Module 2: The Chemical Level of Organization

Lesson 8: Organic Compounds Essential to Human Functioning: Proteins

Các Hợp Chất Hữu Cơ Cần Thiết Cho Hoạt Động Của Con Người: Protein

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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.
You might associate proteins with muscle tissue, but in fact, proteins are critical components of all tissues and organs. A protein is an organic molecule composed of amino acids linked by peptide bonds. Proteins include the keratin in the epidermis of skin that protects underlying tissues, the collagen found in the dermis of skin, in bones, and in the meninges that cover the brain and spinal cord. Proteins are also components of many of the body’s functional chemicals, including digestive enzymes in the digestive tract, antibodies, the neurotransmitters that neurons use to communicate with other cells, and the peptide-based hormones that regulate certain body functions (for instance, growth hormone). While carbohydrates and lipids are composed of hydrocarbons and oxygen, all proteins also contain nitrogen (N), and many contain sulfur (S), in addition to carbon, hydrogen, and oxygen.
Proteins are polymers made up of nitrogen-containing monomers called amino acids. An amino acid is a molecule composed of an amino group and a carboxyl group, together with a variable side chain. Just 20 different amino acids contribute to nearly all of the thousands of different proteins important in human structure and function. Body proteins contain a unique combination of a few dozen to a few hundred of these 20 amino acid monomers. All 20 of these amino acids share a similar structure (Figure 1). All consist of a central carbon atom to which the following are bonded:

  • a hydrogen atom an alkaline (basic) amino group NH2 (see Table 1)
  • an acidic carboxyl group COOH (see Table 1)
  • a variable group

Notice that all amino acids contain both an acid (the carboxyl group) and a base (the amino group) (amine = “nitrogen-containing”). For this reason, they make excellent buffers, helping the body regulate acid–base balance. What distinguishes the 20 amino acids from one another is their variable group, which is referred to as a side chain or an R-group. This group can vary in size and can be polar or nonpolar, giving each amino acid its unique characteristics. For example, the side chains of two amino acids—cysteine and methionine—contain sulfur. Sulfur does not readily participate in hydrogen bonds, whereas all other amino acids do. This variation influences the way that proteins containing cysteine and methionine are assembled.

Amino acids join via dehydration synthesis to form protein polymers (Figure 2). The unique bond holding amino acids together is called a peptide bond. A peptide bond is a covalent bond between two amino acids that forms by dehydration synthesis. A peptide, in fact, is a very short chain of amino acids. Strands containing fewer than about 100 amino acids are generally referred to as polypeptides rather than proteins.

The body is able to synthesize most of the amino acids from components of other molecules; however, nine cannot be synthesized and have to be consumed in the diet. These are known as the essential amino acids.

Free amino acids available for protein construction are said to reside in the amino acid pool within cells. Structures within cells use these amino acids when assembling proteins. If a particular essential amino acid is not available in sufficient quantities in the amino acid pool, however, synthesis of proteins containing it can slow or even cease.
Shape of Proteins Just as a fork cannot be used to eat soup and a spoon cannot be used to spear meat, a protein’s shape is essential to its function. A protein’s shape is determined, most fundamentally, by the sequence of amino acids of which it is made (Figure 3a). The sequence is called the primary structure of the protein.

Although some polypeptides exist as linear chains, most are twisted or folded into more complex secondary structures that form when bonding occurs between amino acids with different properties at different regions of the polypeptide. The most common secondary structure is a spiral called an alpha-helix. If you were to take a length of string and simply twist it into a spiral, it would not hold the shape. Similarly, a strand of amino acids could not maintain a stable spiral shape without the help of hydrogen bonds, which create bridges between different regions of the same strand (see Figure 3b). Less commonly, a polypeptide chain can form a beta-pleated sheet, in which hydrogen bonds form bridges between different regions of a single polypeptide that has folded back upon itself, or between two or more adjacent polypeptide chains.

