Module 2: The Chemical Level of Organization

Lesson 1: Elements and Atoms: The Building Blocks of Matter

Các Thành Tố Và Nguyên Tử: Các Khối Xây Dựng Nên Vật Chất

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Dưới đây là danh sách những thuật ngữ Y khoa của module The Chemical Level of Organization.
Khái quát được số lượng thuật ngữ sẽ xuất hiện trong bài đọc và nghe sẽ giúp bạn thoải mái tiêu thụ nội dung hơn. Sau khi hoàn thành nội dung đọc và nghe, bạn hãy quay lại đây và luyện tập (practice) để quen dần các thuật ngữ này. Đừng ép bản thân phải nhớ các thuật ngữ này vội vì bạn sẽ gặp và ôn lại danh sách này trong những bài học (lesson) khác của cùng một module.

Medical Terminology: The Chemical Level of Organization

acid
compound that releases hydrogen ions (H+) in solution
activation energy
amount of energy greater than the energy contained in the reactants, which must be overcome for a reaction to proceed
adenosine triphosphate (ATP)
nucleotide containing ribose and an adenine base that is essential in energy transfer
amino acid
building block of proteins; characterized by an amino and carboxyl functional groups and a variable side-chain
anion
atom with a negative charge
atom
smallest unit of an element that retains the unique properties of that element
atomic number
number of protons in the nucleus of an atom
base
compound that accepts hydrogen ions (H+) in solution
bond
electrical force linking atoms
buffer
solution containing a weak acid or a weak base that opposes wide fluctuations in the pH of body fluids
carbohydrate
class of organic compounds built from sugars, molecules containing carbon, hydrogen, and oxygen in a 1-2-1 ratio
catalyst
substance that increases the rate of a chemical reaction without itself being changed in the process
cation
atom with a positive charge
chemical energy
form of energy that is absorbed as chemical bonds form, stored as they are maintained, and released as they are broken
colloid
liquid mixture in which the solute particles consist of clumps of molecules large enough to scatter light
compound
substance composed of two or more different elements joined by chemical bonds
concentration
number of particles within a given space
covalent bond
chemical bond in which two atoms share electrons, thereby completing their valence shells
decomposition reaction
type of catabolic reaction in which one or more bonds within a larger molecule are broken, resulting in the release of smaller molecules or atoms
denaturation
change in the structure of a molecule through physical or chemical means
deoxyribonucleic acid (DNA)
deoxyribose-containing nucleotide that stores genetic information
disaccharide
pair of carbohydrate monomers bonded by dehydration synthesis via a glycosidic bond
disulfide bond
covalent bond formed within a polypeptide between sulfide groups of sulfur-containing amino acids, for example, cysteine
electron
subatomic particle having a negative charge and nearly no mass; found orbiting the atom’s nucleus
electron shell
area of space a given distance from an atom’s nucleus in which electrons are grouped
element
substance that cannot be created or broken down by ordinary chemical means
enzyme
protein or RNA that catalyzes chemical reactions
exchange reaction
type of chemical reaction in which bonds are both formed and broken, resulting in the transfer of components
functional group
group of atoms linked by strong covalent bonds that tends to behave as a distinct unit in chemical reactions with other atoms
hydrogen bond
dipole-dipole bond in which a hydrogen atom covalently bonded to an electronegative atom is weakly attracted to a second electronegative atom
inorganic compound
substance that does not contain both carbon and hydrogen
ion
atom with an overall positive or negative charge
ionic bond
attraction between an anion and a cation
isotope
one of the variations of an element in which the number of neutrons differ from each other
kinetic energy
energy that matter possesses because of its motion
lipid
class of nonpolar organic compounds built from hydrocarbons and distinguished by the fact that they are not soluble in water
macromolecule
large molecule formed by covalent bonding
mass number
sum of the number of protons and neutrons in the nucleus of an atom
matter
physical substance; that which occupies space and has mass
molecule
two or more atoms covalently bonded together
monosaccharide
monomer of carbohydrate; also known as a simple sugar
neutron
heavy subatomic particle having no electrical charge and found in the atom’s nucleus
nucleotide
class of organic compounds composed of one or more phosphate groups, a pentose sugar, and a base
organic compound
substance that contains both carbon and hydrogen
peptide bond
covalent bond formed by dehydration synthesis between two amino acids
periodic table of the elements
