Chapter 3 – The Molecules of Cells

3.1 Life’s molecular diversity is based on the properties of carbon

  • Almost all of the molecules a cell makes are composed of carbon. Next to water, carbon is the most common substance in living organisms. Carbon based molecules are considered organic. Carbon completes its outer shell by sharing electrons in up to 4 covalent bonds. Different bonds and angles are created depending on the bond being a single or double bond.
  • Large organic molecules can have very elaborate shapes due to carbon’s ability to bond. Compounds composed of only carbon and hydrogen are considered hydrocarbons. The chain of carbon atoms in the molecule is called a carbon skeleton, and this skeleton is the basis for the formation of large organic compounds. The skeleton may branch or form rings.
  • These large organic molecules can have elaborate shapes, and these shapes will help determine function of the compound.
  • Carbon skeletons may also include double bonds (where two pairs of electrons are shared). Depending on where the double bond is determines what compound is present.
  • For example, C4H8 is either 1-butene or 2-butene, depending on the placement of the double bond.
  • Isomers: Compounds with the same molecular formula but differ in the position of their bonds. Different isomers have different properties and add to the diversity of organic compound.

3.2 A few chemical groups are key to the functioning of biological molecules

  • The properties of organic compounds depend on the size and shape of the carbon skeleton, but also on the atoms that attach to the skeleton. They are called functional groups. They affect a molecule’s function by participating in chemical reactions in a particular way. These groups are polar because oxygen or nitrogen exert a strong pull on shared electrons. This polarity makes them hydrophilic, or water loving, which necessary for functionality in a cell.
  • There are five groups that are important to the chemistry of life. The sixth group, a methyl group, is non polar and non-reactive, but it affects molecular shape and therefore, function.
  1. Hydroxyl (-OH) Hydrogen bonded to an oxygen, which will bond to the carbon skeleton. Compounds containing hydroxyls are called alcohols. Example: ethanol
  2. Carbonyl (-C=O) Carbon double bonded to an oxygen.
  3. If the carbon attaches to the carbon skeleton, then the compound is an aldehyde. Example: sugars. Sugars contain a carbonyl and several hydroxyls
  4. If the oxygen attaches to the carbon skeleton, then the compound is a ketone.
  5. Carboxyl ( -COOH) Carbon double bonded to an oxygen and single bonded to a hydroxyl. The carboxyl group acts as an acid by contributing H+ to solution. Compounds are called carboxylic acids. Example: acetic acid
  6. Amino ( -NH2) Nitrogen bonded to two hydrogens. Acts as a base by picking up H+ in solutions. Compounds are called amines. Amino acids are the basis of proteins and will contain both an amino group and a carboxyl group.
  7. Phosphate ( -OPO32-) A phosphorous usually bonded to four oxygens. Usually attaches to the carbon skeleton by one of its oxygens. Compounds are called organic phosphates and are usually involved with energy transfers. Ex: ATP
  8. Methyl ( -CH3) A carbon bonded to three hydrogens. Compounds with this are called methylated compounds. In DNA, a methyl group addition can affect the expression of genes.

3.3 Cells make a huge number of large molecules from a limited set of small molecules

  • Despite the amazing variety of life on earth, there are only four important groups of organic compounds. The four main macromolecules are carbohydrates, lipids, proteins, and nucleic acids. Macromolecules are made from joining smaller molecules, monomers, into chains called polymers.
  • Cells link different monomers by a dehydration reaction – one that removes water. Unlinked monomers have both hydroxyl groups (-OH) and hydrogen atoms (H). For each monomer added to a chain, one water (H2O) is made. As this occurs, a new covalent bond is made linking the two monomers
  • Cells will also have to break down macromolecules. To digest these substances and make the monomers usable, a hydrolysis reaction is performed. Hydrolysis means to break (lyse) with water (hydro-). The bond between monomers is broken by the addition of water.
  • Cells are able to make this vast number using only 40-50 different monomers (for example, proteins are made of only 20 different amino acids).

