BIO 141: Chapter 5 (The Structure and Function of Large Biological Molecules) Review

Lipid - monomer, characteristic bond/functional group, example

"Monomer": Glycerol, fatty acids Characteristic bond/functional group: Ester linkage, hydroxyl group, carboxyl group, phosphate group Example: Waxes, phospholipids, steroids, cholesterol

Carbohydrates

Carbohydrates include sugars and polymers of sugars. The simplest carbohydrates are the monosaccharides, or simple sugars; these are the monomers from which more complex carbohydrates are built. Disaccharides are double sugars, consisting of two monosaccharides joined by a covalent bond. Carbohydrate macromolecules are polymers called polysaccharides, composed of many sugar building blocks.

All living things are made up of the same four kinds of biological macromolecules:

Carbohydrates, proteins, nucleic acids, lipids

Glucose, ribose, and deoxyribose

Glucose (C6H12O6), the most common monosaccharide, is of central importance to the chemistry of life. Glucose is an aldose and a hexose. In aqueous solutions, glucose molecules, as well as most other five- and six-carbon sugars, form rings. Monosaccharides, particularly glucose, are major nutrients for cells. In the process known as cellular respiration, cells extract energy from glucose molecules by breaking them down in a series of reactions. In DNA, the sugar is deoxyribose; in RNA it is ribose. The only difference between these two sugars is that deoxyribose lacks an oxygen atom on the second carbon in the ring, hence the name deoxyribose.

Structure of nucleic acids

Nucleic acids are macromolecules that exist as polymers called polynucleotides. As indicated by the name, each polynucleotide consists of monomers called nucleotides. The linkage of nucleotides into a polynucleotide involves a dehydration reaction. In the polynucleotide, adjacent nucleotides are joined by a phosphodiester linkage, which consists of a phosphate group that links the sugars of two nucleotides.

Phospholipids

Phospholipids are essential for cells because they are major constituents of cell membranes. Their structure provides a classic example of how form fits function at the molecular level. A phospholipid is similar to a fat molecule but has only two fatty acids attached to glycerol rather than three. The third hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge in the cell. Typically, an additional small charged or polar molecule is also linked to the phosphate group. The two ends of phospholipids show different behaviors with respect to water. The hydrocarbon tails are hydrophobic and are excluded from water. However, the phosphate group and its attachments form a hydrophilic head that has an affinity for water. When phospholipids are added to water, they self-assemble into a double-layered sheet called a "bilayer" that shields their hydrophobic fatty acid tails from water. The phospholipid bilayer forms a boundary between the cell and its external environment and establishes separate compartments within eukaryotic cells.

Function of polysaccharides

Polysaccharides are macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages. Some polysaccharides serve as storage material, hydrolyzed as needed to provide sugar for cells. Other polysaccharides serve as building material for structures that protect the cell or the whole organism. The architecture and function of a polysaccharide are determined by its sugar monomers and by the positions of its glycosidic linkages.

Protein structure (primary, secondary, tertiary, quaternary)

The chemical nature of the molecule as a whole is determined by the kind and sequence of the side chains, which determine how a polypeptide folds and thus its final shape and chemical characteristics. A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape. And it is the amino acid sequence of the polypeptide that determines what three-dimensional structure the protein will have under normal cellular conditions. Many proteins are roughly spherical (globular proteins), while others are shaped like long fibers (fibrous proteins).

Hydrophobic vs. hydrophilic: What is a molecule called that has regions of both?

The two ends of phospholipids show different behaviors with respect to water. The hydrocarbon tails are hydrophobic and are excluded from water. However, the phosphate group and its attachments form a hydrophilic head that has an affinity for water. When phospholipids are added to water, they self-assemble into a double-layered sheet called a "bilayer" that shields their hydrophobic fatty acid tails from water. A molecule that has regions of both is called amphipathic.

Types of nucleic acids

The two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), enable living organisms to reproduce their complex components from one generation to the next. Unique among molecules, DNA provides directions for its own replication. DNA also directs RNA synthesis and, through RNA, controls protein synthesis; this entire process is called gene expression.

Peptide bond

When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined by a dehydration reaction, with the removal of a water molecule. The resulting covalent bond is called a peptide bond. Repeated over and over, this process yields a polypeptide, a polymer of many amino acids linked by peptide bonds. The repeating sequence of atoms is called the polypeptide backbone. Extending from this backbone are the different side chains (R groups) of the amino acids. One end of the polypeptide chain has a free amino group (the N-terminus), while the opposite end has a free carboxyl group (the C-terminus).

