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Covalent Bonding
Functional Groups & Reactivity

Explore how atoms share electrons to form covalent bonds, discover the functional groups that define molecular behavior, and understand how bond polarity drives chemical reactivity in biological systems.

Biochemistry

What Is a Covalent Bond?

A covalent bond forms when two atoms share one or more pairs of valence electrons. Unlike ionic bonds, where electrons transfer completely, covalent bonds involve mutual sharing so both atoms achieve a more stable electron configuration.

O O Shared Electrons
\(\text{O}=\text{O}\) Double Bond

Single, Double, and Triple Bonds

Single Bond
One shared electron pair. Written as \( \text{C-C} \). Longest and weakest of the three. Allows free rotation.
Double Bond
Two shared electron pairs. Written as \( \text{C=C} \). Shorter and stronger. Restricts rotation, creating rigid geometry.
Triple Bond
Three shared electron pairs. Written as \(\text{C}\equiv\text{C}\). Shortest and strongest. Found in \(\text{N}_2\) and alkynes.

Electronegativity and Bond Polarity

Electronegativity is an atom's ability to attract shared electrons. When two atoms with different electronegativities form a covalent bond, the electrons are pulled toward the more electronegative atom, creating a polar covalent bond.

Nonpolar Covalent H H
\(\Delta\text{EN} = 0\)
 Equal sharing Polar Covalent O H
\(\Delta\text{EN} = 1.24\)
 Unequal sharing
\(\delta^-\)
\(\delta^+\)

What Are Functional Groups?

A functional group is a specific cluster of atoms within a molecule that determines its chemical properties and reactivity. The carbon backbone of an organic molecule is relatively inert: it is the functional groups that make each molecule unique.

1
They determine reactivity: functional groups are the sites where chemical reactions occur.
2
They determine polarity: polar functional groups make molecules water-soluble (hydrophilic).
3
They determine biological function: amino groups, carboxyl groups, and phosphate groups define amino acids, fatty acids, and nucleotides.

The Major Functional Groups in Biology

Hydroxyl
\(\text{-OH}\)
 Polar, hydrophilic Carboxyl
\(\text{-COOH}\)
 Acidic, donates H+ Amino
\(-\text{NH}_2\)
 Basic, accepts H+ Carbonyl
\( \text{C=O} \)
 Aldehyde or ketone Phosphate
\(-\text{PO}_4\)
 Energy transfer (ATP) Sulfhydryl
\(\text{-SH}\)
 Disulfide bridges Methyl
\(-\text{CH}_3\)
 Nonpolar, gene regulation R Group Variable side chain Defines amino acid identity

Core Rule: Polarity Determines Solubility

Hydrophilic Region Glucose 5 x -OH Acetic acid -COOH Amino acid
\(-\text{NH}_2\)
 Hydrophobic Region Fatty acid tails Cholesterol Mostly -CH

Functional Groups and Acid-Base Behavior

In aqueous solution at physiological pH (~7.4), certain functional groups ionize. This determines a molecule's charge, its solubility, and how it interacts with other molecules.

\(\text{-COOH}\) (Carboxyl)
Donates \(\text{H}^+\) at pH 7.4, becoming \(-\text{COO}^-\). Acts as an acid. Gives the molecule a negative charge.
\(-\text{NH}_2\) (Amino)
Accepts \(\text{H}^+\) at pH 7.4, becoming \(-\text{NH}_3^+\). Acts as a base. Gives the molecule a positive charge.

Polar vs Nonpolar Covalent Bonds

Polar Covalent Nonpolar Covalent
Electronegativity Difference 0.4 - 1.7 < 0.4
Electron Sharing Unequal Equal
Dipole Moment Yes No
Solubility in Water Generally soluble Generally insoluble
Biological Examples \( \text{O-H} \), \( \text{N-H} \), \( \text{C=O} \) \( \text{C-H} \), \( \text{C-C} \)

How to Identify Functional Groups

1
Find the carbon backbone: Locate the chain or ring of carbon atoms that forms the molecule's skeleton.
2
Look for heteroatoms: Identify any atom that is not carbon or hydrogen: oxygen, nitrogen, sulfur, phosphorus.
3
Match the pattern: Compare the cluster of atoms around each heteroatom to the seven major functional groups (hydroxyl, carboxyl, amino, carbonyl, phosphate, sulfhydryl, methyl).
4
Predict properties: Each functional group tells you about polarity, charge at pH 7.4, and the types of reactions the molecule can undergo.

