2.1 Nature of Life
Atoms
The greek philosopher, Democritus, first came up with the concept of the basic unit of matter, the atom. (atomos means unable to be cut)
Atoms are made up of subatomic particles called protons, neutrons, and electrons.
Protons and neutrons have about the same mass.
Protons are positively charged particles (+)
Neutrons carry on charge.
Strong forces bind protons and neutrons together to form the nucleus, the center of the atom.
Electrons are negatively charged particles (-) with only 1/1840 the mass of a proton.
Electrons are in constant motion in the space outside of and surrounding the nucleus and are attracted to the positively charged nucleus by the opposite charges.
Atoms have equal numbers of electrons and protons so their charges balance out. Therefore, they are electrically neutral.
Atoms are made up of subatomic particles called protons, neutrons, and electrons.
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| Atoms are incredibly small. Placed side by side, 100 million atoms would make a row only 1 cm long. |
Protons are positively charged particles (+)
Neutrons carry on charge.
Strong forces bind protons and neutrons together to form the nucleus, the center of the atom.
Electrons are negatively charged particles (-) with only 1/1840 the mass of a proton.
Electrons are in constant motion in the space outside of and surrounding the nucleus and are attracted to the positively charged nucleus by the opposite charges.
Atoms have equal numbers of electrons and protons so their charges balance out. Therefore, they are electrically neutral.
Elements and Isotopes
An element is a pure substance that consists entirely of one type of atom. There are more than 100 known elements, but only about 24 of them reside in living organisms.
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| Mercury, a silvery-white metallic element, is liquid at room temperature and forms droplets. It is extremely poisonous. |
Atoms of the same element may have different numbers of neutrons. These are known as isotopes.
Isotopes of the same element have the same number of protons but a different number of neutrons.
The total number of protons + neutrons in the nucleus is called its mass number.
mass # = protons + neutrons
Isotopes are identified by their mass numbers
Because they have the same number of electrons, all isotopes of an element have the same chemical properties.
(it is the number of electrons in the outer (valence) shell which determines an elements chemical properties)
Some isotopes have such uneven ratios of protons to neutrons, their nuclei are unstable and break down at a constant rate over time. This means they are radioactive.
Radiation is dangerous, but these isotopes have a number of important scientific and practical uses such as C14 dating, medical diagnostics and treatments.
Chemical Compounds
In nature, most elements are found combined with other elements in compounds. A chemical compound is a substance formed by the chemical combination of two or more elements in definite proportions.
The composition of compounds is like an exact recipe. It tells how many atoms of each element are contained within the compound.
H2O - two hydrogen atoms for every one oxygen atom
NaCl - one sodium atom for every chlorine atom
The physical and chemical properties of a compound are usually very different from those of the elements from which it is formed.
ex: NaCl (table salt)
Na - silver-colored metal
Cl - poisonous yellow-green gas
Chemical Bonds
There are 2 main types of chemical bonds.
Ionic and Covalent bonds.
Bond formation involves the electrons in the outermost shell surrounding the nucleus.
Ionic Bonds
An ionic bond is formed when one or more electrons are transferred from one atom to another.
When an atom loses an electron (-) to another atom it becomes positively charged. When an atom gains an electron (-), it becomes negatively charged. These charged atoms are called ions.
This transfer of electrons causes the ions to have a strong attractions to each other forming an "ionic bond."
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| The compound sodium chloride forms when sodium loses its valence electron to chlorine. |
Covalent Bonds
Sometimes electrons are shared by atoms instead of being transferred. This means that the moving electrons are actually traveling about about the nuclei of both atoms, forming a covalent bond.
When atoms share 2 bond, the bond is called a single covalent bond, and so on.
share 2 bonds - single covalent bond
share 4 bonds - double covalent bond
share 6 bonds - triple covalent bond
Molecule - structure that results when atoms are joined together by covalent bonds.
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| In a water molecule, each hydrogen atom shares two electrons with the oxygen atom. |
Van der Waals Forces
Because of their structures, atoms of different elements do not all have the same ability to attract electrons. Some atoms have a stronger attraction for electrons than do other atoms. When the atomsin a covalent bond share electrons, the sharing is not always equal. This can create regions on a molecule that have a tiny positive or negative charge.
When molecules are close together, a slight attraction can develop between the oppositely charged regions of nearby molecules call van der Waals forces.
These are not as strong as bonds, but they can hold different molecules together.
A gecko foot is covered by as many as half a million tiny hairlike projections. Each projection is further divided into hundreds of tiny, flat-surfaced fibers. This design allows the gecko's foot to come in contact with an extremely large area of the wall at the molecular level. Van der Waals forces form between molecules on the surface of the gecko's foot and molecules on the surface of the wall.
