Biochemistry: The Basic Ingredients of Life 3 Biochemistry: The Basic Ingredients of Life

Multimedia Asset Directory Slide 45 Carbohydrates Animation Slide 52 Lipids Animation Slide 56 Proteins Animation Slide 59 DNA Animation Slide 75 Biochemists Video

Introduction Chemistry is the study of atoms and molecules and their interactions. Physiology is largely about the interactions between molecules in our cells and tissues or, more specifically, how chemistry relates to a living organism.

Introduction This special division of chemistry is known as biochemistry. In order to understand how the body works and to lay a foundation for the upcoming cell chapter you need at least a basic understanding of biochemistry.

Learning Objectives Differentiate between atoms, elements and ions. Define pH, acids and bases and their role in the body. Describe chemical bonding and the role of water. Describe the properties of a solution. Distinguish among the types of biological molecules.

Learning Objectives Explain metabolism. Explain cellular respiration. Explain the role of enzymes in physiology.

Pronunciation Guide adenosine triphosphate (uh DEN oh seen) Click on the megaphone icon before each item to hear the pronunciation. adenosine triphosphate (uh DEN oh seen) amino (ah MEAN oh) anabolism (ah NAB oh lizm) catabolism (kah TAB oh lizm) covalent (coh VAY lent) disaccharide (die SACK eh ride) glycerol (GLIS er oll) glycogen (GLIE koh jen) metabolism (meh TAB oh lizm)

Pronunciation Guide monosaccharide (mon oh SACK eh ride) Click on the megaphone icon before each item to hear the pronunciation. monosaccharide (mon oh SACK eh ride) organelles (OR guh NELLS) phospholipid (FOS foh LIP id)

Atoms, Elements, and Ions All matter, whether living, like our bodies, or non-living like this textbook, is made of elements. An element is the smallest unit that retains the unique chemical properties of that specific type of matter. Elements cannot be broken into smaller pieces by routine chemical techniques. Elements are usually abbreviated using the first two letters of their technical names. For example, the element sodium (Latin name natrium) is abbreviated Na, while the element chlorine is abbreviated Cl.

Atoms, Elements, and Ions Two or more elements joined together form a molecule. Molecules with more than one type of element are known as compounds. Following on our previous example, the molecule you know as table salt is sodium chloride, abbreviated NaCl.

Atoms, Elements, and Ions The smallest recognizable unit of an element is called an atom. Atoms consist of a nucleus, containing protons (positively charged particles) and neutrons (neutral particles). The nucleus is surrounded by electrons (negatively charged particles).

Table 3-1 Some Important Trace Elements in the Body

Table 3-1 (continued) Some Important Trace Elements in the Body

Figure 3-1 The atom.

Figure 3-2 the periodic table Figure 3-2 The periodic table.

Atoms, Elements, and Ions In a typical atom, the number of positively charged protons (+) equals the number of negatively charged electrons (-). This balance of electrons and protons results in an atom with a neutral charge. However, under certain conditions, atoms can gain or lose electrons. These atoms are called ions and have either a positive or negative charge.

Atoms, Elements, and Ions Atoms which have lost an electron will be positively charged, while atoms that have gained an electron will be negatively charged. Again, we can use sodium and chlorine as examples. When NaCl (salt) is formed it is neutral and, therefore, has no charge. However, if the elements are separated (ionization), sodium loses an electron becoming Na+, sodium ion, while chlorine gains an electron becoming Cl-, a chloride ion.

Atoms, Elements, and Ions Atoms which have lost an electron will be positively charged, while atoms that have gained an electron will be negatively charged. Ions are also said to be polar, because they have charges, like the poles on a battery. The positively charged atom is attracted to the negatively charged one. (Conversely, negative charges repel negative charges and positive repel positive.)

Atoms, Elements, and Ions Atoms which have lost an electron will be positively charged, while atoms that have gained an electron will be negatively charged. The reason why this is important is that electrolytes are charged ions found within the body. They influence the nervous system, muscle activity, and fluid balance. Important electrolytes include sodium (Na+), potassium (K+), calcium (Ca2+), magnesium (Mg2+), chloride (Cl-), hydrogen phosphate (HPO4-) and bicarbonate (HCO3-).

