Learning Outline

Biological Chemistry

BIO 095

Basic structural concepts

Macromolecule: giant molecules (many atoms, not just a few)

Polymer: macromolecule made up of many smaller molecules called "monomers"

Polymers are assembled by dehydration synthesis

Polymers are disassembled by hydrolysis

Carbohydrates

Saccharides (C₆H₁₂O₆)—sugar groups that make up many carbohydrates

• Monosaccharides—just one saccharide group
  
  
  • Examples: glucose, fructose, galactose
    
    
  • Also called "simple sugars" or "single sugars"
    
    
• Disaccharides—have two saccharide groups
  
  
  • Examples: sucrose, maltose, lactose
    
    
  • Also called "double sugars"
  • 
    
• Polysaccharides—have many saccharide groups
  
  
  • Example: glycogen
    
    

Examples of function: fuel, fuel storage

Lipids

Triglycerides: three fatty acid "tails" and one glycerol holding them together

• Nonpolar; hydrophobic
  
  
• Fuel
  
  

Phospholipids: two fatty acid "tails" with a "head" containing glycerol and phosphate

• Tails are nonpolar; head is polar
  
  
• Form bilayers in water
  
  
• Form cellular membranes
  
  

Cholesterol

• Source of steroid lipids
  
  
  • For example, the body converts cholesterol into steroid hormones
    
    
• Stabilizes phospholipid bilayers
  
  
  • Strengthens cellular membranes that are made up primarily of phospholipids
    
    

Proteins

Protein structure

Proteins are folded/twisted chains of amino acids

• Proteins have 50 or more amino acids; polypeptides 10-50, peptides less than 10
  
  
  • These different categories are used very loosely in real life
    
    
• Levels of protein structure (increasing degrees of structural complexity)
  
  
  • Primary - sequence of amino acids (determined by shape)
    
    
  • Secondary - folded (pleated sheets), twisted (helices) version of primary structure
    
    
  • Tertiary - folded and/or twisted version of secondary structure
    
    
  • Quaternary (optional) - combination of two or more tertiary proteins
    
    
• Chaperone molecules assist proteins in folding properly
  
  
  • The proper (functioning) shape of a protein is called its "native state"
    
    
• Denaturation is loss of proper 3D shape (native state)
  
  
  • May be caused by extreme temp, extreme pH, chemical reactions, other extreme conditions
    
    
  • Renatured proteins are those that have regained their native state after having been previously denatured
    
    
  • Chaperone molecules may assist in refolding denatured proteins
    
    
• Misfolded proteins must be destroyed (and recycled) or they may cause damage
  
  
  • May form deadly plaque (gunk)
    
    
• Categories of protein shape
  
  
  • Fibrous proteins
    
    
  • Globular proteins (globulus "small globe or sphere")
    
    
    • Nearly any shape that isn't "fibrous"
      
      
    • Also sometimes called globins
      
      
• Structure of molecule determines function (it's all about shape)
  
  
• Protein folding has become a vital part of our understanding of how proteins function in the body
  
  

Types of proteins

Structural proteins

• Form structures, e.g. collagen, keratin
  
  

Functional proteins

• Act as "chemists" or "regulators", e.g. hormones, neurotransmitters, enzymes
  
  
• Enzyme action
  
  
  • Lower "activation energy" of chemical reactions to body temp--that is, make chemistry happen that otherwise wouldn't happen
    
    
  • Lock-and-key model
    
    
    • Enzyme fits substrate as a key fits into a lock
      
      
  • Active site
    
    
  • Allosteric site (allosteric "shape changing" effect)
    
    
  • Cofactors help enzymes
    
    
    • Organic cofactors are coenzymes, e.g. vitamins
      
      
  • Enzymes are specific (only work with one type of substrate)
    

Nucleic acids

• Examples:
  
  
  • deoxyribonucleic acid (DNA)
    
    
  • ribonucleic acid (RNA)
    
    
• Encode genetic information
  
  
  • Structure/function of DNA discovered in 1953 by
    
    
    • James Watson
      
      
    • Francis Crick
      
      
    • Maurice Wilkins
      
      
    • Rosalind Franklin
      
      
• Nucleotide is the subunit, made of three components
  
  
  • Sugar (ribose in RNA; deoxyribose in DNA)
    
    
  • Phosphate
    
    
  • Nitrogen base
    
    
    • Different types of nitrogen base
      
      
      • cytosine, guanine, adenine, thymine (DNA only), uracil (RNA only)
        
        
      • First letters are used as abbreviations: C, G, A, T, U
        
        
    • Bases may link C-G or G-C and T-A or A-T (in RNA, U-A or A-U)
      
      
      • This rule is complementary or obligatory "base-pairing"
        
        
• RNA nucleotides link to form strands that sometimes fold
  
  
  • Some RNA types do form double strands
    
    
• DNA nucleotides form a double strand that twists (double helix)
  
  
• Information is encoded in the sequence of nitrogen bases
  
  
  • Every three bases is one codon or "word" in "genetish"
    
    
    • Each codon represents one amino acid in a sequence to form a protein
      
      
    • Genetish is what science author Matt Ridley calls the language of the genetic code
      
      
• ATP (adenosine triphosphate) is a modified nucleotide
  
  
  • Breaking of last phosphate bond can release energy for cell work
    
    
  • [Very] temporary energy-storage "battery" of cell
    
    
  • Other modified nucleotides similarly transfer energy
    
    
    • NAD, FAD, CP
      
      
    • The role of each of these molecules will be discussed later in the course

 

Combined forms

• Molecule made up of more than one type of macromolecule
  
  
  • Sometimes called "hybrid" molecules
    
    
• Examples:
  
  
  • Glycoprotein
    
    
  • Proteoglycan
    
    
  • Glycolipid
    
    
  • Ribonucleoprotein
    
    
  • Lipoprotein