Recap: A little chemistry helps to understand a lot of biology Covalent Bonds Polar and Non-Polar Electronegativity is key! Non-covalent bonds: Intra and inter molecular interactions Hydrogen Bonds Ionic Bonds Van der Waals Attraction Hydrophobic Effect intramolecular intermolecular Acid base chemistry going on inside the cell Most small molecules and larger biomolecules have functional groups that can act as weak acids and bases 1
Recap: A little chemistry helps to understand a lot of biology Biology is the interplay between covalent and non-covalent chemistry Molecule Cell 2
What is the importance of Molecular Shape and Function? Ex. Morphine has similar shape to endorphins therefore it activates endorphin receptors similarly! 3
Carbon Chemistry Why is carbon key to molecular shape and function? C has 4e- in its outer shell, can form 4 different bonds - tetravalence 4
Carbon Chemistry Why is carbon key to molecular shape and function? Carbon skeletons can vary in length, branching, double bonds and rings leads to diversity! 5
Carbon Chemistry Why is carbon key to molecular shape and function? Isomers Same number of atoms but different structures Structural isomers Geometric isomers 3 variations - pentane (C 5 H 12 ) 18 possibilities of C 8 H 18 366,319 possibilities of C 20 H 42 cis and trans isomers 6
Carbon Chemistry Why is carbon key to molecular shape and function? Isomers Same number of atoms but different structures Geometric isomers cis and trans isomers 11 cis - retinal is found photoreceptor cells to transduce light signals from the eye to the brain 7
Emergent properties of chemistry and biology 03-31-16: Lecture 2 Photoreceptor rod cell 8
Carbon Chemistry Why is carbon key to molecular shape and function? Isomers Same number of atoms but different structures Structural isomers Geometric isomers 3 variations - pentane (C 5 H 12 ) 18 possibilities of C 8 H 18 366,319 possibilities of C 20 H 42 cis and trans isomers Enantiomers (mirror images) 9
Carbon Chemistry Why is carbon key to molecular shape and function? Isomers Same number of atoms but different structures Enantiomers (mirror images) 10
Macromolecules: Polymers in biology Most macromolecules are polymers (built from monomers) Four major types of macromolecules Carbohydrates (polysaccharides) monomer Proteins *Lipids (fats, phospholipids) Nucleic Acids (DNA, RNA) 11
Macromolecules: Polymers in biology Synthesis Most macromolecules are polymers (built from monomers) Breakdown 12
*Lipids Fatty Acids Carboxylic acid with a long unbranched aliphatic tail (hydrocarbon chain), which is either saturated or unsaturated 03-31-16: Lecture 2 Not a polymer but they are large molecules that are assembled by dehydration rxn. Examples: Stearic acid CH 3 (CH 2 ) 16 CO 2 H O C OH Oleic acid CH 3 (CH 2 ) 7 CH=CH(CH 2 ) 7 CO 2 H C C 13 13
Common Fatty acids 03-31-16: Lecture 2 Formula Common Name Melting Point CH 3 (CH 2 ) 10 CO 2 H lauric acid 45 ºC CH 3 (CH 2 ) 12 CO 2 H myristic acid 55 ºC CH 3 (CH 2 ) 14 CO 2 H palmitic acid 63 ºC CH 3 (CH 2 ) 16 CO 2 H stearic acid 69 ºC CH 3 (CH 2 ) 18 CO 2 H arachidic acid 76 ºC Formula Common Name Melting Point CH 3 (CH 2 ) 5 CH=CH(CH 2 ) 7 CO 2 H palmitoleic acid 0 ºC CH 3 (CH 2 ) 7 CH=CH(CH 2 ) 7 CO 2 H oleic acid 13 ºC CH 3 (CH 2 ) 4 CH=CHCH 2 CH=CH(CH 2 ) 7 CO 2 H linoleic acid -5 ºC CH 3 CH 2 CH=CHCH 2 CH=CHCH 2 CH=CH(CH 2 ) 7 CO 2 H linolenic acid -11 ºC CH 3 (CH 2 ) 4 (CH=CHCH 2 ) 4 (CH 2 ) 2 CO 2 H arachidonic acid -49 ºC 14
Remember Phospholipids: They solve the Containment Problem! 2 Fatty acid tails Glycerol Phosphate Head group Phospholipid can differ in: Head groups serine, ethanolamine, choline Fatty acids length unsaturation (double bonds) Cholesterol amount fluidity of membrane Non-polar proteins 15
Polysaccharides (carbohydrates)- sugars and polymers of sugars Formula (CH2O)n Glucose = C 6 H 12 O 6 Ribose = C 5 H 10 O 5 6C = hexose 5C = pentose (ribose) 3C = triose (simplest polysaccharide) 03-31-16: Lecture 2 2 major functions: 1. Store energy animals: glycogen Plants: starch 2. Structural support Plants: cellulose (wood) Insects: exoskeleton (chitin) 1 2 3 4 5 6 1 2 3 4 5 6 16
Polysaccharides (carbohydrates)- sugars and polymers of sugars 03-31-16: Lecture 2 When placed in water ring form is much more favored 17
Polysaccharides (carbohydrates)- forming polymers Glycosidic bond Polymers of this Below ring alpha glycosidic bond Above ring beta glycosidic bond 18
Polysaccharides (carbohydrates)- important for solving the information problem Sugars in Nucleic Acids: DNA: RNA: deoxyribose missing 2 OH group ribose RNA DNA 19
Proteins (polypeptides) Polymer of amino acids generic amino acid structure R NH 2 C COOH H 20 different R groups (side chains) In the cell; ph 7 ionize! 20
Proteins (polypeptides) Polymer of amino acids Work horse macromolecule inside the cell! >50% of cellular mass responsible for most all work done in the cell Enzymes, which speed up chemical reactions Structural support Storage Transport Communication Movement Defense Assemble and destroy other macromolecules (proteins, DNA, RNA) 21
Proteins (polypeptides) Forming a polypeptide bond (protein) Create a peptide bond 22
Proteins (polypeptides) Types of Amino acids - 20 different depends on R group (side chain) Nonpolar
Proteins (polypeptides) Types of Amino acids - 20 different depends on R group (side chain) Polar 24
Proteins (polypeptides) Types of Amino acids - 20 different depends on R group (side chain) Electrically Charged 25
Proteins (polypeptides) Unique Glycine Types of Amino acids - 20 different depends on R group (side chain) Smallest a.a. Tiny space filler Introduces a kink/turn in a.a. chain Increases flexibility Proline Fixed structure Increased rigidity Introduces a kink in a.a. chain Cysteine Disulfide bridge - covalent Increase rigidity Stabilize protein structure 26