Biochemistry and the Organization of Cells MODULE 1 PDF

# Biochemistry and the Organization of Cells ## Chapter Outline - **1-1 Basic Themes** - Biochemistry and Life - Origin of Life on Earth - **1-2 Chemical Foundations of Biochemistry** - Amino Acids - Carbohydrates - Nucleotides - Lipids - Functional Groups Important in...

# Biochemistry and the Organization of Cells ## Chapter Outline - **1-1 Basic Themes** - Biochemistry and Life - Origin of Life on Earth - **1-2 Chemical Foundations of Biochemistry** - Amino Acids - Carbohydrates - Nucleotides - Lipids - Functional Groups Important in biochemistry - **1-3 The Beginnings of Biology** - The Earth and Its Age - Biomolecules - Molecules to Cells - **1-4 The Biggest Biological Distinction - Prokaryotes and Eukaryotes** - Prokaryotic Cells - Eukaryotic Cells - **1-5 How We Classify Eukaryotes and Prokaryotes** - Five-Kingdom Classification System - 1A Biochemical Connections: Biotechnology: Extremophiles: The Toast of the Industry - Three-Domain Classification System - Eukaryotic Origins - ** 1- 6 Biochemical Energetics** - Thermodynamic Principles - Energy Changes - Spontaneity in Biochemical Reactions - Life and Thermodynamics - 1B Biochemical Connections: Thermodynamics: Predicting Reactions **Biochemistry and Life** How does biochemistry describe life processes? Living organisms are enormously complex and diverse. However, certain unifying features are common to all living things. Biochemistry is the chemistry of life. It combines biology and chemistry. Biochemistry draws on many disciplines, allowing it to use results from many sciences to answer questions about the molecular nature of life processes. **Origin of Life on Earth** The fundamental similarity of cell types makes speculating on the origins of life a worthwhile question. Living cells must have arisen ultimately from very simple molecules, such as water, methane, carbon dioxide, ammonia, nitrogen, and hydrogen. **How did living things originate?** Simple molecules were formed by combining atoms, and reactions of simple molecules led to more complex molecules. The molecules that play a role in living cells today are the same molecules as those encountered in organic chemistry; they simply operate in a different context. ## 1-2 Chemical Foundations of Biochemistry **Organic Chemistry** Organic chemistry is the study of compounds of carbon and hydrogen and their derivatives. Because the cellular apparatus of living organisms is made up of carbon compounds, biomolecules are part of the subject matter of organic chemistry. The small molecules found in the cell can usually be lumped into four basic classes: - Amino acids - Carbohydrates - Nucleotides - Lipids **Amino Acids** The simplest compounds are the amino acids. They get their name from the fact that they all contain an amino group and a carboxyl group. Amino acids have a basic structure where a central carbon atom is bonded to a carboxyl group, an amino group, a hydrogen, and a variable group, called the R group. It is the difference between the R groups that makes each amino acid unique. **Carbohydrates** Carbohydrates are compounds made up of carbon, hydrogen, and oxygen, with a general formula of (CH2O)n, where n is at least 3. The simplest forms are called monosaccharides, or sugars. The most common monosaccharide is glucose, which has the formula C6H12O6. Simple sugars often make up much larger polymers and are used for energy storage and structural components. **Nucleotides** Nucleotides are the basic unit of the hereditary materials DNA and RNA. They also form the molecular currency of the cell, adenosine triphosphate (ATP). A nucleotide is composed of a five-carbon sugar, a nitrogen-containing ring, and one or more phosphate groups. **Lipids** The fourth major group of biochemicals consists of lipids. They are the most diverse and cannot be shown with a simple structure common to all lipids. However, they all have the common trait that they are poorly soluble in water. This is because they are composed of long chains of hydrocarbons. **Can a chemist make the molecules of life in a laboratory?** Until the early part of the 19th century, there was a widely held belief in the idea that the compounds found in living organisms could not be produced in the laboratory. This belief was disproved in 1828 by German chemist Friedrich Wöhler. He synthesized urea from ammonium cyanate, a compound obtained from mineral (i.e., nonliving) sources. The reactions of biomolecules can be described by the methods of organic chemistry, which requires the classification of compounds according to their functional groups. The reactions of molecules are based on the reactions of their respective functional groups. ## 1-3 The Beginnings of Biology **The Earth and Its Age** The most widely accepted cosmological theory for the origin of the Universe is the big bang. The Universe was originally confined to a comparatively small volume of space. As a result of a tremendous explosion, this "primordial fireball" started to expand with great force. The most abundant isotopes of biologically important elements such as carbon, oxygen, nitrogen, phosphorus, and sulfur have particularly stable nuclei. **How and when did the Earth come to be?** The atmosphere of the early Earth was very different from the one we live in. The early Earth was constantly irradiated with ultraviolet light from the Sun because there was no ozone layer in the atmosphere to block it. The gases usually postulated to have been present in the atmosphere of the early Earth include NH3, H2S, CO, CO2, CH4, N2, H2, and (in both liquid and vapor forms) H2O. **How were biomolecules likely to have formed on the early Earth?