Chapter 2: The Chemical Context of Life BIO151 PDF

Chapter 2 The Chemical Context of Life © 2021 Pearson Education, Inc. © 2021 Pearson Education, Inc. Figure 2.1 © 2021 Pearson Education, Inc. Figure 2.1a CONCEPT 2.1: Matter consists of chemical elements in pure form and in combinations called compounds Organisms are composed of matter...

Chapter 2 The Chemical Context of Life © 2021 Pearson Education, Inc. © 2021 Pearson Education, Inc. Figure 2.1 © 2021 Pearson Education, Inc. Figure 2.1a CONCEPT 2.1: Matter consists of chemical elements in pure form and in combinations called compounds Organisms are composed of matter Matter is anything that takes up space and has mass © 2021 Pearson Education, Inc. Elements and Compounds Matter is made up of elements An element is a substance that cannot be broken down to other substances by chemical reactions A compound is a substance consisting of two or more elements in a fixed ratio A compound has characteristics (emergent properties) different from those of its elements © 2021 Pearson Education, Inc. The emergent properties of a compound © 2021 Pearson Education, Inc. Figure 2.2 The Elements of Life About 20–25% of the 92 natural elements are required for life (essential elements) Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur Trace elements are required by an organism in only minute quantities © 2021 Pearson Education, Inc. © 2021 Pearson Education, Inc. Case Study: Evolution of Tolerance to Toxic Elements Some elements can be toxic Some species can become adapted to environments containing toxic elements – For example, some plant communities are adapted to serpentine © 2021 Pearson Education, Inc. Serpentine plant community © 2021 Pearson Education, Inc. Figure 2.3 CONCEPT 2.2: An element’s properties depend on the structure of its atoms Each element consists of unique atoms An atom is the smallest unit of matter that still retains the properties of an element © 2021 Pearson Education, Inc. Subatomic Particles Atoms are composed of subatomic particles Relevant subatomic particles include: – Neutrons (no electrical charge) – Protons (positive charge) – Electrons (negative charge) © 2021 Pearson Education, Inc.  Neutrons and protons form the atomic nucleus Electrons form a “cloud” of negative charge around the nucleus Neutron mass and proton mass are almost identical and are measured in daltons Electrons are so small they are ignored when calculating the total mass of an atom © 2021 Pearson Education, Inc. Simplified models of a helium (He) atom © 2021 Pearson Education, Inc. Figure 2.4 Atomic Number and Atomic Mass Atoms of the various elements differ in their number of subatomic particles An element’s atomic number is the number of protons in its nucleus An element’s mass number is the sum of protons plus neutrons in the nucleus Atomic mass, the atom’s total mass, can be approximated by the mass number © 2021 Pearson Education, Inc. © 2021 Pearson Education, Inc. UNF02-01 Isotopes All atoms of an element have the same number of protons but may differ in the number of neutrons Isotopes are two atoms of an element that differ in the number of neutrons Radioactive isotopes decay spontaneously, giving off particles and energy © 2021 Pearson Education, Inc. Radioactive Tracers Radioactive isotopes are often used as diagnostic tools in medicine Radioactive tracers can be used to track atoms through metabolism They can also be used in combination with sophisticated imaging instruments PET scanners can monitor the growth and metabolism of cancers in the body © 2021 Pearson Education, Inc. A PET scan, a medical use for radioactive isotopes © 2021 Pearson Education, Inc. Figure 2.5 Radiometric Dating A “parent” isotope decays into its “daughter” isotope at a fixed rate, expressed as the half-life of the isotope In radiometric dating, scientists measure the ratio of different isotopes and calculate how many half- lives have passed since the fossil or rock was formed Half-life values vary from seconds or days for some isotopes to billions of years for others © 2021 Pearson Education, Inc. The Energy Levels of Electrons Energy is the capacity to cause change Potential energy is the energy that matter possesses because of its location or structure Matter has a natural tendency to move toward the lowest possible state of potential energy © 2021 Pearson Education, Inc.  The electrons of an atom differ in their amounts of potential energy based on their distance from the nucleus Changes in potential energy of electrons can occur only in steps of fixed amounts Electrons are found in different electron shells, each with a characteristic average distance and energy level © 2021 Pearson Education, Inc. Energy levels of an atom’s electrons © 2021 Pearson Education, Inc. Figure 2.6 Electron Distribution and Chemical Properties The chemical behavior of an atom is determined by the distribution of electrons in the electron shells The periodic table of the elements shows the electron distribution for each element The left-to-right sequence of elements in each row corresponds to the sequential addition of electrons and protons © 2021 Pearson Education, Inc.  