has an atomic number of 8. This means that all oxygen atoms have 8 protons in their nucleus. |
When atoms combine they form molecules: when two hydrogen atoms combine with an oxygen atom they form a single molecule of water (H2O). Just as atoms are the smallest unit of elements, molecules are the smallest units of compounds, substance composed of two or more elements chemically bound together. Water (H2O), carbon dioxide (the gas released from combustion and metabolic activities such as cellular respiration), glucose (a simple sugar produced through photosynthesis) and calcium carbonate (the substance shellfish and corals use to build sea shells) are examples of compounds. However, you should note that some molecules are in fact elements, so long as the molecule contains only a single type of atom. This is true of oxygen and nitrogen gas (O2 and N2 respectively) because it each contains only 1 atom type. In contrast to a compound, a mixture will also contain multiple types of atoms, but these atoms will not be chemically bound.
Atomic Mass
Each protons and neutron has a mass of 1 atomic mass unit (amu) and these two subatomic particles contribute to the atom's atomic mass. A helium atom consists of 1 proton and 1 neutron, giving it an atomic mass of 2 amu. You may notice that in the periodic table of elements, none of the listed elements have integer atomic masses, including helium. This is because the periodic table lists the weighted average atomic mass of all the known isotopes of each element. Electrons do have mass, but the value is so small it does not significantly contribute to the atomic mass and scientists generally consider electrons to have an atomic mass of 0. |
Isotopes and Ions
While all atoms of the same element must have identical numbers of protons, the same is not true for neutrons and electrons. Consider carbon, the so called backbone of living organisms. As an atom, carbon can have 6, 7 or 8 neutrons in its nucleus. These different forms of carbon are called isotopes; each isotope has a different number of neutrons. Carbon-12 is the most common isotope of carbon with Carbon-13 occurring in smaller amounts and Carbon-14 being the rarest isotope. While all three isotopes have the same chemical properties (they all have the same number of protons), each has a different atomic masses because of the varying numbers of neutrons. |
All carbon atoms have an atomic number of 6 and therefore 6 protons in their nucleus and we can use this information to calculate the number of neutrons in each of the isotopes. For example, Carbon-12 has an atomic mass of 12 amu (hence the name Carbon-12), so it has 6 neutrons, Carbon-13 has 7 neutrons and Carbon-14 has 8 neutrons.
Remember that protons have a positive charge (+1) and electrons have a negative charge (-1). In an atom, the number of protons and electrons is always equal which gives the atom an overall charge of 0. However, sometimes atoms can gain or lose electrons creating an imbalance. The atom no longer has an overall charge of 0 and is no longer considered an atom, instead it is an ion. Let's try another example with carbon. Again, carbon has an atomic number of 6 and therefore 6 protons. This means that a carbon atom must have 6 electrons; the 6 positive charges are canceled out by 6 negative charges resulting in a stable atom with no charge. But let's remove one electron from carbon; now there are 6 protons and 5 electrons. The carbon is now considered an ion and has a +1 charge to it. Ions with a positive charge are known as cations and ions with a negative charge are known as anions.
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Isomers
Some substances have the same chemical formula, but are in face unique molecules. At first glance, that might sound really weird, how could two substances with the same atoms be two different molecules? This is the idea of isomers, molecules with the same chemical formula, but different arrangements of their atoms. The example to the right depicts glucose and fructose, which have the same chemical formula (C6H12O6), but have their own unique structures. Most notably, glucose has a hexagon ring, while fructose has a pentagon ring. |
Intramolecular Bonding
Left on their own, most atoms are not stable. The electrons that orbit the nucleus of atoms and ions occupy specific shells or orbitals around the nucleus. To be stable, these orbitals must be filled. So in order to fill these orbitals and become stable, atoms with look to share or transfer electrons and thereby establish bonds with other atoms to form molecules. This type of bonding is called intramolecular bonding because it occurs within molecules and forms between atoms. In general there are two types of intramolecular bond: covalent bonds and ionic bonds. Covalent bonds occur when atoms share electrons, neither atom has complete sovereignty over the electrons involved in the bond. Water molecules themselves are formed by covalent bonds between the hydrogen atoms and the oxygen. |
Ionic bonds exist when 1 or more electrons are transferred from one atom to another. For example, sodium (Na) has a single valence electron, meaning it has only a single electron in its outer most orbital and a chlorine (Cl) atom has 7 valence electrons (the inner orbitals are already full). To fill their outer orbitals and become stable, both sodium and chlorine require a total of 8 valence electrons. This means the sodium atom require 7 more electrons to be stable...or it could donate away its one 1 valence electron, emptying the outer most orbital and achieve a more stable arrangement since the remaining inner electron orbitals are already full. This is exactly what happens when sodium and chlorine atoms meet; sodium donates its one valence electron to chlorine and both become stable and "happy." And because these two ions have opposite charge (Na+ and Cl-) they remain bound together as NaCl.
Polarity
Recall that in a covalent bond, electrons are shared between atoms, as is the case between hydrogen and oxygen in a water molecule. In a perfect world, these atoms would share their electrons equally, but chemistry is anything but a perfect world. Each atom/ion has a different electronegativity, a tendency to pull electrons closer to their nuclei. Think of this as a desire or thirst for electrons. Atoms/ions with higher electronegativities have more valence electrons because they are closer to having a complete orbital and becoming stable. So atoms/ions that have no valence electrons like helium, have very low electronegativities while atoms that have many valence electrons like chlorine have very high electronegativities.
