Organic Chemistry and the Carbon Atom

The Carbon Atom

• Organic molecules contain carbon
• Organic molecules are abundant in living organisms
• Macromolecules are large, complex organic molecules

Organic Chemistry

• Organic chemistry is the science of carbon-containing molecules
• Vitalism was a 19th-century concept that organic molecules were created by and imparted with a vital life force within a plant or animal’s body

Carbon

• Carbon has 4 electrons in its outer shell, needing 4 more to fill it
• Carbon can make up to four bonds, usually single or double bonds
• Carbon can form nonpolar or polar bonds
  • Molecules with polar bonds are water soluble
  • Molecules with nonpolar bonds (like hydrocarbons) are not very water soluble

Functional Groups

• Groups of atoms with special chemical features that are functionally important
• Each type of functional group exhibits the same properties in all molecules in which it occurs

Isomers

• Two molecules with an identical molecular formula but different structures and characteristics
• Structural isomers contain the same atoms but in different bonding relationships
• Stereoisomers have identical bonding relationships, but the spatial positioning of the atoms differs in the two isomers
  • Cis-trans isomers have a different positioning around a double bond
  • Enantiomers are mirror image molecules
    • Difference in orientation leads to different binding abilities
    • Enzymes that recognize one enantiomer usually do not recognize the other

Synthesis and Breakdown of Organic Molecules and Macromolecules

• Macromolecules are composed of thousands or millions of atoms
• Polymers are formed by linking monomers
• A condensation reaction produces a larger organic molecule plus a water molecule

Polymer Formation by Dehydration (Condensation) Reactions

• A water molecule is removed each time a new monomer is added
• The process repeats to form long polymers
• A polymer can consist of thousands of monomers
• Dehydration is catalyzed by enzymes

Breakdown of a Polymer by Hydrolysis Reactions

• A water molecule is added back each time a monomer is released
• The process repeats to break down long polymers
• Hydrolysis is catalyzed by enzymes

Four Major Classes of Organic Molecules Found in Living Cells

• Carbohydrates
• Lipids
• Proteins
• Nucleic acids

Carbohydrates

• Composed of carbon, hydrogen, and oxygen atoms
• Most of the carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl group
• The general formula is Cn(H2O)n

Monosaccharides

• Simplest sugars
• Most common are 5 or 6 carbons
  • Pentoses: Ribose (C5H10O5) and Deoxyribose (C5H10O4)
  • Hexose: Glucose (C6H12O6)

Glucose Isomers

• Stereoisomers of glucose are α- and β-glucose, where the hydroxyl group of carbon 1 is above or below the ring
• D- and L-glucose are enantiomers with mirror image structures
  • D-glucose is commonly found in living cells
  • L-glucose is rarely found in living cells
• Galactose is a glucose isomer where the hydroxyl group on carbon 4 of glucose is above the plane of the ring instead of below it

Disaccharides

• Composed of two monosaccharides
• Joined by a dehydration or condensation reaction, forming a glycosidic bond
• Examples: sucrose, maltose, lactose

Polysaccharides

• Many monosaccharides linked together to form long polymers
• Examples:
  • Energy storage: starch, glycogen
  • Structural: cellulose, chitin, glycosaminoglycans, peptidoglycan

Lipids

• Composed predominantly of hydrogen and carbon atoms, and some oxygen
• Defining feature of lipids is that they are nonpolar and very insoluble in water
• Include fats, phospholipids, steroids, waxes.
• Lipids comprise about 40% of the organic matter in the average human body

Fats

• Also known as triglycerides
• Formed by bonding glycerol to 3 fatty acids
• Joined by dehydration, forming an ester bond

Fatty Acids

• Saturated: All carbons have the maximal amount of hydrogens, tend to be solid at room temperature
• Unsaturated: Contain one or more double bonds, tend to be liquid at room temperature (known as oils)
  • Cis forms naturally
  • Trans forms artificially
  • Trans fats are linked to disease

Fats

• Fats are important for energy storage, 1 gram of fat stores more energy than 1 gram of glycogen or starch
• Fats can also be structural, providing cushioning and insulation

Phospholipids

• Formed from glycerol, two fatty acids, and a phosphate group
• Phospholipids are amphipathic molecules
  • Phosphate head is polar and hydrophilic
  • Fatty acid tail is nonpolar and hydrophobic

Steroids

• Four interconnected rings of carbon atoms
• Usually insoluble in water
• Example: Cholesterol
• Tiny differences in structure can lead to profoundly different, specific biological properties, such as estrogen versus testosterone

Waxes

• Many plants and animals produce lipids called waxes that are secreted onto their surface
• May contain hundreds of different compounds but all contain one or more hydrocarbons and long structures that resemble a fatty acid attached by its carboxyl group to another long hydrocarbon chain
• Very nonpolar, forming a barrier to water loss

Proteins

• Composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of other elements, notably sulfur
• The building blocks of proteins are amino acids, 20 different amino acids
• Each amino acid has a common structure with a variable sidechain that determines structure and function

Polypeptide Formation

• Amino acids are joined by a dehydration reaction, where the carboxy + amino forms a peptide bond
• Polymers of amino acids are known as polypeptides
• The free amino group of a polypeptide is the N-terminus
• The free carboxyl end is the C-terminus
• Proteins may be formed from one or several polypeptides

Proteins Have a Hierarchy of Structure

• Four progressive levels:
  • Primary
  • Secondary
  • Tertiary
  • Quaternary

Primary Structure

• The amino acid sequence of a protein
• It is determined by genes

Secondary Structure

• Chemical and physical interactions cause protein folding
• Forms α helices and β pleated sheets
  • These are key determinants of a protein’s characteristics

Tertiary Structure

• Folding gives a protein its complex 3D shape
• This is the final level of structure for a single polypeptide chain

Quaternary Structure

• Made up of two or more polypeptides
  • Individual polypeptide chains are protein subunits
• A protein can be formed from several copies of the same polypeptide

Five Factors That Promote Protein Folding and Stability

• Hydrogen bonds
• Ionic bonds and other polar interactions
• Hydrophobic effects
• Van der Waals forces - link the –SH groups in two cysteine side chains together

Protein-Protein Interactions

• Many cellular processes involve steps in which two or more different proteins interact
• Specific binding at the surface of proteins uses the following four factors:
  • Hydrogen bonds
  • Ionic bonds and other polar interactions
  • Hydrophobic effects
  • Van der Waals forces

Anfinsen Showed That the Primary Structure of Ribonuclease Determines Its Three-Dimensional Structure

• Prior to the 1960s, the mechanisms by which proteins assume their 3D structures were not understood.

This quiz covers key concepts related to organic chemistry, focusing on carbon atoms and their behavior in organic molecules. Explore the significance of functional groups, isomerism, and the structural properties of carbon. Ideal for students studying foundational concepts in organic chemistry.