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Biology Chapter 6: The Chemistry of Life Name_____________________________________ Per_______________ Learning Goals o You will be able to describe the parts of an atom and how atoms interact with each other o You will be able to describe the different methods of how elements are able to bond together to form molecules and compounds o You will be able to explain the importance of hydrogen bonds and water to organisms o You will be able to explain the process and importance of diffusion o You will be able to identify and describe the base structures and functions of the four types of biomolecules Atoms o When constructing a picture of how our world is built, scientists begin with the atom. o Atoms are the basic building blocks of all matter o Essentially, every living and non-living thing in our universe is a series of atoms held together by electrical charges o Though they come in different sizes, atoms all have the same basic shape o The center of the atom is the nucleus. o Inside of the nucleus are two types of particles, protons and neutrons Protons are positively charged, like the positive end of a battery Neutrons are the same size and shape as a proton, but with no charge (they are neutral) o Surrounding the nucleus in specific “shells” are electrons. o Electrons are negatively charged particles, and are much smaller than protons. o If the atom is stable, then the number of electrons will equal the number of protons in an atom. o The overall charge of the atom is zero, but the nucleus is positively charged and the outside shells are negatively charged. Electrons o Electrons are peculiar. They tend to hang out in specific shells surrounding the nucleus o The first shell has only two electrons. Almost every shell after that has 8 (not really, but this is simplified) o If an atom’s outer shell does not have the right amount of electrons, it will be unstable. o Each atom can donate or accept other electrons to become more stable Protons o “Elements” and “atoms” are the same thing o Each element is a different type of atom. o The number of protons in an atom’s nucleus determines the element Oxygen has 8 protons, therefore any atom with 8 protons must be an oxygen. The number of neutrons and electrons doesn’t matter Sketch Area Isotopes of Elements o An isotope is an element with the same number of protons but different numbers of neutrons o Sometimes the extra neutrons cause the atom to be unstable and the neutrons break off of the nucleus o When they break off, the energy that held them in the nucleus is released o This energy is called radiation Compounds and Bonds o Compounds are combinations of elements that make a new substance H2O is…? Water NaCl is…? Table Salt NH3 is…? Ammonia o Atoms combine with other atoms to form a compound more stable than the atom by itself o The key to stability is getting the outer shell to 8 electrons The one exception is Hydrogen, which only needs two o Covalent bonds share the outermost electrons to make a completed outer shell o Since all atoms are stable, the bond is also stable o The second type of bond is an Ionic bond o Ionic bonds form when one atom uses another atom to fill it’s shell o The second atom’s shell isn’t completely filled, so it’s still unstable and highly reactive. Reactions occur when two atoms FORM a bond or BREAK a bond Covalent bonds: atoms share electrons; not reactive Ionic bonds: one atom borrows electrons from another atom; highly reactive o Why do we care in biology? o Compounds held together by covalent bonds are stable and are typically used by organisms as a form of storage or structure Food and Energy; Bones; Tissues o Compounds held together by ionic bonds are unstable. Organisms use them for any type of reaction Nerve conduction; Muscle contraction Sketch Area Acids and Bases o Acids and Bases are compounds that undergo reactions when in contact with water. Since most organisms contain or react with water, acids and bases react with water as well o The type of reaction determines whether or not the compound is an acid or a base o Acidity or Basicity is determined by the pH scale. If a substance has a pH under 7, it’s an acid If a substance has a pH over 7, it’s a base o An acid is any substance that forms Hydrogen (H+) ions in water o A base is any substance that forms Hydroxide (OH-) ions in water Water o It’s the most important molecule on the planet by far. o Water makes up important molecules Blood, tears, sap, o Water transports materials Oxygen to lungs, nutrients through roots o Water insulates and protects Sweating, Atmosphere o Water is a polar covalent molecule Hydrogen and Oxygen share electrons, but not equally The result is that each molecule has a slightly positive end and a slightly negative end. Hydrogen Bonds o Hydrogen bonds form between two polar molecules (molecules with charges) o Hydrogen bonds are easy to break and easy to form o Hydrogen bonds allow water molecules to cling to each other o Hydrogen bonds also allow water to cling to other molecules like salt and sugar (dissolving) Properties of Water o Each oxygen in water (the negative charge of the molecule) forms a hydrogen bond with the hydrogen’s (positive charge) of a different water molecule o This allows for several important properties of water Specific Heat: water can absorb and hold lots of heat energy without changing temperature This makes it difficult for water to gain heat or lose heat. Solvent: water breaks apart molecules by using it’s charge to bond with parts of other molecules NaCl—Sodium (Na) is positively charged. Chlorine (Cl) is negatively charged. In the presence of water, Na+ will attract to oxygen and the Cl- will attract to the hydrogens Cohesion. Water molecules can bond to each other Water flows freely without breaking up This makes water excellent for transport Water