Organic Molecules - VOCABULARY Flashcards (BIOL 1020 Chapter 4)

I. Importance of organic molecules for life

• Organic compounds have at least one carbon atom covalently bound to another carbon atom or to hydrogen.
• Life is largely organized around carbon; organic molecules are built around a carbon backbone (CARBON).
• CHNOPS: six most important elements for biological molecules = Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), Phosphorus (P), Sulfur (S).
• The chemistry of carbon:
  • Carbon has 6 protons and 6 electrons; it has 4 valence electrons, giving it the ability to form up to 4 covalent bonds.
  • Carbon does not readily form ionic bonds under typical biological conditions; it almost always shares electrons in covalent bonds.
  • Therefore, carbon can form diverse, stable, four-way bonds, enabling large diversity of molecules.
• Bonding behavior of carbon (typical examples):
  • Methane: $ext{CH}_4$
  • Ethane: $ext{C}<em>2 ext{H}</em>6$
  • In most cases, carbon (often the central atom) forms 4 covalent bonds.
• There are MANY organic compounds (>5 million identified to date); diversity arises because carbon bonds to:
  • Other Carbons, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur → CHNOPS are the six most important elements for biology.
  • This explains how carbon scaffolds link with other elements to form carbohydrates, lipids, proteins, nucleic acids, etc.
• Hydrocarbons:
  • Contain only hydrogen and carbon: “hydro-” + “-carbon”.
  • Single C–C bonds allow rotation around them, lending flexibility to biological molecules.
  • Example shown: butane, $ext{C}<em>4 ext{H}</em>{10}$ (the same molecule shown in different orientations).
• Rotation about C–C bonds:
  • Free rotation about single bonds allows conformational isomers and flexibility in three-dimensional shape.
• Building organic macromolecules:
  • Carbon acts as a molecular backbone for long chains and networks.
  • Stronger C–C bonds can be formed with double or triple bonds, enabling multiple bond types.
  • Carbon chains can branch, creating a variety of structures with different properties.
• Shapes of organic molecules:
  • With single bonds (C–C, C–H, etc.), bond angles around carbon are approximately $109.5^\circ$, giving a tetrahedral geometry.
  • When a carbon forms a double bond (C=C), the geometry is planar around the double bond with bond angles of $120^\circ$; rotation about C=C is restricted.
  • Examples:
  • Methane (single bonds): $ext{CH}_4$ with bond angles $109.5^\circ$.
  • Ethene (double bond): $ext{C}<em>2 ext{H}</em>4$ with bond angles $120^\circ$.
  • Observation: compounds with single bonds (ane) vs double bonds (ene) often have different suffixes, reflecting bond types.
• What dictates the shape of a molecule?
  • Bonding behavior of carbon (ability to form up to four covalent bonds).
  • Angles formed by bonding (tetrahedral vs planar for double bonds).
  • Rotation about bonds (single bonds allow rotation; double bonds restrict rotation).

II. Isomers

• Isomers are molecules with the same molecular formula but different structures.
• Two main types:
  • 1) Structural (constitutional) isomers – same formula, different covalent arrangements of atoms. Example: two C4H10 isomers (n-butane and isobutane) have the same formula but different connectivity.
  • 2) Stereoisomers – same covalent bonds, but different spatial arrangement of atoms.
• Stereoisomers have subtypes:
  • 1) Cis/trans isomers – associated with C=C bonds; no rotation about double bonds, so substituents can be on the same side (cis) or opposite sides (trans).
  • Cis = same side, Trans = different sides.
  • 2) Enantiomers – non-superimposable mirror images; typically organisms use only one form of an enantiomer pair.
  • Designations include: + vs. - (e.g., D vs. L is used in sugars and amino acids).
  • R vs. S notation can be used to describe absolute configuration.
• Biological relevance example:
  • Thalidomide (1950s–60s) demonstrated that small chemical differences can have huge biological consequences: marketed as antiemetic/ sedative, but caused birth defects (teratogenic).
  • This underscores the importance of stereochemistry in biology and pharmacology.