Recall that in a covalent bond, electrons are shared between atoms, as is the case between hydrogen and oxygen in a water molecule. In a perfect world, these atoms would share their electrons equally, but chemistry is anything but a perfect world. Each atom/ion has a different electronegativity, a tendency to pull electrons closer to their nuclei. Think of this as a desire or thirst for electrons. Atoms/ions with higher electronegativities have more valence electrons because they are closer to having a complete orbital and becoming stable. So atoms/ions that have no valence electrons like helium, have very low electronegativities while atoms that have many valence electrons like chlorine have very high electronegativities.
Let's return to our example with water. When a covalent bond forms between oxygen and hydrogen the electrons are not shared evenly. This is because oxygen, with 6 valence electrons, has a higher electronegativity then hydrogen which only has 1 valence electron. This allows oxygen to pull harder on the shared electrons which tend to stay around the oxygen more often than the hydrogen. A simpler way to think about this is to say that oxygen is greedy and this greediness leads to polarity. Molecules that exhibit polarity have a separation of charges; one end of the molecule has a small positive charge and the other end has a small negative charge. In the water molecule, the "greedy" oxygen will have a small negative charge and the "weak" hydrogens will have a small positive charge. This is because the shared electrons of the covalent bonds tend to remain closer to the oxygen atom and electrons have a negative charge. The polarity of water makes it "sticky" meaning water molecules can stick to one another as well as other surfaces
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Intermolecular Bonds
Intermolecular bonds form between molecules. While there are a wide variety of intermolecular bonds in chemistry, we will be focusing only on 1 in particular, the hydrogen bond, a type of bond that forms between molecules that contain a hydrogen atom bound to a highly electronegative (greedy) atom including Nitrogen, Oxygen and Fluorine. Hydrogen bonding occurs between water molecules (H bound to O) making water "sticky". Hydrogen bonding exists because water is polar. As you already know, the oxygen in water has a slight negative charge and the hydrogens have slight positive charges. This means that the oxygen of one water molecule can attach to the hydrogen of a completely different water molecule, almost like an ionic bond, but much weaker. Hydrogen bonds are relatively weak compared to covalent and ionic bonds. Hydrogen bonds are generally only temporary, constantly breaking and reforming; they do not permanently bind molecules together. Despite this, hydrogen bonds have interesting effects on the molecules they hold together: the reason water has such a high boiling point is because of hydrogen bonding. Before the liquid water can be converted to gas, all hydrogen bonds must be broken and that requires energy/heat. |
The Properties of Water
Properties of Water
Water is one of the most important molecules for life; so far no known organism can survive in the absence of water. Even at a chemical level, water is very special- it has a number of unique properties, properties that have enabled life to flourish here on earth. Water owes many of these properties to its electrochemical structure. As you know, water is composed of three atoms: 1 atom of oxygen and 2 hydrogen atoms. These atoms are held together by covalent bonds, the atoms share electrons in order to become more stable. Earlier, we saw that oxygen is more electronegative than hydrogen resulting in a separation of charges within the molecule called polarity. Overall, water molecules have no charge, but different regions or poles with have small electrical charges. These poles have granted water a variety of different properties, outlined below.
Water is one of the most important molecules for life; so far no known organism can survive in the absence of water. Even at a chemical level, water is very special- it has a number of unique properties, properties that have enabled life to flourish here on earth. Water owes many of these properties to its electrochemical structure. As you know, water is composed of three atoms: 1 atom of oxygen and 2 hydrogen atoms. These atoms are held together by covalent bonds, the atoms share electrons in order to become more stable. Earlier, we saw that oxygen is more electronegative than hydrogen resulting in a separation of charges within the molecule called polarity. Overall, water molecules have no charge, but different regions or poles with have small electrical charges. These poles have granted water a variety of different properties, outlined below.
Cohesion: the ability of water molecules to stick to themselves. Cohesion exists as a direct extension of hydrogen bonding. Recall from earlier that because hydrogen and oxygen have differing electronegative, they have small charges. These small charges allow hydrogen bonds to form between water molecules causing them to stick together. You can observe cohesion in action when you observe a drop of water on a penny or the surface of water in a beaker. The water molecules stick to one another, allowing a bubble to form. The water molecules hold on to other and prevent themselves from spilling over (to a point obviously).
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Adhesion: the ability of water molecules to stick to other surfaces. Adhesion is very similar to cohesion, both exist as a consequence of hydrogen bonding. But unlike cohesion, where water molecules stick to each other, adhesion refers to when water molecules stick to other surfaces, not other water molecules. If you have ever looked out a window in the rain you have seen adhesion in action. The water droplets on the surface of the glass should fall to the ground as a result of gravity, but they don't. Instead, the water molecules adhere to the glass, allowing the water droplet to stay in place (again, to a point, if the droplet becomes to heavy the force of adhesion will be overcome and the droplet will fall to the ground).
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Capillary action: the tendency of water to move up a narrow space, with no assistance and against gravity. Capillary action exists as a combination of cohesion and adhesion. If you place a narrow, glass tube in a beaker of water, the water will move up the tube. This is because the water molecules adhere to the glass and are pulled up into the tube. But the water molecules are cohesive and stick together, forming a chain of water molecules that gets pulled up into the tube. The general rule of capillary is that the more narrow the opening/tube is, the farther the water will travel; this is extremely important for plants as it allows them to transport water to their leaves through vascular tissue as we will see later on.
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Surface Tension: the ability of water to resist a force applied to its surface. Surface tension exists largely as a consequence of cohesion and hydrogen bonding. Because the water molecules stick to each other, they do not give way to forces applied to them. Obviously, there is a limit to the strength of surface tension, if enough force is applied the water molecules will separate. This is why people cannot walk on water, we are simply to heavy. But surface tension allows us to float paper slips and leaves on water surfaces. In fact, small insects and spiders are even able to walk on the surface of ponds and other bodies of water.
