2.1 Chemical Bonds and Simple Reactions
Key Takeaways
Carbon, hydrogen, oxygen, and nitrogen (CHON) make up most living mass, and each carbon atom forms four covalent bonds.
Ionic bonds transfer electrons, as in sodium chloride; nonpolar covalent bonds share electrons equally, and polar covalent bonds share them unequally, as in an oxygen-hydrogen bond.
A hydrogen bond is a weaker attraction between a hydrogen already held in a polar bond and nitrogen, oxygen, or fluorine; it does not transfer electrons, and it is not the covalent peptide bond that joins amino acids.
Hydroxyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl groups have predictable behavior; dehydration synthesis joins monomers and releases water, while hydrolysis splits polymers by adding water.
pH is the negative logarithm of hydrogen-ion concentration, so each unit is a tenfold change: pH 3 has 1,000 times the hydrogen-ion concentration of pH 6, and buffers such as carbonic acid and bicarbonate resist pH change.
2.1 Chemical Bonds and Simple Reactions
Most living mass comes from four elements: carbon, hydrogen, oxygen, and nitrogen, remembered as CHON. Water holds much of the hydrogen and oxygen, and both elements also sit inside sugars, fats, proteins, and nucleic acids. Carbon forms molecular skeletons. Nitrogen is concentrated in amino groups and in the bases of DNA and RNA. Phosphorus, sulfur, and ions such as sodium, potassium, calcium, and chloride are essential, yet they are a smaller share of body mass. An item that asks which elements dominate living matter is asking for CHON.
Carbon's four bonds and electronegativity
Carbon has four valence electrons and forms four covalent bonds, single, double, or triple, to carbon, hydrogen, oxygen, nitrogen, phosphorus, or sulfur. Carbon can bond to other carbons and still have valence left, so chains, branches, and rings form. Methane, , shows the limit in a small molecule: four bonds on carbon, and a fifth bond is impossible.
Electronegativity is an atom's pull on electrons in a bond. Oxygen and nitrogen pull harder than carbon or hydrogen. Similar pulls give nearly equal sharing. A much stronger pull shifts the shared electrons toward one atom and creates partial charges. Use that comparison to judge whether a covalent bond is polar. A complete handover of electrons is a different event: ionic bonding.
Five interactions to keep distinct
| Interaction | What the electrons do | Strength in cells | Example |
|---|---|---|---|
| Ionic bond | Transferred; opposite ions attract | Strong as a crystal; often loosened in water | Sodium chloride, |
| Nonpolar covalent bond | Shared about equally | Strong; builds skeletons | Carbon-carbon and carbon-hydrogen |
| Polar covalent bond | Shared unequally | Strong inside one molecule | Oxygen-hydrogen in water |
| Hydrogen bond | No transfer; partial charges attract | Weaker than covalent | Between water molecules |
| Van der Waals forces | Brief uneven electron clouds | Weakest and short-lived | Packed nonpolar chains |
An ionic bond transfers electrons. Sodium loses one electron and becomes . Chlorine gains it and becomes . Opposite charges attract, which is why solid sodium chloride is an ionic lattice. In water, many ionic compounds separate into free ions. Sharing is the covalent pattern. Transfer is the ionic pattern.
A covalent bond is a shared electron pair. A nonpolar covalent bond shares that pair about equally, so neither end keeps a lasting partial charge. Carbon-carbon and carbon-hydrogen bonds are the usual nonpolar bonds in organic molecules. A polar covalent bond shares unequally. In water, oxygen pulls the electrons of each oxygen-hydrogen bond closer, so oxygen is partially negative, hydrogen is partially positive, and the molecule as a whole remains neutral. Partial charges are smaller than the full charges of ions.
A hydrogen bond does not share electrons and does not transfer them. It forms when a hydrogen already held in a polar bond, usually to nitrogen, oxygen, or fluorine, is attracted to nitrogen, oxygen, or fluorine on another molecule. In water, hydrogen is covalently bonded to oxygen inside its own molecule and attracted to oxygen on a neighbor. Hydrogen bonds are weaker than covalent bonds and break and re-form often. They help DNA base pairing and protein folding. They do not join amino acids into a chain. Those links are peptide bonds, covalent bonds made by dehydration synthesis. A hydrogen bond may pull parts of a finished protein toward each other. It does not build the backbone.