arrangement of the elements in a table according to their atomic number; elements having similar properties because of their electron arrangements compose columns in the table, while elements having the same number of valence shells compose rows in the table
pH
negative logarithm of the hydrogen ion (H+) concentration of a solution
phospholipid
a lipid compound in which a phosphate group is combined with a diglyceride
phosphorylation
addition of one or more phosphate groups to an organic compound
polar molecule
molecule with regions that have opposite charges resulting from uneven numbers of electrons in the nuclei of the atoms participating in the covalent bond
polysaccharide
compound consisting of more than two carbohydrate monomers bonded by dehydration synthesis via glycosidic bonds
potential energy
stored energy matter possesses because of the positioning or structure of its components
product
one or more substances produced by a chemical reaction
prostaglandin
lipid compound derived from fatty acid chains and important in regulating several body processes
protein
class of organic compounds that are composed of many amino acids linked together by peptide bonds
proton
heavy subatomic particle having a positive charge and found in the atom’s nucleus
purine
nitrogen-containing base with a double ring structure; adenine and guanine
pyrimidine
nitrogen-containing base with a single ring structure; cytosine, thiamine, and uracil
radioactive isotope
unstable, heavy isotope that gives off subatomic particles, or electromagnetic energy, as it decays; also called radioisotopes
reactant
one or more substances that enter into the reaction
ribonucleic acid (RNA)
ribose-containing nucleotide that helps manifest the genetic code as protein
solution
homogeneous liquid mixture in which a solute is dissolved into molecules within a solvent
steroid
(also, sterol) lipid compound composed of four hydrocarbon rings bonded to a variety of other atoms and molecules
substrate
reactant in an enzymatic reaction
suspension
liquid mixture in which particles distributed in the liquid settle out over time
synthesis reaction
type of anabolic reaction in which two or more atoms or molecules bond, resulting in the formation of a larger molecule
triglyceride
lipid compound composed of a glycerol molecule bonded with three fatty acid chains
valence shell
outermost electron shell of an atom
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Dưới đây là các bài văn nằm ở bên trái. Ở bên phải là các bài luyện tập (practice) để đánh giá khả năng đọc hiểu của bạn. Sẽ khó khăn trong thời gian đầu nếu vốn từ vựng của bạn còn hạn chế, đặc biệt là từ vựng Y khoa. Hãy kiên nhẫn và đọc nhiều nhất có kể, lượng kiến thức tích tụ dần sẽ giúp bạn đọc thoải mái hơn.
The substance of the universe—from a grain of sand to a star—is called matter. Scientists define matter as anything that occupies space and has mass. An object’s mass and its weight are related concepts, but not quite the same. An object’s mass is the amount of matter contained in the object, and the object’s mass is the same whether that object is on Earth or in the zero-gravity environment of outer space. An object’s weight, on the other hand, is its mass as affected by the pull of gravity. Where gravity strongly pulls on an object’s mass its weight is greater than it is where gravity is less strong. An object of a certain mass weighs less on the moon, for example, than it does on Earth because the gravity of the moon is less than that of Earth. In other words, weight is variable, and is influenced by gravity. A piece of cheese that weighs a pound on Earth weighs only a few ounces on the moon.
All matter in the natural world is composed of one or more of the 92 fundamental substances called elements. An element is a pure substance that is distinguished from all other matter by the fact that it cannot be created or broken down by ordinary chemical means. While your body can assemble many of the chemical compounds needed for life from their constituent elements, it cannot make elements. They must come from the environment. A familiar example of an element that you must take in is calcium (Ca). Calcium is essential to the human body; it is absorbed and used for a number of processes, including strengthening bones. When you consume dairy products your digestive system breaks down the food into components small enough to cross into the bloodstream. Among these is calcium, which, because it is an element, cannot be broken down further. The elemental calcium in cheese, therefore, is the same as the calcium that forms your bones. Some other elements you might be familiar with are oxygen, sodium, and iron. The elements in the human body are shown in Figure 1, beginning with the most abundant: oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). Each element’s name can be replaced by a one- or two-letter symbol; you will become familiar with some of these during this course. All the elements in your body are derived from the foods you eat and the air you breathe.

