Biology 2.1
How many elements occur naturally?
92 elements. The remaining elements are synthesized in laboratories and are unstable.
Accounting for the sizes of protons, neutrons, and electrons, most of the volume of an atom—greater than
99 percent—is, in fact, empty space.
electrolyte
ion necessary for nerve impulse conduction, muscle contractions and water balance
Some of the most abundant elements in living organisms include carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. These form the
nucleic acids, proteins, carbohydrates, and lipids that are the fundamental components of living matter. Biologists must understand these important building blocks and the unique structures of the atoms that make up molecules, allowing for the formation of cells, tissues, organ systems, and entire organisms.
inert gas
(also, noble gas) element with filled outer electron shell that is unreactive with other atoms
There are how many elements?
118 elements
The number of neutrons is variable, resulting in what?
Isotopes, which are different forms of the same atom that vary only in the number of neutrons they possess.
Even though all of the reactants and products of this reaction are molecules (each atom remains bonded to at least one other atom), in this reaction only hydrogen peroxide and water are representatives of compounds: they contain
atoms of more than one type of element. Molecular oxygen, on the other hand, as shown in Figure,consists of two doubly bonded oxygen atoms and is not classified as a compound but as a mononuclear molecule.
According to the law of conservation of matter, the number of atoms before and after a chemical reaction should
be equal, such that no atoms are, under normal circumstances, created or destroyed.
Chemical reactions occur when two or more atoms bond together to form molecules or when
bonded atoms are broken apart.
atomic mass
calculated mean of the mass number for an element's isotopes
electronegativity
ability of some elements to attract electrons (often of hydrogen atoms), acquiring partial negative charges in molecules and creating partial positive charges on the hydrogen atoms
Although useful to explain the reactivity and chemical bonding of certain elements, the Bohr model of the atom does not
accurately reflect how electrons are spatially distributed surrounding the nucleus. They do not circle the nucleus like the earth orbits the sun, but are found in electron orbitals. These relatively complex shapes result from the fact that electrons behave not just like particles, but also like waves.
Some atoms are more stable when they gain or lose
an electron (or possibly two) and form ions. This fills their outermost electron shell and makes them energetically more stable. Because the number of electrons does not equal the number of protons, each ion has a net charge.
electron configuration
arrangement of electrons in an atom's electron shell (for example, 1s22s22p6)
In the periodic table, shown in Figure, the elements are organized and displayed according to their
atomic number and are arranged in a series of rows and columns based on shared chemical and physical properties. In addition to providing the atomic number for each element, the periodic table also displays the element's atomic mass. Looking at carbon, for example, its symbol (C) and name appear, as well as its atomic number of six (in the upper left-hand corner) and its atomic mass of 12.11.
Covalent bonds are commonly found in
carbon-based organic molecules, such as our DNA and proteins. Covalent bonds are also found in inorganic molecules like H2O, CO2, and O2. One, two, or three pairs of electrons may be shared, making single, double, and triple bonds, respectively. The more covalent bonds between two atoms, the stronger their connection. Thus, triple bonds are the strongest.
An early model of the atom was developed in 1913 by Danish scientist Niels Bohr (1885-1962). The Bohr model shows the atom as a
central nucleus containing protons and neutrons, with the electrons in circular orbitals at specific distances from the nucleus, as illustrated in Figure. These orbits form electron shells or energy levels, which are a way of visualizing the number of electrons in the outermost shells. These energy levels are designated by a number and the symbol "n." For example, 1n represents the first energy level located closest to the nucleus.
law of mass action
chemical law stating that the rate of a reaction is proportional to the concentration of the reacting substances
The periodic table groups elements according to
chemical properties. The differences in chemical reactivity between the elements are based on the number and spatial distribution of an atom's electrons.
reversible chemical reaction
chemical reaction that functions bi-directionally, where products may turn into reactants if their concentration is great enough va
irreversible chemical reaction
chemical reaction where reactants proceed uni-directionally to form products
Electrons fill orbitals in a consistent order: they first fill the orbitals
closest to the nucleus, then they continue to fill orbitals of increasing energy further from the nucleus. If there are multiple orbitals of equal energy, they will be filled with one electron in each energy level before a second electron is added. The electrons of the outermost energy level determine the energetic stability of the atom and its tendency to form chemical bonds with other atoms to form molecules.
