Chem 106: Exam 2 Notes (Ch. 14, 16, 18-20)

• The following are Chem 106 exam 2 study notes, covering chapters 14, 16, 18-20

Chapter 14: Aldehyde/Ketone Addition Reactions

• Aldehydes and ketones undergo addition reactions to form hemiacetals and acetals
• For hemi/acetal formation, the new group must come off the same carbon atom

Chapter 16: Carboxylic Acids and Esters

• Esters are named by first naming the group on the oxygen (without the C=O) with the suffix "-yl"
• The longest chain with the C=O is named second, ending in "-oate," separated as the O separates them
• Acids are named with the suffix "-oic acid"

Properties of Acids and Esters

• Functional groups, ranked by boiling point (lowest to highest): alkanes, alkenes, alkynes, ethers, esters, aldehydes, ketones, thiols, amines, alcohols, carboxylic acids, amides

Carboxylic Acids

• Carboxylic acids have higher boiling points compared to similar mass alcohols, ketones, and aldehydes
• Carboxylic acids exhibit high solubility due to dimer formation enabled by hydrogen bonds between polar carboxyl groups
• As the number of carbons increase, boiling points increase, but solubility decreases

Esters

• Esters contribute to fragrances and flavors of flowers and fruits
• Esters have boiling points higher than alkanes and ethers, but lower than alcohols and acids
• Smaller esters show greater water solubility

Preparing Acids & Reactions of Acids

• Acids are prepared via the oxidation of primary alcohols, yielding an aldehyde, then an acid
• Neutralization of acids result in an organic salt, represented by: Acid + base -> acid salt
• Acids ionize in water : Acid + water -> salt (H3O+ is one product)
• Esterification, an acid reacts with an alcohol to make an ester: Acid + alcohol -> ester + water

Reactions of Esters

• Acid hydrolysis of an ester yields the acid and alcohol that makes the ester

• Ester + water -> acid + alcohol

• Saponification reaction of ester

• Ester + base -> salt + alcohol

Chapter 18: Amines and Amides

Classes of Amines

• Amines are classified based on the number of carbon groups attached to the nitrogen (N) atom:
  • One carbon group attached to the N atom
  • Two carbon groups attached to the N atom
  • Three carbon groups attached to the N atom

Classes of Amides

• Amides are classified based on the carbonyl groups attached to the nitrogen (N) atom:
  • One carbonyl group attached to the N atom
  • One carbonyl group and one carbon groups attached to the N atom
  • One carbonyl group and two carbon groups attached to the N atom

Nomenclature of Amines and Amides

• Amines use the "-amine" ending
  • Prefixes indicate number of alkyl groups attached to N
  • 1- no N's in name
  • 2- 1 N's in name
  • 3-2 N's in name
• Amides use the "-amide" ending
• Numbering system is the same as naming amines
• The parent chain will always be the one with the (C=O)

Properties of Amines and Amides

Amines:

• Higher boiling points than esters, aldehydes, and ketones, but lower than alcohols, acids, and amides
  • Amines that can form 1 H bond have the highest boiling point
• Amines with 1-5 carbons are soluble in water -1 carbon will be the most soluble

Amides:

• H-bonding
  • Primary amides have exceptionally strong H-bonding due to the -CONH2 group
  • 1 and 2 can both form H bonds
  • 3 have no H bonds and a low MP
• Boiling Point
  • Amides have the highest boiling points out of all functional groups especially 1 and 2
• Solubility
  • Soluble in water if they have 1-5 carbons
  • 3 have low boiling point because they lack a NH group

Reactions of Amines

• Amines react as bases
• Amine + water -> salt
• Neutralization: Amine + acid -> salt

Heterocyclic Compounds

• Cyclic organic compounds with a 5 or 6 atom ring; contains 1 or more atom in the ring that is NOT carbon

Alkaloids

• Physiologically active, N-containing compounds produced by plants, used as stimulants, anesthetics, and antidepressants
• Examples: caffeine, nicotine, morphine, and codeine

Neurotransmitters

• Chemical messengers that transmit signals between neurons in the nervous system
  • Acetylcholine: learning and short-term memory, low levels in Alzheimer's
  • Dopamine: gives energy
  • Serotonin: gives a feeling of well-being
  • Histamine: immune response to pathogens & allergic reactions
  • Gamma-aminobutyric acid (GABA): regulates anxiety, muscle tone, sleep, and anxiety

Preparation and Hydrolysis of Amides

• Preparation of amide: Acid + 1 or 2 amine -> amide + H2O
• Hydrolysis of amide: Amide + water + HCl -> acid + salt