Acids and Bases Acids and bases are also electrolytes because they can conduct electricity and breakdown (dissociate) in water. Acids can dissolve metals and literally burn a hole through material (don’t try this at home!). The definition of an acid is something that can release hydrogen ions. Acids taste sour. Acids dissolved in water release hydrogen ions that can easily react with other atoms.

Acids and Bases Bases, which have a bitter taste, can accept hydrogen ions; for example, bicarbonate (HCO3-) can accept hydrogen ions, forming carbonic acid (H2CO3), which is a weak acid. Hydroxides (OH-) are common bases, which accept spare hydrogen ions.

Acids and Bases The concentration or amount of hydrogen and hydroxides are measured using the pH scale. The pH scale is from 0 to 14, where a value between 0 and 6.9 means there are more hydrogen ions compared to hydroxide or hydroxyl ions, and so it is said to be acidic. Neutral pH, where there are the same number of hydrogen and hydroxyl ions, is 7. A pH greater than (>) 7 indicates that there are more hydroxyl ions, and therefore it is said to be alkali. To give some examples, the pH of blood is between 7.35 and 7.45; bleach has a pH of 11 and grapefruit juice has a pH of 3.

Acids and Bases The systems that help regulate the acid/base balance include the respiratory and renal systems. The role of the respiratory system is to take in air and get rid of carbon dioxide (CO2). Carbon dioxide is a weak acid. If we stop breathing, there is a build-up of CO2 in the body and this build-up of acid is detected in the brain which gives you an overwhelming desire to breathe.

Acids and Bases If there is a problem with the respiratory system, the kidneys come to the rescue and enable excess acid to be lost in the urine.

Table 3-2 The pH Scale.

Bonding Elements can be joined together to form molecules. The individual elements in molecules are held together by bonds between electrons in the atoms.

Bonding If one atom donates electrons to the other atom, an ionic bond results. Because one atom has lost electrons and the other has gained them, the atoms involved in an ionic bond are ions, and carry a positive or negative charge. Using our previous example, the bond between sodium and chlorine in table salt (NaCl) is an ionic bond and if NaCl were to dissociate (break apart) it would form Na+ ions and Cl- ions respectively.

Figure 3-3 Formation of sodium chloride ions.

Bonding If the electrons are shared by the atoms involved in the bond, a covalent bond results. Covalent bonds may sometimes be unequal because one atom takes more than its share of the shared electrons. This type of covalent bond, a polar covalent bond, results in weak charges on the elements in the molecule. Polar covalent bonds are more polar (slight charge) than covalent bonds, but less polar than the higher charged ionic bonds.

Figure 3-4 Covalent bonding.

Figure 3-4 (continued) Covalent bonding.

Table 3-3 Summary of Bonds and Their Properties

Water Water (H20) is the chief liquid in biological systems. All of the fluid in your body is water-based. Water is a polar solvent because the bonds between the H and O in water are polar covalent. Oxygen takes more than its share of electrons. Thus, charged molecules will be attracted to one end or the other of a water molecule.

Water Charged molecules containing elements like oxygen, phosphorus, and nitrogen, mix easily with water. Such molecules are called hydrophilic (water-loving). Other molecules which do not carry a charge, like fats and oils, do not mix well with water. They are called hydrophobic (water-fearing).

Figure 3-5 The polar covalent bonding of water.

Water In addition, the polarity of water causes the development of hydrogen bonds between water molecules. The hydrogen on one water molecule binds weakly to the oxygen on another water molecule. The bonds between the water molecules increases water’s heat capacity. Water can store heat, meaning water heats up and cools down more slowly than air.

Solutions When one substance is dissolved in another the combination is called a solution. The substance dissolved is called the solute. The substance doing the dissolving, usually water in living things, is called the solvent. Electrolytes, those important ions necessary for fluid balance, are the solutes dissolved in your water-based body fluids. The amount of solute dissolved in a solvent is called the solute concentration.