** Experiments have been performed in which the simple compounds of the early atmosphere were allowed to react under the varied sets of conditions that might have been present on the early Earth. These results indicate that these simple compounds react abiotically to give rise to biologically important compounds such as the components of proteins and nucleic acids. According to one theory, reactions such as these took place in the Earth's early oceans; other researchers postulate that such reactions occurred on the surfaces of clay particles that were present on the early Earth. Recent theories of the origin of life focus on RNA, not proteins, as the first genetic molecules. **Living cells today are assemblages that include very large molecules, such as proteins, nucleic acids, and polysaccharides.** ## 1-4 The Biggest Biological Distinction - Prokaryotes and Eukaryotes - **Prokaryotes** are microorganisms that lack a distinct nucleus and membrane-enclosed organelles. These include bacteria and cyanobacteria. - **Eukaryotes** are organisms whose cells have a well-defined nucleus and membraneenclosed organelles. These include yeasts, Paramecium, and all multicellular organisms. **What is the difference between a prokaryote and a eukaryote?** The word eukaryote means “true nucleus.” Eukaryotes are more complex organisms and the biggest difference is that a nucleus is set off from the rest of the cell by a membrane. Also, eukaryotic cells are more complex and usually much larger than prokaryotic cells. **Prokaryotic Cells** Although no well-defined nucleus is present in prokaryotes, the DNA of the cell is concentrated in one region called the nuclear region. The DNA of prokaryotes is not complexed with proteins in extensive arrays with specified architecture, as is the DNA of eukaryotes. In general, there is only a single, closed, circular molecule of DNA in prokaryotes. This circle of DNA, which is the genome, is attached to the cell membrane. Before a prokaryotic cell divides, the DNA replicates itself, and both DNA circles are bound to the plasma membrane. The cell then divides, and each of the two daughter cells receives one copy of the DNA. **Cytoplasm** refers to the portion of the cell outside the nucleus, and the **cytosol** is the aqueous portion of the cell that lies outside the membrane-bounded organelles. **Every cell is separated from the outside world by a cell membrane, or plasma membrane, an assemblage of lipid molecules and proteins.** In addition to the cell membrane and external to it, a prokaryotic bacterial cell has a cell wall. The chemical natures of prokaryotic and eukaryotic cell walls differ somewhat, but a common feature is that the polymerization of sugars produces the polysaccharides found in both bacteria and plant cells. ## 1-5 How We Classify Eukaryotes and Prokaryotes **Five-Kingdom Classification System** The kingdom **Monera** consists only of prokaryotic organisms that are made up of eukaryotic organisms. **Protista** includes unicellular organisms. The kingdom **Fungi** includes yeasts, molds, and mushrooms. The three kingdoms that consist of multicellular eukaryotes are **Fungi**, **Plantae**, and **Animalia**. One group of organisms can be classified as prokaryotes in the sense that the organisms lack a well-defined nucleus. These organisms are called **archaebacteria** because there are marked differences between the two kinds of organisms. Archaebacteria are found in extreme environments. Most of the differences between archaebacteria and other organisms are biochemical features such as the molecular structure of the cell walls, membranes, and some types of RNA. **Three-Domain Classification System** Another system exists for classifying organisms, called the three-domain system. There are two divisions of prokaryotes: - **Bacteria** are the most common and found in normal habitats. - **Archaea** are prokaryotes that inhabit extreme environments. ** Eukaryotic Origins** The complexity of eukaryotes raises many questions about how such cells arose from simpler progenitors. Symbiosis plays a large role in current theories of the origin of eukaryotes. The type of symbiosis called mutualism is a relationship that benefits both species involved, as opposed to parasitic symbiosis, in which one species gains at the other's expense. A classic example of mutualism is the lichen, which consists of a fungus and an alga. *Another example is the rootnodule system formed by a leguminous plant and anaerobic nitrogen-fixing bacteria.* **Did symbiosis play a role in the development of eukaryotes?** In hereditary symbiosis, a larger host cell contains a genetically determined number of smaller organisms. An example is the protist *Cyanophora paradoxa*, a eukaryotic host that contains a genetically determined number of cyanobacteria. This relationship is an example of **endosymbiosis**. According to one theory, chloroplasts arose from the past existence of cyanobacteria and mitochondria arose from the past existence of aerobic bacteria. ## 1-6 Biochemical Energetics **What is the source of energy in life processes?