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Heat Capacity: The amount of energy required to raise the temperature of water by 1 degree. Water has a very high heat capacity and therefore it takes a large amount of energy to raise its temperature. As mentioned earlier under "Intermolecular bonds", this is because water molecules are held together by hydrogen bonds. Although they are not as strong as covalent or ionic bonds, hydrogen bonds are strong enough to increase the amount of energy required to convert liquid water to gas. Water's high heat capacity is what causes areas located near large bodies of water to experience more moderate temperates. Because the temperature of water does not change quickly, the water moderates the temperature of the surrounding land surfaces.
For instance, imagine two cities in the summer, one on an island and one in land away from any major bodies of water. On the island, the land will heat up very quickly, but the surrounding ocean will warm up more slowly and keeps the island cooler. The land locked has no body of water to keep it cooler and so it becomes hotter than the island city. In the winter the opposite occurs and the city on the island will remain warmer than the landlocked one.
For instance, imagine two cities in the summer, one on an island and one in land away from any major bodies of water. On the island, the land will heat up very quickly, but the surrounding ocean will warm up more slowly and keeps the island cooler. The land locked has no body of water to keep it cooler and so it becomes hotter than the island city. In the winter the opposite occurs and the city on the island will remain warmer than the landlocked one.
Universal Solvent
Because of its chemistry, water serves as an excellent solvent, capable of dissolving a wide range of solutes. In fact, water is capable of dissolving more substances than any other liquid earning it the title "universal solvent." Don't be fooled though, this title is not literal, there are substances that do not dissolve in water. Recall again that water is polar; in general polar solvents are effective at dissolving other polar substance, but not non-polar substances which readily dissolve in non-polar solvents. In other words, like dissolves like. So while water can dissolve salts and to some degree sugars, non-polar substances like oil will not mix with water. |
Ice is Less Dense than Water
Unlike most other forms of matter, water actually expands when it freezes which means that ice is actually less dense than liquid water. That may sound mundane, but it is actually hugely important for living organisms. Consider a pond during the winter. As the temperature decreases, the water becomes colder and starts to freeze. If ice was more dense than water, the bottom of the lake would freeze over and the top portion would follow suit until the entire pond is frozen solid. All life in the pond would be destroyed. But, that's not what happens because ice floats in liquid water, meaning the top of the pond will freeze into solid ice while the bottom portion remains liquid. Because of its crystalline design, the ice actually traps heat, insulating the water below, keeping it warmer and allowing organisms to survive the winter. |
Xylem: Properties of Water in Action
Trees and other land plants face a major challenge. Like nearly most plants, trees undergo photosynthesis to convert water, carbon dioxide and sunlight into glucose which they use for food. Of course, photosynthesis occurs in the leaves which can be very high off the ground. When gathering carbon dioxide and sunlight, this really does not pose a problem as both of these resources can be readily accessed by the leaves. The challenge emerges with water, because water is taken up by the roots of the plant, underground. The question then becomes, how do trees able to get water to their leaves to form glucose? The answer is both stunningly simple and amazingly complex.
Trees and other land plants face a major challenge. Like nearly most plants, trees undergo photosynthesis to convert water, carbon dioxide and sunlight into glucose which they use for food. Of course, photosynthesis occurs in the leaves which can be very high off the ground. When gathering carbon dioxide and sunlight, this really does not pose a problem as both of these resources can be readily accessed by the leaves. The challenge emerges with water, because water is taken up by the roots of the plant, underground. The question then becomes, how do trees able to get water to their leaves to form glucose? The answer is both stunningly simple and amazingly complex.
Trees contain vascular tissue- networks of tiny tubes that transport resources around the organism like a primitive circulatory system. There are two major types of vascular tissue, xylem and phloem. Xylem conducts water water and minerals throughout the plant and phloem moves sugars and other carbohydrates. The xylem tissue is extremely narrow having a microscopic diameter. This promotes strong capillary action that moves water up through the plant against gravity. In other words, the tree has taken advantage of one of water's unique properties and used it to transport water to the leaves without exerting any energy.
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But trees and other vascular plants don't stop with just capillary action. As you know, water has a cohesive property that allows water molecules to stick together. Cohesion forms a chain of water molecules to from within the xylem tissue, running all the way from the leaves down to the roots. Water at the top of the chain in the leaves has two possible fates: it can be used for photosynthesis or it can be released through the stomata of the leaf during gas exchange, a process called transpiration. In either case, the water molecule at the top of the chain is removed. This generates a negative pressure like in a vacuum, and forces the entire chain of water molecules to be pulled up the plant. This negative pressure is extremely important to very tall trees that would be unable to move water via capillary action alone. The final force at play is known as water potential, which refers to the potential energy of the water itself. Water naturally moves from the high water potential in the ground to low the water potential in the atmosphere.
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One of the most dangerous issues tall, vascular plants can face is an embolism. An embolism is blockage in vascular tissue; for plants it is usually an air bubble. When plants develop an embolism in their xylem, the air bubble (or whatever the blockage is) breaks the water chain, preventing water from moving up the tree. Generally, once an embolism forms in a tree there is nothing the tree can do to fix it, so trees produce many, many xylem as a type of insurance. This way if one xylem forms an embolism there are still other xylem that can function and the tree can survive.