For example, in human blood, excess hydrogen ions (H+) bind to bicarbonate ions (HCO3-) forming an equilibrium state with carbonic acid (H2CO3). If carbonic acid were added to this system, some of it would be
converted to bicarbonate and hydrogen ions. HCO3−+ H+↔H2CO3 HCO3− + H+ ↔ H2CO3 In biological reactions, however, equilibrium is rarely obtained because the concentrations of the reactants or products or both are constantly changing, often with a product of one reaction being a reactant for another.
The formation of water molecules provides an example of
covalent bonding. The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds.
In the non-living world, elements are found in what?
different proportions, and some elements common to living organisms are rare on the earth as a whole. For example, the atmosphere is rich in nitrogen and oxygen but contains little carbon and hydrogen, while the earth's crust, although it contains oxygen and a small amount of hydrogen, has little nitrogen and carbon.
The strength of different levels of covalent bonding is one of the main reasons living organisms have a
difficult time in acquiring nitrogen for use in constructing their molecules, even though molecular nitrogen, N2, is the most abundant gas in the atmosphere. Molecular nitrogen consists of two nitrogen atoms triple bonded to each other and, as with all molecules, the sharing of these three pairs of electrons between the two nitrogen atoms allows for the filling of their outer electron shells, making the molecule more stable than the individual nitrogen atoms. This strong triple bond makes it difficult for living systems to break apart this nitrogen in order to use it as constituents of proteins and DNA.
To return to the example of excess hydrogen ions in the blood, the formation of carbonic acid will be the major
direction of the reaction. However, the carbonic acid can also leave the body as carbon dioxide gas (via exhalation) instead of being converted back to bicarbonate ion, thus driving the reaction to the right by the chemical law known as law of mass action. These reactions are important for maintaining the homeostasis of our blood. HCO3− + H+ ↔ H2CO3 ↔ CO2 + H2O
The small contribution of mass from electrons is what?
disregarded in calculating the mass number. This approximation of mass can be used to easily calculate how many neutrons an element has by simply subtracting the number of protons from the mass number.
The second electron shell may contain
eight electrons. This shell contains another spherical s orbital and three "dumbbell" shaped p orbitals, each of which can hold two electrons, as shown in Figure. After the 1s orbital is filled, the second electron shell is filled, first filling its 2s orbital and then its three p orbitals. When filling the p orbitals, each takes a single electron; once each p orbital has an electron, a second may be added. Lithium (Li) contains three electrons that occupy the first and second shells. Two electrons fill the 1s orbital, and the third electron then fills the 2s orbital. Its electron configuration is 1s22s1. Neon (Ne), on the other hand, has a total of ten electrons: two are in its innermost 1s orbital and eight fill its second shell (two each in the 2s and three p orbitals); thus, it is an inert gas and energetically stable as a single atom that will rarely form a chemical bond with other atoms. Larger elements have additional orbitals, making up the third electron shell. While the concepts of electron shells and orbitals are closely related, orbitals provide a more accurate depiction of the electron configuration of an atom because the orbital model specifies the different shapes and special orientations of all the places that electrons may occupy.
Reversible reactions are those that can go in
either direction. In reversible reactions, reactants are turned into products, but when the concentration of product goes beyond a certain threshold (characteristic of the particular reaction), some of these products will be converted back into reactants; at this point, the designations of products and reactants are reversed.
Certain salts are referred to in physiology as
electrolytes (including sodium, potassium, and calcium), ions necessary for nerve impulse conduction, muscle contractions and water balance. Many sports drinks and dietary supplements provide these ions to replace those lost from the body via sweating during exercise.
This movement of electrons from one element to another is referred to as
electron transfer.
