Biological Molecules: The Building Blocks of Cells | L3 Fall 2021 KF

Biological Molecules: The Building Blocks of Cells Alberts MBotC Chapter 2  The Big Picture Cells are made from a distinctive and restricted set of small carbon-based molecules that are fundamentally the same for all li...

Biological Molecules: The Building Blocks of Cells Alberts MBotC Chapter 2  The Big Picture Cells are made from a distinctive and restricted set of small carbon-based molecules that are fundamentally the same for all living species. The major molecules that provide structure and function to a cell are polymers of the smaller subunit molecules (called monomers) Carbohydrates are made up of sugar monomers and serve as energy storage and structural support for cells Lipids are composed of fatty acids, usually linked to glycerol. They serve as energy storage, and can also assemble into membranes Proteins are made up of amino acids and perform most cellular functions Nucleic acids are built from nucleotide monomers. They are the units of information storage, and also short-term energy storage Cells are able to build order (reduce entropy) but must expend energy to do so Table 2-2 Molecular Biology of the Cell (© Garland Science 2008) Figure 2-29 Molecular Biology of the Cell (© Garland Science 2008) Figure 2-17 Molecular Biology of the Cell (© Garland Science 2008) Monomers are linked together to form polymers via ondensation reactions – pecifically, dehydration reactions (because a water molecule is formed in the process) Glycosidic bond Peptide bond Phosphodiester bond Figure 2-19 Molecular Biology of the Cell (© Garland Science 2008)  Carbohydrates: energy source, structural support, binding surface hemical features: linear chain ring, several OH groups hemical nature: highly polar Figure 2-18 Molecular Biology of the Cell (© Garland Science 2008) Describing sugar linkages: The carbons in the ring are numbered clockwise from the oxygen in the ring. 6 5 β1 1 4 The positions of the OH 3 2 groups attached to each carbon in the ring are described as being either: UP (above the plane of the ring) = β DOWN (below the plane of the ring) =  Figure 2-20 Molecular Biology of the Cell (© Garland Science 2008) Describing sugar linkages: Condensation reaction between a β1 OH on sugar A and an 4 OH on Sugar B. 6 6 5 5 A 1 B 1 4 4 2 2 3 3 Linkages are made from left to right, so this would be a glycosidic β 14 linkage. Figure 2-20 Molecular Biology of the Cell (© Garland Science 2008) A given sugar molecule has multiple OH groups located at various positions throughout the structure. So…. inked sugars are capable of forming a vast array f branched polysaccharide structures There are 11 different ways just to form D- glucose disaccharides! Figure 2-20 Molecular Biology of the Cell (© Garland Science 2008)  Starch and cellulose are both polymers made up of glucose subunits. Why are we ? able to digest starch but not cellulose? A) Because starch is an energy storage molecule, but cellulose is a structural molecule ? B) We have enzymes that digest the a linkages of starch, but not the b linkages of cellulose C) Trick question – we can actually digest both! ? ?  Lipids: Hydrophobic membrane barriers, energy source Triglyceride (energy storage in animal Chemical features: hydrocarbon chains with polar COOH at one end Chemical nature: amphipathic Figure 2-21 Molecular Biology of the Cell (© Garland Science 2008)  Phospholipids: Phosphatidyl choline example Figure 2-22 Molecular Biology of the Cell (© Garland Science 2008) Tay-Sachs Disease: A Case of Lipid Storage Another class of lipids are called gangliosides - similar to phospholipids, but the phosphate/polar head group is replaced by a carbohydrate. The GM2 ganglioside is found in small amounts in the plasma membrane and is involved in cell-cell communication and neuronal plasticity (learning, etc.) Tay-Sachs Disease: A Case of Lipid Storage A mutation in the enzyme b-hexosaminidase A prevents cells from properly metabolizing GM2, causing it to accumulate to abnormally high levels in brain neurons. The result is a genetic disorder, Tay-Sachs disease Symptoms generally begin around the age of 6 months. Neurodegeneration in the CNS leads to blindness, deafness, paralysis, cognitive defects, and eventually death by the age of 4 years old. No current therapy or cure, but gene therapy is being studied to correct the mutation. Otherwise, the only option is genetic screening of parents (especially Jews of Easter European descent, French Canadians, and Cajun population in Louisiana)  Amino acids: Building blocks of proteins, can be metabolized for