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Acid, Bases and pH
Acids, Bases and pH
Acids are molecules/ions that contribute H+ ions in solution including hydrochloric acid (HCl) and carbonic acid (H2CO3). Bases are substances that contribute OH- (hydroxide) ions in solution including sodium hydroxide (NaOH) and ammonia (NH3). Both acids and bases come in varying strengths and are corrosive- strong acids and/or bases can harm or kill organisms.
pH stands for "potential of hydrogen" and is used to measure the relative strength of acids and bases. The pH scale is ranges in value from 0 to 14. Substances with pH's below 7 are considered acidic, with a pH of 0 being the most acidic. Substance with pH's greater than 7 are considered basic with a pH of 14 being the most basic. Pure water has a pH of 7 is neutral, neither acidic or basic. The pH scale is logarithmic which means every time you move one integer value on the pH scale, the relative strength of the acid or base changes by a factor of 10. For example, an acid with a pH of 3 is 10x more acidic than a pH of 4. And the same acid with a pH of 3 is 10x less acidic than an acid with a pH of 2. The pH of a substance can be lowered by adding an acid or raised by adding a base.
Acids are molecules/ions that contribute H+ ions in solution including hydrochloric acid (HCl) and carbonic acid (H2CO3). Bases are substances that contribute OH- (hydroxide) ions in solution including sodium hydroxide (NaOH) and ammonia (NH3). Both acids and bases come in varying strengths and are corrosive- strong acids and/or bases can harm or kill organisms.
pH stands for "potential of hydrogen" and is used to measure the relative strength of acids and bases. The pH scale is ranges in value from 0 to 14. Substances with pH's below 7 are considered acidic, with a pH of 0 being the most acidic. Substance with pH's greater than 7 are considered basic with a pH of 14 being the most basic. Pure water has a pH of 7 is neutral, neither acidic or basic. The pH scale is logarithmic which means every time you move one integer value on the pH scale, the relative strength of the acid or base changes by a factor of 10. For example, an acid with a pH of 3 is 10x more acidic than a pH of 4. And the same acid with a pH of 3 is 10x less acidic than an acid with a pH of 2. The pH of a substance can be lowered by adding an acid or raised by adding a base.
Buffers
As you can imagine, acids and bases pose a problem for living organisms. The byproducts of many biological processes are acids and/or bases which can drastically shift the pH of the organism and cause a great deal of harm. Luckily the concept of neutralization provides a homeostatic defense mechanism for the organism to control its pH, buffers. A buffer is a solution that can resist pH change upon the addition of an acidic or basic components (remember, one of the characteristics of life is maintaining a stable internal environment- homeostasis). The buffer is able to neutralize small amounts of added acid or base, thus keeping the pH of the solution relatively stable. This is important for organisms and/or reactions which require specific and stable pH ranges. Buffer solutions have a working pH range and capacity which dictate how much acid/base can be neutralized before pH changes, and the amount by which it will change.
As you can imagine, acids and bases pose a problem for living organisms. The byproducts of many biological processes are acids and/or bases which can drastically shift the pH of the organism and cause a great deal of harm. Luckily the concept of neutralization provides a homeostatic defense mechanism for the organism to control its pH, buffers. A buffer is a solution that can resist pH change upon the addition of an acidic or basic components (remember, one of the characteristics of life is maintaining a stable internal environment- homeostasis). The buffer is able to neutralize small amounts of added acid or base, thus keeping the pH of the solution relatively stable. This is important for organisms and/or reactions which require specific and stable pH ranges. Buffer solutions have a working pH range and capacity which dictate how much acid/base can be neutralized before pH changes, and the amount by which it will change.
Buffers can be seen in many living things. For instance, your body uses the bicarbonate buffer system to prevent your blood's pH from shifting too much. As you perform various metabolic reactions, your body produces different acids and the presence of H+ in your blood stream increases, thereby lowering the pH of your blood. When the pH of your blood drops, your kidneys release bicarbonate (HCO3-) ion. The bicarbonate works as a buffer and combines with the excess H+ forming carbonic acid (H2CO3). That carbonic acid is then broken down into water and carbon dioxide, the latter of which can be exhaled. In other words, as you exhale carbon dioxide you actually help remove excess H+ from your blood, making your body less acidic and increasing the pH of your blood.
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Monomers, Polymers and Polymerization
The Backbone of Life
As far as elements go, carbon is unique. It can form up to 4 covalent bonds and can even bond with other carbon atoms, allowing it to form the literal backbone of organic molecules. These properties have earned carbon the nickname "the backbone of life." Organic molecules contain carbon and hydrogen atoms bound together, meaning that methane (CH4) is organic, but carbon dioxide (CO2) is inorganic. Carbon is one of the most common elements found in living things alongside hydrogen, oxygen, nitrogen, phosphorous and sulfur (CHONPS).
As far as elements go, carbon is unique. It can form up to 4 covalent bonds and can even bond with other carbon atoms, allowing it to form the literal backbone of organic molecules. These properties have earned carbon the nickname "the backbone of life." Organic molecules contain carbon and hydrogen atoms bound together, meaning that methane (CH4) is organic, but carbon dioxide (CO2) is inorganic. Carbon is one of the most common elements found in living things alongside hydrogen, oxygen, nitrogen, phosphorous and sulfur (CHONPS).
In biology there are four major classes of organic macromolecules: carbohydrates, lipids, nucleic acids and proteins. These macromolecules are also known as polymers because they are large molecules composed of many smaller units known as monomers. Monomers combine to form polymers through a process called polymerization.
Sometimes when monomers combine to form polymers a water molecule is released such as when monosaccharides combine to form polysaccharides. One of the sugar molecules (monosaccharide) will contribute a hydrogen atom, while the other contributes an alcohol group (OH). This generates water and binds the monomer units together. This process can be "undone" through hydrolysis in which water is added to a polymer chain, separating the monomers again.
Dehydration Synthesis |
Hydrolysis |
The Macromolecules
The macromolecules can be divided into 4 major groups: carbohydrates, lipids, nucleic acids and proteins. Each group contains a wide variety of different molecules, but within each group these molecules share similar uses in the body as well as similar structures and functions.
