Macromolecules | Biology | Science | Khan Academy
Carbohydrates, proteins and lipids are biological molecules. lipids (fats and oils) This means that they all contain carbon atoms, covalently bonded to the atoms of other elements. As we've learned, there are four major classes of biological macromolecules: Let's take a closer look at the differences between the difference classes. . gains a hydrogen atom (H+) and the other gains a hydroxyl molecule (OH–) from a split in our bodies, food is hydrolyzed, or broken down, into smaller molecules by. The atomic weight of an atom, or the molecular weight of a molecule, is its factor describing the relationship between everyday quantities and quantities .. The Principal Types of Weak Noncovalent Bonds that Hold Macromolecules Together. . Fatty acids serve as a concentrated food reserve in cells, because they can.
The first is the alpha-helix. The alpha-helix is a major structural component of proteins. The hydrogen bonds are all intrachain, between different parts of the same chain.
Chapter 05 - The Structure and Function of Macromolecules
A lthough a single hydrogen bond is weak, cooperation of many hydrogen bonds can be strongly stabilizing. Alpha-helices must have a minimum length to be stable so there will be enough hydrogen bonds.
All peptide bonds are trans and planar. So, if the amino acid R-groups do not repel one another helix formation is favored.
The net electric charge should be zero or low charges of the same sign repel. Adjacent R-groups should be small, to avoids steric repulsion. R-groups that repel one another favor extended conformations instead of the helix.
Examples include large net electric charge and adjacent bulky R-groups. Proline is incompatible with the alpha-helix. The ring formed by the R-group restricts rotation of a bond that would otherwise be free to rotate.
The restricted rotation prevents the polypeptide chain from coiling into an alpha-helix. Occurrence of proline necessarily terminates or kinks alpha-helical regions in proteins. Occurrence of the alpha-helix. A component of typical globular proteins. A component of some fibrous proteins, like alpha-keratin.
Alpha-keratin has high tensile strength, as first observed by Rapunzel. It is found in hair, feathers, horn; the physical strength and elasticity of hair make it useful in ballistas, onagers, etc. The beta-pleated sheet is a second major structural component of proteins. The beta-pleated sheet resembles cellulose in that both consist of extended chains -- degenerate helices -- lying side by side and hydrogen bonded to one another. The polypeptide chains of a beta-pleated sheet can be arranged in two ways: An edge-on view shows the pleats.
Stabilizing factors for the pleated sheet resemble those for the alpha-helix.
The hydrogen bonds here are all interchain, unlike those of the alpha-helix. Small R-groups prevent steric destabilization. Large R-groups destabilize due to crowding. Sheets can stack one upon the other, with interdigitating R-groups of the amino acids. Occurrence of the beta-pleated sheet. In some fibrous proteins. Egg stalks of certain moths. Collagen has an unusual structure.
It consists of three polypeptide chains in a triple helix. This is the structure: Three extended helices of a type called polyproline II helices because polyproline can take this form hydrogen bonded to one another interchain ; no intrachain hydrogen bonds form because each helix is too extended, and hydrogen bonds cannot reach from one level of the helix up or down to the next level placed at the corners of a triangle.
The entire assembly is twisted into a superhelix. The stability of the collagen triple helix is due to its unusual amino acid composition and sequence. One third of the amino acid residues is glycine, and the glycyl residues are evenly spaced: Gly X Y n, where X and Y are other amino acids is the amino acid sequence of collagen. This places a glycyl residue at each position where the chain is in the interior of the triple helix.
There would be no room for a bulky R-group in this position glycine's R-group is H. The high glycine content with its small R-group would otherwise permit too much conformational freedom and favor a random coil. Proline and hydroxyproline together comprise about one third of the total amino acid residues, and Gly Pro Hypro is a common sequence. The relative inflexibility of the prolyl and hydroxyprolyl residues stiffens the chains.
Collagen occurs in tough, inelastic tissues, like tendon. The collagen helix is already fully extended. Unlike the alpha-helix, it cannot stretch; tendon ought not to stretch under heavy load.
Collagen is the single most abundant protein in the body; fortunately collagen defects are rare. Tertiary structure is the three dimensional arrangement of helical and nonhelical regions of macromolecules. Let's look first at the Tertiary structure of nucleic acids. Most circular double-stranded DNA is partly unwound before the ends are sealed to make the circle.
Partial unwinding is called negative superhelicity. Overwinding before sealing would be called positive superhelicity. Superhelicity introduces strain into the molecule. Think of holding a coil spring by the two ends and twisting it to unwind it; it takes effort to introduce this strain The strain of superhelicity can be relieved by forming a supercoil.
The identical phenomenon occurs in retractable telephone headset cords when they get twisted. The twisted circular DNA is said to be supercoiled. The supercoil is more compact. This is exemplified by yeast tRNA. There are four regions in which the strand is complementary to another sequence within itself.
