Cells: The Fundamental Units of Life PDF

# Chapter 1 ## Cells: The fundamental Units of Life - UNITY AND DIVERSITY OF CELLS - BACKGROUND AND SCALES - THE EUKARYOTIC CELL - MODELL ORGANISMS - ESSENTIAL CONCEPTS ## Cells come in a variety of shapes and sizes. Note the very different scales of these micrographs. - (A) Drawing of a single n...

# Chapter 1 ## Cells: The fundamental Units of Life - UNITY AND DIVERSITY OF CELLS - BACKGROUND AND SCALES - THE EUKARYOTIC CELL - MODELL ORGANISMS - ESSENTIAL CONCEPTS ## Cells come in a variety of shapes and sizes. Note the very different scales of these micrographs. - (A) Drawing of a single nerve cell from a mammalian brain. This cell has a single, unbranched extension (axon), projecting toward the top of the image, through which it sends electrical signals to other nerve cells, and it possesses a huge branching tree of projections (dendrites) through which it receives signals from as many as 100,000 other nerve cells. - (B) Paramecium. This protozoan—a single giant cell-swims by means of the beating cilia that cover its surface. - (C) The surface of a snapdragon flower petal displays an orderly array of tightly packed cells. - (D) A macrophage spreads itself out as it patrols animal tissues in search of invading microorganisms. - (E) A fission yeast is caught in the act of dividing in two. The medial septum (stained red with a fluorescent dye) is forming a wall between the two nuclei (also stained red) that have been separated into the two daughter cells; in this image, the cells' membranes are stained with a green fluorescent dye. ## How big are cells and their components? - This chart lists sizes of cells and their component parts, the units in which they are measured, and the instruments needed to visualize them. - Drawings convey a sense of scale between living cells and atoms. Each panel shows an image that is magnified by a factor of 10 compared to its predecessor-producing an imaginary progression from a thumb, to skin, to skin cells, to a mitochondrion, to a ribosome, and ultimately to a cluster of atoms forming part of one of the many protein molecules in our bodies. - Note that ribosomes are present inside mitochondria (as shown here), as well as in the cytoplasm. Details of molecular structure, as shown in the last two bottom panels, are beyond the power of the electron microscope. ## Background and Scales ### Length | Unit | Measurement | |---|---| | 1 km (kilometer) | 10³ m | | 1 m (meter) | 10⁰ m | | 1 cm (centimeter) | 10⁻² m | | 1 mm (millimeter) | 10⁻³ m | | 1 μm (micrometer) | 10⁻⁶ m | | 1 nm (nanometer) | 10⁻⁹ m | | 1 Å (Ångström) | 10⁻¹⁰ m | ### Mass | Unit | Measurement | |---|---| | 1 kg (kilogram) | 10³ g | | 1 g (gram) | 10⁰ g | | 1 mg (milligram) | 10⁻³ g | | 1 μg (microgram) | 10⁻⁶ g | | 1 ng (nanogram) | 10⁻⁹ g | ### Volume | Unit | Measurement | |---|---| | 1 l (liter) | (10⁻¹ m)³ | | 1 ml (milliliter) | 10⁻³ l | (10⁻² m)³ | 1 cm³ | | 1 μl (microliter) | 10⁻⁶ l | (10⁻³ m)³ | 1 mm³ | | 1 nl (nanoliter) | 10⁻⁹ l | (10⁻⁴ m)³ | ## Mole and Concentration | Unit | Measurement | |---|---| | 1 M (molar) | 1 mole/l = 6.02 x 10²³ molecules/l | | 1 mM (millimolar) | 10⁻³ M | | 1 μM (micromolar) | 10⁻⁶ M | | 1 nM (nanomolar) | 10⁻⁹ M | # The Eukaryotic cell - bigger and more elaborate than bacteria and archaea - By definition, all eukaryotic cells have a nucleus - possession of a nucleus goes hand-in-hand with possession of a variety of other organelles, most of which are membrane-enclosed and common to all eukaryotic organisms. - In this section, we take a look at the main organelles found in eukaryotic cells from the point of view of their functions, and we consider how they came to serve the roles they have in the life of the eukaryotic cell. ## Nucleus - This drawing of a typical animal cell shows its extensive system of membrane-enclosed organelles. The nucleus is colored brown, the nuclear envelope is green, and the cytoplasm (the interior of the cell outside the nucleus) is white. - An electron micrograph of the nucleus in a mammalian cell. Individual chromosomes are not visible because at this stage of the cell-division cycle the DNA molecules are dispersed as fine threads throughout the nucleus. ## Mitochondria - An electron micrograph of a cross section of a mitochondrion reveals the extensive infolding of the inner membrane. - This three-dimensional representation of the arrangement of the mitochondrial membranes shows the smooth outer membrane (gray) and the highly convoluted inner membrane (red). - The inner membrane contains most of the proteins responsible for energy production in eukaryotic cells; it is highly folded to provide a large surface area for this activity. - In this schematic cell, the innermost compartment of the mitochondrion is colored orange. ## Endoplasmic Reticulum (ER) - Schematic diagram of an animal cell showing the endoplasmic reticulum. - An electron micrograph of a thin section of a mammalian pancreatic cell shows a small part of the ER, of which there are vast amounts in this cell type, which is specialized for protein secretion. - Note that the ER is continuous with membranes of the nuclear envelope. - The black particles, studding the region of the ER (and nuclear envelope) shown here are ribosomes, structures that translate mRNAs into proteins. - Because of its appearance, ribosome-coated ER is often called rough ER, to distinguish it from the "smooth ER," which does not have ribosomes bound to it. ## Golgi apparatus - Schematic diagram of an animal cell with the Golgi apparatus colored red. - More realistic drawing of the Golgi apparatus. Some of the vesicles seen nearby have pinched off from the Golgi stack; others are destined to fuse with it. - Only one stack is shown here, but several can be present in a cell. - Electron micrograph that shows the Golgi apparatus from a typical animal cell. ## Membrane-enclosed organelles are distributed throughout the eukaryotic cell cytoplasm. - (A) The various types of membrane-enclosed organelles, shown in different colors, are each specialized to perform a different function. - (B) The cytoplasm that fills the space outside of these organelles is called the cytosol (colored blue). ## Cytosol - This atomically detailed model of the cytosol of E. coli is based on the sizes and concentrations of 50 of the most abundant large molecules present in the bacterium. RNAs, proteins, and ribosomes are shown in different colors ## Cytoskeleton - The three major types of filaments can be detected using different fluorescent stains. - Shown here are (A) actin filaments, (B) microtubules, and (C) intermediate filaments. - Intermediate filaments are not found in the cytoplasm of cells with cell walls, such as plant cells. ## Yeast Saccharomyces cerevisiae is a model eukaryote - Yeasts are simple, free-living eukaryotes. - The cells shown in this micrograph belong to the species of yeast, Saccharomyces cerevisiae, used to make dough rise and turn malted barley juice into beer. - As can be seen in this image, the cells reproduce by growing a bud and then dividing asymmetrically into a large mother cell and a small daughter cell; for this reason, they are called budding yeast. ## Fruit Fly Drosophila melanogaster - Drosophila melanogaster is a favorite among developmental biologists and geneticists. - Molecular genetic studies on this small fly have provided a key to the understanding of how all animals develop. ## Model organisms | Organism | Genome Size* (Nucleotide Pairs) | Approximate Number of Protein-coding Genes | |---|---|---| | Homo sapiens (human) | 3200 x 10⁶ | 19,000 | | Mus musculus (mouse) | 2800 x 10⁶ | 22,000 | | Drosophila melanogaster (fruit fly) | 180 x 10⁵ | 14,000 | | Arabidopsis thaliana (plant) | 103 x 10⁶ | 28,000 | | Caenorhabditis elegans (roundworm) | 100 x 10⁶ | 22,000 | | Saccharomyces cerevisiae (yeast) | 12.5 x 10⁶ | 6600 | | Escherichia coli (bacterium) | 4.6 x 10⁶ | 4300 | *Genome size includes an estimate for the amount of highly repeated, noncoding DNA sequence, which does not appear in genome databases. # Essential Concepts of Chapter 1 - Cells are the fundamental units of life. All present-day cells are believed to have evolved from an ancestral cell that existed more than 3 billion years ago. - All cells are enclosed by a plasma membrane, which separates the inside of the cell from its environment. - All cells contain DNA as a store of genetic information and use it to guide the synthesis of RNA molecules and proteins. This molecular relationship underlies cells' ability to self-replicate. - Cells in a multicellular organism, though they all contain the same DNA, can be very different because they turn on different sets of genes according to their developmental history and to signals they receive from their environment. - Animal and plant cells are typically 5-20 µm in diameter and can be seen with a light microscope, which also reveals some of their internal components, including the larger organelles. - The simplest of present-day living cells are prokaryotes-bacteria and archaea: although they contain DNA, they lack a nucleus and most other organelles and probably resemble most closely the original ancestral cell. - Different species of prokaryotes are diverse in their chemical capabilities and inhabit an amazingly wide range of habitats. - Eukaryotic cells possess a nucleus and other organelles not found in prokaryotes. They probably evolved in a series of stages, including the acquisition of mitochondria by engulfment of aerobic bacteria and (for cells that carry out photosynthesis) the acquisition of chloroplasts by engulfment of photosynthetic bacteria. - The nucleus contains the main genetic information of the eukaryotic organism, stored in very long DNA molecules. # Essential Concepts of Chapter 1 - The cytoplasm of eukaryotic cells includes all of the cell's contents outside the nucleus and contains a variety of membrane-enclosed organelles with specialized functions: mitochondria carry out the final oxidation of food molecules and produce ATP; the endoplasmic, reticulum and the Golgi apparatus synthesize complex molecules for export from the cell and for insertion in cell membranes; lysosomes digest large molecules; in plant cells and other photosynthetic ,eukaryotes, chloroplasts perform photosynthesis. - Outside, the membrane-enclosed organelles in the cytoplasm is the cytosol, a highly concentrated mixture of large and small molecules that carry out many essential biochemical processes. - The cytoskeleton is composed of protein filaments that extend throughout the cytoplasm and are responsible for cell shape and movement and for the transport of organelles and large molecular complexes from one intracellular location to another. - Free-living, single-celled eukaryotic microorganisms are complex cells that, in some cases, can swim, mate, hunt, and devour other microorganisms. - Animals, plants, and some fungi are multicellular organisms that consist of diverse eukaryotic cell types, all derived from a single fertilized egg cell; the number of such cells cooperating to form a large, multicellular organism such as a human runs into thousands of billions. - Biologists have chosen a small number of model organisms to study intensely, including the bacterium E. coli, brewer's yeast, a nematode worm, a fly, a small plant, a fish, mice, and humans themselves. - The human genome has about 19,000 protein-coding genes, which is about five times as many as E. coli and about 5000 more than the fly. # Chapter 2 ## The Chemistry behind it all - CHEMICAL BONDS - ACIDS AND BASES # Calculate with Mol - **atomic weight** = The mass of an atom relative to the mass of a hydrogen atom; equal to the number of protons plus the number of neutrons that the atom contains - **molecular weight** = Sum of