Carbohydrates
Carbohydrates are composed of carbon, hydrogen and oxygen atoms (hence the name Carbo-hydrates) usually in the ratio of 1:2:1. For example, glucose has the chemical formula (C6H12O6). Carbohydrates provide the primary source of energy for living things: they are formed by photosynthesis where solar energy is converted to chemical energy. in plants and other autotrophs. That energy is later released for use in cells when carbohydrates are broken down by cellular respiration. Carbohydrates can be classified as two different types: simple and complex carbohydrates.
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Carbohydrate Types
Simple carbohydrates are known as monosaccharides because they contain a single molecule of sugar. Monosaccharides are actually considered monomers, they are not polymers. Glucose and fructose are both examples of monosaccharides. Simple carbohydrates provide quick energy, while complex carbohydrates (polysaccharides) store excess sugars and are built from monosaccharide monomer subunits. For example, plants (like the potato) store excess sugars (usually glucose) in underground organs called tubers (in the potato plant's case, the potato) as the polysaccharide starch. Starch is the polysaccharide found in plants, while glycogen refers to polysaccharides in animals. A special type of carbohydrate known as a dissaccharide is formed from two sugar molecules as is the case with sucrose (glucose + fructose). For our purposes, we will consider disaccharides to be a simple carbohydrate. Polysaccharides (complex carbohydrates) are the true polymer form of carbohydrates while monosaccharides and disaccharides (the simple carbohydrates) are considered monomer units.
Simple carbohydrates are known as monosaccharides because they contain a single molecule of sugar. Monosaccharides are actually considered monomers, they are not polymers. Glucose and fructose are both examples of monosaccharides. Simple carbohydrates provide quick energy, while complex carbohydrates (polysaccharides) store excess sugars and are built from monosaccharide monomer subunits. For example, plants (like the potato) store excess sugars (usually glucose) in underground organs called tubers (in the potato plant's case, the potato) as the polysaccharide starch. Starch is the polysaccharide found in plants, while glycogen refers to polysaccharides in animals. A special type of carbohydrate known as a dissaccharide is formed from two sugar molecules as is the case with sucrose (glucose + fructose). For our purposes, we will consider disaccharides to be a simple carbohydrate. Polysaccharides (complex carbohydrates) are the true polymer form of carbohydrates while monosaccharides and disaccharides (the simple carbohydrates) are considered monomer units.
Carbohydrate Identification Tests
Benedict's Solution can test for simple sugars and their relative concentration. A green color indicates a small concentration of simple sugars while a red color indicates a very high concentration of simple sugars. Lugol's Iodine Test can be used to detect complex carbohydrates like starch or glycogen as iodine changes color to black in the presence of complex carbohydrates (see image on right below). |
Stat Line
Important terminology
Types: Simple (monomer) and complex (polymer).
Uses: Primarily energy source, some energy storage (complex carbohydrates like starch).
Elements present: Carbon, hydrogen and oxygen (1:2:1)
Identification Test
Important terminology
- Monosaccharide: single sugar molecule such as glucose and fructose
- Disaccharide: two sugar molecules such as sucrose
- Polysaccharide: many monosaccharide sugar molecules bound together to form one long chain such as starch or glycogen
Types: Simple (monomer) and complex (polymer).
Uses: Primarily energy source, some energy storage (complex carbohydrates like starch).
Elements present: Carbon, hydrogen and oxygen (1:2:1)
Identification Test
- Simple: Benedict's Solution Test (blue = no simple carbs, green = low, yellow and orange = medium, red = high, brown = very high)
- Complex: Lugol's Iodine Test (black indicates positive result, red/yellow indicates a negative result)
Lipids
Structure and Function
Lipid molecules can take a variety of forms including fats, waxes, oils and even steroids. Lipids are composed primarily of hydrogen and carbon with oxygen present in very small concentrations. Because carbon and hydrogen have similar electronegativities (desire for electrons or "greediness"), lipid molecules are nonpolar and do not dissolve in water. In other words, lipids are hydrophobic, making them useful in cellular membranes and waterproof coverings as well as other biological purposes including energy storage and chemical communication. As macromolecules, lipids are composed of two types of monomers: a glycerol "head" with numerous fatty acid "tails". The fatty acids earn their name from the presence of a carboxyl group (-COOH); organic compound with this functional group are known as carboxylic acids. The carboxyl group is located where the fatty acid is bonded to the glycerol. |
Functional Groups
In chemistry, functional groups refer to specific arrangements of atoms that have specific properties. There are a wide variety of these functional groups, but we will only be focusing on 2: carboxyl groups (COOH) and amine groups (NH2). Lipids or rather fatty acids contain carboxyl groups and amino acids (the monomer unit of proteins) contain both carboxyl and amine groups. If you examine the figure to the right which depicts the structure of a variety of functional groups. Notice that carboxyl groups and amine groups enable hydrogen bonds to form since each group contains a hydrogen atom bound to oxygen and nitrogen respectively (remember the NOF rule). |
Triglycerides
The lipids we find in food and are often the subject of so much dietary scrutiny contain a single glycerol molecule with three fatty acid chains. This gives them the scientific name of "triglycerides" and can either be saturated or unsaturated. The saturation refers to the carbon atoms in the fatty acid tails. On the other hand saturated triglycerides (known as fats) are saturated with hydrogens; they have formed as many carbon-to-hydrogen bonds as possible in their fatty acid chains. This saturation causes the fatty acid to remain straight allowing the fat molecules to pack together more closely, resulting in a higher melting temperature, explaining why fat is solid at room temperature. Triglycerides (saturated and unsaturated) are primarily used for storing energy. |
Unsaturated triglycerides (known as oils) do not have the maximum number of hydrogen atoms possible; the presence of carbon-to-carbon double bonds excludes some hydrogen atoms. This organization causes the fatty acid chains to not be straight, but rather bend and kink. This bending prevents oil molecules from packing together tightly, resulting in a low melting point which is why oils are liquid at room temperature.