The secondary structure of proteins further folds into a compact three-dimensional shape, referred to as the protein’s tertiary structure (see Figure 3c). In this configuration, amino acids that had been very distant in the primary chain can be brought quite close via hydrogen bonds or, in proteins containing cysteine, via disulfide bonds. A disulfide bond is a covalent bond between sulfur atoms in a polypeptide. Often, two or more separate polypeptides bond to form an even larger protein with a quaternary structure (see Figure 3d). The polypeptide subunits forming a quaternary structure can be identical or different. For instance, hemoglobin, the protein found in red blood cells is composed of four tertiary polypeptides, two of which are called alpha chains and two of which are called beta chains.

When they are exposed to extreme heat, acids, bases, and certain other substances, proteins will denature. Denaturation is a change in the structure of a molecule through physical or chemical means. Denatured proteins lose their functional shape and are no longer able to carry out their jobs. An everyday example of protein denaturation is the curdling of milk when acidic lemon juice is added.

The contribution of the shape of a protein to its function can hardly be exaggerated. For example, the long, slender shape of protein strands that make up muscle tissue is essential to their ability to contract (shorten) and relax (lengthen). As another example, bones contain long threads of a protein called collagen that acts as scaffolding upon which bone minerals are deposited. These elongated proteins, called fibrous proteins, are strong and durable and typically hydrophobic.

In contrast, globular proteins are globes or spheres that tend to be highly reactive and are hydrophilic. The hemoglobin proteins packed into red blood cells are an example (see Figure 3d); however, globular proteins are abundant throughout the body, playing critical roles in most body functions. Enzymes, introduced earlier as protein catalysts, are examples of this. The next section takes a closer look at the action of enzymes.
If you were trying to type a paper, and every time you hit a key on your laptop there was a delay of six or seven minutes before you got a response, you would probably get a new laptop. In a similar way, without enzymes to catalyze chemical reactions, the human body would be nonfunctional. It functions only because enzymes function.

Enzymatic reactions—chemical reactions catalyzed by enzymes—begin when substrates bind to the enzyme. A substrate is a reactant in an enzymatic reaction. This occurs on regions of the enzyme known as active sites (Figure 4). Any given enzyme catalyzes just one type of chemical reaction. This characteristic, called specificity, is due to the fact that a substrate with a particular shape and electrical charge can bind only to an active site corresponding to that substrate.

Due to this jigsaw puzzle-like match between an enzyme and its substrates, enzymes are known for their specificity. In fact, as an enzyme binds to its substrate(s), the enzyme structure changes slightly to find the best fit between the transition state (a structural intermediate between the substrate and product) and the active site, just as a rubber glove molds to a hand inserted into it. This active-site modification in the presence of substrate, along with the simultaneous formation of the transition state, is called induced fit. Overall, there is a specifically matched enzyme for each substrate and, thus, for each chemical reaction; however, there is some flexibility as well. Some enzymes have the ability to act on several different structurally related substrates.

Binding of a substrate produces an enzyme–substrate complex. It is likely that enzymes speed up chemical reactions in part because the enzyme–substrate complex undergoes a set of temporary and reversible changes that cause the substrates to be oriented toward each other in an optimal position to facilitate their interaction. This promotes increased reaction speed. The enzyme then releases the product(s), and resumes its original shape. The enzyme is then free to engage in the process again, and will do so as long as substrate remains.
Advertisements for protein bars, powders, and shakes all say that protein is important in building, repairing, and maintaining muscle tissue, but the truth is that proteins contribute to all body tissues, from the skin to the brain cells. Also, certain proteins act as hormones, chemical messengers that help regulate body functions, For example, growth hormone is important for skeletal growth, among other roles.

As was noted earlier, the basic and acidic components enable proteins to function as buffers in maintaining acid–base balance, but they also help regulate fluid–electrolyte balance. Proteins attract fluid, and a healthy concentration of proteins in the blood, the cells, and the spaces between cells helps ensure a balance of fluids in these various “compartments.” Moreover, proteins in the cell membrane help to transport electrolytes in and out of the cell, keeping these ions in a healthy balance. Like lipids, proteins can bind with carbohydrates. They can thereby produce glycoproteins or proteoglycans, both of which have many functions in the body.

