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Carbon & the Molecular Diversity of Life - Chapter 3 (Powerpoint Notes)

A. Carbon atoms can form diverse molecules by bonding to 4 other atoms (1)

  • Carbon forms bonds with four other atoms, enabling branching in four directions and the creation of large, complex molecules.
  • Key ideas:
    • Carbon has 6 electrons: 2 in the first energy level and 4 in the valence shell.
    • Carbon tends to share its 4 electrons to complete its valence shell with 8 electrons.
    • This tetravalence allows carbon to form diverse, multi-directional skeletons.
  • Formation of bonds with carbon (summary):
    • i. Carbon has 6 electrons, with 2 in the first energy level and 4 in the valence shell.
    • ii. Carbon wants to share its 4 electrons so that its valence shell is full with 8 electrons.
    • iii. Each carbon can branch in 4 directions, enabling large, complex molecules.

A. Carbon atoms can form diverse molecules by bonding to 4 other atoms (2)

  • When carbon forms bonds, it creates diverse molecular geometries and varieties of organic compounds.
  • Examples of simple carbon compounds:
    • (a) Methane, $CH_4$, tetrahedral geometry when a carbon atom has four single bonds to other atoms.
    • (b) Ethane, $C2H6$, composed of two tetrahedral groups of single-bonded atoms.
    • (c) Ethene (ethylene), $C2H4$, where two carbons are joined by a double bond; all attached atoms lie in the same plane (the molecule is planar).
    • Note: A triple bond is also possible (e.g., acetylene, $C2H2$). Double and triple bonds affect planarity and reactivity.

B. The Chemical Groups Most Important to Life (1)

  • The distinctive properties of organic molecules depend on:
    • The arrangement of the carbon skeleton.
    • The chemical groups attached to the skeleton.
  • Some chemical groups influence molecular shape (e.g., sex hormones).
  • Other chemical groups participate directly in chemical reactions; these are called functional groups.

B. The Chemical Groups Most Important to Life (2)

  • Functional groups and their general classes (examples):
    • Carbonyl functional class:
    • Aldehydes and ketones
    • Hydroxyl group: $-OH$; example: ethanol, $CH3CH2OH$.
    • Aldehyde: $R-CHO$; example: acetaldehyde.
    • Ketone: $R-CO-R'$; example: acetone.
    • Carboxyl group: $-COOH$ (carboxylic acids); example: acetic acid.
    • Amino group: $-NH_2$ (amines); example: methylamine.
    • Phosphate group: $-OPO_3^{2-}$ (organic phosphates).
    • Sulfhydryl group: $-SH$ (thiols); example: mercaptoethanol.
    • Methyl group: $-CH_3$; example: 5-methylcytosine.

C. ATP: An Important Source of Energy for Cellular Processes (1)

  • ATP stands as a key energy-currency molecule with a phosphate group.
  • Structure: adenosine attached to 3 phosphate groups.
  • Energy release: One phosphate can be released via hydrolysis, releasing energy usable by the cell.
  • General idea: $ATP
    ightarrow ADP + P_i + ext{energy}$ (via hydrolysis).

D. Macromolecules are polymers, built from monomers (1)

  • Macromolecules in 3 of 4 major classes of organic compounds – carbohydrates, proteins, and nucleic acids – are polymers.
  • A polymer is a long molecule consisting of many similar or identical building blocks linked by covalent bonds.
  • Each building block is a monomer.

D. Macromolecules are polymers, built from monomers (2)

  • Synthesis and breakdown of polymers follow a common pattern across classes:
    • Enzymes facilitate both processes.
    • Monomers are connected when two molecules form a covalent bond, with the loss of a water molecule (dehydration reaction).
  • Dehydration reaction:
    • ext{Monomer} + ext{Monomer}
      ightarrow ext{Polymer} + H_2O

D. Macromolecules are polymers, built from monomers (3)

  • Polymers are disassembled to monomers by hydrolysis:
    • Add water to break the bond: ext{Polymer} + H_2O
      ightarrow ext{Monomer} + ext{Monomer}

E. Carbohydrates serve as fuel & building blocks (1)

  • Carbohydrates include sugars and polymers of sugars.
  • Monosaccharides typically have formulas that are some multiple of CH2O; glucose is the most common monosaccharide: C6H{12}O_6.
  • Sugars contain a carbonyl group ($C=O$) and multiple hydroxyl groups ($OH$).

E. Carbohydrates serve as fuel & building blocks (2)

  • The carbonyl group is either an aldehyde or a ketone.
  • Carbon skeletons range from 3 to 7 carbons long.
  • Most names for sugars end in -ose.
  • In aqueous solution, most 5- and 6-carbon sugars form rings.

