The Chemistry of Life Lesson 2 by Owen Borville August 10, 2024 Biology, Biosciences, Intelligent Design
Matter is any substance that occupies space and has mass. Elements are individual atoms with unique chemical and physical properties, and which are the smallest unit of matter involved in biology and chemical reactions. There are at least 118 different elements that are known, but only about 90-100 of these elements occur naturally on Earth, while some of the other elements can be produced in a laboratory. Oxygen makes up 65 percent of humans, 21 percent of the atmosphere, and 46 percent of the Earth's crust. Carbon makes up 18 percent of humans. Hydrogen makes up 10 percent of humans. Nitrogen makes up 78 percent of the atmosphere.
The atom of an element is the smallest unit of matter that keeps the same properties as other atoms of the same element. All atoms of a particular element will have the same properties (such as oxygen atoms, carbon atoms, hydrogen atoms, or nitrogen atoms).
Inside the atom is the nucleus, which contains subatomic particles protons (positive charged) and neutrons (neutral charge) and has a net positive charge. The outermost part of the atom is the electrons, negative charged particles that orbit around the atom. Protons and neutrons have similar mass, while electrons have much smaller mass.
Atomic number is the number of protons in the atom.
Mass number is the number of protons and neutrons in the atom's nucleus.
An isotope is an element with the same number of protons but different number of neutrons. The number of protons defines the atom or element.
Atomic mass is the average mass of all isotopes of an element.
Radioactive isotopes or radioisotopes emit neutrons, protons, and electrons to become more stable, which is a process called radioactive decay.
The Periodic Table of the Elements was organized by Dimitri Mendeleev, who recognized that when elements are organized as table groups, elements in the same table group share similar properties. These similar properties include specific chemical reactivity with other elements.
Molecules are two or more atoms chemically bonded together.
Model of Atom and Electron Shells: Neils Bohr in 1913 developed an early model of the atom with electron shells and a nucleus with protons and neutrons.
Each electron shell is an energy level, the first of which is closest to the nucleus and other shells are spaced further out and increasing energy.
Electrons fill the lowest energy levels closest to the nucleus first, and then fill increasingly higher energy levels.
The innermost shell can hold only 2 electrons, but the next two shells can hold 8 electrons each.
Octet Rule=atoms are most stable when they have a full 8 electrons in the outer shell, which is called the valence shell.
Atoms in the far right column of the Periodic Table have filled electrons in the outer shell. Helium has 2 electrons and the rest have 8 electrons in the outer shell. These elements are called Noble gasses because they do not react with other substance.
Ions=molecules that loose an electron (-)
Bohr model does not explain how electrons spatially distribute themselves around the nucleus.
Later atomic models created subshells around the nucleus that better describe the location and movement of electrons.
These subshells are labeled s, p, d, f.
The s subshell is spherical in shape and has one orbital with 2 electrons.
The p subshell has 3 orbitals shaped like dumbells, with 2 electrons in each orbital, for a total of 6 plus the s subshell makes 8 electrons.
The d subshell has 5 orbitals and the f subshell has 7 orbitals. The shapes of the d and f subshells are more complex.
Electron configuration is a listing of all subshells of an element or ion.
Chemical bonds form between atoms of atoms if the outermost electron shells are not full.
When two or more atoms bonded together, it is called a molecule.
Water has the formula H2O, which has two hydrogen atoms and one oxygen atom.
Chemical reactions occur when two or more atoms bond together to form molecules, or when bonded atoms break apart.
The original elements or molecules in the reaction are called reactants, and the final elements or molecules in the reaction are called products.
A balanced equation contains the correct number of atoms on each side of the chemical equation.
2H + O -> H2O (water) Hydrogen and oxygen atoms combine to form a water molecule in this reaction.
2H2O2 (hydrogen peroxide) -> 2H2O (water) + O2 (oxygen) Hydrogen peroxide breaks down into water and oxygen in this reaction.
Compounds are molecules with different elements bonded together.
Irreversible reactions only move in one direction.
Reversible reactions can move in two directions, or forward and reverse.
Reversible reactions occur in order to produce equilibrium conditions.
Some reactions occur where elements or compounds produce a third new substance, instead of reversing back to the original substance. This is called the law of mass action.
An ion is made when an atom loses or gains an electron, and has a net charge of negative or positive.
Cation is a positive charged ion formed by losing electrons.
Anion is a negative charged ion formed by gaining electrons.
Electron transfer occurs when an electron is transferred from one atom to another atom.
Ionic Bonds form between ions of opposite charges, or positive and negative.
Electrolyte is an ion needed for nerve impulse conduction, muscle contractions, or water balance
Atoms can also share electrons to form a covalent bond and complete the octet rule of 8 electrons in the outer shell.
Types of covalent bonds: polar and non-polar.