Figure 3-6 Solutions.

FROM THE STREETS: Intravenous Fluids IV fluids often administered in prehospital care. Primary reasons for IV fluid therapy Water replacement Administration of essential electrolytes Provision of calories Provision of open vein for administration of emergency medications It is important to choose the correct IV fluid.

FROM THE STREETS: Intravenous Fluids Table 3-4 The Most Commonly Used Prehospital IV Fluids

Biological Molecules Most of your anatomy is made of molecules called biological molecules. Biological molecules are molecules found in living systems that contain mainly the elements carbon (C) and hydrogen (H), with lesser amounts of oxygen (O), nitrogen (N), sulfur (S), phosphorous (P) and other elements. These molecules fall into four broad categories: carbohydrates, lipids, proteins and nucleic acids.

Biological Molecules Carbohydrates Carbohydrates are sugars and starches. They are used as energy sources and as structural molecules. The name carbohydrate literally means “watered carbon”. Carbohydrate molecules all have carbon, hydrogen, and oxygen in the ratio of 1 carbon, to 2 hydrogens, to 1 oxygen (CH2O). Monosaccharides, or simple sugars, have 5 or 6 carbons. Glucose (C6H12O6), your body’s chief fuel, is a monosaccharide.

Biological Molecules Carbohydrates If two monosaccharides are hooked together, a disaccharide is formed. Sucrose, table sugar, consists of a glucose and a fructose hooked together. Polysaccharides are made when many monosaccharides are hooked together. Glycogen, a molecule in your liver that is used to store energy, consists of many, many glucose molecules in a long chain and therefore can be called upon to break down and release more glucose into the blood when needed.

Figure 3-7 Carbohydrates

Click here to view an animation on the topic of carbohydrates. Back to Directory

Biological Molecules Lipids Lipids consist of mainly carbon and hydrogen. They have very little oxygen. Because they have little oxygen or any other ions in them, lipids are hydrophobic. Lipids are used for energy storage, communication, and protection. There are many types of lipids. Fats and oils are probably the lipids most familiar to you. Fats and oils consist of three fatty acid chains and a glycerol molecule. They are energy storage molecules and can be broken down when needed by the body.

Biological Molecules Lipids (cont’d) Waxes are lipids that consist of a fatty acid chain with an alcohol molecule. They are some of the most hydrophobic substances known and are used mainly for protection, particularly water-proofing. (Why do you wax the car?)

Biological Molecules Lipids (cont’d) A phospholipid molecule has two fatty acid “tails” and a phosphate (PO4-) “head”. The tails are hydrophobic but the head is hydrophilic. Phospholipids are key molecules in the structure and function of cell membranes.

Biological Molecules Lipids (cont’d) The last category of lipids is steroids. Steroids are lipids with the carbon atoms arranged in rings. Steroids are structural molecules or are used for communication between cells. Examples of steroids are cholesterol, testosterone, and estrogen.

Figure 3-8 Lipids.

Figure 3-8 (continued) Lipids.

Click here to view an animation on the topic of lipids. Back to Directory

Biological Molecules Proteins Molecules made of long chains of amino acids. Because amino acids have nitrogen in them, proteins are always recognizable by the nitrogen molecules in the backbone of the molecule. A special linkage called a peptide bond ties the amino acids together and is unique to protein molecules. The structure of a protein is determined by the order of amino acids in the molecule.

Biological Molecules Proteins (cont’d) The most versatile of all biological molecules act as structural molecules (collagen in tendons and ligaments), speeding up biological reactions (enzymes), storing energy (egg white albumin), moving your body (muscle protein), protecting against infection (antibodies) and allowing cells to communicate (the hormone, insulin), to name just a few functions of proteins.

Figure 3-9 Amino acids and proteins.

Click here to view an animation on the topic of proteins. Back to Directory

Nucleic Acids The last category of biological molecules is nucleic acids. There are only two nucleic acids in nature, RNA and DNA. They are involved in controlling the activities of cells and are the molecules that contain your genetic code. You will learn more about nucleic acids when we discuss cellular reproduction.

