Week 3 - Chemistry Comes to Life Chemistry PDF

Chapter 2 Chemistry Comes to Life Lecture Presentation by Tonya Bates, UNC Charlotte © 2017 Pearson Education, Inc. Life is Hierarchical atom...

Chapter 2 Chemistry Comes to Life Lecture Presentation by Tonya Bates, UNC Charlotte © 2017 Pearson Education, Inc. Life is Hierarchical atom Molecule organelle cell tissue organ organ system organism population community ecosystem biosphere (hydrogen (water) (nucleus) (neuron) (nervous tissue) (brain) (nervous system) (sea lion) (colony) (giant kelp (southern California (Earth) forest) coast) Figure 1.6  Chemistry Comes to Life Outline:  The Nature of Atoms  Chemical Bonds and Compounds  The Role of Water in Life  Major Molecules of Life © 2017 Pearson Education, Inc.  2.1 The Nature of Atoms  Everything that takes up space and has mass is called matter  All matter is made of atoms, each containing a nucleus with protons and neutrons surrounded by a cloud of electrons Atoms are units of matter that cannot be broken down into simpler substances by ordinary chemical means © 2017 Pearson Education, Inc. F Figure 2.1 Electrons spin in shells around the nucleus. Electron shell Proton () Electron () 2p 8p 2n 8n Nucleus Neutron (no charge) Helium (He) Helium (He) Oxygen (O) (a) A three-dimensional representation of an atom (b) A two-dimensional representation (c) A two-dimensional representation of an of helium, showing protons and neutrons in the of an atom of helium atom of oxygen nucleus and electrons occupying a region around the nucleus © 2017 Pearson Education, Inc. Unstable, very reactive atoms Stable, unreactive atoms hydrogen (H) helium (He) carbon (C) neon (Ne) sodium (Na) argon (Ar) Outermost electron Outermost electron shells unfilled shells filled Figure 2.7 Table 2.1 © 2017 Pearson Education, Inc.  2.1 The Nature of Atoms  Element An element is a form of matter that cannot be broken down into simpler substances It is made of many atoms that are all the same Examples include gold, iron, oxygen © 2017 Pearson Education, Inc.  2.1 The Nature of Atoms  Each element has an atomic number and atomic mass Atomic number  The number of protons in the nucleus Atomic mass  The number of protons plus the number of neutrons, as electrons have an insignificant mass © 2017 Pearson Education, Inc. Figure 2.2 Group number Element symbol 1 8 Atomic Atomic mass number 1 2 3 4 5 6 7 Nonmetals 2 Metals 3 Transition elements 4 5 6 7 Metals Nonmetals Lanthanides Actinides © 2017 Pearson Education, Inc.  2.1 The Nature of Atoms  Elements with the same number of protons but different numbers of neutrons are called isotopes  Example of carbon atom All carbon atoms have six protons in the nucleus Common isotopes of carbon include:  12C with six neutrons  13C with seven neutrons  14C with eight neutrons © 2017 Pearson Education, Inc. © 2017 Pearson Education, Inc.   A radioisotope, also known as a radioactive isotope, is an atom that has an unstable nucleus and undergoes radioactive decay, emitting radiation in the process.  Isotopes are variants of chemical elements that have the same number r of protons in their nuclei but differ in the number of neutrons. Radioisotopes have an excess or deficiency of neutrons compared to stable isotopes of the same element, which makes their nuclei unstable. © 2017 Pearson Education, Inc.  2.1 The Nature of Atoms  Radiation is energy moving through space, such as radio waves, light, and heat  Some elements have isotopes, which can be stable (do not change over time) or unstable (emit radiation to regain a stable state)  A radioisotope is an unstable radiation-emitting isotope  Radiation can be harmful, causing the death of cells, or beneficial, as evidenced by its use in medicine © 2017 Pearson Education, Inc.  2.1 The Nature of Atoms  Examples of important isotopes used in medicine Radioactive iodine can be used for thyroid imagery in diagnosing metabolic disorders Radiation can also be used as a treatment for cancer, as cancer cells are more susceptible to damage © 2017 Pearson Education, Inc. Figure 2.4 Thyroid gland Trachea (windpipe) (a) An image of a normal (b) An image of an enlarged thyroid gland thyroid gland © 2017 Pearson Education, Inc. © 2017 Pearson Education, Inc. © 2017 Pearson Education, Inc. © 2017 Pearson Education, Inc.  Scans with Radioisotopes A thyroid scan shows the accumulation of radioactive iodine- 131 in the thyroid. Figure 2.5 Figure 2.5 Logo for irradiated foods. https://www.youtube.com/watch?v=U0SZHGfP_1A&t=3s © 2017 Pearson Education, Inc.  