The body can use proteins for energy when carbohydrate and fat intake is inadequate, and stores of glycogen and adipose tissue become depleted. However, since there is no storage site for protein except functional tissues, using protein for energy causes tissue breakdown, and results in body wasting.

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.

Different amino acids join together to form peptides, polypeptides, or proteins via dehydration synthesis. The bonds between the amino acids are peptide bonds R1 and R2 may be the same or different side chains.

(a) The primary structure is the sequence of amino acids that make up the polypeptide chain. (b) The secondary structure, which can take the form of an alpha-helix or a beta-pleated sheet, is maintained by hydrogen bonds between amino acids in different regions of the original polypeptide strand. (c) The tertiary structure occurs as a result of further folding and bonding of the secondary structure. (d) The quaternary structure occurs as a result of interactions between two or more tertiary subunits. The example shown here is hemoglobin, a protein in red blood cells which transports oxygen to body tissues.

According to the induced-fit model, the active site of the enzyme undergoes conformational changes upon binding with the substrate.(a) Substrates approach active sites on enzyme. (b) Substrates bind to active sites, producing an enzyme–substrate complex. (c) Changes internal to the enzyme–substrate complex facilitate interaction of the substrates. (d) Products are released and the enzyme returns to its original form, ready to facilitate another enzymatic reaction.

Functional groupStructural formulaImportance
Hydroxyl—O—HHydroxyl groups are polar. They are components of all four types of organic compounds discussed in this chapter. They are involved in dehydration synthesis and hydrolysis reactions.
CarboxylR is single bonded to C, C is double bonded to one O and single bonded to another O. The second O is single bonded to H.Carboxyl groups are found within fatty acids, amino acids, and many other acids.
Amino—N—H2Amino groups are found within amino acids, the building blocks of proteins.
Methyl—C—H3Methyl groups are found within amino acids.
Phosphate—P—O42–Phosphate groups are found within phospholipids and nucleotides.
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Script:
  1. Organic compounds essential to human functioning include carbohydrates, lipids, proteins, and nucleotides.
  2. These compounds are said to be organic because they contain both carbon and hydrogen.
  3. Carbon atoms in organic compounds readily share electrons with hydrogen and other atoms, usually oxygen, and sometimes nitrogen.
  4. Carbon atoms also may bond with one or more functional groups such as carboxyls, hydroxyls, aminos, or phosphates.
  5. Monomers are single units of organic compounds.
  6. They bond by dehydration synthesis to form polymers, which can in turn be broken by hydrolysis.
  7. Carbohydrate compounds provide essential body fuel.
  8. Their structural forms include monosaccharides such as glucose, disaccharides such as lactose, and polysaccharides, including starches, glycogen, and fiber.
  9. Starches are polymers of glucose, while glycogen is the storage form of glucose.
  10. All body cells can use glucose for fuel.
  11. It is converted via an oxidation-reduction reaction to ATP.
  12. Lipids are hydrophobic compounds that provide body fuel and are important components of many biological compounds.
  13. Triglycerides are the most abundant lipid in the body, and are composed of a glycerol backbone attached to three fatty acid chains.
  14. Phospholipids are compounds composed of a diglyceride with a phosphate group attached at the molecule’s head.
  15. The result is a molecule with polar and nonpolar regions.
  16. Steroids are lipids formed of four hydrocarbon rings.
  17. The most important is cholesterol.
  18. Prostaglandins are signaling molecules derived from unsaturated fatty acids.
  19. Proteins are critical components of all body tissues.
  20. They are made up of monomers called amino acids, which contain nitrogen, joined by peptide bonds.
  21. Protein shape is critical to its function.
  22. Most body proteins are globular.
  23. An example is enzymes, which catalyze chemical reactions.
  24. Nucleotides are compounds with three building blocks: one or more phosphate groups, a pentose sugar, and a nitrogen-containing base.
  25. DNA and RNA are nucleic acids that function in protein synthesis.
  26. ATP is the body’s fundamental molecule of energy transfer.
  27. Removal or addition of phosphates releases or invests energy.
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