BIOMOLECULES

• Biochemistry


  • The study of chemical interactions of living organisms
  • The study of the chemical reactions that take place inside organisms. It combines elements from both biology and chemistry
• Biochemists have established several principles central to our understanding of living organisms
• Principles established by biochemists

  • Life is complex and dynamic
  • Life is organized and self-sustaining
  • Life is cellular
  • Life is information-based
  • Life adapts and evolves
• Life is complex and dynamic—All organisms are primarily composed of organic (carbon-based) molecules that have intricate, 3d shapes. Living processes involve thousands of chemical reactions
• Life is organized and self-sustaining—Living organisms are hierarchically organized systems. Biomolecules become linked to form macromolecules like nucleic acids, proteins, and polysaccharides
• Life is cellular—cells differ widely in structure and function, but each is surrounded by a membrane that controls the transport of chemical substances
• Life is information-based—Living organisms can be considered information-processing systems. Biological information is expressed in the form of coded messages inherent in the unique three-dimensional structure of biomolecules
• Life adapts and evolves—All life on earth has a common origin, with new forms arising from other forms. Over many generations, environmental change and genetic variation can lead to the accumulation of favorable traits and different forms of life
• Life adapts and evolves

  Individual organism reproduces itself, stress-induced DNA modifications and errors can result in mutations or sequence changes. Over many generations, environmental change and genetic variation can lead to accumulation of favorable traits and different forms of life
• Levels of organization in a multicellular organism

  • Organ systems
  • Organs
  • Tissues
  • Cells
  • Organelles
  • Molecules
  • Atoms
• The liver is a multifunctional organ that has several digestive functions, such as producing bile and processing food molecules absorbed in the small intestine
• Genetic information stored in genes specifies the linear sequence of amino acids in proteins and how and when those proteins are synthesized
• Almost all the molecules in living organisms are organic, derived from hydrocarbons, which are nonpolar and not water-soluble
• 50-95% of a cell’s content by weight consists of water, while ions such as Na+, K+, Mg2+, and Ca2+ may account for another 1%
• Almost all other kinds of molecules in living organisms are organic
• Hydrocarbons


  Nonpolar and not water-soluble, hence hydrophobic
• The basic structural units of all living organisms are cells, where thousands of chemical reactions take place
• All organisms use the same molecules, and the instructions for growth, development, and reproduction are encoded in nucleic acid
• Living things are composed of

  • Prokaryotic cells
  • Eukaryotic cells
• Prokaryotic cells


  Lack a nucleus
• Eukaryotic cells


  Contain a complex membrane-bound structure called a nucleus that holds genetic information in the form of chromosomes, primarily DNA
• Organic compounds are characterized by the presence of carbon atoms
• Major classes of biomolecules

  • Amino acids
  • Sugars
  • Fatty acids
  • Nucleotides
• Polarization


  Occurs when an electric field distorts the negative cloud of electrons around positive atomic nuclei, resulting in a separation of charge
• All life processes consist of chemical reactions catalyzed by enzymes, collectively known as metabolism
• Metabolism is the sum of all reactions in a living organism
• Primary functions of metabolism

  • Acquisition and utilization of energy
  • Synthesis of molecules needed for cell structure and functioning
  • Removal of waste products
• While the number of reactions is large, the number of reaction types is relatively small in metabolism
• The mechanism used in biochemical reactions is relatively simple
• Reactions of central importance in biochemistry are relatively few in number
• Common reaction types in biochemical processes

  • Nucleophilic substitution
  • Elimination
  • Addition
  • Isomerization
  • Oxidation-reduction
• Nucleophilic substitution reactions


  One atom or group is substituted for another
• In nucleophilic substitution reactions, the attacking species is called a nucleophile, which can be anions or neutral species with non-bonding electron pairs
• Electrophiles are easily attacked by nucleophiles and are deficient in electron density
• The reaction of glucose with ATP is an example of nucleophilic substitution, where the hydroxyl oxygen on carbon 6 of the sugar acts as the nucleophile and phosphorus as the electrophile
• Reaction between glucose and phosphorus

  Glucose is the nucleophile attacking the polarized phosphorus atom, resulting in the expulsion of ADP
• Hydrolysis reactions


  A kind of nucleophilic reaction where oxygen of water serves as the nucleophile, usually targeting the carbonyl group of ester, amide, or anhydride
• Hydrolysis reactions


  • Ester + H2O (hydrolyze) = carboxylic acid + alcohol
• The digestion of many food molecules involves hydrolysis
• The hydrolysis of ATP is used to drive an astonishing diversity of energy-requiring biochemical reactions