Biomolecules Energetics in biology Biomolecules inside the cell
Energetics in biology The production of energy, its storage, and its use are central to the economy of the cell. Energy may be defined as the ability to do work, a concept applicable to automobile engines and electric power plants in our physical world and to cellular engines in the biological world. The energy associated with chemical bonds can be harnessed to support chemical work and the physical movements of cells. Several Forms of Energy Are Important in Biological Systems Kinetic energy is the energy of movement, the motion of molecules, for example. Potential energy, or stored energy, is particularly important in the study of biological or chemical systems. Thermal Radiant Mechanical Electric Chemical potential energy Concentration gradient Electric potential
Thermodynamic principles Open and closed systems We will review the first and second laws of thermodynamics focusing on their relationship to energy flow in living organisms.
The first law of thermodynamics states that the total energy of a system plus its environment remains constant. Cells Can Transform One Type of Energy into Another: In photosynthesis, the radiant energy of light is transformed into the chemical potential energy of the covalent bonds between the atoms in a sucrose or starch molecule. In muscles and nerves, chemical potential energy stored in covalent bonds is transformed, respectively, into the kinetic energy of muscle contraction and the electric energy of nerve transmission. In all cells, potential energy, released by breaking certain chemical bonds, is used to generate potential energy in the form of concentration and electric potential gradients. Similarly, energy stored in chemical concentration gradients or electric potential gradients is used to synthesize chemical bonds or to transport molecules from one side of a membrane to another to generate a concentration gradient. This latter process occurs during the transport of nutrients such as glucose into certain cells and transport of many waste products out of cells. The standard unit of energy for biochemists is calorie (1 joule 0.239 calories).
The second law of thermodynamics states that a system and its surroundings always proceed to a state of maximum disorder or maximum entropy, a state in which all available energy has been expended and no work can be performed. Many biological reactions lead to an increase in order, and thus a decrease in entropy (S < 0). An obvious example is the reaction that links amino acids together to form a protein. A solution of protein molecules has a lower entropy than does a solution of the same amino acids unlinked, because the free movement of any amino acid in a protein is restricted when it is bound into a long chain. reactants products All systems change in such a way that free energy [G] is minimized. In the conversion of complex foods such as glucose [C6(H2O)6] to simpler products such as CO2 and H2O, energy conversions, allowed by the first law of thermodynamics, take place.
The free energy of a chemical system can be defined as G= H -TS, where H is the bond energy, or enthalpy, of the system; T is its temperature in degrees Kelvin (K); and S is the entropy, a measure of its randomness or disorder. If temperature remains constant, a reaction proceeds spontaneously only if the free-energy change G in the following equation is negative:
An Unfavorable Chemical Reaction Can Proceed If It Is Coupled with an Energetically Favorable Reaction Many processes in cells are energetically unfavorable (G > 0) and will not proceed spontaneously. Examples include the synthesis of DNA from nucleotides and transport of a substance across the plasma membrane from a lower to a higher concentration. Cells can carry out an energyrequiring reaction (G1 > 0) by coupling it to an energy-releasing reaction (G2 < 0) if the sum of the two reactions has a net negative G. Energetically unfavorable reactions in cells often are coupled to the hydrolysis of ATP, as we discuss next.
Hydrolysis of ATP Releases Substantial Free Energy and Drives Many Cellular Processes In almost all organisms, adenosine triphosphate, or ATP, is the most important molecule for capturing, transiently storing, and subsequently transferring energy to perform work (e.g., biosynthesis, mechanical motion). The useful energy in an ATP molecule is contained in phosphoanhydride bonds, which are covalent bonds formed from the condensation of two molecules of phosphate by the loss of water: An ATP molecule has two key phosphoanhydride bonds. Hydrolysis of a phosphoanhydride bond (~) in each of the following reactions has a highly negative Gº of about 7.3 kcal/mol: (ATP Is Generated During Photosynthesis and Respiration)
Biomolecules inside the cell Cells contain four major families of small organic molecules: Sugars, Fatty acids, Amino acids, and Nucleotide
Bond type
Sugars: Sugars provide an energy source for cells and are the subunits of polysaccharides. H H HO C C C O OH H The molecules made from sugars, are also called carbohydrates. I (CH 2 O) n or H - C - OH I H C OH H C OH CH 2 OH D-glucose C 6 H 12 O 6 Monosaccharides - simple sugars with multiple OH groups. Based on number of carbons (3, 4, 5, 6), a monosaccharide is a triose, tetrose, pentose or hexose. Disaccharides - 2 monosaccharides covalently linked. Oligosaccharides - a few monosaccharides covalently linked. Polysaccharides - polymers consisting of chains of monosaccharide or disaccharide units.
Fatty acids: Fatty acids, the simplest lipids, consist of a hydrocarbon chain with a carboxylic acid at one end. an 16-C fatty acid: CH 3 (CH 2 ) 14 -COO - Non-polar polar Fatty acids are components of cell membranes as well as a source of energy and are stored in the form of triacylglycerols.
Bipolarity Cell membrane
Amino acids: Amino acids are the subunits of proteins Every amino acid has a similar basic structure NH 3 CHRCOOH Except for glycine (R = H), all amino acids have at least one asymmetric carbon atom and exists as two stereoisomers (D or L) Only L form exists in proteins
20 common amino acids
Peptide band
Protein structures Organization levels determining protein structure Level of structure Basis of Structure Bonds involved Primary Amino acid sequence Covalent bonds Secondary Tertiary Quaternary Folding into a helix, b sheet or random coil 3D folding of a single polypeptide Association of 2 or more folded subunits Hydrogen bonds Hydrogen and disulfide bonds, electrostatic and hydrophobic interactions Same as tertiary
Protein structure Primary structure Carbon Nitrogen Secondary structure Tertiary structure Quaternary structure
Protein function
Functions of membrane proteins: Outside Plasma membrane Inside Transporter Enzyme activity Cell surface receptor Cell surface identity marker Cell adhesion Attachment to the cytoskeleton
Nucleotids: Nucleotids are the subunits of DNA and RNA A nucleotide is made of 3 components: A Pentose sugar A Phosphate group A Nitogenous base In DNA the four bases are: Thymine (T) Adenine (A) Cytosine (C) Guanine (G) In RNA the four bases are: Uracil (U) Adenine (A) Cytosine (C) Guanine (G) Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)
Chemical structures of the principal bases in nucleic acids: Five different nucleotides are used to build nucleic acids
DNA STRUCTURE hydrogen bonded nucleotides on opposite helices DNA helices are antiparallel carbons on sugar define ends... 5' and 3' pyrimidines bond with purines T A C G
RNA structure mrna Ribonucleic acid (RNA). RNA is a single strand of nucleotides that relays instructions from genes to ribosomes, guiding the chemical reactions in the synthesis of amino acids into protein. trna rrna
Adenosine tri phosphate (ATP)
Energy transfer
Summary
Macromolecules