All elements are most stable when their outermost shell is filled with
electrons according to the octet rule. This is because it is energetically favorable for atoms to be in that configuration and it makes them stable. However, since not all elements have enough electrons to fill their outermost shells, atoms form chemical bonds with other atoms thereby obtaining the electrons they need to attain a stable electron configuration. When two or more atoms chemically bond with each other, the resultant chemical structure is a molecule. The familiar water molecule, H2O, consists of two hydrogen atoms and one oxygen atom; these bond together to form water, as illustrated in Figure. Atoms can form molecules by donating, accepting, or sharing electrons to fill their outer shells.
Negative ions are formed by gaining
electrons and are called anions. Anions are designated by their elemental name being altered to end in "-ide": the anion of chlorine is called chloride, and the anion of sulfur is called sulfide, for example.
Two weak bonds that occur frequently are
hydrogen bonds and van der Waals interactions. Without these two types of bonds, life as we know it would not exist. Hydrogen bonds provide many of the critical, life-sustaining properties of water and also stabilize the structures of proteins and DNA, the building block of cells.
An example of a simple chemical reaction is the breaking down of
hydrogen peroxide molecules, each of which consists of two hydrogen atoms bonded to two oxygen atoms (H2O2).
When considering atomic mass, it is customary to do what?
ignore the mass of any electrons and calculate the atom's mass based on the number of protons and neutrons alone.
chemical bond
interaction between two or more of the same or different atoms that results in the formation of molecules
The periodic table is arranged in columns and rows based on the number of
electrons and where these electrons are located. Take a closer look at the some of the elements in the table's far right column in Figure. The group 18 atoms helium (He), neon (Ne), and argon (Ar) all have filled outer electron shells, making it unnecessary for them to share electrons with other atoms to attain stability; they are highly stable as single atoms. Their non-reactivity has resulted in their being named the inert gases (or noble gases). Compare this to the group 1 elements in the left-hand column. These elements, including hydrogen (H), lithium (Li), and sodium (Na), all have one electron in their outermost shells. That means that they can achieve a stable configuration and a filled outer shell by donating or sharing one electron with another atom or a molecule such as water. Hydrogen will donate or share its electron to achieve this configuration, while lithium and sodium will donate their electron to become stable. As a result of losing a negatively charged electron, they become positively charged ions. Group 17 elements, including fluorine and chlorine, have seven electrons in their outmost shells, so they tend to fill this shell with an electron from other atoms or molecules, making them negatively charged ions. Group 14 elements, of which carbon is the most important to living systems, have four electrons in their outer shell allowing them to make several covalent bonds (discussed below) with other atoms. Thus, the columns of the periodic table represent the potential shared state of these elements' outer electron shells that is responsible for their similar chemical characteristics.
Another way the octet rule can be satisfied is by the sharing of
electrons between atoms to form covalent bonds. These bonds are stronger and much more common than ionic bonds in the molecules of living organisms.
With all this empty space, one might ask why so-called solid objects do not just pass through one another. The reason they do not is that the
electrons that surround all atoms are negatively charged and negative charges repel each other.
Ionic and covalent bonds between elements require
energy to break. Ionic bonds are not as strong as covalent, which determines their behavior in biological systems. However, not all bonds are ionic or covalent bonds. Weaker bonds can also form between molecules.
This back and forth continues until a certain relative balance between reactants and products occurs—a state called
equilibrium. These situations of reversible reactions are often denoted by a chemical equation with a double headed arrow pointing towards both the reactants and products.
electron orbital
how electrons are spatially distributed surrounding the nucleus; the area where an electron is most likely to be found
The properties of water and the formation of hydrogen bonds are
key to understanding living processes. Recognizing the properties of acids and bases is important, for example, to our understanding of the digestive process. Therefore, the fundamentals of physics and chemistry are important for gaining insight into biological processes.
Cations are positive ions that are formed by
losing electrons.
Together, the number of protons and the number of neutrons determine an element's what?
mass number.
