Week 2Chapter 3 The Chemistry of Life: Atoms, Molecules and Reactions
We are going to spend the day talking about inorganic chemistry…
An Element is any substance that cannot be broken down into a simpler substance and still maintain its characteristics.
There are 92 known naturally occurring elements that are designated by one or two letters and are given latin - english names.
O is the symbol for Oxygen, C for Carbon, pb for lead, N for nitrogen and Na for sodium (natrium), etc.
Some elements are more plentiful than others, some are fairly rare.
The smallest complete unique unit of an element. While there are a variety of subatomic particles we are concerned with only three: Protons, Neutrons, and Electrons.
Protons carry a positive electrical charge.
Neutrons have no charge or are uncharged and have about the same mass as protons.
Most of the mass of the atom is made up of protons and nuetrons. They are clustered together in the atomic nucleus.
Electrons carry a negative electrical charge and have an extremely small mass (about 1/800th of a proton). Electrons spin around the atomic nucleus.
Each element has a fixed number of protons in its nucleus. The number of protons is an element’s atomic number and is written as a small number subscript to the left of the atomic symbol.
1H indicates that hydrogen has one proton in its nucleus.
Oxygen has 8. The number of protons gives the element its chemical identity….any atom with one proton is always hydrogen.
The total number of protons plus nuetrons is called an elements atomic mass and is designated as a superscript to the left of the atomic symbol…
2311Na means that sodium has 11 protons and 12 nuetrons and an atomic mass of 23.
Pg 39 of text shows two different illustrations of an atom…
An atom contains the same number of electrons and protons so that an atom has no net charge Some chemical reactions will change the number of electrons but do not effect the atomic nucleus.
The electrical attraction between protons (+) and electrons (-), and the fact that like charged electrons will repel each other helps to explain the location of electrons around the atomic nucleus.
Whenever two or more atoms combine chemically they are said to have formed a molecule. When two atoms of oxygen combine a molecule of oxygen is said to have formed.
A chemical compound is formed when molecules of different elements combine into a fixed ratio. Water is a chemical compound created by a combination of hydrogen and oxygen atoms at a ration of 2H to 1O.
A chemical formula then is a short hand way of describing a compound…H20.
Chemical formulas are written descriptions of the reactions that occur between atoms and molecules…you book describes the reaction between methane (CH4) and oxygen:
CH4 + 2O2 --- CO2 + 2H2O + energy
Reactants, that is, the compounds participating in the reaction are written on the left and the products or the result of the reaction are written on the right.
Atoms combine by forming chemical bonds. The electrons in the outer ring or energy level of an atom are called the valence electrons. When the outer shell of an atom has fewer than eight electrons, it tends to lose or gain or share electrons to achieve a complete outer shell. (Some lighter elements use fewer than 8.)
Compounds that are held together by these forces of attraction are called chemical bonds. The two principle chemical bonds are covalent bonds and ionic bonds.
Covalent bonds involve sharing pairs of electrons between atoms.
Single bonds refer to the sharing of one electron, double bonds sharing 2 electrons, triple bonds sharing three… Nonpolar covalent bonds – when atoms have equal affinity for electrons, that is equal electronegativity.
Polar Covalent bonds – when atoms have different electronegativity example H2O where hydrogen atoms are electropositive and oxygen atoms are electronegative
IONIC BONDS are formed in an extreme case of polarity in which the electrons from one atom are transferred from one atom to another. When an atom gains or loses an electron it becomes a charged particle called an ion. Atoms with 1,2or 3 electrons in the outer shell tend to lose electrons t5o other atoms. As they lose electrons they begin to become positively charged as the protons in the atomic nucleus outnumber the electrons. Positively charged ions are called cations
Atoms with 5, 6, or 7 valence electrons tend to gain electrons from other atoms and become negatively charged and are called anions.
An ionic compound is a substance that consists of anions and cations held together by their opposite charges.
An example of an ionic compound is the combination of sodium and chlorine…
See page 47 of your book…
Sodium has three rings of electrons, 2 in the inner shell, 8 in the second and 1 in the third…Sodium cannot add electrons to its outer ring because it would begin to have a very negative charge and be out of balance with its atomic nucleus, it would be out of balance. So instead sodium tends to give up its electron in the outermost shell to some other atom which leaves the second ring complete.
A chlorine atom has an atomic number of 17 (17 protons in its nucleus) and is balanced by 2 electrons in its inner shell, 8 in its second and 7 in its third. If the chlorine atoms were to shed its seven electrons in effort to have a complete ring it would have a heavily positive charge, instead it accepts an electron “donated” by another atom to complete its third ring.
When sodium “donates” its on electron to chlorine it has 11 protons and 10 electrons or a positive charge of +1. When the chlorine accepts the electron it has 17 protons and 18 electrons or a negative charge of –1. They are held together y this electrical attraction, they become sodium chloride…salt.
When an ionic compound is held together in its solid form it takes incredible energy to overcome the electrical attraction, but When ionic compounds are placed in water they separate or disassociate easily.
Water is an excellent solvent because of the partial positive charge on the hydrogen atoms and the partial negative charge on the oxygen atom on each water molecule attract the anions and cations on the surfaces of ionic solids…the solid dissolves
As it dissolves, each cation and anion is surrounded by the opposite charged ends of water molecules…this is called hydration. (see page 46 and 47)
WATER
Water is unique. It is important because it accounts for about 80% of the weight of a cell, you are about 70% water by weight.
Water is the biological solvent for many of the reactions we need to survive, from the metabolism of oxygen producing plants to activities in our own bodies.
The hydrogen bonds between water molecules are weak. Each water molecule can from bonds with up to four other water molecules by aligning the partial positive charged hydrogen to a corresponding partial negative charged oxygen.