Glycerol, fatty acids, and ester bonds

A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids. Glycerol is an alcohol; each of its three carbons bears a hydroxyl group. A fatty acid has a long carbon skeleton, usually 16 or 18 carbons atoms in length. The carbon at one end of the skeleton is part of a carboxyl group, the functional group that gives these molecules the name fatty acids. The rest of the skeleton consists of a hydrocarbon chain. The relatively nonpolar C-H bonds in the hydrocarbon chains of fatty acids are the reason fats are hydrophobic. Fats separate from water because the water molecules hydrogen-bond to one another and exclude the fats. In making a fat, three fatty acids molecules are each joined to glycerol by an ester linkage, a bond formed by a dehydration reaction between a hydroxyl group and a carboxyl group. The resulting fat, also called triacylglycerol, thus consists of three fatty acids linked to one glycerol molecule.

Glycosidic bonds (alpha α and beta β)

A glycosidic linkage is a covalent bond formed between two monosaccharides by a dehydration reaction. There are actually two slightly different ring structures for glucose. When glucose forms a ring, the hydroxyl group attached to the number 1 carbon is positioned either below or above the plane of the ring. These two rings forms for glucose are called alpha α and beta β, respectively. In starch, all the glucose monomers are in the α configuration. In contrast, the glucose monomers of cellulose are all in the β configuration, making every glucose monomer "upside down" with respect to its neighbors.

Components of nucleotides

A nucleotide, in general, is composed of three parts: a five-carbon sugar (a pentose), a nitrogen-containing (nitrogenous) base, and one to three phosphate groups. The beginning monomer used to build a polynucleotide has three phosphate groups, but two are lost during the polymerization process. The portion of a nucleotide without any phosphate groups is called a nucleoside. Each nitrogenous base has one or two rings that include nitrogen atoms. There are two families of nitrogenous bases: pyrimidines and purines. A pyrimidine has one six-membered ring of carbon and nitrogen atoms (cytosine (C), thymine (T), and uracil (U)). Purines are larger, with a six-membered ring fused to a five-membered ring (adenine (A) and guanine (G)). Adenine, guanine, and cytosine are found in both DNA and RNA; thymine is found only in DNA and uracil only in RNA. In DNA, the sugar is deoxyribose; in RNA it is ribose. The only difference between these two sugars is that deoxyribose lacks an oxygen atom on the second carbon in the ring, hence the name deoxyribose. To complete the construction of a nucleotide, we attach one to three phosphate groups to the 5' carbon of the sugar. With one phosphate, this is a nucleoside monophosphate, more often called a nucleotide.

Proteins

A protein is a biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific three-dimensional structure. Proteins account for more than 50% of the dry mass of most cells, and they are instrumental in almost everything organisms do. Some proteins speed up chemical reactions, while others play a role in defense, storage, transport, cellular communication, movement, or structural support. A human has tens of thousands of different proteins, each with a specific structure and function; proteins, in fact, are the most structurally sophisticated molecules known. Consistent with their diverse functions, they vary extensively in structure, each type of protein having a unique three-dimensional shape.

Function of nucleic acids

DNA is the genetic material that organisms inherit from their parents. Each chromosome contains one long DNA molecule, usually carrying several hundred or more genes. When a cell reproduces itself by dividing, its DNA molecules are copied and passed along from one generation of cells to the next. The information that programs all the cell's activities is encoded in the structure of DNA. A given gene along a DNA molecule can direct synthesis of a type of RNA called messenger RNA (mRNA). The mRNA molecule interacts with the cell's protein-synthesizing machinery to direct production of a polypeptide, which folds into all or part of a protein (DNA → RNA → protein). DNA resides in the nucleus. RNA conveys genetic instructions for building proteins from the nucleus to the cytoplasm. Prokaryotic cells lack nuclei but still use mRNA to convey a message from the DNA to ribosomes and other cellular equipment.

The different types of macromolecules

Important large molecules found in all living things can be sorted into just four main classes: carbohydrates, lipids, proteins, and nucleic acids. On the molecular scale, three of these classes - carbohydrates, proteins, and nucleic acids - are huge and are therefore called macromolecules. Large biological molecules exhibit unique emergent properties arising from the orderly arrangement of their atoms.

Polymer and monomer

Large carbohydrates, proteins, and nucleic acids are chain-like molecules called polymers. A polymer is a long molecule consisting of many similar or identical building blocks linked by covalent bonds. The repeating units that serve as the building blocks of a polymer are smaller molecules called monomers. In addition to forming polymers, some monomers have functions of their own.

Are lipids polymers or monomers?

Lipids are the one class of large biological molecules that does not include true polymers, and they are generally not big enough to be considered macromolecules. Although fats are not polymers, they are large molecules assembled from smaller molecules by dehydration reactions.