These regions are antiparallel, fulfilling the conditions for stable double helix formation. X-ray crystallography shows that the three dimensional structure of tRNA contains the expected double helical regions.Macromolecules-A Beginners Guide
Large RNA molecules have extensive regions of self-complementarity, and are presumed to form complex three-dimensional structures spontaneously. Tertiary structure in Proteins The formation of compact, globular structures is governed by the constituent amino acid residues. Folding of a polypeptide chain is strongly influenced by the solubility of the amino acid R-groups in water.
Hydrophobic R-groups, as in leucine and phenylalanine, normally orient inwardly, away from water or polar solutes. Polar or ionized R-groups, as in glutamine or arginine, orient outwardly to contact the aqueous environment. Some amino acids, such as glycine, can be accommodated by aqueous or nonaqueous environments. The rules of solubility and the tendency for secondary structure formation determine how the chain spontaneously folds into its final structure.
Forces stabilizing protein tertiary structure. Hydrophobic interactions -- the tendency of nonpolar groups to cluster together to exclude water. Hydrogen bonding, as part of any secondary structure, as well as other hydrogen bonds. Ionic interactions -- attraction between unlike electric charges of ionized R-groups.
Disulfide bridges between cysteinyl residues. The disulfide bridge is a covalent bond. It strongly links regions of the polypeptide chain that could be distant in the primary sequence. It forms after tertiary folding has occurred, so it stabilizes, but does not determine tertiary structure. Globular proteins are typically organized into one or more compact patterns called domains. This concept of domains is important. In general it refers to a region of a protein.
But it turns out that in looking at protein after protein, certain structural themes repeat themselves, often, but not always in proteins that have similar biological functions. This phenomenon of repeating structures is consistent with the notion that the proteins are genetically related, and that they arose from one another or from a common ancestor.
In looking at the amino acid sequences, sometimes there are obvious homologies, and you could predict that the 3-dimensional structures would be similar. But sometimes virtually identical 3-dimensional structures have no sequence similarities at all!
The four-helix bundle domain is a common pattern in globular proteins. Helices lying side by side can interact favorably if the properties of the contact points are complementary. Hydrophobic amino acids like leucine at the contact points and oppositely charged amino acids along the edges will favor interaction. If the helix axes are inclined slightly 18 degreesthe R-groups will interdigitate perfectly along 6 turns of the helix.
Sets of four helices yield stable structures with symmetrical, equivalent interactions. Interestingly, four-helix bundles diverge at one end, providing a cavity in which ions may bind. All-beta structures comprise domains in many globular proteins. Beta-pleated sheets fold back on themselves to form barrel-like structures. Part of the immunoglobulin molecule exemplifies this. The interiors of beta-barrels serve in some proteins as binding sites for hydrophobic molecules such as retinol, a vitamin A derivative.
What keeps these proteins from forming infinitely large beta-sheets is not clear. They consist of a beta-barrel surrounded by a wheel of alpha-helices. Examples Triose phosphate isomerase. Domain 1 of pyruvate kinase. Beta-sheet surrounded by alpha-helices also occur. This is a variation on the theme of beta-structure inside and alpha-helix outside. Examples Lactate dehydrogenase domain 1 Phosphoglycerate kinase domain 2 Now that we are familiar with the structures of single chain macromolecules, we are in a position to look at some of the interactions of macromolecules with other macromolecules and with smaller molecules.
Macromolecular interactions involving proteins. Quaternary structure refers to proteins formed by association of polypeptide subunits. Individual globular polypeptide subunits may associate to form biologically active oligomers. The association is specific. A limited number of subunits is involved.
Chapter 05 - The Structure and Function of Macromolecules | CourseNotes
The subunits may be identical or they may be different. In contrast, both RNA and proteins are normally single-stranded. Therefore, they are not constrained by the regular geometry of the DNA double helix, and so fold into complex three-dimensional shapes dependent on their sequence.
These different shapes are responsible for many of the common properties of RNA and proteins, including the formation of specific binding pocketsand the ability to catalyse biochemical reactions. DNA is optimised for encoding information[ edit ] DNA is an information storage macromolecule that encodes the complete set of instructions the genome that are required to assemble, maintain, and reproduce every living organism.
On the other hand, the sequence information of a protein molecule is not used by cells to functionally encode genetic information. First, it is normally double-stranded, so that there are a minimum of two copies of the information encoding each gene in every cell. Second, DNA has a much greater stability against breakdown than does RNA, an attribute primarily associated with the absence of the 2'-hydroxyl group within every nucleotide of DNA.
Third, highly sophisticated DNA surveillance and repair systems are present which monitor damage to the DNA and repair the sequence when necessary. Analogous systems have not evolved for repairing damaged RNA molecules.
Consequently, chromosomes can contain many billions of atoms, arranged in a specific chemical structure. Proteins are optimised for catalysis[ edit ] Proteins are functional macromolecules responsible for catalysing the biochemical reactions that sustain life.
- Biological molecules
In addition, the chemical diversity of the different amino acids, together with different chemical environments afforded by local 3D structure, enables many proteins to act as enzymescatalyzing a wide range of specific biochemical transformations within cells.