CH - Chapter 8: The Major Macromolecules - Chemistry
Monomer + = Polymer Macromolecule glucose glycogen smaller subunits long Carbohydrate molecule with carbon atoms is called monosaccharide. Aug 8, “We must be clear that when it comes to atoms, language can be used only as in poetry. The poet, too, is not nearly so concerned with. As nouns the difference between molecule and macromolecule is that molecule is two or more atoms held together by chemical bonds while macromolecule is.
New amino acids are always added onto the carboxylic acid tail, never onto the amine of the first amino acid in the chain. In addition, because the R-groups can be quite bulky, they usually alternate on either side of the growing protein chain in the trans conformation. The cis conformation is only preferred with one specific amino acid known as proline. The addition of two amino acids to form a peptide requires dehydration synthesis.
Proteins are very large molecules containing many amino acid residues linked together in very specific order. Proteins range in size from 50 amino acids in length to the largest known protein containing 33, amino acids. Macromolecules with fewer than 50 amino acids are known as peptides. The identity and function of a peptide or a protein is determined by the primary sequence of amino acids within its structure.
There are a total of 20 alpha amino acids that are commonly incorporated into protein structures Figure Due to the large pool of amino acids that can be incorporated at each position within the protein, there are billions of different possible protein combinations that can be used to create novel protein structures!
For example, think about a tripeptide made from this amino acid pool. At each position there are 20 different options that can be incorporated. Now think about how many options there would be for a small peptide containing 40 amino acids. There would be options, or a mind boggling 1.
Each of these options would vary in the overall protein shape, as the nature of the amino acid side chains helps to determine the interaction of the protein with the other residues in the protein itself and with its surrounding environment. Thus, it is useful to learn a little bit about the general characteristics of the amino acid side chains. The different amino acid side chains can be grouped into different classes based on their chemical properties Figure For example, some amino acid side chains only contain carbon and hydrogen and are thus, very nonpolar and hydrophobic.
Others contain electronegative functional groups with oxygen or nitrogen and can form hydrogen bonds forming more polar interactions. Still others contain carboxylic acid functional groups and can act as acids or they contain amines and can act as bases, forming fully charged molecules. The character of the amino acids throughout the protein help the protein to fold and form its 3-dimentional structure. It is this 3-D shape that is required for the functional activity of the protein ie.
For proteins found inside the watery environments of the cell, hydrophobic amino acids will often be found on the inside of the protein structure, whereas water-loving hydrophilic amino acids will be on the surface where they can hydrogen bond and interact with the water molecules.
Proline is unique because it has the only R-group that forms a cyclic structure with the amine functional group in the main chain. This cyclization is what causes proline to adopt the cis conformation rather than the trans conformation within the backbone.
This shift is structure will often mean that prolines are positions where bends or directional changes occur within the protein. Methionine is unique, in that it serves as the starting amino acid for almost all of the many thousands of proteins known in nature.
Cysteines contain thiol functional groups and thus, can be oxidized with other cysteine residues to form disulfide bonds within the protein structure Figure Disulfide bridges add additional stability to the 3-D structure and are often required for correct protein folding and function Figure Disulfide bonds are formed between two cysteine residues within a peptide or protein sequence or between different peptide or protein chains.
In the example above the two peptide chains that form the hormone insulin are depicted. Disulfide bridges between the two chains are required for the proper function of this hormone to regulate blood glucose levels.
Protein Shape and Function The primary structure of each protein leads to the unique folding pattern that is characteristic for that specific protein. Recall that this is the linear order of the amino acids as they are linked together in the protein chain Figure These specific motifs or patterns are called secondary structure. Common secondary structural features include alpha helix and beta-pleated sheet Figure Within these structures, intramolecular interactions, especially hydrogen bonding between the backbone amine and carbonyl functional groups are critical to maintain 3-dimensional shape.
Every helical turn in an alpha helix has 3. The R groups are attached to the carbons and extend above and below the folds of the pleat. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive nitrogen atom in the amino group and the partially negative oxygen atom in the carbonyl group of the peptide backbone.