3.4 Monosaccharides are the simplest carbohydrates

  • Carbohydrate refers to a class of molecules ranging from simple sugars to complex starches. The carbohydrate monomers are called monosaccharides (Greek monos- meaning single and sacchar meaning sugar). Both glucose and fructose have the same molecular formula, but different arrangements, making them isomers.
  • Monosaccharides generally have a molecular formula that is a multiple of CH2O. For example, glucose is C6H12O6. Fructose, a sugar common in fruits is also C6H12O6, but it differs in arrangement, thus making it an isomer to glucose. While both fructose and glucose are six carbon sugars (hexose), many other monosaccharides are five carbon (pentose); with these being the two most common arrangements. Three to seven carbon sugars also exist.
  • Monosaccharides are the main fuel for cellular work. They provide the raw material for constructing other organic molecules, including proteins. Monosaccharides not immediately used are incorporated into disaccharides or polysaccharides.

3.5 Two monosaccharides are linked to form a disaccharide

  • Cells construct a disaccharide from two monosaccharides by a dehydration reaction. For example, two glucose monomers can be connected to form maltose, a common sugar found in malted milk shakes and candy. The most common disaccharide is made from glucose linked to fructose to form sucrose, table sugar.

3.7 Polysaccharides are long chains of sugar units

  • Polysaccharides are groups of monosaccharides linked together by dehydration reactions. These polymers can be hundreds to thousands of units long. They may function as storage molecules or as structural components. They are storage units that are broken down as needed to obtain sugar.
  • Starch – storage polysaccharides in the roots and tissues of plants. Made entirely of glucose that coil into a helical shape.
  • Glycogen – animals store excess sugar in the form of a glucose polysaccharide
  • In some cases, they serve as structural components. Cellulose forms fibrils in the walls that enclose plant cells. It resembles starch and glycogen because it is made entirely of glucose, but they are linked in a different orientation. Animals do not have enzymes that can hydrolyze the bonds in cellulose, so it does not serve as a nutrient for humans; however, it does serve as fiber to help the digestive system. Some microorganisms can break down cellulose; termites and cows house these in their digestive tracts to help them derive energy from cellulose.
  • Chitin is another structural polysaccharide. Insects and crustaceans use it to build an exoskeleton. Chitin is found in the cell walls of fungus. Humans use chitin in surgical thread that decomposes after a wound or incision heals.
  • Almost all carbohydrates are hydrophilic, due to the hydroxyls attached to the sugar monomers.

3.8 Fats are lipids that are mostly energy storage molecules

  • Lipids are diverse compounds consisting of mostly carbons and hydrogens linked by nonpolar covalent bonds. Being nonpolar, they are not attracted to water (which is polar). Lipids are hydrophobic (water fearing). They differ from other organic compounds in that they are not polymers built from similar monomers; lipids vary in structure and function.
  • A fat is a large lipid made from two smaller molecules, glycerol and fatty acids. Glycerol is an alcohol with three carbons having a hydroxyl group (-OH). A fatty acid is a carboxyl group (-COOH) attached to a carbon chain. These nonpolar chains make fats hydrophobic.
  • Oils are liquid fats. Fats are large lipids made from two smaller molecules, glycerol and fatty acids. A synonym for this is triglyceride, since three fatty acids bond to one glycerol.
  • Some fatty acids contain one or more double bonds; they are termed unsaturated fats. The double bonds put kinks in the chains and prevent them from solidifying at room temperature (ex: vegetable oils, olive oil). Fatty acids with no double bonds are termed saturated fats. Most animal fats are saturated and solid at room temperature. Trans fats are created when hydrogen is added to solidify a fat.
  • The main function of lipids is energy storage. A gram of fat stores more than twice the amount of energy of a gram of polysaccharides. This compact energy storage enables mobile animals to get around easier than if they had to carry the same amount of energy in carbohydrate form. Fat serves as cushions for vital organs and insulates the body.

3.9 Phospholipids and steroids are lipids with a variety of functions

  • Fats are only one type of lipid important to living organisms. Other lipids are major constituents of cell membranes or perform vital functions such as protecting body surfaces and regulating cell and body functions.
  • Phospholipids (component of the cell membrane) are similar to fats in structure, but contain phosphorous and have two fatty acids instead of three.
  • Waxes consist of one fatty acid linked to an alcohol. They are more hydrophobic than fats and make them an effective coating for fruits, insects, and birds.
  • Steroids are fats whose carbon structure is bent to form four fused rings. All steroids have the same ring pattern: three 6-sided rings and one 5-sided ring. Cholesterol is a common substance in animal cell membranes, and animal cells will used it to make other steroids, such as male and female sex hormones.