the atomic weights of the atoms in a molecule; as a ratio of molecular masses, it is a number without units. - 1 Mol = 6 x 10²³ molecules of the substance - **A mole** is X grams of a substance, where X is the molecular weight of the substance. A mole will contain 6 x 10²³ molecules of the substance. - 1 mole of carbon weighs 12 g - 1 mole of glucose weighs 180 g - 1 mole of sodium chloride weighs 58 g - **A one molar solution** has a concentration of 1 mole of the substance in 1 liter of solution. A 1 M solution of glucose, for example, contains 180 g/L, and a one millimolar (1 mM) solution contains 180 mg/L. - The standard abbreviation for gram is g; the abbreviation for liter is L. ## Chemical Bonds - Matter is made of combinations of elements-substances such as hydrogen or carbon that cannot be broken down or interconverted by chemical means. The smallest particle of an element that still retains its distinctive chemical properties is an atom. - The characteristics of substances other than pure elements-including the materials from which living cells are made-depend on which atoms they contain and the way that these atoms are linked together in groups to form molecules. To understand living organisms, therefore, it is crucial to know how the chemical bonds that hold atoms together in molecules are formed. ## An atom consists of a nucleus surrounded by an electron cloud - Schematic representations of an atom of carbon and an atom of hydrogen are shown. The nucleus of every atom except hydrogen consists of both positively charged protons and electrically neutral neutrons; the atomic weight equals the number of protons plus neutrons. The number of electrons, in an atom is equal to, the number of protons, so that the atom has no net charge. ## Geometry - The spatial arrangement of the covalent bonds that can be formed by oxygen, nitrogen, and carbon. - Molecules formed from these atoms therefore have precise three-dimensional structures defined by the bond angles and bond lengths for each covalent linkage. A water molecule, for example, forms a "V" shape with an angle close to 109°. ## Covalent Bonds Form by Sharing of Electrons - Each hydrogen atom in isolation has a single electron, which means that its first (and only) electron shell is incompletely filled. By coming together to form a hydrogen molecule (H2, or hydrogen gas), the two atoms are able to share their electrons, so that each obtains a completely filled first shell, with the shared electrons adopting modified orbits around the two nuclei. - The covalent bond between the two atoms has a defined length-0.074 nm, which is the distance between the two nuclei. If the atoms were closer together, the positively charged nuclei would repel each other; if they were farther apart, they would not be able to share electrons as effectively. ## Distribution of electrons - Comparison of electron distributions in the polar covalent bonds in a molecule of water (H₂O) and the nonpolar covalent bonds in a molecule of oxygen (O₂). - In H₂O, electrons are more strongly attracted to the oxygen nucleus than to the H. nucleus, as indicated by the distributions of the partial negative (δ-) and partial positive (δ+) charges. ## lonic Bonds - An atom of sodium (Na) reacts with an, atom of chlorine (Cl). Electrons of each atom are shown in their different shells; (incompletely filled) outermost shells are shown in red. The reaction takes place with transfer of a single electron from sodium to chlorine, forming two electrically charged atoms, or ions, each with complete, sets of electrons in their outermost shells. The two ions have opposite charge and are held together by electrostatic attraction. - The product of the, reaction between sodium and chlorine, crystalline sodium chloride, contains sodium and chloride ions packed closely together in a regular array in which the charges are exactly balanced. - Color photograph of crystals of sodium chloride ## Molecular Interaction - A large molecule, such as a protein, can bind to another protein through noncovalent interactions on the surface of a cell, many individual weak, interactions could cause the two proteins to recognize each other specifically and form a tight complex. - Shown here is a set of electrostatic attractions between complementary positive and negative charges. ## Hydrogen Bonds - Hydrogen bonds have only about 1/20 the strength of a covalent bond. - Noncovalent hydrogen bonds form between water molecules and between many other polar molecules. - A hydrogen bond forms between two water molecules. The slight positive charge associated with the hydrogen atom is electrically attracted to the slight negative charge of the oxygen atom. - In cells, hydrogen bonds commonly form between molecules, that contain an oxygen or nitrogen. The atom bearing the hydrogen is considered the H-bond donor and the atom that interacts with the hydrogen is the H-bond acceptor. ## Examples of Hydrogen bonds - Amino acids in a polypeptide chain can be hydrogen-bonded together in a folded protein. - Two bases, G and C, are hydrogen-bonded in a DNA double helix. ## Chemical properties of water - Molecules of water join together transiently in a hydrogen-bonded lattice. The cohesive nature of water is responsible for many of its unusual properties, such as high surface tension, high specific heat capacity, and high heat of vaporization. ## Hydrophobic molecules in water - Substances that contain a preponderance of nonpolar bonds are usually insoluble in water and are termed hydrophobic. - Water molecules are not attracted to such hydrophobic molecules and so have little tendency to surround them and bring them into solution. - Hydrocarbons, which contain many C-H bonds, are especially hydrophobic ## Hydrophilic Molecules in Water - Substances that dissolve readily in water are termed hydrophilic. - lonic substances such as sodium chloride dissolve because water molecules are attracted to the positive (Na+) or negative (Cl-) charge of each ion. - Polar substances such as urea dissolve because their molecules form hydrogen bonds with the surrounding water molecules. ## Parameter of chemical bonds | Bond Type | Length* (nm) | Strength (kJ/mole) In Vacuum | Strength (kJ/mole) In Water | |---|---|---|---| | Covalent | 0.10 | 377 [90]** | 377 [90]| | Noncovalent: ionic bond | 0.25 | 335 [80] | 12.6 [3] | | Noncovalent: hydrogen bond | 0.17 | 16.7 [4] | 4.2 [1] | | Noncovalent: van der Waals attraction (per atom) | 0.35 | 0.4 [0.1] | 0.4 [0.1] | *The bond lengths and strengths listed are approximate, because the exact values will depend on the atoms involved. **Values in brackets are kcal/mole. 1 kJ = 0.239 kcal and 1 kcal = 4.184 kJ. ## Autoproteolysis of water - Water can react as acid or as base in proteolysis. - Even multiply distilled water (= very pure water) has a specific conductivity, which would not be possible without the presence of the ions (H₃O⁺ and OH⁻). - H₂O + H₂O ⇌ H₃O⁺ + OH⁻ - Like any protolysis, the autoprotolysis of water is an equilibrium reaction, with the equilibrium being strongly left. ## The law of mass action for the autoproteolysis of water. K = [H₃O⁺][OH⁻] / [H₂O]² ## The lon product of water - Although, the equilibrium exists, the number of water particles, i.e. the concentration of water in this container, has not changed noticeably. Therefore, the concentration of water can be considered constant and is therefore shifted to the side of the constant K. This results in a new constant Kw, which is called the ion product of water. - K = [H₃O⁺][OH⁻] / [H₂O]² - Kw = K* [H₂O]² = [H₃O⁺][OH⁻] - Kw = 1*10⁻¹⁴ mol²L⁻² (bei 25°C) ## Acids - Substances that release hydrogen ions (protons) into solution are called acids. - HCI ⇌ H⁺ + Cl⁻ - hydrochloric acid (strong acid) - hydrogen ion - chloride ion ## The Law of Mass action - How strong an acid is, depends on the dissociation equilibrium