The alpha helix and beta-pleated sheet are common structural motifs found in most proteins. They are held together by hydrogen bonding between the amine and the carbonyl oxygen within the amino acid backbone. Secondary Protein Structure in Silk There were many trade routes throughout the ancient world. The most highly traveled and culturally significant of these was called the Silk Road. The reason that the Silk road was so culturally significant was because of the great distance that it covered.
Essentially the entire ancient world was connected by one trade route. The silk road had an astounding effect on the creation of many societies. It was able to bring economic wealth into areas along the route, and new ideas traveled the distance and influence many things including art. An example of this is Buddhist art that was found in India. The painting has many western influences that can be identified in it, such as realistic musculature of the people being painted. Also, the trade of gun powder to the West helped influence warfare, and in turn shaped the modern world.
The real reason the Silk Road was started though was for the product that it takes its name from: The Silk showed that the rulers had power and wealth because the silk was not easy to come by, and therefore was definitely not cheap.
Silk was first developed in China, and is made by harvesting the silk from the cocoons of the mulberry silkworm. The silk itself is called a natural protein fiber because it is composed of a pattern of amino acids in a secondary protein structure.
The secondary structure of silk is the beta pleated sheet.
What is the relationship between atoms, bonding and macromolecules?
The primary structure of silk contains the amino acids of glycine, alanine, serine, in specific repeating pattern. These amino acids are used as side chains and affect things such as elasticity and strength. The beta pleated sheet of silk is connected by hydrogen bonds. The hydrogen bonds in the silk form beta pleated sheets rather than alpha helixes because of where the bonds occur.
The hydrogen bonds go from the amide hydrogens on one protein chain to the corresponding carbonyl oxygen across the way on the other protein chain. This is in contrast to the alpha helix because in that structure the bonds go from the amide to the carbonyl oxygen, but they are not adjacent. Figure The abundances of some chemical elements in the nonliving world the Earth's crust compared with their abundances in the tissues of an animal.
The abundance of each element is expressed as a percentage of the total number of atoms present in the sample. The Outermost Electrons Determine How Atoms Interact To understand how atoms bond together to form the molecules that make up living organisms, we have to pay special attention to their electrons. Protons and neutrons are welded tightly to one another in the nucleus and change partners only under extreme conditions—during radioactive decay, for example, or in the interior of the sun or of a nuclear reactor.
In living tissues, it is only the electrons of an atom that undergo rearrangements. They form the exterior of an atom and specify the rules of chemistry by which atoms combine to form molecules. Electrons are in continuous motion around the nucleusbut motions on this submicroscopic scale obey different laws from those we are familiar with in everyday life.
These laws dictate that electrons in an atom can exist only in certain discrete states, called orbitals, and that there is a strict limit to the number of electrons that can be accommodated in an orbital of a given type—a so-called electron shell. The electrons closest on average to the positive nucleus are attracted most strongly to it and occupy the innermost, most tightly bound shell. This shell can hold a maximum of two electrons.
The second shell is farther away from the nucleus, and its electrons are less tightly bound. This second shell can hold up to eight electrons. The third shell contains electrons that are even less tightly bound; it can also hold up to eight electrons. The fourth and fifth shells can hold 18 electrons each.
Atoms with more than four shells are very rare in biological molecules. The electron arrangement of an atom is most stable when all the electrons are in the most tightly bound states that are possible for them—that is, when they occupy the innermost shells. Therefore, with certain exceptions in the larger atoms, the electrons of an atom fill the orbitals in order—the first shell before the second, the second before the third, and so on.
An atom whose outermost shell is entirely filled with electrons is especially stable and therefore chemically unreactive. Hydrogen, by contrast, with only one electron and therefore only a half-filled shell, is highly reactive. Likewise, the other atoms found in living tissues all have incomplete outer electron shells and are therefore able to donate, accept, or share electrons with each other to form both molecules and ions Figure Figure Filled and unfilled electron shells in some common elements.