energy Chemical features: uniform chemical structure with directionality (Amino terminus --- Carboxyl terminus) and side (R) group variability hemical nature: varies by R group. Figure 2-23 Molecular Biology of the Cell (© Garland Science 2008)  Amino acid side chains have different chemical properties Figure 2-25 Molecular Biology of the Cell (© Garland Science 2008)  5 of the naturally occurring amino acid side chains that readily ionize at neutral pH Acidic amino acids: Aspartic acid / Aspartate Glutamic acid / Glutamate Basic amino acids: Histidine Lysine Arginine pK = pH at which ½ of all molecules of an ionizable substance are charged. Figure 2-25 Molecular Biology of the Cell (© Garland Science 2008)  Nucleotides: Building blocks of nucleic acids, short term energy carriers Chemical features: uniform chemical structure with some side group variability (nitrogenous base component) Chemical nature: polar, charged Figure 2-26 Molecular Biology of the Cell (© Garland Science 2008)  Adenosine triphosphate (ATP) – major short term energy carrier in the cell Figure 2-26 Molecular Biology of the Cell (© Garland Science 2008)  One property of living things above all that makes them seem almost miraculously different from living matter: they create and maintain order in a universe that is tending always to greater disorder. (Molecular Biology of the Cell, p.65) Examples of biological order on various scales Figure 2-33 Molecular Biology of the Cell (© Garland Science 2008)  Cells and Thermodynamics In order to discuss how cells acquire and utilize energy, we must consider those laws that govern the use of energy: thermodynamics.  Cells and Thermodynamics All components of the universe are subject to the same laws, so cells must follow the laws of thermodynamics. The 1st Law of Thermodynamics: The amount of energy in a system is constant. Within that system, energy can be converted from one form to another, but cannot be created or destroyed Cells and Thermodynamics As these conversions are never 100% efficient – some energy is always lost as heat, which is NOT confinable or useable energy  Everyday examples of Energy Conversions Figure 2-39 Molecular Biology of the Cell (© Garland Science 2008)  Cells and Thermodynamics The 2nd Law of Thermodynamics: All processes in the universe are driven in the direction that increases disorder (entropy). This is to say that USEABLE energy or AVAILABLE energy tends to decrease. Remember, energy is only useable if it is confinable (stored).  Cells and Thermodynamics From a chemical perspective, this means that: Reactions that decrease the availability of useable energy ARE energetically favorable and will occur spontaneously Reactions that increase the availability of useable energy) are not energetically favorable and will NOT occur spontaneously  What do we actually mean by a “spontaneous” reaction? ? A) A reaction that will occur without a net addition of energy ? B) A reaction that occurs immediately when the reactants are mixed together C) Both ? ?  Cells and Thermodynamics Yet cells must increase biological order in order to survive. Do cells, then, violate this 2nd law? Figure 2-37 Molecular Biology of the Cell (© Garland Science 2008)  Cells and Thermodynamics Cells are not isolated systems; they are able to exchange energy with their environment. Figure 2-38 Molecular Biology of the Cell (© Garland Science 2008) Energy input to the cell is used to generate order within the cell, and this energy from outside the cell was generated by processes that increase entropy (chemical fusion in the sun, for example) In addition, in the course of order-generating reactions, the cell converts part of the energy into heat. This heat is released into the cell’s environment, thereby disordering it and thus also increasing entropy overall.  The Big Picture - Review Cells are made from a distinctive and restricted set of small carbon-based molecules that are fundamentally the same for all living species. The major molecules that provide structure and function to a cell are polymers of the smaller subunit molecules (called monomers) Carbohydrates are made up of sugar monomers and serve as energy storage and structural support for cells Lipids are composed of fatty acids, usually linked to glycerol. They serve as energy storage, and can also assemble into membranes Proteins are made up of amino acids and perform most cellular functions Nucleic acids are built from nucleotide monomers. They are the units of information storage, and also short-term energy storage Cells are able to build order (reduce entropy) but must expend energy to do so