Protons and neutrons have approximately the same what?
mass, about 1.67 × 10-24 grams. Scientists arbitrarily define this amount of mass as one atomic mass unit (amu) or one Dalton, as shown in Table.
Elements are unique forms of what?
matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions.
Elements in various combinations comprise all
matter, including living things.
At its most fundamental level, life is made up of
matter.
reactant
molecule found on the left side of a chemical equation
product
molecule found on the right side of a chemical equation
Atoms that chemically react and bond to each other form
molecules. Molecules are simply two or more atoms chemically bonded together. Logically, when two atoms chemically bond to form a molecule, their electrons, which form the outermost region of each atom, come together first as the atoms form a chemical bond.
Either way, the atom's relative electronegativity contributes to the development of partial charges whenever one element is significantly
more electronegative than the other, and the charges generated by these polar bonds may then be used for the formation of hydrogen bonds based on the attraction of opposite partial charges. (Hydrogen bonds, which are discussed in detail below, are weak bonds between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules.) Since macromolecules often have atoms within them that differ in electronegativity, polar bonds are often present in organic molecules.
Isotopes are different forms of an element that have the same number of protons but a different number of
neutrons. Some elements—such as carbon, potassium, and uranium—have naturally occurring isotopes. Carbon-12 contains six protons, six neutrons, and six electrons; therefore, it has a mass number of 12 (six protons and six neutrons). Carbon-14 contains six protons, eight neutrons, and six electrons; its atomic mass is 14 (six protons and eight neutrons). These two alternate forms of carbon are isotopes.
It should be stressed that there is a connection between the number of protons in an element, the atomic number that distinguishes one element from another, and the
number of electrons it has. In all electrically neutral atoms, the number of electrons is the same as the number of protons. Thus, each element, at least when electrically neutral, has a characteristic number of electrons equal to its atomic number.
Matter is any substance that
occupies space and has mass.
Some chemical reactions, such as the one shown above, can proceed in
one direction until the reactants are all used up. The equations that describe these reactions contain a unidirectional arrow and are irreversible.
Ionic bonds are formed between ions with
opposite charges.
valence shell
outermost shell of an atom
The four elements common to all living organisms are what?
oxygen (O), carbon (C), hydrogen (H), and nitrogen (N).
Water is a polar molecule, with the hydrogen atoms acquiring a
partial positive charge and the oxygen a partial negative charge. This occurs because the nucleus of the oxygen atom is more attractive to the electrons of the hydrogen atoms than the hydrogen nucleus is to the oxygen's electrons. Thus oxygen has a higher electronegativity than hydrogen and the shared electrons spend more time in the vicinity of the oxygen nucleus than they do near the nucleus of the hydrogen atoms, giving the atoms of oxygen and hydrogen slightly negative and positive charges, respectively. Another way of stating this is that the probability of finding a shared electron near an oxygen nucleus is more likely than finding it near a hydrogen nucleus.
The properties of elements are responsible for their what?
physical state at room temperature: they may be gases, solids, or liquids. Elements also have specific chemical reactivity, the ability to combine and to chemically bond with each other.
All biological processes follow the laws of
physics and chemistry, so in order to understand how biological systems work, it is important to understand the underlying physics and chemistry. For example, the flow of blood within the circulatory system follows the laws of physics that regulate the modes of fluid flow. The breakdown of the large, complex molecules of food into smaller molecules—and the conversion of these to release energy to be stored in adenosine triphosphate (ATP)—is a series of chemical reactions that follow chemical laws.
When polar covalent bonds containing hydrogen form, the hydrogen in that bond has a slightly
positive charge because hydrogen's electron is pulled more strongly toward the other element and away from the hydrogen. Because the hydrogen is slightly positive, it will be attracted to neighboring negative charges. When this happens, a weak interaction occurs between the δ+of the hydrogen from one molecule and the δ- charge on the more electronegative atoms of another molecule, usually oxygen or nitrogen, or within the same molecule. This interaction is called a hydrogen bond. This type of bond is common and occurs regularly between water molecules. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, creating a major force in combination. Hydrogen bonds are also responsible for zipping together the DNA double helix.