Polar covalent bond is when the electrons are unequally shared to one nucleus than another, and results in a charge (positive or negative). Non-polar covalent bond is when electrons are equally shared. (such as an O2 molecule).
Water is one of the most important polar bonds and is the reason for many of the characteristics of water. In the water molecule, the electrons are unequally shared between the two hydrogen atoms and one oxygen atom. The hydrogen electrons are more attracted to the larger oxygen nucleus than the smaller hydrogen nucleus.
Electronegativity is the ability of an atom or charged ion to attract electrons. The higher the electronegativity of an atom, the more attractive the electrons are to the atom.
Hydrogen bond is a common but weak bond between slightly positive hydrogen ions and another negative ion, usually oxygen in water molecules. Hydrogen bonds are also important to DNA structure.
Van der Waals forces are weak interactions between molecules close together that help keep them together, but allow them to be flexible. These forces are important in protein structures along with ionic, covalent, and hydrogen bonds.
Water's Polarity: causes a slight positive charge on hydrogen atoms and slight negative charge on oxygen atoms. Water molecules are attracted to each other because of polarity and form hydrogen bonds with each other and other polar molecules.
Hydrophilic: polar substance that interacts readily or dissolves in water.
Hydrophobic: non-polar compounds (do not interact readily or dissolve in water)
Water States: Gas, Liquid, Solid; water is essential for life and most living things have a high water content.
Ice or water in frozen form is one solid that is less dense than its liquid form. This allows ice to float in water. In ice, hydrogen bonds are positioned to give more space, and make ice less dense than water.
Water has a high heat capacity because of hydrogen bonding. Water has the highest specific heat capacity of any liquid on earth.
Specific Heat Capacity: the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius.
Specific Heat Capacity of Water is one calorie. Therefore water heats and cools slowly compared to other substances, and this phenomenon is very important to the biosphere as it helps organisms maintain temperature in their water-based bodies.
Heat of Vaporization is the amount of energy required to change one gram of liquid into gas.
Water has a high Heat of Vaporization, because of hydrogen bonding. Therefore, a large amount of energy is needed to change water into vapor gas (586 calories) and break the hydrogen bonds.
Vapor creation is evaporation
Water is a solvent=ions and polar molecules can easily dissolve in water because of water's polarity. The added ion will form hydrogen bonds with the water molecules. (sphere of hydration)
Solvent=substance that can easily dissolve another substance.
Dissociation: when atoms break off from molecules and form ions; occurs when a substance is added to water, the substance dissociates into ions, such as NaCl as the water molecules surround each ion of Na and Cl and cause them to break apart because of the water's polarity.
Cohesion of water: forms a dome of water above an over a full glass or cup of water because hydrogen bonding keeps the water molecules together.
Cohesion causes surface tension that keeps water molecules together at the surface of a container. This also causes water droplets on a dry surface to stay together and not flatten
Adhesion is the attraction between water molecules and other molecules
Capillary action is when water "climbs up" a tube inside a container, as the water molecules are attracted to the molecules of the inner tube walls, and the water level is higher inside the tube than outside the tube. The water will also rise more against the tube walls than the center of the tube. These properties of water are important and allow living organisms to live on and around water surfaces. These forces also allow water to move easier through the bodies of plants and animals.
pH of a solution is the measure of acidity or basicity.
Acid is a substance that increases hydrogen ions H+ concentration in a solution, commonly as hydrogen ions dissociate and lower the pH
Base is a substance that increases hydroxide ions OH- or other negative ions that combine with hydrogen ions, reducing the hydrogen concentration and raising the pH
pH Scale is an inverse logarithm scale that ranges from 0 to 14, below 7 is considered acidic and above 7 is considered basic.
Buffers are substances inside an organism that absorb or release excess acid H+ or base OH- when another substance is injected to keep the organism's pH as neutral as possible
Organic Molecules are any solid, liquid, or gas containing carbon.
Hydrocarbons are organic molecules that consist entirely of carbon and hydrogen atoms (eg. methane CH4, ethane C2H6, ethene C2H4, benzene C6H6)
Hydrocarbon chains can form between carbon atoms and have a variety of shapes: linear (aliphatic), branches, angles, planar, tetrahedral, single, double, and triple bonds
Hydrocarbon rings include single bonds between carbons; Aliphatic hydrocarbons include cyclopentane and cyclohexane.
