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UNIT 1: Biochemistry THINK ABOUT IT Think about important news stories you’ve heard. Bird flu spreads around the world, killing birds and threatening a human epidemic. Users of certain illegal drugs experience permanent damage to their brains and nervous systems. Reports surface about efforts to clone human cells. These and many other stories involve biology—the science that employs scientific methodology to study living things. The Greek word bios means “life,” and -logy means “study of.” Unit 1 Content Expectations LIFE Describe the 8 characteristics of life. B2.4f - recognize and describe that both living and nonliving things are composed of compounds, which are themselves made up of elements joined by energy-containing bonds, such as those in ATP. B2.5A Recognize and explain that macromolecules such as lipids contain high energy bonds. B2.2B - Recognize the six most common elements in organic molecules (C, H, N, O, P, S). B2.2A - Explain how carbon can join to other carbon atoms in chains and rings to form large and complex molecules. B2.2C - Describe the composition of the four major categories of organic molecules (carbohydrates, lipids, proteins, and nucleic acids). B2.2D - Explain the general structure and primary functions of the major complex organic molecules that compose living organisms. B2.2E Describe how dehydration and hydrolysis relate to organic molecules. B2.2f - Explain the role of enzymes and other proteins in biochemical functions (e.g., the protein hemoglobin carries oxygen in some organisms, digestive enzymes, and hormones). Unit 1 Big Idea Living things are made up of energy rich complex chemical structures. Unit 1 Core Concepts Living things are made up of four major types of organic molecules: carbohydrates, lipids, proteins and nucleic acids. Organisms are made up of different arrangements of these molecules, giving all life a biochemical framework. Carbohydrates and lipids contain many C-H bonds that store energy. Peer Review Scientists share their findings with the scientific community by publishing articles that have undergone peer review. In peer review, scientific papers are reviewed by anonymous, independent experts. Reviewers read them looking for oversights, unfair influences, fraud, or mistakes in techniques or reasoning. They provide expert assessment of the work to ensure that the highest standards of quality are met. IN YOUR NOTES Predict what might happen if an article is published without undergoing peer review. Scientific Theories What is a scientific theory? In science, the word theory applies to a well-tested explanation that unifies a broad range of observations and hypotheses and that enables scientists to make accurate predictions about new situations. Scientific Theories Evidence from many scientific studies may support several related hypotheses in a way that inspires researchers to propose a scientific theory that ties those hypotheses together. In science, the word theory applies to a well-tested explanation that unifies a broad range of observations and hypotheses and that enables scientists to make accurate predictions about new situations. A useful theory that has been thoroughly tested and supported by many lines of evidence may become the dominant view among the majority of scientists, but no theory is considered absolute truth. Science is always changing; as new evidence is uncovered, a theory may be revised or replaced by a more useful explanation. Avoiding Bias The way that science is applied in society can be affected by bias, which is a particular preference or point of view that is personal, rather than scientific. Science aims to be objective, but scientists are human, too. Sometimes scientific data can be misinterpreted or misapplied by scientists who want to prove a particular point. Recommendations made by scientists with personal biases may or may not be in the public interest. But if enough of us understand science, we can help make certain that science is applied in ways that benefit humanity. • LIFE Describe the 8 characteristics of life. Characteristics of Living Things Biology is the study of life. But what is life? No single characteristic is enough to describe a living thing. Also, some nonliving things share one or more traits with organisms. Some things, such as viruses, exist at the border between organisms and nonliving things. Characteristics of Living Things Despite these difficulties, we can list characteristics that most living things have in common. Both fish and coral, for example, show all the characteristics common to living things. Characteristics of Living Things Living things are based on a universal genetic code. All organisms store the complex information they need to live, grow, and reproduce in a genetic code written in a molecule called DNA. That information is copied and passed from parent to offspring and is almost identical in every organism on Earth. Characteristics of Living Things Living things grow and develop. During development, a single fertilized egg divides again and again. As these cells divide, they differentiate, which means they begin to look different from one another and to perform different functions. Characteristics