Chapter 2 Basic Chemistry Chapter 2 Basic Chemistry
Chapter 2: Basic Chemistry
Chapter 2: Basic Chemistry
“Life is Chemistry” Photosynthesis DNA replication Protein synthesis
Atomic structure is the basis for life’s chemistry. Living and non-living matter is composed of atoms. What is matter?
Chapter 2: Basic Chemistry • Matter – anything that takes up space and has mass. • Element – A pure substance that contains only one kind of atom. • Atom – The most basic component of matter, or the smallest unit of matter that retains the properties of an element.
Chapter 2: Basic Chemistry • Chemistry: The study of the properties and interactions of the elements.
Important definitions: • Chemical: A substance of defined molecular composition. • Molecule: The smallest unit of a chemical. • Compound: A substance made up of two or more elements in a specific ration. CO 2 H 2 O C 6 H 12 O 6 O 2 What about oxygen gas? • Chemical reaction: A process that transforms one or more molecules into substances with different chemical identities, different compositions of atoms, and different bond arrangements.
Important definitions: Photosynthesis CO 2 H 2 O Reactants C 6 H 12 O 6 O 2 Products • Reactants: The elements or compounds that participate in a chemical reaction. • Products: The elements or compounds produced by a chemical reaction.
Atoms and Isotopes • Atomic structure: Bohr model Positive and negative forces attract each other. How strong is this attraction? A million trillion times the force of gravity!!! Electron orbital: the 3 D space occupied by an electron Electrons “zoom” around the nucleus of an atom at the speed of light, forming an “electron cloud. ”
Atoms and Isotopes The number of subatomic particles is what makes the atoms of an element unique. How to read the periodic table of the elements.
Common Elements in Biology (know symbols for these!) • Carbon* • Hydrogen* • Oxygen* • Nitrogen* • Phosphorous* • Potassium • Calcium • Iron • Chlorine • Sodium • Sulfur* • Magnesium • Iodine *6 most abundant elements in living things!
What is an isotope? • Every element has its own atomic number based on the number of protons in the nucleus. • Isotope: A different form of the same element with the SAME number of protons, but a different number of neutrons. Unstable
Electrons • What do electrons do? • Electrons define the chemical reactivity of elements.
Electrons • Carry a negative charge • Repel one another • Are attracted to protons in the nucleus • Move in orbitals -- An area of around the nucleus with a high probability of finding an electron
Bohr model For atomic structure: atom is largely empty space; the electrons occur in orbits, or electron shells.
Shell/Bohr Model: these are NOT orbitals but energy levels!!! • First shell – Lowest energy – Holds 1 orbital with up to 2 electrons • Second shell – 4 orbitals hold up to 8 electrons CALCIUM 20 p+ , 20 e-
Electron Vacancies • Unfilled shells make atoms likely to react • Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells CARBON 6 p+ , 6 e- NITROGEN 7 p+ , 7 e- HYDROGEN 1 p+ , 1 e-
Octet rule: • For elements 6– 20, an atom will lose, gain, or share electrons in order to achieve a stable configuration of 8 electrons in its outermost shell. • When atoms share electrons, they form stable associations called molecules.
Chemical Bonds • Covalent bonds: Atoms can form molecules by sharing electrons equally. “Covalent bonds store energy. When chemical bonds are broken, some of the energy stored in bonds is lost as heat. This is the process of basic biological chemistry: food molecules are taken in and broken down, and the energy in the bonds is captured to form new bonds. “
Ionic bonds: one atom surrenders an electron more strongly.
Atoms start out electrochemically neutral. Or, # protons = # electrons. When one atom gives up an electron to another atom, both atoms become IONS (atoms with a net electrical charge). Cation (+) Anion (-) The cation and anion are attracted to each other because of their opposite electrical charges.
Hydrogen bonds: is like an ionic bond, but without the transfer of an electron between the bonding partners to form positive and negative ions.
Other interactions: • van der Waals interactions: weak intermolecular attractions due to instantaneous charge differences between two surfaces that produce a slight “stickiness”
Bond Energies
Drawing chemical formulas:
Simplified structural formula. • For organic compounds (they contain carbon), sometimes simplified structural formulas are used. • Connecting lines represent carbon atoms. Simplified structural formula
Functional groups: • Certain groups of atoms, called functional groups, are consistently found together in very different biological molecules. • Each functional group has a specific set of chemical properties. • When attached to a larger molecule, it can transfer its properties to that molecule. • One of the properties is polarity. • Large biological molecules often contain many different functional groups (Ex. hydrophobic, charged, and polar groups within a large protein).