CH103 – Chapter 8: The Major Macromolecules
All the elements commonly found in living organisms have unfilled outermost shells red and can thus participate in chemical reactions with other atoms. For comparison, some elements that have more Because an unfilled electron shell is less stable than a filled one, atoms with incomplete outer shells have a strong tendency to interact with other atoms in a way that causes them to either gain or lose enough electrons to achieve a completed outermost shell.
This electron exchange can be achieved either by transferring electrons from one atom to another or by sharing electrons between two atoms.
These two strategies generate two types of chemical bonds between atoms: Often, the pair of electrons is shared unequally, with a partial transfer between the atoms; this intermediate strategy results in a polar covalent bond, as we shall discuss later.
Figure Comparison of covalent and ionic bonds. Atoms can attain a more stable arrangement of electrons in their outermost shell by interacting with one another. An ionic bond is formed when electrons are transferred from one atom to the other. A covalent bond more An H atom, which needs only one more electron to fill its shell, generally acquires it by electron sharing, forming one covalent bond with another atom; in many cases this bond is polar.
The other most common elements in living cells—C, N, and O, with an incomplete second shell, and P and S, with an incomplete third shell see Figure —generally share electrons and achieve a filled outer shell of eight electrons by forming several covalent bonds.
The number of electrons that an atom must acquire or lose either by sharing or by transfer to attain a filled outer shell is known as its valence. The crucial role of the outer electron shell in determining the chemical properties of an element means that, when the elements are listed in order of their atomic number, there is a periodic recurrence of elements with similar properties: The metals, for example, have incomplete outer shells with just one or a few electrons, whereas, as we have just seen, the inert gases have full outer shells.
Ionic Bonds Form by the Gain and Loss of Electrons Ionic bonds are most likely to be formed by atoms that have just one or two electrons in addition to a filled outer shell or are just one or two electrons short of acquiring a filled outer shell. They can often attain a completely filled outer electron shell more easily by transferring electrons to or from another atom than by sharing electrons.
For example, from Figure we see that a sodium Na atom, with atomic number 11, can strip itself down to a filled shell by giving up the single electron external to its second shell. By contrast, a chlorine Cl atom, with atomic number 17, can complete its outer shell by gaining just one electron. Consequently, if a Na atom encounters a Cl atom, an electron can jump from the Na to the Cl, leaving both atoms with filled outer shells.
The offspring of this marriage between sodium, a soft and intensely reactive metal, and chlorine, a toxic green gas, is table salt NaCl. When an electron jumps from Na to Cl, both atoms become electrically charged ions.
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The Cl atom that gained an electron now has one more electron than it has protons and has a single negative charge Cl. Positive ions are called cations, and negative ions, anions. Ions can be further classified according to how many electrons are lost or gained. Substances such as NaCl, which are held together solely by ionic bonds, are generally called salts rather than molecules. Ionic bonds are just one of several types of noncovalent bonds that can exist between atoms, and we shall meet other examples.
Figure Sodium chloride: A An atom of sodium Na reacts with an atom of chlorine Cl. Electrons of each atom are shown schematically in their different energy levels; electrons in the chemically reactive incompletely filled more In contrast, covalent bond strengths are not affected in this way. Covalent Bonds Form by the Sharing of Electrons All the characteristics of a cell depend on the molecules it contains. A molecule is defined as a cluster of atoms held together by covalent bonds ; here electrons are shared between atoms to complete the outer shells, rather than being transferred between them.Atoms and Molecules - Class 9 Tutorial
In the simplest possible molecule —a molecule of hydrogen H2 —two H atoms, each with a single electronshare two electrons, which is the number required to fill the first shell.
These shared electrons form a cloud of negative charge that is densest between the two positively charged nuclei and helps to hold them together, in opposition to the mutual repulsion between like charges that would otherwise force them apart.
The attractive and repulsive forces are in balance when the nuclei are separated by a characteristic distance, called the bond length. A further crucial property of any bond—covalent or noncovalent—is its strength.