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