of Living Things Living things respond to their environment. A stimulus is a signal to which an organism responds. For example, some plants can produce unsavory chemicals to ward off caterpillars that feed on their leaves. Characteristics of Living Things Living things reproduce, which means that they produce new similar organisms. Most plants and animals engage in sexual reproduction, in which cells from two parents unite to form the first cell of a new organism. Other organisms reproduce through asexual reproduction, in which a single organism produces offspring identical to itself. Beautiful blossoms are part of an apple tree’s cycle of sexual reproduction. Characteristics of Living Things Living things maintain a relatively stable internal environment, even when external conditions change dramatically. All living organisms expend energy to keep conditions inside their cells within certain limits. This conditionprocess is called homeostasis. For example, specialized cells help leaves regulate gases that enter and leave the plant. Characteristics of Living Things Living things obtain and use material and energy to grow, develop, and reproduce. The combination of chemical reactions through which an organism builds up or breaks down materials is called metabolism. For example, leaves obtain energy from the sun and gases from the air. These materials then take part in various metabolic reactions within the leaves. Characteristics of Living Things Living things are made up of one or more cells—the smallest units considered fully alive. Cells can grow, respond to their surroundings, and reproduce. Despite their small size, cells are complex and highly organized. For example, a single branch of a tree contains millions of cells. Characteristics of Living Things Taken as a group, over generations, organisms evolve, or change over time. Evolutionary change links all forms of life to a common origin more than 3.5 billion years ago. Characteristics of Life video THINK ABOUT IT... What are you made of? Just as buildings are made from bricks, steel, glass, and wood, living things are made from chemical compounds. When you breathe, eat, or drink, your body uses the substances in air, food, and water to carry out chemical reactions that keep you alive. The first job of a biologist is to understand the chemistry of life. Atoms What three subatomic particles make up atoms? The subatomic particles that make up atoms are protons (+), neutrons(O), and electrons (-). Atoms The study of chemistry begins with the basic unit of matter, the atom. The concept of the atom came first from the Greek philosopher Democritus, nearly 2500 years ago. Democritus asked, can you divide a substance without limit, or does there come a point at which you cannot divide the substance without changing it into something else? Democritus thought that there had to be a limit, and he called the smallest fragment the atom, from the Greek word atomos, which means “unable to be cut.” Atoms Atoms are incredibly small. Placed side by side, 100 million atoms would make a row only about 1 centimeter long—about the width of your little finger! Despite its extremely small size, an atom contains subatomic particles that are even smaller. The subatomic particles that make up atoms are protons, neutrons, and electrons. The subatomic particles in a carbon atom are shown. Protons and Neutrons Protons and neutrons have about the same mass. Protons are positively charged particles (+) and neutrons carry no charge at all. Strong forces bind protons and neutrons together to form the nucleus, at the center of the atom. Electrons The electron is a negatively charged particle (–) with only 1/1840 the mass of a proton. Electrons are in constant motion in the space surrounding the nucleus. They are attracted to the positively charged nucleus but remain outside the nucleus because of the energy of their motion. Electrons Because atoms have equal numbers of electrons and protons, their positive and negative charges balance out, and atoms themselves are electrically neutral. The carbon atom shown has 6 protons and 6 electrons. Elements and Isotopes A chemical element is a pure substance that consists entirely of one type of atom. More than 100 elements are known, but only about two dozen are commonly found in living organisms. Elements are represented by one- or two-letter symbols. For example, C stands for carbon, H for hydrogen, Na for sodium, and Hg for mercury (shown). Elements and Isotopes The number of protons in the nucleus of an element is called its atomic number. Carbon’s atomic number is 6, meaning that each atom of carbon has six protons and, consequently, six electrons. Chemical Compounds In what ways do compounds differ from their component elements? The physical and chemical properties of a compound are usually very different from those of the elements from which it is formed. For example, sodium is a silver-colored metal that is soft enough to cut with knife. It reacts explosively with cold water. Chlorine is a very reactive, poisonous, greenish gas that was used in battles during World War I. However, the compound sodium chloride--table salt--is a white solid that dissolves easily in water, is not poisonous, and