** All cells require energy for a number of purposes. Many reactions that take place in the cell, particularly those involving synthesis of large molecules, cannot take place unless energy is supplied. The Sun is the ultimate source of energy for all life on Earth. Photosynthetic organisms trap light energy and use it to drive the energy-requiring reactions that convert carbon dioxide and water to carbohydrates and oxygen. Nonphotosynthetic organisms consume these carbohydrates and use them as energy sources. **Thermodynamic Principles** One of the most important questions about any process is whether energy changes favor the process. Thermodynamics is the branch of science that deals with this question. **The key point is that processes that release energy are favored.** Conversely, processes that require energy are disfavored. The change in energy depends only on the state of the molecules present at the start of the process and the state of those present at the end of the process. **Energy Changes** Energy can take several forms, and it can be converted from one form to another. All living organisms require and use energy in varied forms. Any process that will actually take place with no outside intervention is **spontaneous** in the specialized sense used in thermodynamics. **Spontaneity in Biochemical Reactions** The most useful criterion for predicting the spontaneity of a process is the free energy, which is indicated by the symbol G. The sign of the change in free energy, ΔG, indicates the direction of the reaction. **Life and Thermodynamics** The laws of thermodynamics can be stated in several ways. The first law states that it is impossible to convert energy from one form to another at greater than 100% efficiency. The second law states that even 100% efficiency in energy transfer is impossible ## 2 Water: The Solvent for Biochemical Reactions **2-1 Water and Polarity** Water is the principal component of most cells. The geometry of the water molecule and its properties as a solvent play major roles in determining the properties of living systems. **Polar Bonds** When two atoms with the same electronegativity form a bond, the electrons are shared equally between the two atoms. However, If atoms with differing electronegativity form a bond, the electrons are not shared equally. **Solvent Properties of Water** The polar nature of water largely determines its solvent properties. Ionic compounds and polar compounds tend to dissolve in water, whereas less polar molecules tend not to dissolve as readily in water, if at all. There are different types of bonds with different strengths depending on these electrostatic attractions. **Ionic Bonds** In a crystal of salt, the positive and negative ions are held together by ionic bonds. Ionic bonds and covalent bonds are the strongest bonds. **Salt Bridges** Biomolecules often have ionizable groups on them. The attraction of these two side chains controls how protein molecules fold in solution. This resulting bond is called a salt bridge. **Ion-Dipole Interactions** Ions in solution can also interact with molecules that have dipoles. **van der Waals Forces** There are several types of weak forces that are called van der Waals forces. These forces are three noncovalent bonds that do not involve an electrostatic interaction of a fully charged ion. - **Dipole-Dipole Interactions** occur between molecules that are dipoles, with the partial positive side of one molecule attracting the partial negative side of another molecule. - **Dipole-Induced Dipole Interactions** are created when a permanent dipole in a molecule comes into close contact with another molecule. - **Induced Dipole-Induced Dipole Interactions** are created when two molecules lacking dipoles bump into each other, they distort each other's electron cloud, thereby creating a brief interaction between these induced dipoles. **Hydrophobic Interactions** Nonpolar compounds tend not to dissolve in water and they are referred to as hydrophobic. **Why do oil and water mixed together separate into layers?** A single molecule may have both polar (hydrophilic) and nonpolar (hydrophobic) portions. Substances of this type are called **amphipathic**. In the presence of water, a compound tends to form structures called **micelles**, in which the polar head groups are in contact with the aqueous environment and the nonpolar tails are sequestered from the water. The separation of oil and water is the result of these nonpolar interactions. ## 2-2 Hydrogen Bonds Hydrogen bonding is a special case of dipoledipole interaction. The hydrogen atom that is covalently bonded to a very electronegative atom such as oxygen or nitrogen has a partial positive charge due to the polar bond. This partial positive charge on hydrogen can interact with an unshared (nonbonding) pair of electrons on another electronegative atom. All three atoms lie in a straight line, forming a hydrogen bond. **Hydrogen Bonds and Water** Water has two hydrogens to enter into hydrogen bonds and two unshared pairs of electrons on the oxygen to which other water molecules can be hydrogen bonded. Each water molecule is involved in four hydrogen bonds-as a donor in two and as an acceptor in two. The geometric arrangement of hydrogen-bonded water molecules has important implications for the properties of water as a solvent. The bond angle in water is 104.3°, and the angle between the unshared pairs of electrons is similar. The result is a tetrahedral arrangement of water molecules. Liquid water consists of hydrogen-bonded arrays that resemble ice crystals; each of these arrays can contain up to 100 water molecules. **2-3. Acids, Bases, and pH** The biochemical behavior of many important compounds depends on their acid-base properties. The degree of dissociation of acids in water ranges from essentially complete