Aromatic hydrocarbons are ring structures with alternating single and double bonds. Example: benzene
Isomers are molecules that have the same chemical formula but different structure of atoms
Structural isomers differ in the placement of their covalent bonds; Butane vs Isobutane C4H10
Geometric isomers have similar bonding patterns but differ in the placement of atoms along a double covalent bond
Enantiomers are molecules that have the same bonding and structure pattern, but are mirror images of each other
Functional groups are groups of atoms that occur within molecules that confer specific chemical properties to those molecules
Substituted hydrocarbons molecules with other elements in their carbon structure
Matter is any substance that occupies space and has mass. Elements are individual atoms with unique chemical and physical properties, and which are the smallest unit of matter involved in biology and chemical reactions. There are at least 118 different elements that are known, but only about 90-100 of these elements occur naturally on Earth, while some of the other elements can be produced in a laboratory. Oxygen makes up 65 percent of humans, 21 percent of the atmosphere, and 46 percent of the Earth's crust. Carbon makes up 18 percent of humans. Hydrogen makes up 10 percent of humans. Nitrogen makes up 78 percent of the atmosphere.
The atom of an element is the smallest unit of matter that keeps the same properties as other atoms of the same element. All atoms of a particular element will have the same properties (such as oxygen atoms, carbon atoms, hydrogen atoms, or nitrogen atoms).
Inside the atom is the nucleus, which contains subatomic particles protons (positive charged) and neutrons (neutral charge) and has a net positive charge. The outermost part of the atom is the electrons, negative charged particles that orbit around the atom. Protons and neutrons have similar mass, while electrons have much smaller mass.
Atomic number is the number of protons in the atom.
Mass number is the number of protons and neutrons in the atom's nucleus.
An isotope is an element with the same number of protons but different number of neutrons. The number of protons defines the atom or element.
Atomic mass is the average mass of all isotopes of an element.
Radioactive isotopes or radioisotopes emit neutrons, protons, and electrons to become more stable, which is a process called radioactive decay.
The Periodic Table of the Elements was organized by Dimitri Mendeleev, who recognized that when elements are organized as table groups, elements in the same table group share similar properties. These similar properties include specific chemical reactivity with other elements.
Molecules are two or more atoms chemically bonded together.
Model of Atom and Electron Shells: Neils Bohr in 1913 developed an early model of the atom with electron shells and a nucleus with protons and neutrons.
Each electron shell is an energy level, the first of which is closest to the nucleus and other shells are spaced further out and increasing energy.
Electrons fill the lowest energy levels closest to the nucleus first, and then fill increasingly higher energy levels.
The innermost shell can hold only 2 electrons, but the next two shells can hold 8 electrons each.
Octet Rule=atoms are most stable when they have a full 8 electrons in the outer shell, which is called the valence shell.
Atoms in the far right column of the Periodic Table have filled electrons in the outer shell. Helium has 2 electrons and the rest have 8 electrons in the outer shell. These elements are called Noble gasses because they do not react with other substance.
Ions=molecules that loose an electron (-)
Bohr model does not explain how electrons spatially distribute themselves around the nucleus.
Later atomic models created subshells around the nucleus that better describe the location and movement of electrons.
These subshells are labeled s, p, d, f.
The s subshell is spherical in shape and has one orbital with 2 electrons.
The p subshell has 3 orbitals shaped like dumbells, with 2 electrons in each orbital, for a total of 6 plus the s subshell makes 8 electrons.
The d subshell has 5 orbitals and the f subshell has 7 orbitals. The shapes of the d and f subshells are more complex.
Electron configuration is a listing of all subshells of an element or ion.
Chemical bonds form between atoms of atoms if the outermost electron shells are not full.
When two or more atoms bonded together, it is called a molecule.
Water has the formula H2O, which has two hydrogen atoms and one oxygen atom.
Chemical reactions occur when two or more atoms bond together to form molecules, or when bonded atoms break apart.
The original elements or molecules in the reaction are called reactants, and the final elements or molecules in the reaction are called products.
A balanced equation contains the correct number of atoms on each side of the chemical equation.
2H + O -> H2O (water) Hydrogen and oxygen atoms combine to form a water molecule in this reaction.
2H2O2 (hydrogen peroxide) -> 2H2O (water) + O2 (oxygen) Hydrogen peroxide breaks down into water and oxygen in this reaction.
Compounds are molecules with different elements bonded together.
Irreversible reactions only move in one direction.
Reversible reactions can move in two directions, or forward and reverse.
Reversible reactions occur in order to produce equilibrium conditions.
Some reactions occur where elements or compounds produce a third new substance, instead of reversing back to the original substance. This is called the law of mass action.
An ion is made when an atom loses or gains an electron, and has a net charge of negative or positive.
Cation is a positive charged ion formed by losing electrons.
Anion is a negative charged ion formed by gaining electrons.
Electron transfer occurs when an electron is transferred from one atom to another atom.
Ionic Bonds form between ions of opposite charges, or positive and negative.
Electrolyte is an ion needed for nerve impulse conduction, muscle contractions, or water balance
Atoms can also share electrons to form a covalent bond and complete the octet rule of 8 electrons in the outer shell.
Types of covalent bonds: polar and non-polar.
Polar covalent bond is when the electrons are unequally shared to one nucleus than another, and results in a charge (positive or negative). Non-polar covalent bond is when electrons are equally shared. (such as an O2 molecule).