Electron distribution diagrams for the first 18 elements in the periodic table © 2021 Pearson Education, Inc. Figure 2.7  Valence electrons are those in the outermost shell, or valence shell The chemical behavior of an atom is mostly determined by the number of valence electrons Elements with a full valence shell are chemically inert © 2021 Pearson Education, Inc. Electron Orbitals An orbital is the three-dimensional space where an electron is found 90% of the time Each electron shell consists of a specific number of orbitals No more than 2 electrons can occupy a single orbital Atoms interact in a way that completes their valence shells © 2021 Pearson Education, Inc. Electron orbitals © 2021 Pearson Education, Inc. Figure 2.8 CONCEPT 2.3: The formation and function of molecules and ionic compounds depend on chemical bonding between atoms Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms These interactions usually result in atoms staying close together, held by attractions called chemical bonds © 2021 Pearson Education, Inc. Covalent Bonds A covalent bond is the sharing of a pair of valence electrons by two atoms In a covalent bond, the shared electrons count as part of each atom’s valence shell © 2021 Pearson Education, Inc. Formation of a covalent bond © 2021 Pearson Education, Inc. Figure 2.9  A molecule consists of two or more atoms held together by covalent bonds A single covalent bond, or single bond, is the sharing of one pair of valence electrons A double covalent bond, or double bond, is the sharing of two pairs of valence electrons © 2021 Pearson Education, Inc.  The notation used to represent atoms and bonding is called a structural formula – For example, H—H represents a single bond – O ═ O represents a double bond This can be abbreviated further with a molecular formula – For example, H2 © 2021 Pearson Education, Inc. Covalent bonding in four molecules © 2021 Pearson Education, Inc. Figure 2.10  Bonding capacity is called the atom’s valence Covalent bonds can form between atoms of the same element or atoms of different elements A compound is a combination of two or more different elements © 2021 Pearson Education, Inc.  Atoms in a molecule attract electrons to varying degrees Electronegativity is an atom’s attraction for the electrons in a covalent bond The more electronegative an atom is, the more strongly it pulls shared electrons toward itself © 2021 Pearson Education, Inc.  In a nonpolar covalent bond, the atoms share the electron equally In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule © 2021 Pearson Education, Inc. Polar covalent bonds in a water molecule © 2021 Pearson Education, Inc. Figure 2.11 Ionic Bonds Atoms sometimes strip electrons from their bonding partners The two resulting oppositely charged atoms or molecules are called ions A positively charged ion is called a cation A negatively charged ion is called an anion Anions and cations attract each other; this attraction is called an ionic bond © 2021 Pearson Education, Inc. Electron transfer and ionic bonding © 2021 Pearson Education, Inc. Figure 2.12  Compounds formed by ionic bonds are called ionic compounds, or salts Salts, such as sodium chloride (NaCl; table salt), are often found in nature as crystals NaCl itself is not a molecule; the formula for an ionic compound indicates the ratio of elements in a crystal of the salt Most salts are quite stable when dry, but dissociate quite easily in water © 2021 Pearson Education, Inc. A sodium chloride (NaCl) crystal © 2021 Pearson Education, Inc. Figure 2.13 Weak Chemical Interactions Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules Many large biological molecules are held in their functional form by weak bonds The reversibility of weak bonds can be an advantage There are several types of weak chemical interactions that are important in organisms © 2021 Pearson Education, Inc. Hydrogen Bonds A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom In living cells, the electronegative partners are usually oxygen or nitrogen atoms © 2021 Pearson Education, Inc. © 2021 Pearson Education, Inc. Figure 2.14 Van der Waals Interactions If electrons are not evenly distributed, they may accumulate by chance in one part of a molecule Van der Waals interactions are attractions between molecules that are close together as a result of these charges Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface © 2021 Pearson Education, Inc.  Figure 2.UN02 © 2021 Pearson Education, Inc. Molecular Shape and Function A molecule’s size and shape are key to its function A molecule’s shape is determined by the positions of its atoms’ orbitals In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes © 2021 Pearson Education, Inc. Molecular shapes due to hybrid orbitals © 2021 Pearson Education, Inc. Figure 2.15  Molecular shape determines how biological molecules recognize and respond to one another Opiates, such as morphine, and naturally produced endorphins have similar effects because their shapes are similar and they bind the same receptors in the brain © 2021 Pearson Education, Inc.  A molecular mimic © 2021 Pearson Education, Inc. Figure 2.16 CONCEPT 2.4: Chemical reactions make and break chemical bonds Chemical reactions are the making and breaking of chemical bonds The starting molecules of a chemical reaction are called reactants The resulting molecules of a chemical reaction are called products © 2021 Pearson Education, Inc.  Water Formation © 2021 Pearson Education, Inc. Figure 2.UN03  Photosynthesis is an important chemical reaction Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen 6 CO2 + 6 H2O → C6H12O6 + 6 O2 © 2021 Pearson Education, Inc. Photosynthesis © 2021 Pearson Education, Inc. Figure 2.UN04  Photosynthesis: a solar-powered rearrangement of matter © 2021 Pearson Education, Inc. Figure 2.17  All chemical reactions are reversible: Products of the forward reaction become reactants for the reverse reaction The two opposite-headed arrows indicate that a reaction is reversible 3 H2 + N ⇌ 2 NH3 © 2021 Pearson Education, Inc.  Chemical equilibrium is reached when the forward and reverse reactions occur at the same rate At equilibrium the relative concentrations of reactants and products do not change © 2021 Pearson Education, Inc. An element’s properties depend on the arrangement of subatomic parts © 2021 Pearson Education, Inc. Figure 2.UN05 © 2021 Pearson Education, Inc. Figure 2.UN06 © 2021 Pearson Education, Inc. Figure 2.UN08