is essential for the survival of most living things. a Parts of an Atom Video • B2.4f recognize and describe that both living and nonliving things are composed of compounds, which are themselves made up of elements joined by energycontaining bonds, such as those in ATP.. Chemical Compounds A chemical compound is a substance formed by the chemical combination of two or more elements in definite proportions. Scientists show the composition of compounds by a kind of shorthand known as a chemical formula. Water, which contains two atoms of hydrogen for each atom of oxygen, has the chemical formula =H2O. The formula for table salt, NaCl, indicates that the elements that make up table salt—sodium and chlorine—combine in a 1:1 ratio. Chemical Bonds The atoms in compounds are held together by various types of chemical bonds. Bond formation involves the electrons that surround each atomic nucleus. The electrons that are available to form bonds are called valence electrons. The main types of chemical bonds are ionic bonds and covalent bonds. Ionic Bonds An ionic bond is formed when one or more electrons are transferred from one atom to another. An atom that loses electrons becomes positively charged. An atom that gains electrons has a negative charge. These positively and negatively charged atoms are known as ions. Ionic Bonds Ionic bonds form between sodium and chlorine to form NaCl, table salt. Ionic Bonds A sodium atom easily loses its one valence electron and becomes a sodium ion (Na+). Ionic Bonds A chlorine atom easily gains an electron (from sodium) and becomes a chloride ion (Cl-). Ionic Bonds These oppositely charged ions have a strong attraction for each other, forming an ionic bond. Ionic Bond Video Covalent Bonds Covalent bonds involve electrons being shared by atoms instead of being transferred. The moving electrons travel about the nuclei of both atoms, forming a covalent bond. When the atoms share two electrons, the bond is called a single covalent bond. Sometimes the atoms share four electrons and form a double bond. In a few cases, atoms can share six electrons, forming a triple bond. Covalent Bonds The structure that results when atoms are joined together by covalent bonds is called a molecule, the smallest unit of most compounds. This diagram of a water molecule shows that each hydrogen atom is joined to water’s lone oxygen atom by a single covalent bond. Each hydrogen atom shares two electrons with the oxygen atom. Covalent Bonds When atoms of the same element join together, they also form a molecule. Oxygen molecules in the air you breathe consist of two oxygen atoms joined by covalent bonds. Covalent Bond Video • B2.5A Recognize and explain that macromolecules such as lipids contain high energy bonds. High Energy Bonds High energy bonds are found in organic molecules such as lipids and ATP. They are covalent bonds that, when broken, release high amounts of energy. So, the energy needed for your cells to function is stored in high energy bonds. When your cell needs energy, it breaks those bonds by breaking down molecules like carbohydrates, lipids, and ATP. Why don't we eat rocks? Our cells break down macromolecules such as lipids and proteins to get energy. Each bond in a macromolecule holds energy. Bonds between Carbon and Hydrogen (as well as those in ATP) hold LOTS of energy and are called HIGH ENERGY BONDS. We eat food to get energy. Our food is made up of macromolecules. Our body breaks down those macromolecules to get energy. In other words, rocks aren't made up of organic macromolecules so we cannot use them for energy!!! High Energy Bonds Movie B2.2B Recognize the six most common elements in organic molecules (C, H, N, O, P, S). The Chemistry of Carbon What elements does carbon bond with to make up life’s molecules? Carbon can bond with many elements, including hydrogen, nitrogen, oxygen, phosphorus, and sulfur to form the molecules of life. B2.2A Explain how carbon can join to other carbon atoms in chains and rings to form large and complex molecules. Carbon videos The Chemistry of Carbon Carbon atoms have four valence electrons, allowing them to form strong covalent bonds with many other elements, including hydrogen, oxygen, phosphorus, sulfur, and nitrogen. Living organisms are made up of molecules that consist of carbon and these other elements. The Chemistry of Carbon Carbon atoms can also bond to each other in chains and rings, which gives carbon the ability to form millions of different large and complex structures. Carbon-carbon bonds can be single, double, or triple covalent bonds. Chains of carbon atoms can even close up on themselves to form rings. B2.2A - Explain how carbon can join to other carbon atoms in chains and rings to form large and complex molecules. THINK ABOUT IT In the early 1800s, many chemists called the compounds created by organisms “organic,” believing they were fundamentally different from compounds in nonliving things. We now understand that the principles governing the chemistry of living and nonliving things are the same, but the term “organic chemistry” is still around. Today, organic chemistry means the study of compounds that contain bonds between carbon atoms, while inorganic chemistry is the study of all