Water Molecules are Polar
Polar compounds are hydrophillic (water loving), nonpolar compounds are hydrophobic (water hating). Nonpolar compounds cluster together and are insoluble in water. (Oil and Water)
Water is an excellent solvent
A Solvent is a fluid capable of dissolving other substances. Because water is polar it is an excellent solvent especially for ionic and polar compounds.
Remember the example of salt? The ability of water to dissolve other compounds is important to water’s biological roles.
Water Molecules are Cohesive and Adhesive
Water molecules like to stick together, they are cohesive, due to the hydrogen bonding we spoke about. They are more attracted to each other than they are to other molecules in the air so that they crowd together at surfaces (Surface tension).
Water molecules also stick to other substances (that have charged atoms at the surface) This adhesive quality is how water makes other things wet.
Adhesive and cohesive forces explain capillary action…as water clings to surfaces it pulls other molecules along with it…defying gravity.
Water helps to stabilize temperatures
The temperature of water changes more slowly and less drastically than most substances. When heat is added to a substance to warm it up, it causes the molecules to move faster. The amount of energy required to raise the temperature of one gram of of a substance 1 degree centigrade is called the substances Specific Heat.
Because of hydrogen bonding the molecules resist the increased motion of added heat so that more heat is required to achieve the same rise in temperature.
Because of the high specific heat of water, water bodies tend to have more constant temperatures.
Water also has a high heat of vaporization…it takes more than 500 calories to change a gram of liquid water into water vapor. Calories are units of heat energy. Because of the heat of vaporization our bodies can cool themselves, get rid of excess heat, by the evaporation of sweat from our skin.
The Density of Water is greatest at 4 degrees centigrade.
It is more dense as an liquid than as a solid…water freezes from the top down and ice floats.
ACIDS PRODUCE HYDROGEN IONS
An acid is a substance that ionizes in water to yield hydrogen ions and an anion. A hydrogen ion is a proton so that an acid is a proton donor. A base is a proton receptor.
Many bases dissociate in water to produce a hydroxide ion and a cation.
PH Scale
The relative strength or weaknesses of an acid or a base are described on the pH scale…
PH is the negative logarithm of the hydrogen ion concentration expressed in moles per liter (A mole is the molecular weight of a substance expressed in grams) See the substances in the pH scale on page 52.
The pH of pure water is 7 or neutral. Because the scale is logarithmic a pH of 6 has ten times fewer hydrogen ions concentration than pH of 7.
Salts- A salt is formed when the hydrogen ion of a compound is replaced by some other cation.
Salts that dissociate in water can conduct electrical current…electrolytes…and are important in the transmission of nerve impulses, muscle contraction, etc.
Chapter 4 Organic Compounds (pg 60)
The primary structural component of living things are organic compounds. Called the “molecules of life”…
The major groups of organic compounds as far as life is concerned are:
- Carbohydrates
- Lipids
- Protiens
- Nucleic acids
All built around carbon atoms…
Hydrogen, oxygen and nitrogen are frequently found bonded to carbon. Organic compounds made up of carbon and hydrogen are known as hydrocarbons, this includes what common materials?
Carbohydrates
“fuel molecules” consist of carbon, hydrogen and oxygen atoms (CH2O). Carbohydrates are further classified as
- Monosaccharides
- Disaccharides
- Polysaccharides
Monosaccharides are simple sugars, contain 3 to 6 carbon atoms. Glucose and fructose are examples which have the same molecular formula but whose atoms are arranged differently. They are called isomers. Same formula but different atomic arrangement.
Disaccharides consit of two monosaccharides covalently bonded to one another. Examples would include maltose and sucrose. Sucrose is a combination of glucose and fructose. A disaccharide can be hydrolized, that is split in water. So that if fructose is mixed with water it divides to form glucose and fructose.
Polyssacharides are also comprised of combined monossacharides. In this case the sugars combine i a long chain of repeating units to form a single molecule. Polysaccharides are the most common carbohydrates, includes starches, glycogen, cellulose and chitin. Polyssacharides stored as starch in plants and as glycogen in animals Cellulose is not water soluble.
Lipids
Most common form is in neutral fats…biologically a form of energy storage. Store more than twice the amount of energy as do carbohydrates. Also serve as insulation, Carbohydrates and proteins can be converted into fats and stored in the cells of adipose (fat) tissues.
A nuetral fat consists of glycerol joined to 1,2 or 3 molecules of fatty acid.
Proteins
Play important roles in a wide range of critical structural and regulatory functions. Such as enzymes (regulate thousands of internal chemical reactions, an enzyme is a biologic catalyst),
Proteins are comprised of hydrogen, carbon, nitrogen, oxygen and usually sulfur. These are combined in different ways to form more than 20 different amino acids
Plants can synthesize all of their required amino acids, but animals cannot
See page 72 for discussion on Amino acids
See page 73 – 76 for discussion on protein organization
Nucleic Acids
Large complex molecules. Two classes are ribonucleic acids (RNA) and deoxyribonucleic acid (DNA).
Nucleic acids are composed of molecular units called nucleotides, each nucleotide is comprised of:
- A 5 carbon sugar, either ribose or deoxyribose,
- A phosphate group,
- A nitrogenous base that might be a double ringer purine or a single ringed pyrimidine
DNA contains the purine adenine (A), and guanine(G) and the pyrimidines cytosine (C) and thymine (T) together with the sugar deoxyribose and phosphate
RNA contains the purines adenine and guanine and the pyrimidines cyotsine and uracil (U) together with the sugar ribose and phosphate.
Adenosine triphosphate (ATP) is a nucleic acid that serves as energy currency of all cells, composed of adenine, ribose and three phosphates.
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