3.10 Anabolic steroids pose health risks

  • Anabolic steroids are synthetic variants of the male hormone testosterone. Testosterone is responsible for the build up of muscle and bone mass in males during puberty, and also responsible for maintaining male characteristics throughout life.
  • Because steroids resemble testosterone, they can mimic the effects of it. Medically, they can be used to treat general anemia and diseases that destroy muscle tissue. However, abuse of steroids has dire consequences ranging from steroid rage to depression and liver damage.

3.11Proteins are made from amino acids linked by peptide bonds

  • Protein comes from the Greek “proteios” meaning first place. A protein is a polymer made of individual amino acids. Each protein has a unique three dimensional structure based on the arrangements of only 20 different amino acids. They are important structures of cells and participate in everything they do.
  • Amino acids have an amino group and a carboxyl group, both bonded covalently to a central carbon atom. Also bonded to this central (alpha) carbon is a chemical group symbolized by the letter “R.” The R group is a side chain and determines the specific properties of the amino acid.
  • Amino acids link together in a dehydration reaction that links the carboxyl of one to the amino in another. One water is removed in the reaction. The resulting covalent link is called a peptide bond. If two amino acids are joined, it is a dipeptide. If more are joined, it is a polypeptide.

3.12 A protein’s specific shape determines its function

  • Proteins are the most elaborate and diverse of the organic compounds. Protein diversity is based on the arrangements of a set of only 20 amino acids.
  • Enzymes may be the most important role played by proteins. As enzymes, proteins will catalyze (speed up) and regulate reactions.
  • Other protein functions include defense (such as antibodies), signaling (hormones and other chemical messengers), coordinating communication between cells, storage (albumin of eggs), and feeding developing embryos of both animals and plants
  • Most enzymes and other proteins are globular in shape. Structural proteins are typically long and thin (fibrous). While the twists of a protein may appear haphazard, they represent the molecule’s specific three-dimensional shape, and this shape determines the protein function.
  • If the polypeptide chain unravels, then the specific shape is lost and the protein can no longer function. This is termed denaturation. Denaturation can be caused by changes in salt, pH, or temperature. Once denatured, proteins cannot function.

3.14 A protein’s shape depends on four levels of structure

  • Primary structure is a unique sequence of amino acids determined by a unique set of inherited genetic information.
  • In the secondary structure, parts of the polypeptide coil and fold into patterns. Coiling can resulting in an alpha helix, while the folding leads to a beta pleated sheet. Pleated sheets may make up the core of globular proteins or can dominate in some fibrous proteins to give them strength (like spider silk).
  • Tertiary structure refers to a roughly globular or fibrous structure. It results from interactions among the R groups and may be further reinforced by a type of covalent bond called a disulfide bridge.
  • Most proteins consist of two or more polypeptide chains, making the quaternary structure.

3.14 DNA and RNA are the two types of nucleic acids

  • Genes determine the amino acid sequence of a polypeptide. Genes are made of DNA, deoxyribonucleic acid, which is one type of nucleic acid. Nucleic comes from their presence in the nucleus of the cell. Genetic material itself is inherited from the parents of an organism.
  • DNA is unique. It provides directions for its own replication, and those directions are passed on to the offspring as the cell divides. Instructions program a cell’s activities by directing protein synthesis. Genes present in DNA do not directly make the proteins.
  • RNA, ribonucleic acid, is the intermediary of DNA and protein synthesis. In the nucleus of a eukaryotic cell, genes direct the synthesis of RNA. DNA is transcribed into RNA. RNA moves out of the nucleus and interacts with the ribosome to build protein (translation). In prokaryotes, both transcription and translation take place in the cytoplasm.

3.16 Nucleic acids are polymers of nucleotides

  • Nucleic acids serve as the blueprints for proteins. The two types are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Nucleic acids are made of nucleotides. A nucleotide consists of a nitrogenous base (adenine, thymine, cytosine, guanine, uracil), a sugar (deoxyribose or ribose), and a phosphate.
  • RNA is a single strand and DNA is a double helix. The two strands of the helix are connected by hydrogen bonds.