Radioisotopes Radioisotopes have a wide range of uses in biomedical research, diagnosis, and therapy due to their ability to emit radiation. Here are some common applications: Medical Imaging: Radioisotopes are widely used in various imaging techniques such as positron emission tomography (PET), single-photon emission computed tomography (SPECT), and gamma camera imaging. For example, ^18F-fluorodeoxyglucose (FDG), a radioisotope, is commonly used in PET scans to visualize metabolic activity in tissues, aiding in the diagnosis and monitoring of various diseases including cancer. Radiopharmaceuticals: Radioisotopes are incorporated into pharmaceuticals to create radiopharmaceuticals used for diagnostic and therapeutic purposes. For instance, radioactive iodine (^131I) is used in the diagnosis and treatment of thyroid disorders such as hyperthyroidism and thyroid cancer. © 2017 Pearson Education, Inc.  Radioisotopes Radiation Therapy: Radioisotopes are used in radiation therapy to treat cancer. Radioactive sources such as cobalt-60 (^60Co) and various isotopes of iridium, cesium, and gold are used to deliver localized radiation doses to tumors, helping to destroy cancer cells while minimizing damage to surrounding healthy tissues. © 2017 Pearson Education, Inc.  Labeling and Tracing: Radioisotopes are used to label molecules such as proteins, antibodies, and drugs for tracing their distribution and metabolism within the body. This technique is valuable for studying physiological processes and disease mechanisms, as well as for developing new drugs and therapies. Research Tools: Radioisotopes are essential tools in biomedical research for studying biological pathways, protein interactions, and cellular processes. They are used in techniques such as autoradiography, radioimmunoassay, and nucleic acid labeling, enabling scientists to investigate molecular mechanisms underlying health and disease. © 2017 Pearson Education, Inc.  Radiation Sterilization: Radioisotopes like gamma-emitting isotopes are used for sterilization of medical equipment and supplies. Gamma radiation effectively kills microorganisms, making it a valuable method for ensuring the safety of medical devices and pharmaceutical products. Blood Volume and Flow Measurement: Radioisotopes such as technetium-99m (^99mTc) are used in blood volume and flow measurements, aiding in the diagnosis of cardiovascular diseases and assessing organ function. These applications demonstrate the versatility and importance of radioisotopes in various aspects of biomedical science, from diagnosis and treatment to basic research and quality control in healthcare settings. © 2017 Pearson Education, Inc.  2.2 Chemical Bonds and Compounds  Two or more elements may combine to form a compound  A compound’s characteristics are usually different from those of the individual elements  The atoms in a compound are held together by chemical bonds © 2017 Pearson Education, Inc. Figure 2.6 (a) The element sodium is a (b) Elemental sodium reacts solid metal. explosively with water. (c) The element chlorine is (d) When the elements sodium a yellow gas. and chlorine join, they form table salt, a compound quite different from its elements. © 2017 Pearson Education, Inc.  2.2 Chemical Bonds and Compounds  Covalent bonds form when 2 or more atoms share electrons  Molecules are chemical structures held together by covalent bonds; compounds are molecules formed with 2 or more elements  Molecules are described in a chemical formula that contains the symbols for all the elements included in them © 2017 Pearson Education, Inc. Figure 2.7 The shell closest to the nucleus can hold up to 2 electrons. 6p 8p The next shell out can 1p hold up to 8 electrons 6n 8n (the shell shown here has 6). Atoms with more than 10 electrons have additional shells. Hydrogen atom Carbon atom Oxygen atom (atomic number  1) (atomic number  6) (atomic number  8) © 2017 Pearson Education, Inc. Figure 2.8 Single covalent bonds Single Single covalent bonds covalent bonds Carbon atom 4 Hydrogen atoms Methane (CH4) (a) The molecule methane (CH4) is formed by the sharing of electrons between one carbon atom and four hydrogen atoms. Because in each case one pair of electrons is shared, the bonds formed are single covalent bonds. Double Double covalent covalent bond bond Double covalent bonds Carbon atom 2 Oxygen atoms Carbon dioxide (CO2) (b) The oxygen atoms in a molecule of carbon dioxide (CO2) form double covalent bonds with the carbon atom. In double bonds, two pairs of electrons are shared. Triple covalent bond Triple covalent bonds Nitrogen atom Nitrogen atom Nitrogen gas (N2) (c) The nitrogen atoms in nitrogen gas (N2) form a triple covalent bond, in which three pairs of electrons are shared. © 2017 Pearson Education, Inc.  2.2 Chemical Bonds and Compounds  Ions are atoms or a group of atoms with a positive or negative electrical charge  The charge results from an uneven number of protons and electrons  An ionic bond results from the mutual attraction of oppositely charged ions  Ionic bonds are weaker than covalent bonds since they do not share electrons © 2017 Pearson Education, Inc. Figure 2.9 An atom of sodium Having given up an Having received an transfers the electron electron, sodium becomes