Monounsaturated triglycerides contain a single carbon-to-carbon bond, while polyunsaturated triglycerides contain two or more double bonds in their fatty acid components. As such, monounsaturated triglycerides have a lower melting point than saturated triglycerides, but a higher melting point relative to polyunsaturated triglycerides.
Monounsaturated triglycerides contain a single carbon-to-carbon bond, while polyunsaturated triglycerides contain two or more double bonds in their fatty acid components. As such, monounsaturated triglycerides have a lower melting point than saturated triglycerides, but a higher melting point relative to polyunsaturated triglycerides.
Phospholipids
Phospholipids contain a single glycerol molecule with two fatty acids which can be saturated or unsaturated) and a phosphate. The glycerol head is polarized by the phosphate making it hydrophilic while the fatty acid tails are non-polar and therefore hydrophobic. Phospholipids are the raw material used to build cell membranes. In fact, a cell membrane is referred to as a phospholipid bilayer because it has two layers of phospholipids. The hydrophobic fatty acid tails remain on the inside with the hydrophilic glycerol heads pointing outward. This organization is extremely important to cells as it creates selective permeability of the cell membrane; only certain molecules may enter and exit the cell. We will explore this concept further in a later unit. |
Steroids and Waxes
The final major group of lipids would include steroids and waxes. Steroids are chemical messengers in the body that include cholesterol and hormones. Waxes are used to waterproof surfaces in animals and plants. For example, the cuticle of a leaf is covered in wax to prevent water loss.
The final major group of lipids would include steroids and waxes. Steroids are chemical messengers in the body that include cholesterol and hormones. Waxes are used to waterproof surfaces in animals and plants. For example, the cuticle of a leaf is covered in wax to prevent water loss.
Lipid Identification Tests
Lipids can be identified using Sudan III Test for lipids. The Sudan III test uses a red die that is "fat soluble" and hence will dissolve in fats, staining them red. If no fat is present, the die will not dissolve into the substance. In the picture, the test tube on the left, is negative for lipids. The Sudan III die did not dissolve into the substance. The test on right does contain lipids because the Sudan III dissolved into the substance. |
Stat Line
Important Terms:
Types: saturated and unsaturated
Uses: Energy storage, membrane construction, waterproofing, chemical signaling (steroids)
Examples: triglycerides (fats and oils), phospholipids, waxes, steroids
Elements present: primarily carbon and hydrogen (nonpolar)
Identification Test
Important Terms:
- Hydrophobic: water hating/fearing; nonpolar
- Hydrophilic: water loving; polar
- Saturated: fatty acid contains only carbon-to-carbon single bonds
- Unsaturated: fatty acid contains at least one carbon-to-carbon double bond
Types: saturated and unsaturated
Uses: Energy storage, membrane construction, waterproofing, chemical signaling (steroids)
Examples: triglycerides (fats and oils), phospholipids, waxes, steroids
Elements present: primarily carbon and hydrogen (nonpolar)
Identification Test
- Sudan III Test: if lipids are present the Sudan III solution will stain them red because Sudan III is "fat soluble". Sudan III dissolves in lipids, but not water or other compounds. If the sample does not contain lipids, the Sudan III die (red) will not dissolve into the sample and so the sample will remain the same color.
Nucleic Acids
Structure and Function
Nucleic acids are some of the most important molecules contain within your body. You are already familiar with DNA (deoxyribose nucleic acid), but RNA (ribonucleic acid) is another critically important nucleic acid. These molecules store hereditary or genetic information, making it possible for life to pass genes from one generation to the next. Nucleic acids are composed of carbon, hydrogen, oxygen, phosphorous and nitrogen and are built from smaller units (monomers) called nucleotides. Nucleotides in turn are composed of a phosphate, a sugar and a nitrogenous base. In DNA, each nucleotide has one of four different nitrogenous bases: adenine, guanine, thymine and cytosine (A,G, T and C). On the other hand, RNA nucleotides contain either adenine, guanine, cytosine or uracil. Thymine is not an option in RNA and is in fact replaced by uracil in RNA. All nucleotides of DNA (regardless of the nitrogenous base they carry) contain the sugar deoxyribose, but RNA nucleotides contain the sugar ribose. DNA actually contains to sets or strings of nucleotides that run antiparallel and are held together by hydrogen bonding. We will discuss DNA and RNA further in a later unit. |
Nucleic Acids and Energy
In addition to their role in storing genetic information, nucleic acids play an interesting role in energy transfer within cells. While energy is primarily supplied by carbohydrates, this energy is not usable by the cell. Instead, energy is converted into adenosine triphosphate (ATP), the so called "energy currency of the cell". To make this more understandable, consider the following metaphor: energy in food is a lot like gold bars. The gold has value, but you cannot go to the store and exchange gold for goods and services. Instead, you must trade your gold in for cash which you can then spend, just like the energy in food (like carbohydrates) must be converted to ATP before the cell can use it.
In addition to their role in storing genetic information, nucleic acids play an interesting role in energy transfer within cells. While energy is primarily supplied by carbohydrates, this energy is not usable by the cell. Instead, energy is converted into adenosine triphosphate (ATP), the so called "energy currency of the cell". To make this more understandable, consider the following metaphor: energy in food is a lot like gold bars. The gold has value, but you cannot go to the store and exchange gold for goods and services. Instead, you must trade your gold in for cash which you can then spend, just like the energy in food (like carbohydrates) must be converted to ATP before the cell can use it.