E. Carbohydrates serve as fuel & building blocks (3)

  • Monosaccharides are major nutrients for cells.
  • In cellular respiration, glucose is broken down to create ATP.
  • Sugar carbon skeletons are also used to make other organic molecules (e.g., amino acids).
  • A disaccharide consists of two monosaccharides joined by a glycosidic linkage.

E. Carbohydrates serve as fuel & building blocks (4)

  • Polysaccharides are polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages.
  • They function as storage material or building material.
  • Structure and function are determined by the types of sugar monomers and the positions of glycosidic linkages.

E. Carbohydrates serve as fuel & building blocks (5)

  • Storage polysaccharides in plants: starch; stored as granules inside cells.
  • Glucose in starch can be mobilized by hydrolysis when energy is needed.

E. Carbohydrates serve as fuel & building blocks (6)

  • Most glucose monomers in starch are joined by 1–4 linkages (carbon 1 to carbon 4).
  • Amylose: unbranched form of starch.
  • Amylopectin: branched form with 1–6 linkages at branch points.

E. Carbohydrates serve as fuel & building blocks (7)

  • Animals store excess glucose as glycogen; similar to amylopectin but more branched; stored mainly in liver and muscle cells.

E. Carbohydrates serve as fuel & building blocks (8)

  • Structural polysaccharides: cellulose found in plant cell walls; most abundant compound on Earth.
  • Like starch and glycogen, cellulose is made of glucose monomers, but linked by 1–4 glycosidic linkages with β glucose instead of α glucose.

E. Carbohydrates serve as fuel & building blocks (9)

  • The different glycosidic linkages lead to different 3-D shapes.
  • Starch and glycogen are helical; cellulose molecules are straight and can form hydrogen bonds with adjacent parallel cellulose molecules to form tough microfibrils.

E. Carbohydrates serve as fuel & building blocks (10)

  • Very few organisms can digest cellulose directly.
  • Ruminants (e.g., cows) and termites rely on symbiotic organisms in their guts to digest cellulose.
  • Chitin is another polysaccharide used by arthropods for exoskeletons and is a major component in fungal cell walls.

F. Lipids are a diverse group of hydrophobic molecules (1)

  • Lipids do not form true polymers and are not considered macromolecules due to their small size.
  • Lipids are hydrophobic and do not mix well with water; many contain hydrocarbons.
  • The major lipid classes are fats, phospholipids, and steroids.

F. Lipids are a diverse group of hydrophobic molecules (2)

  • Fats are composed of glycerol and fatty acids.
  • Glycerol is an alcohol with a hydroxyl group on each of its three carbons.
  • A fatty acid is a hydrocarbon chain (commonly 16 or 18 carbons) with a carboxyl group at one end.

F. Lipids are a diverse group of hydrophobic molecules (3)

  • Three fatty acids bond to glycerol via dehydration reactions to form a triacylglycerol (triglyceride).
  • The covalent bond formed is an ester linkage between a hydroxyl group and a carboxyl group.

F. Lipids are a diverse group of hydrophobic molecules (4)

  • The three fatty acids need not be identical; they can vary in carbon number or level of hydrogen saturation.
  • Saturated fatty acids have no double bonds and are fully hydrogenated.
  • Unsaturated fatty acids contain at least one double bond and have fewer hydrogens, creating kinks in the tail.

F. Lipids are a diverse group of hydrophobic molecules (5)

  • Fats with saturated fatty acids pack closely and are solid at room temperature (e.g., animal fats like lard and butter).
  • Fats from plants and fish are unsaturated and are liquids at room temperature (oils).
  • Saturated fats are more energy-dense and advantageous to mobile animals.
  • Why fish use unsaturated fats? (Discussion prompt in lecture; relates to fluidity at lower temperatures.)

F. Lipids are a diverse group of hydrophobic molecules (6)

  • Phospholipids: major component of cell membranes.
  • They are similar to fats but have only two fatty acids and a phosphate-containing head group, which is hydrophilic.
  • Additional molecules can be attached to the phosphate, producing a variety of phospholipids.

F. Lipids are a diverse group of hydrophobic molecules (7)

  • Phospholipid structure: hydrophobic tails (fatty acid chains) and a hydrophilic phosphate-containing head.
  • In water, phospholipids self-assemble into a bilayer with tails facing inward and heads facing outward.

F. Lipids are a diverse group of hydrophobic molecules (8)

  • Steroids: lipids with a