Figure 3-10 Nucleic acids.

Click here to view an animation on the topic of DNA. Back to Directory

Metabolism Metabolism refers to all of the chemical operations going on within our bodies. Metabolism requires various nutrients or fuel to function and produces waste products much like a car consumes gas for power and produces waste, or exhaust. Metabolism, for now, can be thought of as “all the life-sustaining reactions within the body.” Metabolism is further subdivided into two opposite processes.

Metabolism Anabolism is the process by which simpler compounds are built up and used to manufacture materials for growth, repair, and reproduction. This is the building phase of metabolism. Many anabolic reactions are dehydration synthesis reactions in which water is removed and biological molecules are hitched together.

Metabolism Catabolism is the process by which complex substances are broken down into simpler substances. Many catabolic reactions are hydrolysis reactions in which water is added to break apart large molecules.

Figure 3-11 Metabolic reactions: Dehydration synthesis builds new compounds while hydrolysis breaks down compounds.

Enzymes In order for your cells to be able to do anything, chemicals must be broken down and others must be made. You need building materials to build the small cell parts called organelles and to make energy. Any of these processes require chemical reactions to occur in the cell.

Enzymes The problem is that these reactions are usually very slow. The hydrolysis and dehydration synthesis reactions used in cellular metabolism cannot happen without help. To solve this problem, cells have special proteins called enzymes.

Enzymes Enzymes speed up the rate of chemical reactions, making them fast enough for your cells to use the materials. Enzymes are protein molecules that have special binding sites on them. Biological molecules bind to the enzymes and are carried through the reaction, much like riders on a roller coaster. When the reaction is finished, the enzyme goes back to get more molecules, called substrates.

Enzymes Because enzymes are a binding system: They are specific. Only certain molecules can be carried by certain enzymes. Substrates can compete for binding sites. If all the binding sites are full, the enzymes are said to be saturated, and molecules must wait for an empty enzyme before going through the reaction. The enzymes can also be blocked or inhibited, preventing the substrate from binding. Enzymes are unchanged by their participation in the reaction.

Figure 3-12 Enzymes: Note the enzyme has the ending ase as in sucrase and the actual substrate is sucrose.

Cell Energy and ATP How does energy get from food to cells? In simple terms, the body takes in food and breaks it down (digestion). During this process, energy is released from the food. The problem is that cells can’t use this energy directly. Only food converted to glucose can be used to make energy.

Cell Energy and ATP Glucose can be used by your cells during a series of chemical reactions called cellular respiration. During cellular respiration, glucose is combined with oxygen and is transformed in your mitochondria into the high energy molecule called Adenosine Triphosphate (ATP).

Cell Energy and ATP ATP is made up of a base, a sugar, and three phosphate groups (hence, triphosphate). The phosphate groups are held together by high-energy bonds. When a bond is broken, a high level of energy is released. Energy in this form can be used by the cells.

Cell Energy and ATP When a bond is used, ATP becomes ADP (adenosine diphosphate), which has only two phosphate groups. ADP now is able to go and pick up another phosphate and form a high-energy bond so energy is stored and the process can begin again.

Figure 3-13 Energy is released from the breaking of the phosphate bond in ATP when converting to ADP.

FROM THE STREETS: A Cellular Toxin Cyanide, a common product of combustion, stops energy production by cells. Cyanide poisoning can be fatal if an antidote is not rapidly administered. Maintain a high index of suspicion for possible cyanide poisoning in victims who have been exposed to the products of combustion of cyanide (often used in mining and jewelry-making).

Click here to view a video on the topic of biochemists. Back to Directory

Snapshots from the Journey The smallest unit that is recognizable chemically is an element. Elements are made of atoms. Atoms consist of a nucleus (neutrons and protons) surrounded by electrons. Elements can be joined together to make molecules. All living matter is composed of elements. Atoms may gain or lose electrons, causing them to have a charge. These atoms are called ions. Physiologically important ions are called electrolytes.