An ATP molecule is nothing more than a nucleotide (adenine is the nitrogenous base) with three phosphates attached. These phosphate bonds contain a large supply of energy that can easily be transferred to the cell to accomplish different tasks. When one of these phosphate bonds is broken, ATP is converted into adenosine diphosphate (ADP) and a free phosphate, plus energy is released. Later, the free phosphate can be reattached to ADP to form ATP using energy from carbohydrates.
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Testing for Nucleic Acids
Nucleic acids can be tested for using NATs (nucleic acid tests), NAATs (nucleic acid amplification tests) and PCR (Polymerase chain reaction), but these methods are expensive, technically demanding and time consuming. We will not be using these in class, but these tests work by amplifying the signal of the nucleic acid: they identify and replicate DNA/RNA sequences over and over again for study.
Nucleic acids can be tested for using NATs (nucleic acid tests), NAATs (nucleic acid amplification tests) and PCR (Polymerase chain reaction), but these methods are expensive, technically demanding and time consuming. We will not be using these in class, but these tests work by amplifying the signal of the nucleic acid: they identify and replicate DNA/RNA sequences over and over again for study.
Nucleic Acid Stat Line
Important Terms:
Uses: Genetic information storage and energy currency
Examples: DNA, RNA, ATP/ADP
Elements present: carbon, hydrogen, oxygen, phosphorous and nitrogen
Identification Tests (we will not use these in class)
Important Terms:
- DNA: deoxyribose nucleic acid, storage form of genetic information in living things
- RNA: ribonucleic acid, supports function of DNA
- ATP: adenosine triphosphate, energy currency of the cell. Can be converted to ADP by removal of a phosphate and release of stored energy.
- ADP: reciprocal, low energy version of ATP. Can be converted back to ATP by reattaching free phosphate using energy.
- Nucleotide: monomer subunit of nucleic acids composed of phosphate, sugar and nitrogenous base
Uses: Genetic information storage and energy currency
Examples: DNA, RNA, ATP/ADP
Elements present: carbon, hydrogen, oxygen, phosphorous and nitrogen
Identification Tests (we will not use these in class)
- NAAT: nucleic acid amplification test
- PCR: polymerase chain reaction
Proteins
Structure and Function
Proteins are the utility players of the cell, they can be used to accomplish virtually any task, from replicating DNA to destroying cellular wastes. The one thing proteins never do is store genetic information. Proteins can provide energy to cells, although cells generally prefer to get their energy from carbohydrates. Proteins contain carbon, hydrogen, oxygen, nitrogen and sulfur. The macromolecule form (polypeptides) are composed of monomer subunits called amino acids. Each amino acid is held together by a peptide bond (hence the term polypeptide when referring to proteins).
Proteins are the utility players of the cell, they can be used to accomplish virtually any task, from replicating DNA to destroying cellular wastes. The one thing proteins never do is store genetic information. Proteins can provide energy to cells, although cells generally prefer to get their energy from carbohydrates. Proteins contain carbon, hydrogen, oxygen, nitrogen and sulfur. The macromolecule form (polypeptides) are composed of monomer subunits called amino acids. Each amino acid is held together by a peptide bond (hence the term polypeptide when referring to proteins).
Amino Acids and Peptide Bonds
The monomer subunits of polypeptides are known as amino acids. Each amino acid shares 3 things in common: an amine group (-NH2), a carboxyl group (-COOH) and one of 20 unique side chains. The amine and carboxyl groups fall into a broader category in chemistry called function groups, which you will learn more about next year. The 20 unique side chain means that there are 20 different amino acids (see below). In other words, if polypeptides were a language (which they essentially are), its alphabet would have 20 letters. Amino acids are joined together by forming peptide bonds. Peptide bonds form via dehydration synthesis in which the carboxyl group of one amino acid bonds to the amine group of another amino acid following the removal of a water molecule. |
Protein Structure and Function
A proteins function is determined by is structure, which can be very complicated. The straight chain of amino acids is called the primary sequence, which can then be folded to form a secondary sequence. As the protein becomes three-dimensional in its folds it forms a tertiary structure. A protein that has achieved tertiary structure is a completed, fully, functioning polypeptide, however, some polypeptides go a step past tertiary structure to quaternary structure. In quaternary structure, multiple chains of amino acids are brought together to form one, very large polypeptide, as is the case with hemoglobin. |
Denaturation
Because a protein's function is determined by its structure, altering the shape of a protein will have huge consequences. This is called denaturation and can occur when a protein is exposed to a change in pH, temperature, pressure or salinity. You can see an example of denaturation when cooking an egg, the heat denatures the proteins of the yolk causing them to change form a clear liquid to a solid, white state. In this case, denaturation is permanent and the protein will remain disfigured and no longer work. In other instances, denaturation is temporary and the protein can revert to its working form. |
Because proteins (especially enzymes) are so important to the health and function of organisms, denaturation is one of the major reasons for why living things must exhibit homeostasis.Most proteins can only operate in a narrow range of temperature and pH conditions, so by maintaining a stable internal environment, organisms can ensure the safety of their vital proteins.
Testing for Proteins
Proteins can be tested for using Biuret's reagent. When Biuret's reagent is applied to a sample containing protein, the reagent with change color from blue to purple. One last thing, enzymes always end with the suffix "-ase" which is a great way to identify them. In a similar manner, sugar tend to end in the suffix -"ose". |
Proteins Stat Line
Important Terms:
Uses: everything except energy supply and storage or storage of genetic information
Examples: hemoglobin, keratin, carbonic anhydrase, etc.
Elements present: carbon, hydrogen, oxygen, nitrogen and sulfur.
Identification Test: Biuret's Reagent test, a color change from blue to violet indicates a positive result. The reagent will remain blue if there are no proteins present.