of the acidic aqueous solution on the product side. Strong acids dissociate completely to their ions. - HA + H₂O ⇌ H₃O⁺ + A⁻ - K = [H₃O⁺][A⁻] / [HA][H₂O] - Applying the law of mass action to the protolysis equilibria leads us to a generally valid characterization of acid strengths. We consider the general case where an acid HA protolyses. ## Acid constant ### Säurekonstante Ks - As we always look at a diluted aqueous acid, it changes the water concentration by adjusting this equilibrium only so little that the concentration of water can be considered constant. Thus, [H₂O] is drawn to the side of the constant K and combined to the acid constant Ks. - Ks = K* [H₂O] = [H₃O⁺][A⁻] / [HA] - Note: The constant Ks is a measure for the strength of an acid and is called the acid constant. The greater, the Ks, the ,stronger the acid. ## Weak Acids - Many of the acids important in the cell, are not completely, dissociated, and they are therefore weak acids-for example, the carboxyl group (-COOH), which dissociates to give a hydrogen ion in solution. - -C-O-H, ⇌ H⁺ + -C-O⁻ - carboxyl group (weak acid) - hydrogen ion - carboxylate ion - Note that this is, a reversible, reaction. ## Hydrogen lon Exchange - Positively charged hydrogen ions (H+) can spontaneously move from one water molecule to another, thereby creating two ionic species. - H₂O ⇌ H₃O⁺ + OH⁻ - hydronium ion - hydroxyl ion - often written as: H₂O ⇌ H⁺ + OH⁻ - hydrogen ion - hydroxide ion - Pure water contains equal concentrations of hydronium ions and hydroxyl ions (both 10⁻⁷ M). ## Protons move continuously from one molecule to another in aqueous solutions. - (A) The reaction that takes place when a molecule of acetic acid dissolves in water. At pH 7, nearly, all of the acetic acid molecules are present as acetate ions. - (B) Water molecules are continually exchanging protons with each other to form hydronium and hydroxyl ions. These ions in turn, rapidly recombine to form water molecules. ## The pH - The acidity of a solution is defined by the concentration (conc.) of hydronium ions (H₃O⁺), It possesses, generally, abbreviated as H+. For convenience, we use the pH scale. - pH = -log₁₀[H⁺] - For pure water - [H⁺] = 10⁻⁷ moles/liter - pH = 7.0 ## Examples - In aqueous solutions, the concentration of hydroxyl (OH⁻) ions increases, as the concentration of H₃O⁺ (or H⁺) ions decreases. The product of the two values -[OH⁻] x [H⁺] - is always 10⁻¹⁴ (moles/liter)². At neutral pH, [OH⁻] = [H⁺], and both ions are present at 10⁻⁷ M. Also shown are examples of common solutions along with their | [H⁺], moles/liter | pH | [OH⁻], moles/liter | Some solutions and their pH values | |---|---|---|---| | 1 | 0 | 10⁻¹⁴ | battery acid (0.5) | | 10⁻¹ | 1 | 10⁻¹³ | stomach acid (1.5) | | 10⁻² | 2 | 10⁻¹² | lemon juice (2.3), cola (2.5) | | ACIDIC | 10⁻³ | 3 | 10⁻¹¹ | orange juice (3.5) | | 10⁻⁴ | 4 | 10⁻¹⁰ | beer (4.5) | | 10⁻⁵ | 5 | 10⁻⁹ | black coffee (5.0), acid rain (5.6) | | 10⁻⁶ | 6 | 10⁻⁸ | urine (6.0), milk (6.5) | | NEUTRAL | 10⁻⁷ | 7 | 10⁻⁷ | pure water (7.0) | | 10⁻⁸ | 8 | 10⁻⁶ | sea water (8.0) | | 10⁻⁹ | 9 | 10⁻⁵ | hand soap (9.5) | | 10⁻¹⁰ | 10 | 10⁻⁴ | milk of magnesia (10.5) | | BASIC | 10⁻¹¹ | 11 | 10⁻³ | household ammonia (11.9) | | 10⁻¹² | 12 | 10⁻² | non-phosphate detergent (12.0) | | 10⁻¹³ | 13 | 10⁻¹ | bleach (12.5) | | 10⁻¹⁴ | 14 | 1 | caustic soda (13.5) | ## Bases - Substances that reduce the number of hydrogen ions in solution, are called bases. - Some bases, such as ammonia, combine directly with hydrogen ions. - NH₃ + H⁺ → NH₄+ - ammonia - hydrogen ion - ammonium ion - Other bases, such as sodium hydroxide, reduce the number of H+ ions indirectly, by producing OH- ions that, then combine directly with H+ ions to make H2O. - NaOH → Na⁺ + OH⁻ - sodium hydroxide (strong base) - sodium ion - hydroxyl ion ## Base constant Kb - For the protolysis equilibrium of a base B, the base constant Kb is obtained in the same way: - B + H₂O ⇌ OH⁻ + BH⁺ - K = [OH⁻][BH⁺] / [B][H₂O] - KB = K* [H₂O] = [OH⁻][BH⁺] / [B] - Note: The constant Kb is a measure for the strength of a base and is called base constant. The greater KB, the stronger the base. ## pKb (base exponent) and pKs (acid exponent) - All concentrations occurring in, the equations of Ks and Kb are equilibrium, concentrations. The unit of the constants is mol/L, thus the unit of a concentration. For many acids and bases the Ks and KB values have, been determined experimentally, and tabulated. However, the Kb and Ks values are not written down there, but the pKb (base exponent) and pKs (acid exponent) values are found there. - pKs = -log (Ks) - pKB = -log (KB) - pKs (HA) + pKB (A⁻) = 14 ## Note - Note: The constant Ks is a measure for the strength of an acid and is called acid constant. The higher the Ks or the lower the pKS, the stronger the acid. - Note: The constant Kb is a measure for the strength of a base and is called base constant. The larger the KB or the smaller the pK, the stronger the base. ## Weak bases - Many bases found in cells are partially associated with H+ ions and are termed weak bases. This is true of compounds that contain an amino group (-NH₂), which has a weak tendency to reversibly accept an H+ ion from water, thereby increasing the concentration of free OH- ions. - -NH₂ + H⁺ ⇌ -NH₃+ - The interior of a cell is kept close to neutral by the presence of buffers: mixtures of weak acids and bases that will adjust proton concentrations around pH 7 by releasing protons (acids) or taking them up (bases) whenever the pH changes. This give-and-take keeps the pH of the cell relatively constant under a variety of conditions. # Chapter 3 ## Chemical Components of Cells - TYPES OF SUGAR - FATTY ACIDS - AMINO ACIDS - NUCLEOTIDES ## Cellular composition - Sugars, fatty acids, amino acids, and nucleotides are the four main families of small organic molecules in cells. They form the monomeric building blocks, or subunits, for larger organic molecules, including most of the macromolecules and other molecular assemblies of the cell. Some, like the sugars and the fatty acids, are also energy sources. ## Distribution by percentage | Substance | Percent of Total Cell Weight | Approximate Number of Types in Each Class | |---|---|---| | Water | 70 | 1 | | Inorganic ions | 1 | 20 | | Sugars and precursors | 1 | 250 | | Amino acids and precursors | 0.4 | 100 | | Nucleotides and precursors | 0.4 | 100 | | Fatty acids and precursors | 1 | 50 | | Other small molecules | 0.2 | 3000 | | Phospholipids | 2 | 4* | | Macromolecules (nucleic acids, proteins, and polysaccharides) | 24 | 3000 | *Estimated number of types ## Outline of some of the types of sugar - **Monosaccharides:** General formula (CH₂O)n, where n is usually 3, 4, 5, or 6 ### ALDOSES | Carbon Count | Name | Structure | |---|---|---| | 3-carbon (TRIOSES) | glyceraldehyde | H-C=O<br>H-C-OH<br>H-C-OH<br>H | | 5-carbon (PENTOSES) | ribose | H-C=O<br>H-C-OH<br>H-C-OH<br>H-C-OH<br>H-C-OH<br>H | | 6-carbon (HEXOSES) | glucose | H-C=O<br>HO-C-H<br>H-C-OH<br>H-C-OH<br>H-C-OH<br>CH₂OH | ### KETOSES | Carbon Count | Name | Structure | |---|---|---| | 3-carbon (TRIOSES) | dihydroxyacetone | H-C-OH<br>C=O<br>H-C-OH<br>H | | 5-carbon (PENTOSES) | ribulose | H-C-OH<br>C=O<br>H-C-OH<br>H-C-OH<br>CH₂OH | | 6-carbon (HEXOSES) | fructose | H-C-OH<br>C=O<br>HO-C-H<br>H-C-OH<br>H-C-OH<br>CH₂OH | ## Ring Formation - In aqueous solution, the aldehyde or ketone group of a sugar molecule tends to react with a hydroxyl group of the same molecule, thereby closing the molecule into a ring. ## Types of display - The structure of glucose, a monosaccharide, can be represented in several ways. - (A) A structural formula in which the atoms are shown as chemical symbols, linked together by solid lines representing the covalent bonds. The thickened lines are used, to indicate the plane of the sugar ring and to show that the H and OH groups are not