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2.2
Properties of Water
The Water Molecule
The Water Molecule
How does the structure of water contribute to its unique properties?
Water is one of the few compounds found in a liquid state over most of the Earth's surface.
Water is neutral. Its positive (+) charges on its 10 protons balance out its negative (-) charges on its 10 electrons.
With 8 protons, water's oxygen nucleus attracts electrons more strongly than the single protons of water's two H nuclei. As a result, water's "shared" electrons spend more time around the O than the H. This causes the end of the molecule which the electrons are pulled toward to become more negative and the end of the molecule the electrons are being pulled away from to become more positive.
A molecule in which the charges are unevenly distributed is said to be polar.
The partial charges on polar molecules are written in parentheses (-) and (+) to show that they are weaker than the charges on ions.
Hydrogen Bonding
Because of their partial positive and negative charges, polar molecules like water can attract each other. This attraction of opposite charges involving a H with a partial positive charge and a partial negative charge on a different molecule is called a Hydrogen Bond.
Hydrogen bonds usually bond with O, N, and F. (FON)
H bonds are not as strong as covalent or ionic bonds. Because water is a polar molecule, it is able to form multiple H bonds which account for many of water's special properties.
Cohesion
Cohesion is an attraction between molecules of the same substance. Water is extremely cohesive and can form as many as 4 H bonds at a time. Cohesion causes the water molecules to stick together. This accounts for why drops of water form beads on a smooth surface, and why some insects can walk on water.
Adhesion
Adhesion is an attraction between molecules of different substances, like water and glass, and is responsible the the meniscus that forms when water is in a glass container. It is also responsible for the capillary action that draws water out of the roots of a plant and up into the stem against gravity.
Heat Capacity
It takes a large amount of heat energy to cause the H bonded molecules of water to move faster, which raises the temperature of water. Water's heat capacity, the amount of heat energy required to increase its temperature, is relatively high. This fact keeps large bodies of water from drastic fluctuations in temperature. This is important for the organisms who live there. At the cellular level, water absorbs the heat produced by cell processes. Cells would not be able to tolerate rapid fluctuations in temperature.
In a solution, the substance in which the solute dissolves is the solvent. The substance being dissolved is the solute.
Water's polarity gives it the ability to dissolve both ionic compounds and other polar molecules.
Water molecules sometimes split apart to form ions.
Each step on the pH scale represents a factor of 10.
Water is one of the few compounds found in a liquid state over most of the Earth's surface.
Water is neutral. Its positive (+) charges on its 10 protons balance out its negative (-) charges on its 10 electrons.
Polarity
A molecule in which the charges are unevenly distributed is said to be polar.
The partial charges on polar molecules are written in parentheses (-) and (+) to show that they are weaker than the charges on ions.
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A water molecule is polar because there is an uneven distribution of electrons between the O and H atoms. The negative pole is near the O atom and the positive pole is between the H atoms. |
Hydrogen Bonding
Because of their partial positive and negative charges, polar molecules like water can attract each other. This attraction of opposite charges involving a H with a partial positive charge and a partial negative charge on a different molecule is called a Hydrogen Bond.
Hydrogen bonds usually bond with O, N, and F. (FON)
H bonds are not as strong as covalent or ionic bonds. Because water is a polar molecule, it is able to form multiple H bonds which account for many of water's special properties.
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| Each molecule of water can form multiple H bonds with other water molecules. |
Cohesion
Cohesion is an attraction between molecules of the same substance. Water is extremely cohesive and can form as many as 4 H bonds at a time. Cohesion causes the water molecules to stick together. This accounts for why drops of water form beads on a smooth surface, and why some insects can walk on water.
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| The strong attraction between water molecules produces a force sometimes called "surface tension," which can support very lightweight objects, such as this raft spider. |
Adhesion
Adhesion is an attraction between molecules of different substances, like water and glass, and is responsible the the meniscus that forms when water is in a glass container. It is also responsible for the capillary action that draws water out of the roots of a plant and up into the stem against gravity.
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| Adhesion between water and glass molecules is responsible for causing the water in these columns to rise. The surface of the water in the glass column dips slightly in the center, forming a curve called a meniscus. |
Heat Capacity
It takes a large amount of heat energy to cause the H bonded molecules of water to move faster, which raises the temperature of water. Water's heat capacity, the amount of heat energy required to increase its temperature, is relatively high. This fact keeps large bodies of water from drastic fluctuations in temperature. This is important for the organisms who live there. At the cellular level, water absorbs the heat produced by cell processes. Cells would not be able to tolerate rapid fluctuations in temperature.