Important Terms:
- Polypeptide: technical name for a protein
- Amino acid: monomer unit of proteins
- Peptide bond: special typed of intramolecular bond that forms between amino acids
- Primary structure: the linear sequence of amino acids in a polypeptide
- Secondary structure: folded primary structure
- Tertiary structure: three-dimensional folded structure of a protein
- Quaternary structure: a protein composed of multiple amino acid sequences such as hemoglobin
- Enzymes: specialized protein that lower the activation energy of chemical reactions
- Activation Energy: energy required to begin a reaction
- Endothermic reactions: absorb energy (energy is a reactant)
- Exothermic reactions: release energy (energy is a product)
- Substrate: the material(s) on which an enzyme acts
- Denaturation: process by which an enzymes changes shape and ceases to function properly. Usually caused by temperature or pH shifts.
Uses: everything except energy supply and storage or storage of genetic information
Examples: hemoglobin, keratin, carbonic anhydrase, etc.
Elements present: carbon, hydrogen, oxygen, nitrogen and sulfur.
Identification Test: Biuret's Reagent test, a color change from blue to violet indicates a positive result. The reagent will remain blue if there are no proteins present.
Enzymes
Chemical Reactions
A chemical reaction is a process that transforms groups of chemicals. During chemical reactions, a reactant(s) are transformed into product(s). For instance, water and carbon dioxide are reactants that combine to form the product carbonic acid. During chemical reactions, chemical bonds (like covalent bonds) must break to allow for the reaction to proceed and new bonds will form later. Recall that atoms bond together in order to achieve complete valence shells and become more stable. This means that forming chemical bonds releases energy and therefore energy must be expended to break a bond. Thus, all chemical reactions require some energy before they can begin called activation energy, the energy required to begin a chemical reaction. Some reactions have very high activation energies, others have very low ones.
In general, there are two major types of chemical reactions: endothermic and exothermic. Both types will absorb and release energy, but endothermic reactions will absorb more energy than they release and exothermic reactions will release more energy than they absorb. For example, an endothermic reaction might use 100 units of energy and release 50 units of energy. Energy was absorbed and released by the reaction, but overall there was a net loss of energy from the system. An exothermic reaction would be the reverse, 50 units of energy might be expended, but 100 units of energy are released, a next gain of 50 units of energy for the system.
A chemical reaction is a process that transforms groups of chemicals. During chemical reactions, a reactant(s) are transformed into product(s). For instance, water and carbon dioxide are reactants that combine to form the product carbonic acid. During chemical reactions, chemical bonds (like covalent bonds) must break to allow for the reaction to proceed and new bonds will form later. Recall that atoms bond together in order to achieve complete valence shells and become more stable. This means that forming chemical bonds releases energy and therefore energy must be expended to break a bond. Thus, all chemical reactions require some energy before they can begin called activation energy, the energy required to begin a chemical reaction. Some reactions have very high activation energies, others have very low ones.
In general, there are two major types of chemical reactions: endothermic and exothermic. Both types will absorb and release energy, but endothermic reactions will absorb more energy than they release and exothermic reactions will release more energy than they absorb. For example, an endothermic reaction might use 100 units of energy and release 50 units of energy. Energy was absorbed and released by the reaction, but overall there was a net loss of energy from the system. An exothermic reaction would be the reverse, 50 units of energy might be expended, but 100 units of energy are released, a next gain of 50 units of energy for the system.
Enzymes are a sub-group of proteins that accelerate the rate at which chemical reactions occur. As "nature's catalysts" enzymes lower the activation energy of reactions and make them go faster. Enzymes DO NOT supply energy to a chemical reaction, but rather induce physical changes that ultimately lower or reduce the amount of activation energy required for a reaction to begin. Each enzyme acts on specific substrates (there can be more than one substrate per enzyme), providing a place for the reactants of a chemical reaction to come in contact with one another.
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Substrates attach to their enzymes at the active site to form the enzyme-substrate complex. Because enzymes and their substrates have such a specific connection, they are often compared to a lock and key. However, enzymes are not indestructible, they can be denatured by a change in temperature or pH. When an enzyme denatures it no longer works correctly because its active site changes shape and can no longer bind the substrates. Enzymes can be recycled endlessly as long as they are not denatured.
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Here's an example of an enzyme: carbonic anhydrase. We already know that carbon dioxide can combine with water to form carbonic acid in our blood stream. This reaction helps regulate blood pH and transport carbon dioxide to the lungs where it can be removed from the body. Without any assistance, this process occurs very slowly, which means carbon dioxide could build up in your blood stream to dangerous, unsafe levels. Luckily, your body has the enzyme carbonic anhydrase which speeds up the reaction of water and carbon dioxide into carbonic acid by a factor of about 10 million (it runs 10,000,000x faster).
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A second example of an enzyme would be catalase. Within cells, including our own, hydrogen peroxide is produced by normal cellular activity, but is toxic to cells. Hydrogen peroxide can be broken down into water and oxygen gas, but left alone, this reaction occurs very slowly and the hydrogen peroxide levels would build to dangerous concentrations for the cell. Catalase is an enzyme that speeds up the degradation of hydrogen peroxide (H2O2) into water (H2O) and oxygen gas (O2). In the lab, you saw that this reaction was exothermic and catalase could be reused over and over again, unless it was denatured by heat or a pH change. In addition, you saw that catalase is present in most cells, including apple, chicken and potatoes, but was in especially high concentrations in the liver. This is because the liver is an organ that specializes in detoxification and therefore has large quantities of catalase available.
Finally, we have amylase, an enzyme found in saliva. Amylase helps to digest complex carbohydrates such as starches, breaking them down into simpler sugars that can be readily absorbed by cells.