Van der Waals forces are brief attractions caused by temporary uneven electron clouds in nearby atoms. One contact is weak. Many close contacts can help nonpolar chains pack, but these forces are not hydrogen bonds and not covalent backbone bonds.
Functional groups
A functional group is a small cluster of atoms with behavior you can predict on different carbon skeletons.
| Group | What to picture | Property |
|---|---|---|
| Hydroxyl | OH attached to carbon | Polar; helps dissolving in water |
| Carbonyl | Carbon double-bonded to oxygen | Polar; aldehydes and ketones, including sugars |
| Carboxyl | COOH | Can release ; acidic |
| Amino | NH2 | Can accept ; basic |
| Phosphate | Phosphorus bonded to oxygens | Negative charge; energy transfer in ATP |
| Sulfhydryl | SH | Two groups can form a disulfide bridge |
A hydroxyl group is attached to carbon, unlike a free hydroxide ion. A carboxyl group can donate and an amino group can accept , so amino acids act as acids and as bases. A carbonyl is the carbon-oxygen double bond in sugars. A phosphate group carries negative charge in ATP. A disulfide bridge between sulfhydryl groups is covalent.
Dehydration synthesis and hydrolysis
Dehydration synthesis joins monomers and releases . One monomer gives hydrogen, the other a hydroxyl, and a covalent bond remains: a glycosidic linkage for sugars, a peptide bond for amino acids, or an ester linkage for a fatty acid on glycerol. Hydrolysis adds water and splits that bond. Digestion is hydrolysis. Water as a product means dehydration synthesis. Water as a reactant means hydrolysis.
Reading pH
pH is the negative logarithm of hydrogen-ion concentration. moles per liter is pH 3, is pH 6, and is pH 7. Each unit is a tenfold change in hydrogen-ion concentration, and a lower pH means more hydrogen ions. Acids are below 7, bases are above 7, and 7 is neutral at 25 C. Stomach fluid is strongly acidic. Blood is held near 7.4.
pH 3 compared with pH 6
A gap from 6 to 3 looks like a factor of 3 on a linear ruler. pH is logarithmic. The hydrogen-ion concentration is 0.001 moles per liter at pH 3 and 0.000001 moles per liter at pH 6. Dividing 0.001 by 0.000001 gives 1,000, because each of the three steps multiplies concentration by 10. The pH 3 solution has a thousandfold higher hydrogen-ion concentration.
Buffers resist that kind of change. A weak acid paired with its related base can donate or accept hydrogen ions. Carbonic acid donates a hydrogen ion and bicarbonate accepts one, so the pair shrinks a pH shift until its capacity is used up.
Warning
Peptide bonds hold amino acids in a chain. They are covalent bonds formed by dehydration synthesis. A hydrogen bond is weaker, transfers no electrons, and only attracts a hydrogen already held in a polar bond toward nitrogen, oxygen, or fluorine.
Which statement correctly describes the bond that joins amino acids in a polypeptide chain?
Hydrogen bonds transfer electrons from one amino acid to the next and are stronger than the covalent bonds in the backbone.
Covalent peptide bonds join the amino acids; hydrogen bonds are weaker attractions and do not build that chain.
Van der Waals forces are the permanent links that polymerize amino acids, and each link requires a hydrogen already bonded to fluorine.
Ionic bonds between free sodium and chloride ions are the covalent links that string amino acids into a chain.
At 25 C, how does the hydrogen-ion concentration of a pH 3 solution compare with that of a pH 6 solution?
The pH 3 solution has 1,000 times the hydrogen-ion concentration of the pH 6 solution.
The pH 6 solution has 1,000 times the hydrogen-ion concentration of the pH 3 solution.
The pH 3 solution has 3 times the hydrogen-ion concentration of the pH 6 solution.
Both solutions have the same hydrogen-ion concentration because both pH values are below 7.
Which description of bonding and a functional group is accurate?
Dehydration synthesis breaks a polymer by adding water, and a carboxyl group cannot donate a hydrogen ion.
Sodium chloride is held together by nonpolar covalent bonds in which sodium and chlorine share electrons equally.
A hydrogen bond transfers electrons between water molecules and is stronger than the covalent bonds inside each molecule.
An oxygen-hydrogen bond is polar covalent because the electrons are shared unequally, and a hydroxyl group is an OH cluster covalently attached to carbon.
Sections you finish are checked off in the contents.