Lipids

Lipids are the one class of large biological molecules that does not include true polymers, and they are generally not big enough to be considered macromolecules. The compounds called lipids are grouped with each other because they share one important trait: They mix poorly, if at all, with water. The hydrophobic behavior of lipids is based on their molecular structure. Although they may have some polar bonds associated with oxygen, lipids consist mostly of hydrocarbon regions. Lipids are varied in form and function. The types of lipids that are most important biologically are fats, phospholipids, and steroids.

Functions of lipids

Lipids are varied in form and function. They include waxes and certain pigments. The major function of fats is energy storage. A gram of fat stores more than twice as much energy as a gram of a polysaccharide, such as starch. Because plants are relatively immobile, they can function with bulky energy storage in the form of starch. Animals, however, must carry their energy stores with them, so there is an advantage to having a more compact reservoir of fuel - fat. Humans and other mammals stock their long-term food reserves in adipose cells, which swell and shrink as fat is deposited and withdrawn from storage. In addition to storing energy, adipose tissue also cushions such vital organs as the kidneys, and a layer of fat beneath the skin insulates the body.

Functions of proteins

Proteins can be enzymatic, defensive, storage, transport, hormonal, receptor, contractile and motor, or structural.

Protein - monomer, characteristic bond/functional group, example

Monomer: Amino acids Characteristic bond/functional group: Peptide bonds, amino group, carboxyl group, side chain (R group) Example: Hemoglobin, Lactase

Polysaccharide - monomer, characteristic bond/functional group, example

Monomer: Monosaccharides Characteristic bond/functional group: Glycosidic linkage, carbonyl group, hydroxyl group Example: Starch, glycogen, cellulose, chitin

Nucleic acid - monomer, characteristic bond/functional group, example

Monomer: Nucleotides Characteristic bond/functional group: Phosphodiester linkage, phosphate group Example: DNA, RNA

Characteristics of fatty acids and molecules associated with membranes that affect fluidity

Most animal fats are saturated: The hydrocarbon chains of their fatty acids - the "tails" of the fat molecules - lack double bonds, and their flexibility allows the fat molecules to pack together tightly. Saturated animal fats are solid at room temperature. The fats of plants and fishes are generally unsaturated, meaning that they are built of or more types of unsaturated fats. Usually liquid at room temperature, plant and fish fats are referred to as oils. The kinks where the cis double bonds are located prevent the molecules from packing together closely enough to solidify at room temperature.

Secondary structure

Most proteins have segments of their polypeptide chains repeatedly coiled or folded in patterns that contribute to the protein's overall shape. These coils and folds, collectively referred to as secondary structure, are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone (not the amino acid side chains). Within the backbone, the oxygen atoms have a partial negative charge, and the hydrogen atoms attached to the nitrogens have a partial positive charge; therefore, hydrogen bonds can form between these atoms. One such secondary structure is the α helix, a delicate coil held together by hydrogen bonding between every fourth amino acid. The other main type of secondary structure is the β pleated sheet. In this structure two or more segments of the polypeptide chain lying side by side (called β strands) are connected by hydrogen bonds between parts of the two parallel segments of polypeptide backbone. β pleated sheets make up the core of many globular proteins.

Some polymer examples (starch vs. cellulose)

Plants store starch, a polymer of glucose monomers, as granules within cellular structures known as plastids (plastids include chloroplasts). Because glucose is a major cellular fuel, starch represents stored energy. The sugar can later be withdrawn by the plant from this carbohydrate "bank" by hydrolysis, which breaks the bonds between the glucose monomers. Most of the glucose monomers in starch are joined by 1-4 linkages (number 1 carbon to number 4 carbon). Organisms build strong materials from structural polysaccharides. For example, the polysaccharide called cellulose is a major component of the tough walls that enclose plant cells. It is the most abundant organic compound on Earth. Like starch, cellulose is a polymer of glucose with 1-4 glycosidic linkages, but the linkages in these two polymers differ. When glucose forms a ring, the hydroxyl group attached to the number 1 carbon is positioned either below or above the plane of the ring. In starch, all the glucose monomers are in the α (below) configuration. In contrast, the glucose monomers of cellulose are in the β (above) configuration.

Polysaccharides

Polysaccharides are macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages. Some polysaccharides serve as storage material, hydrolyzed as needed to provide sugar for cells (ex: starch, glycogen). Other polysaccharides serve as building material for structures that protect the cell or the whole organism (ex: cellulose, chitin). The architecture and function of a polysaccharide are determined by its sugar monomers and by the positions of its glycosidic linkages.