In nature, elements rarely occur alone. Instead, they combine to form compounds. A compound is a substance composed of two or more elements joined by chemical bonds. For example, the compound glucose is an important body fuel. It is always composed of the same three elements: carbon, hydrogen, and oxygen. Moreover, the elements that make up any given compound always occur in the same relative amounts. In glucose, there are always six carbon and six oxygen units for every twelve hydrogen units. But what, exactly, are these “units” of elements?
An atom is the smallest quantity of an element that retains the unique properties of that element. In other words, an atom of hydrogen is a unit of hydrogen—the smallest amount of hydrogen that can exist. As you might guess, atoms are almost unfathomably small. The period at the end of this sentence is millions of atoms wide.

A. Atomic Structure and Energy

Atoms are made up of even smaller subatomic particles, three types of which are important: the proton, neutron, and electron. The number of positively-charged protons and non-charged (“neutral”) neutrons, gives mass to the atom, and the number of protons determines the element. The number of negatively-charged electrons that “spin” around the nucleus at close to the speed of light equals the number of protons. An electron has about 1/2000th the mass of a proton or neutron.

Figure 2 shows two models that can help you imagine the structure of an atom—in this case, helium (He). In the planetary model, helium’s two electrons are shown circling the nucleus in a fixed orbit depicted as a ring. Although this model is helpful in visualizing atomic structure, in reality, electrons do not travel in fixed orbits, but whiz around the nucleus erratically in a so-called electron cloud.

An atom’s protons and electrons carry electrical charges. Protons, with their positive charge, are designated p+. Electrons, which have a negative charge, are designated e–. An atom’s neutrons have no charge: they are electrically neutral. Just as a magnet sticks to a steel refrigerator because their opposite charges attract, the positively charged protons attract the negatively charged electrons. This mutual attraction gives the atom some structural stability. The attraction by the positively charged nucleus helps keep electrons from straying far. The number of protons and electrons within a neutral atom are equal, thus, the atom’s overall charge is balanced.

B. Atomic Number and Mass Number

An atom of carbon is unique to carbon, but a proton of carbon is not. One proton is the same as another, whether it is found in an atom of carbon, sodium (Na), or iron (Fe). The same is true for neutrons and electrons. So, what gives an element its distinctive properties—what makes carbon so different from sodium or iron? The answer is the unique quantity of protons each contains. Carbon by definition is an element whose atoms contain six protons. No other element has exactly six protons in its atoms. Moreover, all atoms of carbon, whether found in your liver or in a lump of coal, contain six protons. Thus, the atomic number, which is the number of protons in the nucleus of the atom, identifies the element. Because an atom usually has the same number of electrons as protons, the atomic number identifies the usual number of electrons as well.

In their most common form, many elements also contain the same number of neutrons as protons. The most common form of carbon, for example, has six neutrons as well as six protons, for a total of 12 subatomic particles in its nucleus. An element’s mass number is the sum of the number of protons and neutrons in its nucleus. So the most common form of carbon’s mass number is 12. (Electrons have so little mass that they do not appreciably contribute to the mass of an atom.) Carbon is a relatively light element. Uranium (U), in contrast, has a mass number of 238 and is referred to as a heavy metal. Its atomic number is 92 (it has 92 protons) but it contains 146 neutrons; it has the most mass of all the naturally occurring elements.

