CHAPTER 6--- CHEMISTRY IN BIOLOGY Miss Queen
SECTION 6.1 Atoms, Elements, Compounds
COMPOSITION OF MATTER Matter - Everything in universe is composed of matter Matter is anything that occupies space or has mass Mass quantity of matter an object has Weight pull of gravity on an object
Atom the smallest unit of matter indivisible Helium atom
The simplest particle of an element that retains all the properties of that element Properties of atoms determine the structure and properties of the matter they compose Our understanding of the structure of atoms based on scientific models, not observation
Central core Consists of positive charged protons and neutral neutrons Positively charged Contains most of the mass of the atom
All atoms of a given element have the same number of protons Number of protons called the atomic number Number of protons balanced by an equal number of negatively charged electrons
The number varies slightly among atoms of the same element Different number of neutrons produces isotopes of the same element
Pure substances that cannot be broken down chemically into simpler kinds of matter More than 100 elements (92 naturally occurring)
90% of the mass of an organism is composed of 4 elements (oxygen, carbon, hydrogen and nitrogen) Each element unique chemical symbol Consists of 1-2 letters First letter is always capitalized
ATOMIC MASS Protons & neutrons are found in the nucleus of an atom Protons and neutrons each have a mass of 1 amu (atomic mass unit) The atomic mass of an atom is found by adding the number of protons & neutrons in an atom
Negatively charged high energy particles with little or no mass Travel at very high speeds at various distances (energy levels) from the nucleus
Atoms have 7 energy levels The levels are K (closest to the nucleus), L, M, N, O, P, Q (furthest from the nucleus) The K level can only hold 2 electrons Levels L Q can hold 8 electrons (octet rule)
Electrons are arranged in Energy Levels or Shells around the nucleus of an atom. first shell a maximum of 2 electrons second shell a maximum of 8 electrons third shell a maximum of 8 electrons
1. The Atomic Number of an atom = number of protons in the nucleus. 2. The Atomic Mass of an atom = number of Protons + Neutrons in the nucleus. 3. The number of Protons = Number of Electrons. 5. Electrons orbit the nucleus in shells. 7. Each shell can only carry a set number of electrons.
Elements are arranged by their atomic number on the Periodic Table The horizontal rows are called Periods & tell the number of energy levels Vertical groups are called Families & tell the outermost number of electrons
Most elements do not exist by themselves Readily combine with other elements in a predictable fashion
A compound is a pure substance made up of atoms of two or more elements The proportion of atoms are always fixed Chemical formula shows the kind and proportion of atoms of each element that occurs in a particular compound
Molecules are the simplest part of a substance that retains all of the properties of the substance and exists in a free state Some molecules are large and complex
Subscript after a symbol tell the number of atoms of each element H 2 0 has 2 atoms of hydrogen & 1 atom of oxygen Coefficients before a formula tell the number of molecules 3O 2 represents 3 molecules of oxygen or (3x2) or 6 atoms of oxygen
PROPERTIES The physical and chemical properties of a compound differ from the physical and chemical properties of the individual elements that compose it
The tendency of elements to combine and form compounds depends on the number and arrangement of electrons in their outermost energy level Atoms are most stable when their outer most energy level is filled
Most atoms are not stable in their natural state Tend to react (combine) with other atoms in order to become more stable (undergo chemical reactions) In chemical reactions bonds are broken; atoms rearranged and new chemical bonds are formed that store energy
COVALENT BONDS Formed when two atoms share one or more pairs of electrons
IONIC BONDS Some atoms become stable by losing or gaining electrons Atoms that lose electrons are called positive ions
Atoms that gain electrons are called negative ions Because positive and negative electrical charges attract each other ionic bonds form
SECTION 6.2 Chemical Reactions, Enzymes
ENERGY AND CHEMICAL REACTIONS Living things undergo thousands of chemical reactions as part of the life process Chemical reaction is the process by which atoms or groups of atoms in substances are reorganized into different substances.
CHEMICAL EQUATIONS represent chemical reactions Reactants are shown on the left side of the equation Products are shown on the right side
The number of each kind of atom must be the same on either side of the arrow (equation must be balanced) Bonds may be broken or made forming new compounds Activation Energy is the minimum amount of energy needed to form products in a chemical reaction.
Enzymes are an important class of catalysts in living organisms Catalyst is a substance that lowers the activation energy needed to start a chemical reaction. Mostly protein Thousands of different kinds Each specific for a different chemical reaction
ENZYME STRUCTURE Enzymes work on substances called substrates Substrates must fit into a place on an enzyme called the active site Enzymes are reusable!
SECTION 6.3 Water and Solutions
H O H
WATER: THE FACTS Water is possibly the most important compound in living organisms. Water consists of 1 atom of oxygen combined with 2 atoms of hydrogen. Water makes up 70 to 95 percent of most organisms.
- water is a polar molecule because oxygen is more electronegative than hydrogen, and therefore electrons are pulled closer to oxygen.
A solution is a mixture in which 2 or more substances are uniformly distributed in another substance
Solute is the substance dissolved in the solution Particles may be ions, atoms, or molecules Solvent is the substance in which the solute is dissolved Water is the universal solvent
SOLUTIONS Solutions can be composed of varying proportions of a given solute in a given solvent --- vary in concentration (measurement of the amount of solute) A saturated solution is one in which no more solute can be dissolved Aqueous solution (water) are universally important to living things
One of the most important aspects of a living system is the degree of acidity or alkalinity
Number of hydronium ions in solutions is greater than the number of hydroxide ions HCl H + + Cl -
Number of hydroxide ions in solution is greater than the number of hydronium ions NaOH Na + + OH -
logarithmic scale for comparing the relative concentrations of hydronium ions and hydroxide ions in a solution ranges from 0 to 14 Each ph is 10X stronger than next e.g. ph 1 is 10 times stronger than ph 2
the lower the ph the stronger the acid the higher the ph the stronger the base ph 7.0 is neutral
Control of ph is very important Most enzymes function only within a very narrow ph Control is accomplished with buffers made by the body Buffers keep a neutral ph (ph 7)
Buffers neutralize small amounts of either an acid or base added to a solution Complex buffering systems maintain the ph values of your body s many fluids at normal and safe levels
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= = = H H-C----O H-C----O H-C----O H O C-CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 3 O C-CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 3 O fatty acids C-CH 2 -CH 2 -CH 2 -CH glycerol 56
= = O C-CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 2 -CH 3 unsaturated O C-CH 2 -CH 2 -CH 2 -CH 57
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PRIMARY STRUCTURE Amino Acids (aa) aa1 aa2 aa3 aa4 aa5 aa6 Peptide Bonds 59
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O O=P-O O 5 CH2 O N C 4 C 1 C 3 C 2 61