Amino acids and general types/classifications

Proteins are all constructed from the same set of 20 amino acids, linked in unbranched polymers. The bond between amino acids is called a peptide bond, so a polymer of amino acids is called a polypeptide. All amino acids share a common structure. An amino acid is an organic molecule with both an amino group and a carboxyl group. At the center of the amino acid is an asymmetric carbon atom called the alpha (α) carbon. Its four different partners are an amino group, a carboxyl group, a hydrogen atom, and a variable group symbolized by R. The R group, also called the side chains, differs with each amino acid. The physical and chemical properties of the side chain determine the unique characteristics of a particular amino acid, thus affecting its functional role in a polypeptide.

Saturated vs. unsaturated fatty acids

Saturated fats and unsaturated fats refer to the structure of the hydrocarbon chains of the fatty acids. If there are no double bonds between carbon atoms composing a chain, then as many hydrogen atoms as possible are bonded to the carbon skeletons. Such a structure is said to be saturated with hydrogen, and the resulting fatty acid is therefore called a saturated fatty acid. An unsaturated fatty acid has one or more double bonds, with one fewer hydrogen atom on each double-bonded carbon. Nearly every double bond in naturally occurring fatty acids is a cis double bond, which creates a kink in the hydrocarbon chain wherever it occurs.

Quaternary structure

Some proteins consist of two or more polypeptide chains aggregated into one functional macromolecule. Quaternary structure is the overall protein structure that results from the aggregation of these polypeptide subunits.

Nucleic acids

The amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance known as a gene. Genes consist of DNA, which belongs to the class of compounds called nucleic acids. Nucleic acids are polymers made up of monomers called nucleotides. The two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), enable living organisms to reproduce their complex components from one generation to the next.

How chemical structures make these biomolecules suited for the different types of functions performed in living organisms

The architecture of a large biological molecule plays an essential role in its function. Like water and simple organic molecules, large biological molecules exhibit unique emergent properties arising from the orderly arrangement of their atoms.

Ability of polymers to create molecular diversity

The diversity of macromolecules in the living world is vast, and the possible variety is effectively limitless. These molecules are constructed from only 40 to 50 common monomers and some others that occur rarely. The key is arrangement - the particular linear sequence that the units follow. Small molecules common to all organisms act as building blocks that are ordered into unique macromolecules. Despite this immense diversity, molecular structure and function can still be grouped roughly by class. For each class, the large molecules have emergent properties not found in their individual components.

Primary structure

The primary structure of a protein is its sequence of amino acids. The primary structure is like the order of letters in a very long word. The precise primary structure of a protein is determined not by the random linking of amino acids, but by inherited genetic information. The primary structure in turn dictates secondary and tertiary structure, due to the chemical nature of the backbone and the side chains (R groups) of the amino acids along the polypeptide.

Dehydration synthesis vs. hydrolysis

The reaction connecting monomers is a good example of a dehydration reaction, a reaction in which two molecules are covalently bonded to each other with the loss of a water molecule. When a bond forms between two monomers, each monomer contributes part of the water molecule that is released during the reaction: One monomer provides a hydroxyl group (-OH), while the other provides a hydrogen (-H). Polymers are disassembled to monomers by hydrolysis, a process that is essentially the reverse of the dehydration reaction. Hydrolysis means water breakage. The bond between monomers is broken by the addition of a water molecule, with a hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other.

What are the monomer units of polysaccharides?

The simplest carbohydrates are the monosaccharides, or simple sugars; these are the monomers from which more complex carbohydrates are built. Polysaccharides are macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages. Monosaccharides generally have molecular formulas that are some multiple of the unit CH2O. The trademarks of a sugar are a carbonyl group and multiple hydroxyl groups. Depending on the location of the carbonyl group, a sugar is either an aldose (aldehyde sugar) or a ketose (ketone sugar). Most sugar names end in -ose. Still another source of diversity for simple sugars is in the way their parts are arranged spatially around symmetric carbons.

Tertiary structure

While secondary structure involves interactions between backbone constituents, tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains (R groups) of the various amino acids. One type of interaction that contributes to tertiary structure is called a hydrophobic interaction. As a polypeptide folds into its functional shape, amino acids with hydrophobic (nonpolar) side chains usually end up in clusters at the core of the protein, out of contact with water. Once nonpolar amino acid side chains are close together, van der Waals interactions help hold them together. Meanwhile, hydrogen bonds between polar side chains and ionic bonds between positively charged and negatively charged side chains also help stabilize tertiary structure. Covalent bonds called disulfide bridges may further reinforce the shape of a protein. Disulfide bridges form when two cysteine monomers, which have sulfhydryl groups (-SH) on their side chains are brought close together by the folding of a protein.