Chapter 19: Protein Functions & Preparation

• Proteins have functions such as structure, contractile, transport, storage, hormone, enzyme, and protection
• Proteins are made of amino acids linked by peptide bonds, formed by linking amino acids together into a long polypeptide chain

Nomenclature of Peptides

• Put "yl" at the end of all names before the last amino acid
• The end peptide is named regularly

Classes of Amino Acids

• Nonpolar (hydrophobic): with hydrocarbon side chains
• Polar (hydrophilic): with polar or ionic side chains
• Acidic (hydrophilic): with acidic side chains
• Basic (hydrophilic): with –NH2 side chains

Protein Structures

• Primary structure: sequence of amino acids in a polypeptide chain

  • Backbone of a peptide chain or protein

• Secondary structure: peptide bonds

  • Alpha helix: corkscrew shape with H bonds between amino acids
    • Coiled shape held in place by H bonds between amine groups and carbonyl groups
  • Beta pleated sheet: polypeptide chains held side by side by H bonds
    • Polypeptide chains arranged side by side
  • Triple Helix: Three peptide chains interwoven like a rope
    • Collagen, CT, skin, tendons, cartilage

• Tertiary structure: side chain interactions

  • Salt bridges
  • Proteins will stay a particular shape
  • Hydrophobic and hydrophilic interactions
  • Examples: globular and fibrous proteins

Ways to Denature a Protein

• Heat and organic compounds
  • Breaks apart H bonds
• Acids and bases
  • Breaks H bonds between polar R groups
• Heavy metal ions
  • React with S-S bonds to form solids
• Agitation
  • Such as whipping that stretches peptide chains

Chapter 20: Enzymes

• Enzymes are used as catalysts to reactions
• They increase the rate of reactions by lowering energy of activation

Classes and Types of Enzymes

• Enzymes usually end in -ase
• Identifies the reacting substance (Ex: sucrase catalyzes the reaction of sucrose)
• Classes of enzymes and their functions:
  • Oxidoreductases: Oxidation-reduction
  • Transferases: Transfer of groups of atoms
  • Hydrolases: Hydrolysis
  • Lyases: Add atoms/remove atoms
  • Isomerases: Rearrange atoms
  • Ligases: Use ATP to combine small molecules
    • Aminase: adds NH3
    • Dehydrogenase: Removes 2 H atoms to form a double bond
    • Synthetase: combines two molecules to make a new compound

How Enzymes Work

• Enzymes have an active site where the substrate sits: Enzyme + substrate -> enzyme-substrate complex (ES)
• After which it turns into the enzyme-product complex (EP), and the products come off, leaving an empty active site.
• Lactase and Lactose are an example of enzymes

Diagnostic Enzymes

• Enzymes like CK, LDH, and AST are diagnostic
• Used by observing how elevated they are after a heart attack to determine its severity

Enzyme Models

• Lock-and-key model
  • The enzyme structure is rigid, only binding to substrates that exactly fit
  • Substrate = key, Lock = enzyme
• Induced fit model
  • The enzyme structure is flexible, changing so that the substrate can bind; these shape changes improve catalyst during the reaction

Optimum Temperature and pH for Enzymes

• pH: 7.4
  • If the pH is anything other than optimal, the rate of reaction will decrease because secondary and tertiary structures are disrupted
• Temperature: 37° C
  • If the temperature is anything other than optimal, the rate of reaction will decrease because of denaturation

Increase Reaction Rate

• More enzymes increases the rate of reaction
• More substrates will increase the rate of reaction, but then plateau when it's reached maximum activity, and new enzyme needs to take place

Enzyme Inhibitors

• Competitive inhibitors: a similar structure to the substrate, competes for the active site
  • Effects can reverse by increasing substrate concentration
• Non-competitive inhibitors: different structure than the substrate, changes the shape and active site
  • Effects aren't reversed by increasing substrate concentration

Irreversible Inhibition

• Occurs when the inhibitor permanently binds to an enzyme via R groups at the active site, destroying enzyme activity (Ex: aspirin)

Zymogens

• Proenzymes, are inactive forms of enzymes
• Requires removal of peptide binds in order to activate enzyme
• Important components in digestive enzymes

Allosteric Enzymes

• These enzymes have a regulator that binds to them:
  • Positive Regulator=> enhances substate binding and reaction rates
  • Negative Regulator=> prevents substance from binding and prevents reaction

Enzyme Cofactors

• Small organic molecules(ex. a vitamin) needed for enzyme activity
• Simple enzymes, active enzymes that are only protein
• Requires Mg 2+ for hydrolysis of phosphate esters
• Simple enzyme example: active with four polypeptide subunits

Vitamins

• Fat-soluble vitamins: A, D, E, & K