Mathematical equations from quantum mechanics known as wave functions can
predict within a certain level of probability where an electron might be at any given time. The area where an electron is most likely to be found is called its orbital.
chemical reaction
process leading to the rearrangement of atoms in molecules
The substances found at the end of the reaction are known as the
products (usually found on the right side of a chemical equation). An arrow is typically drawn between the reactants and products to indicate the direction of the chemical reaction; this direction is not always a "one-way street." For the creation of the water molecule shown above, the chemical equation would be:
Understanding that the organization of the periodic table is based on the total number of
protons (and electrons) helps us know how electrons are distributed among the outer shell.
Atoms of each element contain a characteristic number of what?
protons and electrons. The number of protons determines an element's atomic number and is used to distinguish one element from another.
Atoms contain what?
protons, electrons, and neutrons, among other subatomic particles. The only exception is hydrogen (H), which is made of one proton and one electron with no neutrons.
Electrons are much smaller in mass than what?
protons, weighing only 9.11 × 10-28 grams, or about 1/1800 of an atomic mass unit. Hence, they do not contribute much to an element's overall atomic mass.
Some isotopes may emit neutrons, protons, and electrons, and attain a more stable atomic configuration (lower level of potential energy); these are called what?
radioactive isotopes, or radioisotopes. Radioactive decay (carbon-14 decaying to eventually become nitrogen-14) describes the energy loss that occurs when an unstable atom's nucleus releases radiation.
The substances used in the beginning of a chemical reaction are called the
reactants (usually found on the left side of a chemical equation)
orbital
region surrounding the nucleus; contains electrons
octet rule
rule that atoms are most stable when they hold eight electrons in their outermost shells
Subshells are designated by the letter
s, p, d, and f. The s subshell is spherical in shape and has one orbital. Principal shell 1n has only a single s orbital, which can hold two electrons. Principal shell 2n has one s and one p subshell, and can hold a total of eight electrons. The p subshell has three dumbbell-shaped orbitals, as illustrated in Figure. Subshells d and f have more complex shapes and contain five and seven orbitals, respectively. These are not shown in the illustration. Principal shell 3n has s, p, and d subshells and can hold 18 electrons. Principal shell 4n has s, p, d and f orbitals and can hold 32 electrons. Moving away from the nucleus, the number of electrons and orbitals found in the energy levels increases. Progressing from one atom to the next in the periodic table, the electron structure can be worked out by fitting an extra electron into the next available orbital.
noble gas
see inert gas
balanced chemical equation
statement of a chemical reaction with the number of each type of atom equalized for both the products and reactants
Recall that the Bohr model depicts an atom's electron shell configuration. Within each electron shell are
subshells, and each subshell has a specified number of orbitals containing electrons. While it is impossible to calculate exactly where an electron is located, scientists know that it is most probably located within its orbital path.
compound
substance composed of molecules consisting of atoms of at least two different elements
chemical reactivity
the ability to combine and to chemically bond with each other
Although not significant contributors to mass, electrons do contribute greatly to what?
the atom's charge, as each electron has a negative charge equal to the positive charge of a proton.
An atom is composed of what?
two regions: the nucleus, which is in the center of the atom and contains protons and neutrons, and the outermost region of the atom which holds its electrons in orbit around the nucleus.
covalent bond
type of strong bond formed between two of the same or different elements; forms when electrons are shared between atoms
To understand how elements come together, we must first discuss the smallest component or building block of an element, which is what?
the atom. An atom is the smallest unit of matter that retains all of the chemical properties of an element. For example, one gold atom has all of the properties of gold in that it is a solid metal at room temperature. A gold coin is simply a very large number of gold atoms molded into the shape of a coin and containing small amounts of other elements known as impurities. Gold atoms cannot be broken down into anything smaller while still retaining the properties of gold.