in the same plane as the ring. - (B) Another kind of structural formula that shows the three-dimensional structure of glucose in a so-called chair configuration. - (C) A ball-and-stick model in which the three-dimensional arrangement of space is indicated. - (D) A space-filling model, which, as well as depicting, the three-dimensional arrangement of the atoms, also shows the relative sizes and surface contours of the molecule (Movie 2.1). The atoms in (C) and (D) are colored as in Figure 2-9: C, black; H, white; O, red. This is the conventional color-coding for these atoms and will be used throughout this book. ## Disaccharides - The carbon that carries the aldehyde, or the ketone can react with any hydroxyl group on a second sugar molecule to form a disaccharide. - Three common disaccharides are - maltose (glucose + glucose) - lactose (galactose + glucose) - sucrose (glucose + fructose) - Two monosaccharides can be linked by a covalent glycosidic bond to form a disaccharide. - This reaction belongs to a general category of reactions termed condensation reactions, in which two molecules join together as a result of the loss of a water molecule. The reverse reaction (in which water is added) is termed hydrolysis. ## Oligosaccharides und Polysaccharides - Large linear and branched molecules can be made from simple repeating sugar subunits. Short chains are called oligosaccharides, and long chains are called polysaccharides. Glycogen, for example, is a polysaccharide made entirely of glucose subunits joined together. ## Complex Oligosaccharides - In many cases, a sugar sequence is nonrepetitive. Many different molecules are possible. Such complex oligosaccharides are usually linked to proteins or to lipids, as is this oligosaccharide, which is part of a cell-surface molecule that defines a particular blood group. ## Fatty Acids - Fatty acids have both hydrophobic and hydrophilic components. The hydrophobic hydrocarbon chain is attached to a hydrophilic carboxylic acid group. - Different fatty acids have different hydrocarbon tails. Palmitic acid is shown here. - (A) Structural formula, showing the carboxylic acid head group in its ionized form, as it exists in water at pH 7. - (B) Ball-and-stick model. - (C) Space-filling model - (D) Space-filling model ## Phospholipids - Phospholipids contain two hydrophobic fatty acid tails and a hydrophilic head. - Phosphatidylcholine is the most common phospholipid in cell membranes. - Diagram showing how, in an aqueous environment, the hydrophobic tails of, phospholipids pack together to form a lipid bilayer. - In the lipid bilayer, the hydrophilic heads of the, phospholipid molecules are on the outside, facing the aqueous environment, and the hydrophobic tails are on the inside, where water is excluded. ## Families of Amino acids - The common amino acids are grouped according to whether their side chains are - acidic - basic - uncharged polar - nonpolar - These 20 amino acids are given both three-letter and one-letter abbreviations. - Thus: alanine = Ala = A - R is commonly one of the 20 different side chains; at pH= 7 both the amino and carboxyl group are ionized ## Amino acids ### Subunits of Proteins - All amino acids have an amino group, a carboxyl group, and a side chain (R) attached to their α-carbon atom. In the cell, where the pH is close to 7, free amino, acids exist in their ionized form, but when they are incorporated into, a polypeptide chain, the charges on their amino and carboxyl groups are lost. - (A) The amino acid shown here is alanine, one of the simplest amino acids, which has a methyl group (CH3) as its side chain. Its amino group is highlighted in blue and its carboxyl, group in red. - (B) A ball-and-stick model - (C) a space-filling model of alanine. - (D) a space-filling model of alanine. In (B) and (C), the N atom is blue and the O atom is red. ## Peptides - Amino acids in a protein are held together by peptide, bonds. The four