The periodic table of the elements, shown in Figure 3, is a chart identifying the 92 elements found in nature, as well as several larger, unstable elements discovered experimentally. The elements are arranged in order of their atomic number, with hydrogen and helium at the top of the table, and the more massive elements below. The periodic table is a useful device because for each element, it identifies the chemical symbol, the atomic number, and the mass number, while organizing elements according to their propensity to react with other elements. The number of protons and electrons in an element are equal. The number of protons and neutrons may be equal for some elements, but are not equal for all.

C. Isotopes

Although each element has a unique number of protons, it can exist as different isotopes. An isotope is one of the different forms of an element, distinguished from one another by different numbers of neutrons. The standard isotope of carbon is 12C, commonly called carbon twelve. 12C has six protons and six neutrons, for a mass number of twelve. All of the isotopes of carbon have the same number of protons; therefore, 13C has seven neutrons, and 14C has eight neutrons. The different isotopes of an element can also be indicated with the mass number hyphenated (for example, C-12 instead of 12C). Hydrogen has three common isotopes, shown in Figure 4.

An isotope that contains more than the usual number of neutrons is referred to as a heavy isotope. An example is 14C. Heavy isotopes tend to be unstable, and unstable isotopes are radioactive. A radioactive isotope is an isotope whose nucleus readily decays, giving off subatomic particles and electromagnetic energy. Different radioactive isotopes (also called radioisotopes) differ in their half-life, the time it takes for half of any size sample of an isotope to decay. For example, the half-life of tritium—a radioisotope of hydrogen—is about 12 years, indicating it takes 12 years for half of the tritium nuclei in a sample to decay. Excessive exposure to radioactive isotopes can damage human cells and even cause cancer and birth defects, but when exposure is controlled, some radioactive isotopes can be useful in medicine. For more information, see the Career Connections.
In the human body, atoms do not exist as independent entities. Rather, they are constantly reacting with other atoms to form and to break down more complex substances. To fully understand anatomy and physiology you must grasp how atoms participate in such reactions. The key is understanding the behavior of electrons.

Although electrons do not follow rigid orbits a set distance away from the atom’s nucleus, they do tend to stay within certain regions of space called electron shells. An electron shell is a layer of electrons that encircle the nucleus at a distinct energy level.

The atoms of the elements found in the human body have from one to five electron shells, and all electron shells hold eight electrons except the first shell, which can only hold two. This configuration of electron shells is the same for all atoms. The precise number of shells depends on the number of electrons in the atom. Hydrogen and helium have just one and two electrons, respectively. If you take a look at the periodic table of the elements, you will notice that hydrogen and helium are placed alone on either sides of the top row; they are the only elements that have just one electron shell (Figure 5). A second shell is necessary to hold the electrons in all elements larger than hydrogen and helium.

Lithium (Li), whose atomic number is 3, has three electrons. Two of these fill the first electron shell, and the third spills over into a second shell. The second electron shell can accommodate as many as eight electrons. Carbon, with its six electrons, entirely fills its first shell, and half-fills its second. With ten electrons, neon (Ne) entirely fills its two electron shells. Again, a look at the periodic table reveals that all of the elements in the second row, from lithium to neon, have just two electron shells. Atoms with more than ten electrons require more than two shells. These elements occupy the third and subsequent rows of the periodic table.

The factor that most strongly governs the tendency of an atom to participate in chemical reactions is the number of electrons in its valence shell. A valence shell is an atom’s outermost electron shell. If the valence shell is full, the atom is stable; meaning its electrons are unlikely to be pulled away from the nucleus by the electrical charge of other atoms. If the valence shell is not full, the atom is reactive; meaning it will tend to react with other atoms in ways that make the valence shell full. Consider hydrogen, with its one electron only half-filling its valence shell. This single electron is likely to be drawn into relationships with the atoms of other elements, so that hydrogen’s single valence shell can be stabilized.