Snapshots from the Journey pH is the measure of acidity or alkalinity of the body. Carbon dioxide is a weak acid and must be appropriately removed to maintain a normal pH in the blood. This is accomplished by a balance between the renal and respiratory systems functions. Atoms are bound together to form molecules. If electrons are shared by the atoms, the bond is covalent. If one atom gains electrons while the other loses them, the bond is ionic and the molecule is polar.

Snapshots from the Journey Water is a polar covalent molecule that is the basis of all body fluids. Molecules that mix with water are polar and are called hydrophilic. Molecules that will not mix with water are non-polar and are called hydrophobic. A solution consists of a substance dissolved (the solute) in a liquid (the solvent). The solvent in biological systems is usually water. Living things are made of biological molecules. Biological molecules fall into four categories based on physical characteristics; proteins, carbohydrates, lipids, and nucleic acids.

Snapshots from the Journey For cells to carry out metabolism they must have energy in the form of ATP. ATP is made via a complex series of reactions called cellular respiration. Enzymes, biological catalysts, are also necessary for cellular metabolism. Metabolism is dependent on the breakdown and manufacture of molecules called biological molecules. Each type, carbohydrates, lipids, proteins, and nucleic acids have unique characteristics. Electrolytes are charged ions that have important roles in body functions.

Case Study Juanita has always been overly concerned about her weight even though she is considered physically attractive and fit by her peers. However, the prom is approaching and she has resorted to the dangerous practice of using diuretics to “slim down” to fit into her gown. During gym class she suddenly became light-headed, had heart palpitations and was taken to the hospital. Her blood studies showed an electrolyte imbalance. Research diuretics and their connection to this case.

FROM THE STREETS You are called to the scene of a 17 year-old female complaining of “feeling confused”. The patient’s blood glucose is 55 mg/dl (normal range 60-120 mg/dl). Her mother describes that her daughter’s prom is approaching and she has been trying to “lose weight” by taking the drug Metformin (Glucophage®). Metformin is a antihyperglycemic drug that blocks glucose absorption in the stomach.

From the Streets Questions Would the patient lose weight by taking the Metformin? Explain why? What type of molecule is glucose? Why is the patient’s blood sugar slightly low? Why is she feeling confused?

From the Streets Questions Would the patient lose weight by taking the Metformin? Yes Explain why? The drug block glucose absorption in the GI tract reducing absorbed calories. What type of molecule is glucose? Carbohydrate Why is the patient’s blood sugar slightly low? The drug blocks glucose absorption Why is she feeling confused? Blood glucose is slightly low

End of Chapter Review Questions The nucleus of an atom consists of Protons Neutrons Electrons a & b a, b & c

End of Chapter Review Questions A person loses body temperature faster in water than in air because water is hydrophilic. has a high heat capacity. is our major body fluid. is polar.

End of Chapter Review Questions Which of the following is not a property of enzymes? Specificity Saturation Polarity Inhibition

End of Chapter Review Questions These biological molecules will not mix with water. Proteins Carbohydrates Lipids Amino acids

End of Chapter Review Questions A new molecule is discovered in a deep sea cave fish. It has the following properties: hydrophilic, very large, used for energy storage. What kind of molecule is it? Lipid Protein Nucleic acid Carbohydrate

End of Chapter Review Questions Atoms or molecules which can gain or lose an electron are called ________________. Unequal sharing of electrons in a bond results in a ______________________ bond. Sodium, potassium, and chloride in body fluids are known as ___________________.

End of Chapter Review Questions NaCl can be in solution in your body. What is the solvent? ____________________ All the chemical reactions in your body are collectively known as ____________________. Your cells need glucose to make this high energy molecule ______________________.

End of Chapter Review Questions Explain the relationship between atoms, elements, molecules, and ions. List and explain the types of bonds between atoms. Distinguish among the four classes of biological molecules. Explain the chemistry of water. Why is water important in biological systems? Explain the functions of enzymes.