Solutions and Suspensions
A mixture is a material composed of two or more elements or compounds that are physically mixed together but not chemically combined. Salt and pepper, sugar and sand, and salad are all mixtures. Living things are in part composed of mixtures, and other gases.
Two types of mixtures that can be made with water:
solutions and suspensions
Solutions
If table salt (NaCl) is placed in a glass of water, the polar ends of the water molecule pull the ions away from each other and "dissolve" them in the water molecules. The water molecules will surround the ions until the NaCl is completely dissolved forming a solution, or until there are no more available and the solution is said to be "saturated." All the components of a solution are evenly distributed throughout the solution.In a solution, the substance in which the solute dissolves is the solvent. The substance being dissolved is the solute.
Water's polarity gives it the ability to dissolve both ionic compounds and other polar molecules.
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| When an ionic compound such as sodium chloride is placed in water, water molecules surround and separate the positice and negative ions. |
Acids, Bases, and pH
Water molecules sometimes split apart to form ions.
In pure water, only 1/550million molecules split into ions. Since the positive ions = the negative ions, water remains neutral.
The pH Scale
The pH scale is a measurement system which indicates the concentration of H ions in solution. It ranges from 0 to 14. A pH of 7 means the concentration of H ions and OH ions is equal. Pure water has a pH of 7. Solutions with a pH below 7 are called acids because they have more H ions that OH ions. The lower the pH, the greater the acidity. Solutions with a pH above 7 are called basic because they have more OH ions than H ions. The higher the pH, the more basic the solution.
pH - the concentration of H ions in solution
Each step on the pH scale represents a factor of 10.
A liter of solution with a pH of 4 has 10x as many H as a liter of solution with a pH of 5.
Acids
An acid is any compound that forms H ions in solution. Acidic solutions contain higher concentrations of H ions than pure water and have pH values below 7. Strong acids have pH values from 1 to 3. (HCl)
Bases
A base is a compound that produces hydroxide (OH) ions in solution. Basic, or alkaline, solutions contain lower concentrations of H ions that pure water and have pH values above 7. Strong bases have pH values ranging from 11 to 14. (Lye soap, NaOH)
Buffers
The pH in the fluids within most cells in the human body must generally be kept between 6.5 and 7.5. If the pH is higher or lower, it will affect the chemical reactions that take place within the cells. Controlling pH is important for maintaining homeostasis.
Buffers are one way organisms can control pH through dissolved compounds. Buffers are weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH.
Buffers dissolved in life's fluids play an important role in maintaining homeostasis in organisms.
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| Buffers help prevent drastic changes in pH. Adding acid to an unbuffered solution causes the pH of the unbuffered solution to drop. If the solution contains a buffer, however, adding the acid will cause only a slight change in pH. |
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2.3
Carbon Compounds
What does "organic" mean?
Two things!
In society, organic means clean, natural, no preservatives, no fertilizers, etc.
In chemistry, organic means the study of compounds that contain bonds between carbon atoms.
Why is carbon so interesting?
Two reasons:
1. Carbon has 4 valence electrons, allowing them to form strong covalent bonds with many other elements.
2. One carbon atom can bond to another, which gives carbon the ability to form chains that are almost unlimited in length.
Carbon to carbon bonds can be since, double, or triple. It has the ability to form millions of different large and complex structures:
Macromolecules
"giant molecules"
Macromolecules are made from thousands or even hundreds of thousands of smaller molecules.
Polymerization - large compounds are built by joining smaller ones together
Monomers are smaller units which are joined together to make Polymers.
Monomers can be identical or different from each other:
The 4 major organic molecules are:
Carbohydrates
Lipids
Nucleic Acids
Proteins
Carbohydrates (sugars)
Made up of Carbon, Hydrogen, and Oxygen in a 1:2:1 ratio.
CHO
1:2:1
Living things use carbohydrates as their main source of energy. Plants, some animals, and other organisms also use carbohydrates for structural purposes.
Sugars (carbs) supply immediate energy for the cells. Complex carbohydrates are ways that organisms store energy such as cellulose in plants and glycogen in animals.
Simple sugars (carbohydrates)
Monosaccharides - single carbohydrate molecule (glucose, galactose, fructose)
Disaccharides - 2 sugar molecules bonded together (sucrose, aka table sugar)
Polysaccharides - (the polymer name of a carbohydrate) more than 2 carb molecules bonded together, sometimes called starches
( cellulose, glycogen)
(cellulose - cell walls of plants for excess energy storage)
(glycogen - stored sugar in animals in the liver and muscles)
Polymerization
When forming polymers, a small molecule (water) is released each time monomers join together.
This is an example of a "condensation" reaction (where water is lost), also known as a dehydration reaction.
When breaking polymers apart, water must enter into the reaction to fill the "spaces" left where the bonds were broken.