electron, chlorine becomes in its outer shell to an a positively charged ion. a negatively charged ion. atom of chlorine. Sodium ion Chloride ion () () Sodium atom  Chlorine atom Sodium chloride (NaCl) The oppositely charged sodium and chloride ions are attracted to one another, forming sodium chloride. © 2017 Pearson Education, Inc.  2.3 The Role of Water in Life  When the electrons of a covalent bond are shared unequally, the bond is called polar The resulting molecules are called polar molecules Water is an example of a polar molecule © 2017 Pearson Education, Inc. Polar and Nonpolar Bonding  A polar covalent bond exists when shared electrons are not shared equally among atoms in a molecule, due to electronegativity differences. Polar and Nonpolar Bonding (a) Polar water molecule (b) Nonpolar methane molecule slight negative charge polar nonpolar because slight charges are positive symmetric charge Figure 2.9  2.3 The Role of Water in Life  Hydrogen bonds form when the slightly positive hydrogen atoms of one water molecule are attracted to the slightly negative oxygen atoms in another water molecule  Hydrogen bonds are the weakest of all the bonds © 2017 Pearson Education, Inc. Figure 2.10a 2 Hydrogen  Oxygen Water (H2O) atoms atom (a) Water is formed when an oxygen atom covalently bonds (shares electrons) with two hydrogen atoms. Because of the unequal sharing of electrons, oxygen carries a slight negative charge, and the hydrogen atoms carry a slight positive charge. © 2017 Pearson Education, Inc. Figure 2.10b (b) The hydrogen atoms from one water molecule are attracted to the oxygen atoms of other water molecules. This relatively weak attraction (shown by dotted lines) is called a hydrogen bond. © 2017 Pearson Education, Inc.  2.3 The Role of Water in Life  The unique properties of water, such as its high heat capacity, high heat of vaporization, and its superior ability as a dissolving agent, can be traced to its polarity 9 © 2017 Pearson Education, Inc.  2.3 The Role of Water in Life © 2017 Pearson Education, Inc. Water is a Major Player in Many of Life’s Processes  A solution is a homogeneous mixture of two or more kinds of molecules, atoms, or ions.  The compound dissolved in solution is the solute; the compound doing the dissolving is the solvent. Homogeneous  Homogeneous – The prefix “homo” – indicate sameness  A homogeneous mixture has the same uniform appearance throughout. Paint  Heterogeneous  Heterogeneous: The prefix “hetero” – indicate difference  Heterogeneous - A heterogeneous mixture consists of visibly different substances or phases. The three phases or states of matter are gas, liquid, and solid. Water is a Major Player in Many of Life’s Processes (a) Attraction (b) Separation (c) Dispersion water (solvent) Sodium and H chloride ions O dissolved H in water Na+ Cl– sodium chloride Sodium chloride’s Pulled from the crystal, This process of (solute) positively charged and separated from separating sodium and sodium ions (Na+) are each other by this chloride ions repeats attracted to water’s attraction, sodium and until both ions are negatively charged chloride ions become evenly dispersed, oxygen atoms, while surrounded by water making this an aqueous its negatively charged molecules. solution. chloride ions (Cl–) are attracted to water’s positively charged hydrogen atoms. Figure 2.15 Water is a Major Player in Many of Life’s Processes  Water is a powerful solvent, with the ability to dissolve more compounds in greater amounts than any other liquid. It is water's chemical composition and physical attributes that make it such an excellent solvent. Water molecules have a polar arrangement of the oxygen and hydrogen atoms— one side (hydrogen) has a positive electrical charge, and the other side (oxygen) had a negative charge. Water’s Structure Gives It Many Unusual Properties ice In ice, the maximum number of hydrogen bonds form, causing the molecules to be spread far apart. liquid water In liquid water, hydrogen bonds constantly break and re-form, enabling a more dense spacing than in ice. Figure 2.16 Water’s Structure Gives It Many Unusual Properties  Water has a great capacity to absorb and retain heat.  Because of this, the oceans act as heat buffers for the Earth, thus stabilizing Earth’s temperature. Water’s Structure Gives It Many Unusual Properties  Water has a high degree of cohesion, which allows water to be drawn up through plants, via evaporation, in one continuous column, from roots through leaves. Hydrophobic and Hydrophilic  Compounds that interact with water are polar or carry an electric charge and are called hydrophilic compounds.  Nonpolar molecules that repel the water molecules are said to be hydrophobic. r Hydrophobic and Hydrophilic  Some compounds do not interact with water.  Hydrocarbons such as petroleum are examples of such hydrophobic compounds.  