AP Biology-UNIT I: CHEMISTRY OF LIFE Study Notes

G. Organic Molecules
➢ Organic compound contains Carbon
➢ Inorganic compound does not contain carbon
➢ Carbon often surrounded by hydrogen
➢ Carbon is a versatile atom

• Can bind with many elements
• Many “slots” to bind with elements
            ■ 4 valence electrons
                       ● Can form 4 covalent bonds
           ■ Makes large, complex molecules possible
• In molecules with multiple carbons, each carbon bonded to 4 other atoms has a tetrahedral shape
           ■ When 2 carbons are formed by a double bond, the atoms joined to the carbons are one the same plane as the carbons
• Electron configuration gives it covalent compatibility with other elements
•  Hydrocarbons consist of only carbon and hydrogen
          ■ Can undergo reactions that release a large amount of energy
          ■ isomers are compounds with the same molecular formula but different
  structures/properties
  ● Usually only one isomer is biologically active
• Functional groups are the components of organic molecules that are most commonly involved in chemical reactions
      ■ Number and arrangement of functional groups give each molecule its unique properties

➢ Most macromolecules are chains of building blocks called polymers. The individual building  blocks of a polymer are called monomers
➢ Carbohydrates

•  Contain carbon, hydrogen, and oxygen in a 1:2:1 ratio
•  Monosaccharides
            ■ Most common are glucose and fructose
   ● Glucose
  • • • Most abundant
      • Part of food humans eat
      •  Made by plants during photosynthesis
                   ■ Broken down to release energy
        ● Fructose
        • • • Common sugar in fruits

                              ● Can be depicted as either straight or rings

                       ■ 6 carbon-sugars
                                  ● Formula: $\mathrm{C}_6\mathrm{H}_{12}\mathrm{O}_6$

• Disaccharides
  ■ 1 monosaccharide+1 monosaccharide=1 Disaccharide
  ■ Formed by dehydration synthesis
  ● Aka condensation
  ● Hydrogen (-H) from one sugar combines with hydroxyl group (-OH) of another sugar molecule to create water as byproduct

● Bond is called glycosidic linkage
                    ■ Broken apart by hydrolysis
● Reverse of dehydration
● Water is used to break apart glycosidic linkage
○ Polysaccharides
                ■ Repeated units of monosaccharides
                ■ Most common
● Starch

• Stores sugar in plants
•  Made up of alpha-glucose molecules
  ● Cellulose
•  Made up of $\beta$-glucose molecules
•  Chitin

                    ■ Structural molecule in walls of fungi/arthropod  exoskeletons
                    ■ Used as surgical thread since it breaks down in body
● Glycogen

•  Stores sugar in animals

➢ Proteins

•  Amino acids=monomer of proteins
              ■ 20 kinds of naturally occurring amino acids
•  Contain:
            ■ Carbon
            ■ Hydrogen
           ■ Oxygen
           ■ Nitrogen
•  4 parts of an amino acid centered around a central carbon
         ■ Amino group $(-NH_2)$
         ■ Carboxyl group (-COOH)
        ■ Hydrogen
        ■ R group
  ● Aka side chain
  ● Interchangeable
  ● Vary in composition, polarity, charge, shape depending on specific side chain
  ● Polar R groups point outward, hydrophobic R groups point inward
•  Polypeptides
        ■ Amino acid + amino acid= dipeptide
  ● Formed by dehydration synthesis
  ● Bond is called a peptide bond
  ● Multiple amino acids= polypeptide
• Once a polypeptide chain twists and folds on itself, it forms a $\text3D$ structure called a protein

•  Higher protein structure (4 levels total)
     ■ Primary structure

              ● Linear sequence of amino acids
               ● Covalent (peptide) bonds
■ Secondary structure
               ● Protein beings to twist–2 options