All atoms (except hydrogen and helium with their single electron shells) are most stable when there are exactly eight electrons in their valence shell. This principle is referred to as the octet rule, and it states that an atom will give up, gain, or share electrons with another atom so that it ends up with eight electrons in its own valence shell. For example, oxygen, with six electrons in its valence shell, is likely to react with other atoms in a way that results in the addition of two electrons to oxygen’s valence shell, bringing the number to eight. When two hydrogen atoms each share their single electron with oxygen, covalent bonds are formed, resulting in a molecule of water, H2O.

In nature, atoms of one element tend to join with atoms of other elements in characteristic ways. For example, carbon commonly fills its valence shell by linking up with four atoms of hydrogen. In so doing, the two elements form the simplest of organic molecules, methane, which also is one of the most abundant and stable carbon-containing compounds on Earth. As stated above, another example is water; oxygen needs two electrons to fill its valence shell. It commonly interacts with two atoms of hydrogen, forming H2O. Incidentally, the name “hydrogen” reflects its contribution to water (hydro- = “water”; -gen = “maker”). Thus, hydrogen is the “water maker.”

OpenStax. (2022). Anatomy and Physiology 2e. Rice University. Retrieved June 15, 2023. ISBN-13: 978-1-711494-06-7 (Hardcover) ISBN-13: 978-1-711494-05-0 (Paperback) ISBN-13: 978-1-951693-42-8 (Digital). License: Attribution 4.0 International (CC BY 4.0). Access for free at openstax.org.

The main elements that compose the human body are shown from most abundant to least abundant.

(a) In the planetary model, the electrons of helium are shown in fixed orbits, depicted as rings, at a precise distance from the nucleus, somewhat like planets orbiting the sun. (b) In the electron cloud model, the electrons of helium are shown in the variety of locations they would have at different distances from the nucleus over time.

(credit: R.A. Dragoset, A. Musgrove, C.W. Clark, W.C. Martin)

Protium, designated 1H, has one proton and no neutrons. It is by far the most abundant isotope of hydrogen in nature. Deuterium, designated 2H, has one proton and one neutron. Tritium, designated 3H, has two neutrons.

Electrons orbit the atomic nucleus at distinct levels of energy called electron shells. (a) With one electron, hydrogen only half-fills its electron shell. Helium also has a single shell, but its two electrons completely fill it. (b) The electrons of carbon completely fill its first electron shell, but only half-fills its second. (c) Neon, an element that does not occur in the body, has 10 electrons, filling both of its electron shells.

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Script:
  1. The human body is composed of elements, the most abundant of which are oxygen, carbon, hydrogen and nitrogen.
  2. You obtain these elements from the foods you eat and the air you breathe.
  3. The smallest unit of an element that retains all of the properties of that element is an atom.
  4. But, atoms themselves contain many subatomic particles, the three most important of which are protons, neutrons, and electrons.
  5. These particles do not vary in quality from one element to another.
  6. Rather, what gives an element its distinctive identification is the quantity of its protons, called its atomic number.
  7. Protons and neutrons contribute nearly all of an atom’s mass.
  8. The number of protons and neutrons is an element’s mass number.
  9. Heavier and lighter versions of the same element can occur in nature because these versions have different numbers of neutrons.
  10. Different versions of an element are called isotopes.
  11. The tendency of an atom to be stable or to react readily with other atoms is largely due to the behavior of the electrons within the atom’s outermost electron shell, called its valence shell.
  12. Helium, as well as larger atoms with eight electrons in their valence shell, is unlikely to participate in chemical reactions because they are stable.
  13. All other atoms tend to accept, donate, or share electrons in a process that brings the electrons in their valence shell to eight (or two in the case of hydrogen).
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