Water cannot break down hydrophobic compounds, which is why oil and water don’t mix.  2.3 The Role of Water in Life  Acids and bases react differently to water Acids release hydrogen ions (H+) when placed in water Bases release hydroxide ions (OH–) when added to water  pH Measure of hydrogen ion concentration The lower the pH on the pH scale, the greater the acidity The higher the pH, the more basic a solution © 2017 Pearson Education, Inc. Acids and Bases pure water (a) Starting with pure water Pure water is a “neutral” substance in terms of its pH levels. (H2O) (b) Making water (c) Making water more acidic HCl more basic NaOH Hydrochloric acid (HCl), An equal concentration of poured into the water, sodium hydroxide, poured into water, dissociates into dissociates into Na+ and OH– ions, H+ and Cl- ions. moving the water toward the basic With a higher end of the scale. concentration of H+ ions in it, the water moves towards the acidic end of the pH scale. (d) Combining acidic and basic solutions When the acid and base solutions are poured together, the OH– ions from (c) accept the H+ ions from (b), forming water and keeping the solution at a neutral pH. acid base neutralized solution Figure 2.18  2.3 The Role of Water in Life  Buffers Prevent dramatic changes in pH Remove excess H+ from solutions when concentrations of H+ increase Add H+ when concentrations t of H+ decrease Many body fluids have the buffering capacity to maintain a stable internal environment © 2017 Pearson Education, Inc. Acids and Bases  The concentration of hydrogen ions that a given solution has determines how basic or acidic that solution is.  The pH scale measures acidity. This scale runs from 0 to 14, with 0 most acidic,14 the most basic, and 7 neutral. Acids and Bases H+ concentration (moles/liter) acidic pH battery acid hydrochloric acid lemon juice, gastric (stomach) juice cola, beer, wine, vinegar tomatoes black coffee urine neutral water human blood seawater human blood is slightly baking soda basic Great Salt Lake household ammonia household bleach oven cleaner lye basic Figure 2.19 Acids and Bases  The pH scale is logarithmic. A substance with a pH of 9 is 10 times as basic as a substance with a pH of 8 \  Living things function best in a near-neutral pH, although some systems in living things have different pH requirements. Biomolecules Molecules that make up living things Dr. Abdullah AlAqel 58  Types of Biological Molecules Proteins Lipids Nucleic acids Carbohydrates Organic Compounds  Most Biomolecules are organic  This means they are based on Carbon and include hydrogen  Includes carbohydrates, lipids, proteins and nucleic acids  Also includes vitamins 60 Carbon is Central to the Living World  Carbon is a central element to life because most biological molecules are built on a carbon framework. Why is Carbon Central to Life?  Complexity of living things – Facilitated by carbon’s linkage capacity  Carbon has great bonding f capacity : Due to its structure Outer shell has four electrons: Can form stable, covalent bonds Why is Carbon Central to Life?  Carbon’s outer shell has only four of the eight electrons necessary for maximum stability in most elements.  Carbon atoms are thus able to form stable, covalent bonds with a wide variety of atoms, including other carbon atoms. 3.2 Functional Groups Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Functional Groups  Groups of atoms known as functional groups can confer special properties on carbon-based molecules.  Carbon is a central element to life because most biological molecules are built on a carbon framework. Functional Groups  For example, the addition of an –OH group to a hydrocarbon molecule always results in the formation of an alcohol. Functional Groups Table 3.1 Functional Groups  Functional groups often impart an electrical charge or polarity onto molecules, thus affecting their bonding capacity.  Each type of organic and biological molecule has its own specific type of functional group.  Functional groups in biological molecules play an important role in the formation of molecules like carbohydrates, lipids, proteins and DNA. Types of Biological Molecules 69  2.4 Major Molecules of Life  Biological macromolecules Biological macromolecules are the giant molecules of life Long chains called polymers made of repeating units called monomers poly = many mono = one © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life  When monomers are joined to form polymers, water is removed, and the reaction is called dehydration synthesis  Conversely, when the same polymers are broken apart, water is added and the reaction is called hydrolysis © 2017 Pearson Education, Inc. Figure 2.13 Two monomers already Third monomer to be bonded to one another added through dehydration synthesis Polymer Dehydration synthesis Hydrolysis Polymer Monomers Monomer (a) Polymers are formed by dehydration synthesis, in which (b) Polymers are broken down by hydrolysis, in