III. Functional groups

• Functional groups determine the most reactive properties and thus the function of organic molecules.
• Definition:
  • Groups of atoms covalently bonded to a carbon backbone that confer properties different from a simple C–H bond.
  • R represents the remainder of the molecule.
• Learn these seven functional groups (major classes discussed in lab and coursework):
  • 1. Hydroxyl group (-OH)
  • Polar; found in alcohols.
  • Note: in visuals the hydroxyl group is highlighted in red; some figures may show other group labels as well.
  • 2. Carbonyl group (-C=O)
  • Polar; found in aldehydes and ketones.
  • Note: some figures color the carbonyl group; some diagrams instruct to ignore the –OH when highlighting this group.
  • 3. Carboxyl group (-COOH)
  • Weakly acidic; found in amino acids; common structural motif in amino acids and fatty acids.
  • 4. Amino group (-NH2)
  • Weakly basic; found in amino acids; central to peptide bonds and protein chemistry.
  • 5. Sulfhydryl group (-SH)
  • Nonpolar; found in amino acids such as cysteine.
  • 6. Phosphate group (-PO4H2)
  • Weakly acidic; found in phospholipids and nucleic acids (DNA/RNA).
  • 7. Methyl group (-CH3)
  • Nonpolar; hydrophobic; found in lipids and membrane components.
• Visual notes and learning tips:
  • The recommended study approach is to make a Quizlet, practice drawing, and identify functional groups in random molecules.
  • Khan Academy resources are suggested as helpful supplementary tools.
• Practice signals from the slides:
  • Several example molecules appear for identification in Pages 32–37; one molecule is an amino acid starting with the letter “L”; another clue mentions Lipitor and Crestor as cholesterol-lowering meds; a third clue hints that a molecule in your nucleus is likely DNA or RNA; another example is Ethanol shown in Ep. 2.
• Quick references to common molecules and structures:
  • Ethanol shown in Ep. 2: $ext{CH}<em>3 ext{CH}</em>2 ext{OH}$.
  • Nucleic acids contain phosphate groups in their backbone and bases that pair via hydrogen bonds; shown in the slide with base-pair schematic (A–T, C–G) and the 3′/5′ notation near the phosphate group.

IV. Carbon & Global Warming

• Carbon-focused videos presented as a series titled "Carbon & Global Warming" (Ep. 1 through Ep. 4):
  • Ep. 1: 3:20
  • Ep. 2: Ethanol! (structure shown as a model) with sample structure $ext{CH}<em>3 ext{CH}</em>2 ext{OH}$.
  • Ep. 3: 4:15
  • Ep. 4: 3:50
• Episode links:
  • Ep. 1: https://www.youtube.com/watch?v=ypbb9Zi5Tao
  • Ep. 2: https://www.youtube.com/watch?v=cOJ3MUpDrfI
  • Ep. 3: https://www.youtube.com/watch?v=Q9u8vM8YjeU
  • Ep. 4: https://www.youtube.com/watch?v=EvphJO8VKlc&t=14s
• Purpose:
  • Reinforce that carbon chemistry is central to understanding global warming and environmental science.

V. Chapter goals/objectives (revisited)

• How does carbon typically bond? To what?
• What sort of shapes, angles, freedoms, etc. are associated with the bonds that carbon makes?
• Draw a tetrahedron.
• What are isomers? Differences between structural isomers and stereoisomers?
• Cis/trans isomers? Enantiomers? Examples of each?
• What are functional groups? Be able to know the names of functional groups and the general chemistry of each.
• Additional emphasis from the text:
  • Rotation about C–C single bonds allows conformational freedom; double bonds restrict rotation and enforce planarity.
  • The suffixes of organic compounds (e.g., -ane vs -ene) reflect bond types.
  • The biological relevance of stereochemistry is highlighted through historical cases like Thalidomide.

Quick reference highlights

• Bonding and geometry:
  • Carbon can form up to 4 covalent bonds: $4$ bonds.
  • Bond angles: $109.5^\circ$ for tetrahedral; $120^\circ$ in alkenes around C=C.
  • Planarity and restricted rotation around double bonds.
• Core formulas to remember:
  • Methane: $ext{CH}_4$
  • Ethane: $ext{C}<em>2 ext{H}</em>6$
  • Butane: $ext{C}<em>4 ext{H}</em>{10}$
  • Ethene: $ext{C}<em>2 ext{H}</em>4$
  • Ethanol: $ext{CH}<em>3 ext{CH}</em>2 ext{OH}$
• Functional groups to know:
  • -OH, -C=O, -COOH, -NH2, -SH, -PO4H2, -CH3
• Real-world relevance:
  • CHNOPS elements form the backbone of biological macromolecules.
  • Isomerism, especially enantiomerism and cis/trans, can drastically alter biological activity (e.g., drugs, amino acids).
  • Environmental carbon chemistry links to climate science and policy.