other compounds. B2.2C Describe the composition of the four major categories of organic molecules (carbohydrates, lipids, proteins, and nucleic acids). B2.2D Explain the general structure and primary functions of the major complex organic molecules that compose living organisms. Carbohydrates Carbohydrates are compounds made up of carbon, hydrogen, and oxygen atoms, usually in a ratio of 1 : 2 : 1. Living things use carbohydrates as their main source of energy. The breakdown of sugars, such as glucose, supplies immediate energy for cell activities. Plants, some animals, and other organisms also use carbohydrates for structural purposes. Carbohydrates Carbohydrates (like Glucose) are actually many subunits called Sugars that have been joined together. When an organism needs energy, it breaks down carbohydrates by breaking the bonds within it. This supplies immediate energy for the organism's cells. Lipids Lipids are a large and varied group of biological molecules. Lipids are made mostly from carbon and hydrogen atoms and are generally not soluble in water. The common categories of lipids are fats, oils, and waxes. Lipids can be used to store energy. Some lipids are important parts of biological membranes and waterproof coverings. Steroids synthesized by the body are lipids as well. Many steroids, such as hormones, serve as chemical messengers. Lipids Many lipids are formed when a glycerol molecule combines with compounds called fatty acids. The picture below shows one Lipid molecule. It is made up of glycerol and fatty acids (subunits). Nucleic Acids Nucleic acids store and transmit hereditary, or genetic, information. Nucleic acids are macromolecules containing hydrogen, oxygen, nitrogen, carbon, and phosphorus. Nucleic acids are assembled from subunits known as nucleotides. Nucleic Acids Nucleotides consist of three parts: a 5carbon sugar, a phosphate group (–PO4), and a nitrogenous base. Some nucleotides, including adenosine triphosphate (ATP), play important roles in capturing and transferring chemical energy. Nucleic Acids Individual nucleotides can be joined by covalent bonds to form nucleic acid. There are two kinds of nucleic acids: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). RNA contains the sugar ribose and DNA contains the sugar deoxyribose. Protein Proteins are macromolecules that contain nitrogen as well as carbon, hydrogen, and oxygen. Proteins are made of subunits called amino acids. Proteins perform many varied functions, such as controlling the rate of reactions and regulating cell processes, forming cellular structures, transporting substances into or out of cells, and helping to fight disease. Protein Amino acids are compounds with an amino group (–NH2) on one end and a carboxyl group (–COOH) on the other end. Covalent bonds called peptide bonds link amino acids together to form a polypeptide. A protein is a functional molecule built from one or more polypeptides. B2.2E Describe how dehydration and hydrolysis relate to organic molecules. Dehydration & Hydrolysis The four macromolecules we just discussed (Carbohydrates, Lipids, Nucleic Acids, and Proteins) are made up of subunits. Those subunits join together to make the macromolecule. Dehydration is when macromolecule subunits join together, the subunits lose an H and an OH. The H and OH pair up to form..... WATER! ( H + OH = H2O ) This is called DEHYDRATION because the subunits are losing a water molecule. Dehydration & Hydrolysis The opposite of dehydration is HYDROLYSIS. Hydrolysis is when a macromolecule breaks into its original subunits and the H and OH are reattached to the subunits. Therefore, in HYDROLYSIS, a water molecule is used up to separate a macromolecule into its subunits. Dehydration & Hydrolysis 1. For which reaction is water used up? 2. Which reaction makes a macromolecule from its subunits? B2.2f - Explain the role of enzymes and other proteins in biochemical functions (e.g., the protein hemoglobin carries oxygen in some organisms, digestive enzymes, and hormones). Enzymes What role do enzymes play in living things and what affects their function? Enzymes speed up chemical reactions that take place in cells and facilitate the breakdown of complex molecules by acting as substrate-specific catalysts. Temperature, pH, and regulatory molecules can affect the activity of enzymes. The Enzyme-Substrate Complex For a chemical reaction to take place, the reactants must collide with enough energy so that existing bonds will be broken and new bonds will be formed. If the reactants do not have enough energy, they will be unchanged after the collision. Enzymes provide a site where reactants can be brought together to react. Such a site reduces the energy needed for reaction. The Enzyme-Substrate Complex The reactants of enzyme-catalyzed reactions are known as substrates. For example, the enzyme carbonic anhydrase converts the substrates carbon dioxide and water into carbonic acid (H2CO3). The Enzyme-Substrate Complex The substrates bind to a site on the enzyme called the active site. The active site and the substrates have complementary shapes. The fit is so precise that the active site and substrates are often compared to a lock and a key. The Enzyme-Substrate Complex Enzyme video 1