Since an element's isotopes will have slightly different mass numbers, scientists also determine what?
the atomic mass, which is the calculated mean of the mass number for its naturally occurring isotopes. Often, the resulting number contains a fraction. For example, the atomic mass of chlorine (Cl) is 35.45 because chlorine is composed of several isotopes, some (the majority) with atomic mass 35 (17 protons and 18 neutrons) and some with atomic mass 37 (17 protons and 20 neutrons).
In uncharged, neutral atoms, the number of electrons orbiting the nucleus is equal to what?
the number of protons inside the nucleus. In these atoms, the positive and negative charges cancel each other out, leading to an atom with no net charge.
The different elements are organized and displayed in what?
the periodic table. Devised by Russian chemist Dmitri Mendeleev (1834-1907) in 1869, the table groups elements that, although unique, share certain chemical properties with other elements.
In spite of their differences in abundance, all elements and the chemical reactions between them obey what?
the same chemical and physical laws regardless of whether they are a part of the living or non-living world.
Nonpolar covalent bonds form between two atoms of
the same element or between different elements that share electrons equally. For example, molecular oxygen (O2) is nonpolar because the electrons will be equally distributed between the two oxygen atoms.
Although similar in mass, protons and neutrons differ in what?
their electric charge. A proton is positively charged whereas a neutron is uncharged. Therefore, the number of neutrons in an atom contributes significantly to its mass, but not to its charge.
Each element is designated by what? i
ts chemical symbol, which is a single capital letter or, when the first letter is already "taken" by another element, a combination of two letters. Some elements follow the English term for the element, such as C for carbon and Ca for calcium. Other elements' chemical symbols derive from their Latin names; for example, the symbol for sodium is Na, referring to natrium, the Latin word for sodium.
Under standard conditions, atoms fill the inner shells first, often resulting in a variable number of electrons in the outermost shell. The innermost shell has a maximum of
two electrons but the next two electron shells can each have a maximum of eight electrons. This is known as the octet rule, which states, with the exception of the innermost shell, that atoms are more stable energetically when they have eight electrons in their valence shell, the outermost electron shell. Examples of some neutral atoms and their electron configurations are shown in Figure.
The closest orbital to the nucleus, called the 1s orbital, can hold up to
two electrons. This orbital is equivalent to the innermost electron shell of the Bohr model of the atom. It is called the 1s orbital because it is spherical around the nucleus. The 1s orbital is the closest orbital to the nucleus, and it is always filled first, before any other orbital can be filled. Hydrogen has one electron; therefore, it has only one spot within the 1s orbital occupied. This is designated as 1s1, where the superscripted 1 refers to the one electron within the 1s orbital. Helium has two electrons; therefore, it can completely fill the 1s orbital with its two electrons. This is designated as 1s2, referring to the two electrons of helium in the 1s orbital. On the periodic table Figure, hydrogen and helium are the only two elements in the first row (period); this is because they only have electrons in their first shell, the 1s orbital. Hydrogen and helium are the only two elements that have the 1s and no other electron orbitals in the electrically neutral state.
There are two types of covalent bonds: polar and nonpolar. In a polar covalent bond, the electrons are
unequally shared by the atoms and are attracted more to one nucleus than the other. Because of the unequal distribution of electrons between the atoms of different elements, a slightly positive (δ+) or slightly negative (δ-) charge develops. This partial charge is an important property of water and accounts for many of its characteristics.
The reactant hydrogen peroxide is broken down into
water, containing one oxygen atom bound to two hydrogen atoms (H2O), and oxygen, which consists of two bonded oxygen atoms (O2). In the equation below, the reaction includes two hydrogen peroxide molecules and two water molecules. This is an example of a balanced chemical equation, wherein the number of atoms of each element is the same on each side of the equation.
Like hydrogen bonds, van der Waals interactions are n.
weak attractions or interactions between molecules. Van der Waals attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities, which are not always symmetrical around an atom. For these attractions to happen, the molecules need to be very close to one another. These bonds—along with ionic, covalent, and hydrogen bonds—contribute to the three-dimensional structure of the proteins in our cells that is necessary for their proper functio