dissociation for a strong acid to practically no dissociation for a very weak acid. **Acid Strength** It is useful to derive a numerical measure of acid strength, which is the amount of hydrogen ion released when a given amount of acid is dissolved in water. This is called the acid dissociation constant, or Ka. **Acids and Bases** Although more than one definition of acid exists, a biologically useful definition of an acid is a molecule that acts as a proton (hydrogen ion) donor. In strict chemistry, this is also known as a Brønsted acid. How readily acids or bases lose or gain protons depends on the chemical nature of the compounds under consideration. **Titration Curves** A titration is an experiment in which measured amounts of base are added to a measured amount of acid. It is convenient and straightforward to follow the course of the reaction with a pH meter. The point in the titration at which the acid is exactly neutralized is called the equivalence point. When 1 mol of base has been added for each mol of acid, the equivalence point is reached, and essentially all the acid has been converted to its conjugate base. The form of the curves in Figure 2.16 represents the behavior of any monoprotic weak acid, but the value of the pK for each individual acid determines the pH values at the inflection point and at the equivalence point. **2-4 Titration Curves** When base is added to a sample of acid, the pH of the solution changes, which is called a titration. It is convenient and straightforward to follow the course of the reaction with a pH meter. The point in the titration at which the acid is exactly neutralized is called the equivalence point. The pH equals the pK of the acid. **2-5 Buffers** **Buffer Definition** A buffer is something that resists change. In terms of acid and base chemistry, a buffer solution tends to resist change in pH when small to moderate amounts of a strong acid or strong base are added. **How do buffers work?** Let us compare the changes in pH that occur on the addition of equal amounts of strong acid or strong base to pure water and to a buffer solution. If 1.0 mL of 0.1 M HCl is added to 99.0 mL of pure water, the pH drops drastically. If the same experiment is conducted with 0.1 M NaOH, the pH rises drastically. **Buffer Selection** A consideration of titration curves can give insight into how buffers work. The pH of a sample being titrated changes very little in the vicinity of the inflection point of a titration curve. **Why do we want to know the pH?** An equation connects the K of any weak acid with the pH of a solution containing both that acid and its conjugate base. This relationship has wide use in biochemistry, especially where it is necessary to control pH for optimum reaction conditions. **2B Biochemical Connections: Buffer Chemistry** The rule of thumb is that the pKa should be ±1 pH unit from the pH of the reaction; ±1½ pH unit is even better. Sometimes a buffer can interfere with a reaction or with the assay method. **How do we choose a buffer?** In many biochemical studies, a strict pH range must be maintained for the experiment to be successful. We can select an appropriate buffer. For instance, if you need a pH close to 9.0, you would look at tables of buffers to find one with a pK close to nine. **How do we make buffers in the laboratory?** To make a buffer, it is usually done in practice. You could start with the HA form and add NaOH until the pH is correct. The pK of a given acid determines the pH values at the inflection point and at the equivalence point. **Biological Buffers** The real importance of buffers is that they are critical to life. The phosphate buffer system is common in living organisms and in the laboratory. The buffering system based on TRIS is also widely used. Zwitterions are compounds that have both a positive charge and a negative charge. Most living systems operate at pH levels close to 7. The practical consequences of this fact are explored in 2C Biochemical Connections and 2D Biochemical Connections. **What naturally occurring pH buffers are present in living organisms?** The H2PO4/HPO pair is the principal buffer in cells. In blood, phosphate ion levels are inadequate for buffering, and a different system operates. The buffering system in blood is based on the dissociation of carbonic acid (H2CO3) . **2C Biochemical Connections: Chemistry of Blood** The maintenance of proper pH is an essential function in all living organisms. The normal pH of human blood, for example, is kept in a very narrow range. When human blood falls below pH 7.35, the condition is called acidosis. This can come from excessive metabolic production of acid or a failure of the kidneys to remove metabolic acid byproducts. If the pH of the blood drops below 7, coma and death can occur. **2D Biochemical Connections: Acids and Sports** The buildup of lactic acid was widely believed to cause muscle pain and muscle fatigue. However, recent evidence suggests that lactic acid actually maintained the muscle membrane's ability to depolarize and repolarize longer, allowing the muscles to continue to contract even though they were fatigued. Since muscle pain seems linked to decreased muscle performance, lactic acid was therefore assumed to also be the cause of the fatigue. This is an active area of research, and there is still much to learn about it. Despite decades of study and popular myth, we still do not really know exactly what causes muscle fatigue, although the athlete shown in Figure 2.20 would most likely tell you it was the lactic acid.