which the addition a water molecule is removed and two monomers are joined. of a water molecule disrupts the bonds between two monomers. © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life  Carbohydrates Polymers, made of monosaccharides (monomer) Serve as fuel for the human body Composed only of C, H, and O Classified by size into monosaccharides, oligosaccharides, and polysaccharides © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life  Monosaccharides Also called simple sugars Glucose and fructose are examples  Oligosaccharides Chains of a few monosaccharides 1 One type is a disaccharide, formed from joining two monosaccharides Sucrose and maltose are examples © 2017 Pearson Education, Inc. Figure 2.14 The straight-chain A ring structure of glucose A ring structure of formula of glucose in which carbon atoms within glucose in which the C the ring are designated with for carbon atoms within the letter C the ring is omitted © 2017 Pearson Education, Inc. Figure 2.15 Glucose Fructose Sucrose (Monosaccharide)  (Monosaccharide) (Disaccharide) © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life  Polysaccharides Chains of monosaccharides that store energy or provide structure The storage polysaccharide in animals is glycogen, which humans store mainly in liver and muscle cells The storage polysaccharide in plants is starch © 2017 Pearson Education, Inc. Figure 2.16 Micrograph of cellulose fibrils in plant cell wall Liver Glycogen granules Liver cell Cell walls Plant cells (a) Glycogen is the storage polysaccharide in animals. (b) Cellulose is a structural polysaccharide found in the Granules of glycogen are stored in cells of the liver. cell walls of plants. © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life  Cellulose A structural polysaccharide made of repeating units of glucose found in cell walls of plants Humans lack the enzyme necessary to digest cellulose However, it is an important form of dietary fiber in the human diet © 2017 Pearson Education, Inc. Four Complex Carbohydrates (a) Potato (b) Liver (c) Algae (d) Tick Starch Glycogen Cellulose Chitin Figure 3.6  Four Complex Carbohydrates 1. Starch is the nutrient storage form of carbohydrates in plants.  Is the chief form of stored energy in plants, especially wheat, corn, rice, and potatoes. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Four Complex Carbohydrates 2. Glycogen is the nutrient storage form of carbohydrates in animals. Your body stores carbohydrate as glycogen in your muscles and liver. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Four Complex Carbohydrates 3. Cellulose is a rigid, structural carbohydrate found in the cells walls of many organisms, such as plant cell walls. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Four Complex Carbohydrates 4. Chitin is a tough carbohydrate that forms the external skeleton of arthropods. It is a primary component of cell walls in fungi. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.  3.4 Lipids Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Lipids Lipids: Provide energy for cells, cell structure, insulation Lipids & Proteins compose the cell membrane Cholesterol: gives cell membrane flexibility. The defining characteristic of all lipids is that they do not readily dissolve in water. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.  Lipids Lipids do not possess the monomers-to-polymers structure seen in other biological molecules; no one structural element is common to all lipids. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.  Lipids Main types of lipids: 1) Triglycerides 2) Steroids 3) Phospholipids 4) Waxes Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.  Lipids Among the most important lipids are the triglycerides, composed of a glyceride and three fatty acids. Most of the fats that human beings consume are triglycerides. Triglycerides are called :  “fat” when they are solid and called “oil” when they are liquid.  Animal fat, olive oil, corn oil, butter, whale oil, fish oil, belly fat Chemically, the main component of all these substances is triglycerides. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. The Triglyceride Tristearin glycerol fatty acids Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Figure 3.9 Steroids Another important variety of lipids is the steroids, all of which have a core of four carbon rings. Examples include cholesterol and such hormones as testosterone and estrogen. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Steroids (a) Four-ring steroid structure (b) Side chains make each steroid unique testosterone estrogen cholesterol Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Figure 3.12  Phospholipids A third class of lipids is the phospholipids, each of which is composed of two fatty acids, glycerol, and a phosphate group. The material forming the outer membrane of cells is largely composed of phospholipids. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.  2.4 Major Molecules of Life Phospholipid molecules have – A glycerol head that is polar and hydrophilic (hydro: Greek for water, philia: to love) and mixes with watery environments inside and outside the cell – A fatty acid tail that is nonpolar and hydrophobic (hydro: water, phobos: fear) that points inward and helps hold the membrane together © 2017 Pearson Education, Inc. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Phospholipids (a) Phospholipid structure — variable phosphate group group polar head nonpolar tails (b) Phospholipid orientation “like attracts like” phospholipids nonpolar hydrophobic tails (fatty acids) exposed to oil oil (nonpolar) polar hydrophilic water (polar) heads exposed to water Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Figure 3.14 Waxes A fourth class of lipids is the waxes, each of which is composed of a single fatty acid linked to a long-chain alcohol. Waxes have an important “sealing” function in the living world. Almost all plant surfaces exposed to air, for example, have a protective covering made largely of wax. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Waxes Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Figure 3.15  s 3.5 Proteins Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.  Proteins Proteins are an extremely diverse group of biological molecules composed of the monomers called amino acids. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.  Proteins Sequences of amino acids are strung together to produce polypeptide chains, which then fold up into working proteins. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Proteins Important groups of proteins include enzymes, which hasten chemical reactions. and structural proteins, which make up such structures as hair. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Types of Protein Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Table 3.3 Levels of Protein Structure The primary structure of a protein is its amino acid sequence; this sequence determines a protein’s secondary structure—the form a protein assumes after having folded up. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Beginnings of a Protein The linkage of several amino acids... ala gln ile ala gln ile A typical protein would consist of hundreds of... produces a polypeptide chain like this: amino acids Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Figure 3.18  Levels of Protein Structure The larger-scale three-dimensional shape that a protein assumes is its tertiary structure, and the way two or more polypeptide chains come together to form a protein results in that protein’s quaternary structure. The activities of proteins are determined by their final folded shapes. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Levels of Protein Structure Four Levels of Structure In Proteins (a) Primary structure The primary structure of any protein is simply its sequence of amino acids. This sequence amino acid sequence determines everything else about the protein’s final shape. (b) Secondary structure Structural motifs, such as the corkscrew-like alpha helix, beta pleated sheets, alpha helix and the less organized “random coils” are parts random coil beta pleated sheet of many polypeptide chains, forming their secondary structure. (c) Tertiary structure These motifs may persist through a set of larger-scale turns that make up the tertiary structure of the folded polypeptide molecule chain (d) Quaternary structure Several polypeptide chains two or more may be linked together in a polypeptide chains given protein, in this case hemoglobin, with their configuration forming its quaternary structure. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Figure 3.20  Lipoproteins Lipoproteins are biological molecules that are combinations of lipids and proteins. High-density and low-density lipoproteins (HDLs and LDLs, respectively), which transport cholesterol in human beings, are important determinants of human heart disease. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.  Glycoproteins Glycoproteins are combinations of carbohydrates and proteins. The signal-receiving receptors found on cell surfaces often are glycoproteins. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.  3.6 Nucleic Acids Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.  Nucleic Acids Nucleic acids are polymers composed of nucleotides. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings.  Nucleotides The nucleic acid DNA (deoxyribonucleic acid) is composed of nucleotides that contain: A sugar (deoxyribose). A phosphate group. and one of four nitrogen-containing bases. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Nucleotides (a) Nucleotides are the building blocks of DNA. Nucleotide nitrogenous DNA consists of two base strands of nucleotides sugar linked by hydrogen (deoxyribose) bonds phosphate group (b) A computer-generated model of DNA The outer “rails” of the double helix are composed of sugar and The rungs phosphate consist of components of bases the molecule hydrogen- bonded together DNA double helix Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Figure 3.21  Nucleic Acids DNA is a repository of genetic information. The sequence of its bases encodes the information for the production of the huge array of proteins produced by living things. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Nucleic Acids A second nucleic acid is RNA (ribonucleic acid), which transports the information encoded in DNA to the sites of protein synthesis—structures called ribosomes—and which helps make up the structure of ribosomes. Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Biological Molecules Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings. Table 3.4  2.4 Major Molecules of sLife © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life  Changes in the chemical environment of a protein can cause it to lose its structure, resulting in a loss of function  This is called denaturation t  Temperature and/or pH changes are the major cause of denaturation © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life  Enzymes are almost always proteins They speed up chemical reactions without being consumed Without enzymes, chemical reactions within our cells would occur too slowly to sustain life An enzyme can’t make a reaction that can’t take place Specificity is due to the unique shape of each enzyme’s active site © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life  Enzymes bind to substrates at the active site, forming an enzyme–substrate complex Sometimes cofactors, often called coenzymes, bind at the active site to facilitate the reaction  The substrate is converted to one or more products © 2017 Pearson Education, Inc. Figure 2.23 2 The substrate binds to the active site of the enzyme, forming an enzyme–substrate complex. 1 The cycle begins when 3 The substrate is converted the active site of the to products that are released enzyme is unoccupied and from the active site, and the the substrate is present. cycle can begin again. Substrate Products Enzyme Enzyme–substrate complex Enzyme (a) A decomposition reaction involving an enzyme Substrates Product Enzyme Enzyme–substrate complex Enzyme (b) A synthesis reaction involving an enzyme © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life  Nucleic acids DeoxyriboNucleic Acid (DNA) and RiboNucleic Acid (RNA) are the two types of nucleic acids  RNA and DNA have structural differences related to the sugar, bases, and number of strands Both are polymers of smaller units called nucleotides  A nucleotide is made up of a five-carbon sugar bonded to one of five nitrogen-containing bases and a phosphate group © 2017 Pearson Education, Inc. Figure 2.24 Nucleotide Phosphate Nitrogen- Pentose containing sugar base © 2017 Pearson Education, Inc. Table 2.4 © 2017 Pearson Education, Inc. Figure 2.25 Phosphate Ribose Phosphate Ribose Phosphate Ribose Phosphate Ribose © 2017 Pearson Education, Inc. Figure 2.26 Hydrogen bonds Phosphate Deoxyribose Nitrogen- Phosphate containing base © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life  A special nucleotide is adenosine triphosphate (ATP) A molecule capable of storing energy in its phosphate-to-phosphate bonds  All energy from the breakdown of molecules, such as glucose, must be channeled through ATP before the body can use it  ATP is often described as the energy currency of cells © 2017 Pearson Education, Inc. Figure 2.27 Bond broken to release energy Adenine Phosphate Phosphate Phosphate Ribose Triphosphate Adenosine ATP (adenosine triphosphate) Adenine Phosphate Phosphate Ribose Diphosphate Adenosine ADP (adenosine diphosphate) Phosphate Energy © 2017 Pearson Education, Inc.  2.4 Major Molecules of Life © 2017 Pearson Education, Inc.  You Should Now Be Able To:  Describe the characteristics of the subatomic particles (protons, neutrons and electrons) and explain the structure of an isotope.  Differentiate between covalent, ionic, and hydrogen bonds in terms of strength and the actions of the electrons.  List the unique properties of water that make it valuable to biological systems. © 2017 Pearson Education, Inc.  You Should Now Be Able To:  Predict what happens when an acid or a base is added to water.  Define pH, explain the range of the pH scale, and tell which values indicate acid and which values indicate base.  Describe the structure of a polymer, including its formation through dehydration synthesis and its breakdown through hydrolysis. © 2017 Pearson Education, Inc.  You Should Now Be Able To:  Describe the structure and biological purpose of carbohydrates, lipids, proteins, and nucleotides and give an example of each.  Describe ATP as the energy currency of the cell. © 2017 Pearson Education, Inc.