This is an example of a "hydrolysis" reaction ( water was split) where the H and OH bond with the larger molecules to fill the holes left from the splitting of the monomers.
Lipids
Lipids include fats, oils, and waxes.
Lipid are made from carbon and hydrogen and oxygen with no exact ration.
CHO
Lipids can be used to store energy. Some lipids are important parts of biological membranes and waterproof coverings.
Lipids are formed when a glycerol molecule combines with compounds called fatty acids.
When each carbon atom is joined to the next carbon atom by a single bond, the lipid is said to be "saturated". This means that the fatty acid contains the maximum possible number of hydrogen atoms.
If there is at least on carbon-carbon double bond the fatty acid is said to be "unsaturated." Lipids whose fatty acids contain more than one double bond are said to be "polyunsaturated."
Saturated fats tend to be solids at room temperature.
Unsaturated fats tend to be liquids at room temperature.
Proteins
Proteins are macromolecules that contain nitrogen as well as carbon, hydrogen, and oxygen.
Proteins are polymers of made of monomers called amino acids. Amino acids are compounds with an amino group (NH2) on one end and a carboxyl group (COOH) on the other end. Covalent bonds called peptide bonds link amino acids together to form a polypeptide.
Jobs of Proteins
Some proteins control the rate of reactions and regulate cell processes. Others form important cellular structures, while still others transport substance into or out of cells or help to fight disease.
More than 20 different amino acids are found in nature. They differ at the place in a side chain called the "R-Group", which have a different range of properties. Some R-groups are acidic and some are basic. Some are polar, some non-polar.
Levels of Organization
Amino acids are assembled into polypeptide chains according to instructions coded in DNA.
Secondary structure is the folding or coiling of the polypeptide chain.
Tertiary structure is the complete, 3D arrangement of a polypeptide chain.
Proteins with more than one chain are said to have a 4th level of structure, describing the way in which the different polypeptides are arranged with respect to each other.
Nucleic acids are macromolecules containing hydrogen, oxygen, nitrogen, carbon, and phosphorus.
CHONP
Nucleic acids are polymers assembled from individual monomers known as nucleotides. Nucleotides consist of 3 parts: a 5-carbon sugar, a phosphate group (PO4), and a nitrogenous base. Nucleotides join together to form the polymers, DNA and RNA.
Nucleic acids store and transmit hereditary information.
The ladder "rails" of DNA are made up of the phosphate group and 5-carbon sugar bonded together by a strong covalent bond. The ladder "steps" are the nitrogenous bases which actually make up the genetic code of an organism.
Lesson 2.4
Chemical Reactions and Enzymes
Everything that happens in an organism- its growth, its interaction with the environment, its reproduction, and even its movement- is based on chemical reactions.
A chemical reaction is a process that changes, or transforms, one set of chemicals into another. Mass and energy are conserved during chemical reactions.
The elements or compounds that enter into a chemical reaction are known as reactants.
The elements or compounds produced by a chemical reaction are known as products.
reactant + reactant ----> product(s)
Chemical reactions involve changes in chemical bonds that join atoms in compounds.
An important chemical reaction in your bloodstream that enables CO2 to be removed from the body is shown here:
Whether or not a chemical reaction will "go" or not depends on the energy involved.
Chemical reactions that release energy (exothermic) often occur on their on, or spontaneously.
Chemical reactions that absorb energy (endothermic) will not occur without a source of energy.
In order to stay alive, organisms need to carry out reactions that require energy. Plants get their energy from the sun. Animals get their energy from consuming plants and animals.
The energy that is needed to get a reaction started is the activation energy.
In an energy-absorbing reaction, energy is put into the reaction to get it started, therefore, the products end up with more energy than the reactants.
In an energy-releasing reaction the products have less energy than the reactants because energy was released with the product(s).
Enzymes
Enzymes are proteins that act as biological catalysts. A catalyst is a substance that speeds up the rate of a chemical reaction.
A catalyst works by lowering the activation energy required to get the reaction started.
Enzymes are very specific, generally catalyzing only one chemical reaction.
Enzymes provide a site where reactants can be brought together to react, thus reducing the amount of energy needed to bring the reactants together.
Each enzymes has a perfect fit, like a lock and a key, called a binding site or "active site" where the reactants, or substrates, fit perfectly. This causes them to react more often, therefore speeding up the reaction.
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| The enxyme carbonic anhydrase converts the substrates carbon dioxide and water into carbonic acid (H2CO3). |
The substrates bind to a site on the enzyme called the active site. The active site and the substrates have complementary shapes. The fit is so precise that the active site and substrates are often compared to a lock and key.
Temperature, pH, and regulatory molecules can affect the activity of enzymes.