•  Forms a coil (alpha-helix)
•  Zigzagging pattern (known as beta-pleated sheets)
  ● Shape depends on R-group
  ● Formed by amino acids that interact with other amino acids closeby in the primary structure
  ● Hydrogen bonds between carbonyl and amino group
  ● Interactions between amino and carboxyl groups of protein backbone
  ● After secondary structure forms, formerly distant amino acids are now closeby–tertiary structure can form
  ■ Tertiary structure
  ● Can be both alpha and beta helix/sheets within structure
  ● Covalent disulfide bridge often stabilizes structure
  ● Bonds between R groups
• Hydrogen bonds
•  Ionic bonds
•  Disulfide bridges
• Hydrophobic interactions
  ■ Quaternary structure
  ● Several different polypeptide chains sometimes interact with each other
  ● Same bonds as above, but between peptide chains rather than between R
  groups
  ■ Mistakes in structure can denature a protein
  ● Change of shape=change of function
•  Ex. pH or heat can denature protein
  ■ Protein folding can involve chaperone proteins (chaperonins)
  ● Help protein fold properly
  ● Make process more efficient

➢ Lipids

•  Like carbs, consist of carbon, hydrogen and oxygen, but not in a fixed ratio
•  Do not form polymers
•  Little-no affinity for water
         ■ Hydrophobic due to nonpolar covalent bonds of hydrocarbon
•  Common examples:
       ■ Triglycerides
  ● Glycerol molecule+3 fatty acid chains attached
•  Fatty acid chain is mostly a long chain of carbons where each carbon is covered in hydrogen; One end of the chain has a carboxyl group $(-COOH)$
     ■ Vary in length and /location(s) of double bonds
•  Glycerol is a 3-carbon alcohol with a hydroxyl group attached to each carbon
  ● Fats separate from water because water forms hydrogen bonds with itself while excluding the fats
  ● In order to be made, each of the carboxyl groups of the 3 fatty acids must react with one of the 3 hydroxyl groups of the glycerol molecule via dehydration synthesis
• bond=ester linkage
  ● Saturated fatty acid
• No double bond
•  Carbon chain completely filled (“saturated”) with hydrogen
•  Usually solid at room temp.
  ● Unsaturated fatty acid
•  Double bond along carbon chain, causing a bend
    ■ Bend allows triglyceride to become LESS dense, making it liquid at room temperature
•  Polyunsaturated fatty acid has multiple double bonds within the fatty acid, causing many bends

■ Phospholipids

➢ Nucleic Acids

•  Contain carbon, hydrogen, oxygen, nitrogen, and phosphorous
•  Structure
         ■ Nitrogenous base
         ■ Pentose sugar
         ■ Phosphate group
         ■ Portion of nucleotide w/o phosphate group is called nucleoside
• Store, transmit, and help expres hereditary information
•  monomer=nucleotides
• Amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene
        ■ Made up of DNA
• Deoxyribonucleic acid (DNA)
             ● sugar=deoxyribose
             ● Contains genetic/hereditary information
             ● Provides directions for its own replication
             ● Directs synthesis of messenger RNA (mRNA), and through mRNA, controls protein synthesis
• Occurs on ribosomes
•  Ribonucleic acid (RNA)
            ● sugar=ribose
            ● Essential for protein synthesis
•  2 families of nitrogenous bases
       ■ Pyrimidines
           ● Single 6-membered ring
          ● Ex.
•  Cytosine
• Thymine (only DNA
• Uracil (only RNA)
  ■ Purines
          ● 6-membered ring fused to a 5-membered ring
           ● Ex.
• Adenine
•  Guanine
•  Nucleotide Polymers
  ■ Nucleotide polymers linked together to build a polynucleotide
  ■ Adjacent nucleotides are joined by covalent bonds that form between the$ -OH$ group on the 3’ carbon of one nucleotide and the phosphate on the 5’ carbon on the next
       ● Links create a backbone of sugar-phosphate units with nitrogenous bases as appendages
  ■ RNA molecules usually exist as single polypeptide chains
  ■ DNA molecules have 2 polynucleotides spiraling around an imaginary axis, forming a double helix
        ● Two backbones run in opposite 5’→3’ directions from each other (antiparallel)
        ● One DNA molecule contains many genes
        ● Nitrogenous bases pair up and form hydrogen bonds
•  Adenine-Thymine
• Guanine-Cytosine
• Complementary base pairing
•  In RNA, thymine is replaced by uracil, so A and U pair