Functional groups:
Water on Mars… Flowing water on the surface of Mars One reason that scientists are so interested in finding water on MARS is that water is one of the essential components of life!!
Biology in the NEWS!
Structure of water • Oxygen attracts electrons more strongly than hydrogen. This created a partial negative charge on the oxygen atom and two partial positive charges on the hydrogen atoms. These partial charges allow water molecules to form up to four hydrogen bonds with other water molecules.
Hydrophilic vs hydrophobic: • Molecules with polar covalent bonds are attracted to polar water (they are hydrophilic). • Molecules with nonpolar covalent bonds show greater attraction to one another than to water (they are hydrophobic). • In the models shown here (gray, H; red, O; black, C)
Properties of water • The hydrogen bonding ability of water has had a profound impact on our planet and effects the large-scale properties of water. Adhesion - the tendency of water to cling to other surfaces Cohesion - the tendency of water molecules to cling together as droplets These forces also allow water to creep up through thin tubes in plants from roots to leaves without other forces pushing from below or pulling from above. As a result, some plants evolved to be hundreds of meters high!
Surface tension • Water molecules sticking to each other at the surface for a “film” between the water and the air that can support some organisms’ weight.
Specific heat of water and homeostasis: • The amount of energy (calories) required to raise the temperature of 1 gram of a liquid by 1 deg. C. • Water has a high specific heat. This means that a large amount of energy is required to heat water. • The tendency of water to resist major fluctuations in temperature, helps living things maintain homeostasis. • Homeostasis: A property of life where an organism’s internal conditions remain stable and relatively constant. • Temperature • p. H • Question: How does the high specific heat of water facilitate homeostasis in living things?
Water as a Solvent: • In its liquid form, water is a solvent (a liquid in which other substances dissolve) • Solute: The dissolved substance. • Solution: A liquid mixture of two or more substances (the solvent and one or more solutes. In animals, water is the solvent in blood (a solution). Sugar, salt and other nutrients are solutes in blood. Cytoplasm and tree sap are other biological solutions.
Acids, Bases, and p. H • In liquid water, a very small # of hydrogen atoms spontaneously break loose from water molecules. H 2 O H+ and OH(1 in 10 million in pure water) • Acids: Can increase the number of hydrogen (H+) ions in a watery solution. Or, they are H+ donors. • Bases: Can increase the number of hydroxide (OH-) ions in a watery solution. Or, they are H+ acceptors.
Acids, Bases, and p. H • At any instant, some water molecules are breaking apart into H+ ions and OH- ions. • The ionization of water is the basis of the p. H scale. • Water has a p. H of 7, which is considered neutral (neither acidic nor basic) • What constitutes a strong of weak acid?
p. H is on a logarithmic scale: •
Weak acids are reluctant H+ donors • Example “carbonic acid” (H 2 CO 3) • Strong acids readily donate electrons when dissolved in water • Examples: • Hydrochloric acid (HCl) • Nitric acid (HNO 3) • Sulfuric acid (H 2 SO 4)
Cells require a neutral p. H 7. 3 -7. 5 p. H 7 Altering the p. H in an organism’s environment can have devastating effects.
Living things are sensitive to small changes in p. H. Strong acids and bases can disrupt or inhibit the chemical processes that keep organisms alive. If the p. H of seawater is lowered from the normal 8. 1 to 7. 5, the larval hardshell clams (Mercenaria mercenaria) cannot incorporate the calcium carbonate needed to build their shells. How can buffers help an organism maintain homeostasis?
Biological buffers. • To counteract relatively minor fluctuations in p. H, organisms have small molecules in their biological solutions that neutralize (or lessen) the impact of strong acids and bases. • These buffers help organisms maintain homeostasis. • They may be able to counter the effects of acids and bases in the environments that exceed the range to which an organisms is adapted. Normal 4 days 7 days • However, this only occurs for a short length of time, and buffers cannot over come exposure to a strong acid or base.
Buffer Systems • Minimize shifts in p. H • Partnership between weak acid and base it forms when dissolved • Two work as pair to counter shifts in p. H
Buffering system in blood. • Metabolic reactions are sensitive to slight shifts in p. H. • Biological systems respond to slight shifts in p. H using buffer systems.
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