Example 1: Ethanol

C C O H H H H H H Hydroxyl (-OH)
\(\text{CH}_3\text{CH}_2\text{OH}\)

Example 2: Glycine (an Amino Acid)

\(\text{C}_\alpha\)
\(\text{NH}_3^+\)
 Amino
\(\text{COO}^-\)
 Carboxyl H H R group (Glycine: just H) + −

Example 3: ATP and Phosphate Groups

Adenine Nitrogenous base Ribose Sugar P
\(\alpha\)
 P
\(\beta\)
 P
\(\gamma\)
 High-energy High-energy Hydrolysis releases energy
\(\text{ATP} \rightarrow \text{ADP} + \text{P}_i\)

Dehydration Synthesis and Hydrolysis

The covalent bonds between monomers in biological macromolecules are formed and broken by two complementary reactions:

Dehydration Synthesis
Two monomers are joined by removing a water molecule (\(\text{H}_2\text{O}\)). One monomer loses an -OH, the other loses an -H, forming a new covalent bond.
Hydrolysis
A polymer is broken apart by adding a water molecule. Water splits across the covalent bond, restoring the -OH and -H to the separated monomers.

How Functional Groups Drive Reactivity

1
Hydroxyl (\( \text{-OH} \)): Participates in dehydration synthesis to form glycosidic bonds (sugars) and ester bonds (lipids).
2
Carboxyl (\( \text{-COOH} \)) + Amino (\(-\text{NH}_2\)): React via dehydration synthesis to form peptide bonds, linking amino acids into proteins.
3
Phosphate (\(-\text{PO}_4\)): Transfers between molecules in phosphorylation reactions, activating enzymes and storing energy in ATP.
4
Sulfhydryl (\( \text{-SH} \)): Two \( \text{-SH} \) groups can oxidize to form a disulfide bridge (\( \text{S-S} \)), stabilizing protein tertiary structure.

Common Mistakes to Avoid

✕ Confusing Ionic and Covalent
Covalent bonds share electrons; ionic bonds transfer them. In biology, most bonds within molecules are covalent.
✕ Ignoring Charge at pH 7.4
\( \text{-COOH} \) is drawn as neutral, but at physiological pH it is deprotonated (\(-\text{COO}^-\)). Similarly, \(-\text{NH}_2\) is protonated (\(-\text{NH}_3^+\)).
✕ Methyl = Hydrophilic
Methyl groups (\(-\text{CH}_3\)) are nonpolar and hydrophobic. They do not increase water solubility: they decrease it.

Summary: Functional Groups at a Glance

Group Formula Polarity Key Role
Hydroxyl \( \text{-OH} \) Polar Alcohols, sugars
Carboxyl \( \text{-COOH} \) Polar Acids, amino acids
Amino \(-\text{NH}_2\) Polar Bases, amino acids
Carbonyl \( \text{C=O} \) Polar Sugars, steroids
Phosphate \(-\text{PO}_4\) Polar ATP, DNA, signaling
Sulfhydryl \( \text{-SH} \) Polar Disulfide bridges
Methyl \(-\text{CH}_3\) Nonpolar Gene regulation

Question 1 of 5

Which functional group acts as an acid by donating \(\text{H}^+\) at physiological pH?

Question 2 of 5

A molecule with many hydroxyl groups (-OH) would most likely be:

Question 3 of 5

During dehydration synthesis, what happens to form a covalent bond between two monomers?

Question 4 of 5

Two sulfhydryl (-SH) groups on different parts of a protein can react to form a:

Question 5 of 5

Why are the bonds between phosphate groups in ATP described as "high-energy" bonds?