can move up plant roots or plumbing (capillary action) Sketch Area Surface Tension Hydrogen bonds cover the surface of water Organisms can float on the surface if they do not break the bonds Density Water is unique because it is less dense as a solid than a liquid, so ice will float on water Life exists below frozen lakes because of this Diffusion o When you pour food coloring into water, does it all sit in one spot? o Diffusion is the net movement of particles from an area of higher concentration to an area of lower concentration The direction of movement is called a concentration gradient o When the number of particles is equally balanced, the particles will still move back and forth, but at an equal rate This rate is called dynamic equilibrium o Diffusion is what allows many biological functions to occur. Nerve conduction Muscle contraction Medicines in the bloodstream Oxygen into the bloodstream Carbon Dioxide out of the bloodstream How you tone your muscles How you distribute your fat storage evenly Carbon o Carbon atoms are very small, very stable, and can bond with up to 4 other molecules o Carbon can form rings, chains, or branched structures o This results in billions of different molecules able to be formed, all of which are one of four types of molecules Proteins, Carbohydrates, Lipids, Proteins o Each of these molecules is made up of monomers and polymers Monomer: A single puzzle piece or link in a chain Polymer: A completed puzzle or multiple links in a chain. Condensation/Dehydration o Monomers and polymers use water to attach to each other and break apart. o Each monomer contains a hydrogen (H) on one end and a hydroxyl (OH) on another end. o Monomers attach due to a condensation reaction Remove the hydrogen off one monomer and the hydroxyl off another. Attach the two monomers in their place The hydrogen and hydroxyl form an H2O—hence, condensation. Hydrolysis o Lysis means “to split”. Hence, hydrolysis is “splitting water.” o Hydrolysis is the exact reverse of condensation. When breaking a polymer into separate monomers, water is required. Split the H2O into a hydrogen (H) and a hydroxyl (OH) Break the polymer into two monomers and attach the hydrogen and hydroxyl to plug the gap This is also one reason why you should drink water if you’re trying to burn fat Biomolecule #1: Carbohydrates o All carbohydrates have a chemical equation that is a multiple of CH2O Example: Glucose is C6H12O6 o Carbohydrates are used by cells as short-term energy sources o Carbohydrates are built from sugars called saccharides A single carbohydrate, such as glucose or fructose, is called a monosaccharide (These are the monomers) The polymers of carbohydrates are called disaccharides (two monosaccharides) or polysaccharides (3 or more monosaccharides) Disaccharide examples: Sucrose, Maltose, Lactose Polysaccharide examples: Starch, Glycogen, Cellulose Biomolecule #2: Lipids o Lipids are large biomolecules consisting almost entirely of chains of carbon and hydrogen o Lipids are not attracted to water molecules and, thus, are not soluble (cannot dissolve in water) o Lipids are used by cells as long-term energy storage (fat), insulation and protective coverings (cell membranes) o Examples of lipids: Butter, Fats, Oils o Monomers of lipids are called “fatty acids”. o A saturated fat is a lipid with the most possible Hydrogen atoms in it’s chain o An unsaturated fat is a lipid missing at least one Hydrogen atom due to a double bond. The double bond creates a kink in the chain o The polymers are 3 fatty acids called triglycerides Biomolecule #3: Proteins o Proteins are made of monomers called amino acids o Amino acids have a Nitrogen (amine), a pair of oxygens (carboxylic acid), a central carbon, and a special group that changes depending on which amino acid you have This special group is called an “R” group o Each amino acid (a.a.) is connected by attaching the amine from one a.a. to the carboxylic acid of another a.a. o The R groups, though, can get in the way. o So instead of one long chain, the protein has to wrap around itself into a 3-D shape o Enzymes Enzymes are proteins that help speed up chemical reactions Each enzyme only reacts with one specific molecule called a substrate. This molecule fits perfectly with the enzyme because of the enzyme’s unique 3-d shape Just like a lock-and-key, the enzyme’s reaction can only react with the right molecule, or key o Enzymes work by lowering the activation energy of a reaction. o Activation energy is the minimum amount of energy required to perform a task. Enzymes reduce this amount to very low levels. o This allows enzymes to perform their specific task fast and efficiently. Digest food, synthesizing hormones, transmit messages through nerves, store energy for exercise Biomolecule #4: Nucleic Acids o DNA and RNA o Nucleic Acids have one function: store and transport genetic information o Nucleic acids are made up of chains of nucleotides. o Each nucleotide has one ribose sugar and a special base. o Each nucleotide is attached to a phosphate, which is used to connect nucleotides to each other. o The different bases are codes. The sequence of the bases tells the cell what type of protein, carbohydrate, lipid, or nucleic acid to make AND where it should go o DNA is always located inside the nucleus of the cell so that it is never lost o RNA is used by the cell to copy the DNA code and transport this message throughout the cell Conclusion o Because water is involved in nearly every reaction on the planet, we study atoms and elements and how they react with water. o Atoms interact in different ways to form different elements o Different elements interact with each other to form the four types of biomolecules o These biomolecules are rearranged and interact with each other in billions of different ways o All these differences create the diversity of life on our planet.