Water is one of the most important polar bonds and is the reason for many of the characteristics of water. In the water molecule, the electrons are unequally shared between the two hydrogen atoms and one oxygen atom. The hydrogen electrons are more attracted to the larger oxygen nucleus than the smaller hydrogen nucleus.
Electronegativity is the ability of an atom or charged ion to attract electrons. The higher the electronegativity of an atom, the more attractive the electrons are to the atom.
Hydrogen bond is a common but weak bond between slightly positive hydrogen ions and another negative ion, usually oxygen in water molecules. Hydrogen bonds are also important to DNA structure.
Van der Waals forces are weak interactions between molecules close together that help keep them together, but allow them to be flexible. These forces are important in protein structures along with ionic, covalent, and hydrogen bonds.
Water's Polarity: causes a slight positive charge on hydrogen atoms and slight negative charge on oxygen atoms. Water molecules are attracted to each other because of polarity and form hydrogen bonds with each other and other polar molecules.
Hydrophilic: polar substance that interacts readily or dissolves in water.
Hydrophobic: non-polar compounds (do not interact readily or dissolve in water)
Water States: Gas, Liquid, Solid; water is essential for life and most living things have a high water content.
Ice or water in frozen form is one solid that is less dense than its liquid form. This allows ice to float in water. In ice, hydrogen bonds are positioned to give more space, and make ice less dense than water.
Water has a high heat capacity because of hydrogen bonding. Water has the highest specific heat capacity of any liquid on earth.
Specific Heat Capacity: the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius.
Specific Heat Capacity of Water is one calorie. Therefore water heats and cools slowly compared to other substances, and this phenomenon is very important to the biosphere as it helps organisms maintain temperature in their water-based bodies.
Heat of Vaporization is the amount of energy required to change one gram of liquid into gas.
Water has a high Heat of Vaporization, because of hydrogen bonding. Therefore, a large amount of energy is needed to change water into vapor gas (586 calories) and break the hydrogen bonds.
Vapor creation is evaporation
Water is a solvent=ions and polar molecules can easily dissolve in water because of water's polarity. The added ion will form hydrogen bonds with the water molecules. (sphere of hydration)
Solvent=substance that can easily dissolve another substance.
Dissociation: when atoms break off from molecules and form ions; occurs when a substance is added to water, the substance dissociates into ions, such as NaCl as the water molecules surround each ion of Na and Cl and cause them to break apart because of the water's polarity.
Cohesion of water: forms a dome of water above an over a full glass or cup of water because hydrogen bonding keeps the water molecules together.
Cohesion causes surface tension that keeps water molecules together at the surface of a container. This also causes water droplets on a dry surface to stay together and not flatten
Adhesion is the attraction between water molecules and other molecules
Capillary action is when water "climbs up" a tube inside a container, as the water molecules are attracted to the molecules of the inner tube walls, and the water level is higher inside the tube than outside the tube. The water will also rise more against the tube walls than the center of the tube. These properties of water are important and allow living organisms to live on and around water surfaces. These forces also allow water to move easier through the bodies of plants and animals.
pH of a solution is the measure of acidity or basicity.
Acid is a substance that increases hydrogen ions H+ concentration in a solution, commonly as hydrogen ions dissociate and lower the pH
Base is a substance that increases hydroxide ions OH- or other negative ions that combine with hydrogen ions, reducing the hydrogen concentration and raising the pH
pH Scale is an inverse logarithm scale that ranges from 0 to 14, below 7 is considered acidic and above 7 is considered basic.
Buffers are substances inside an organism that absorb or release excess acid H+ or base OH- when another substance is injected to keep the organism's pH as neutral as possible
Organic Molecules are any solid, liquid, or gas containing carbon.
Hydrocarbons are organic molecules that consist entirely of carbon and hydrogen atoms (eg. methane CH4, ethane C2H6, ethene C2H4, benzene C6H6)
Hydrocarbon chains can form between carbon atoms and have a variety of shapes: linear (aliphatic), branches, angles, planar, tetrahedral, single, double, and triple bonds
Hydrocarbon rings include single bonds between carbons; Aliphatic hydrocarbons include cyclopentane and cyclohexane.
Aromatic hydrocarbons are ring structures with alternating single and double bonds. Example: benzene
Isomers are molecules that have the same chemical formula but different structure of atoms
Structural isomers differ in the placement of their covalent bonds; Butane vs Isobutane C4H10
Geometric isomers have similar bonding patterns but differ in the placement of atoms along a double covalent bond
Enantiomers are molecules that have the same bonding and structure pattern, but are mirror images of each other
Functional groups are groups of atoms that occur within molecules that confer specific chemical properties to those molecules
Substituted hydrocarbons molecules with other elements in their carbon structure