Chapter 3 Notes: The Chemistry of Life (Unit 1)
Concept 3.1: Carbon atoms can form diverse molecules by bonding to four other atoms
Carbon is central to all life; all life built on carbon.
Carbon atoms are versatile building blocks because they form four covalent bonds (tetravalence).
This allows carbon to form: chains, branched molecules, and rings, yielding a huge diversity of molecules.
In cells, composition includes:
~72% H2O
~25% carbon compounds (carbohydrates, lipids, proteins, nucleic acids)
~3% salts (Na, Cl, K, etc.)
Arrangements of carbon bonds yield structural isomers (same atoms, different arrangement) and stereoisomers (different spatial arrangement).
Hydrocarbons: molecules consisting only of C and H
Hydrophobic
Relatively nonpolar; relatively nonreactive among molecules
Structure can vary (straight chains, branched chains, rings)
Functional groups: the parts of organic molecules involved in chemical reactions
Replace hydrogen on a carbon skeleton, conferring distinctive properties and reactivity
Increase molecular diversity and biological activity
Often influence solubility and polarity (hydrophilicity when groups like –OH or –COOH are present)
Example contrast: propane (nonpolar) vs propanol (–OH present, polar)
Have significant effects on biological behavior and reactivity
Viva la difference! Hormones example
Basic carbon skeleton can be identical between male and female hormones
Attachment of different functional groups changes targets and effects in the body
Functional Groups: quick reference
Hydroxyl group (−OH): Alcohol
Example: Ethanol; structure: \text{–OH attached to carbon chain}
Carbonyl group (C=O): Ketone, Aldehyde
Examples: Acetone (ketone), Propanal (aldehyde)
Carboxyl group (−COOH): Carboxylic acid (organic acid)
Example: Acetic acid
Amino group (−NH2): Amine (base form)
Example: Glycine (in zwitterion form at physiological pH)
Sulfhydryl group (−SH): Thiol
Example: Cysteine
Phosphate group (−OPO3^2−): Organic phosphate
Important in energy transfer (ATP) and nucleic acid chemistry
Methyl group (−CH3): Methylated compounds
ATP: An Important Source of Energy for Cellular Processes
Structure: adenosine with three phosphate groups linked by high-energy phosphoanhydride bonds
ATP hydrolysis releases energy:
Overall: \text{ATP} + \text{H}2\text{O} \rightarrow \text{ADP} + \text{P}i + \text{energy}
ADP and Pi can be re-synthesized into ATP via cellular processes
ATP serves as immediate energy currency for cellular activities
Think About It (concept reinforcement)
Think About It 1: Is this molecule soluble in water? A. yes B. no
Think About It 2: What does the term “amino acid” signify about the structure of such a molecule?
Concept 3.2: Macromolecules are polymers, built from monomers
Macromolecules are large molecules formed by linking small building blocks (monomers) into polymers.
Major types of macromolecules in biology: carbohydrates, lipids, proteins, nucleic acids
Key terms
Monomer: a single subunit building block
Dimer: two monomers covalently bonded
Polymer: many monomers covalently bonded
Dehydration synthesis (condensation)
Process by which monomers covalently bond to form polymers
Water is removed as a byproduct
Enzymes assist in catalyzing the reaction
General form: \text{Monomer}1 + \text{Monomer}2 \rightarrow \text{Dimer} + \text{H}_2\text{O}
Example: glucose + fructose → sucrose + H2O (sucrose formation)
Hydrolysis
Breakdown of polymers into monomers using water
Catabolic process; releases energy when polymers are broken down
Enzymes facilitate the reaction; water is consumed
General form: \text{Polymer} + \text{H}2\text{O} \rightarrow \text{Monomer}1 + \text{Monomer}_2 + \text{…}
Example illustrations
Dehydration synthesis of glucose + glucose → maltose (water released)
Hydrolysis of disaccharide (e.g., sucrose) → glucose + fructose (water added)
Think About It (concept reinforcement)
Label a diagram showing short polymer, monomer, longer polymer, dehydration synthesis, hydrolysis.
Consider how many water molecules are required to hydrolyze a polymer that is 10 monomers long.
Concept 3.3: Carbohydrates serve as fuel and building material
Carbohydrates are composed of carbon, hydrogen, and oxygen with the general formula \text{CH}2\text{O} or (\text{CH}2\text{O})x ; empirical formula often written as \text{CH}2\text{O} per unit; common carbohydrate formula example: \text{C}6\text{H}{12}\text{O}_6
Functions
Fuel for cells
Energy storage (starch in plants; glycogen in animals)
Raw material for synthesis of other molecules
Structural materials (cell wall components like cellulose in plants, chitin in arthropods)
Monomer: sugars (monosaccharides)
Most names end with -ose (e.g., glucose, fructose, galactose)
Size-based categorization
Monosaccharides: single-unit sugars (e.g., glucose, fructose, galactose)
Disaccharides: two monosaccharides linked by a glycosidic bond (e.g., sucrose, lactose, maltose)
Polysaccharides: long polymers of monosaccharide units (e.g., starch, glycogen, cellulose, chitin)
Examples of polysaccharides in nature
Starch (plant storage)
Glycogen (animal storage, branched)
Cellulose (plant cell walls; linear, hydrogen-bonding network)
Chitin (exoskeletons of arthropods, fungal cell walls)
Bonding and synthesis
Glycosidic bonds form via dehydration synthesis between hydroxyl groups of monosaccharides
Condensation reactions release water; hydrolysis reverses this process
Branched vs. linear polysaccharides
Starch (amylose is linear; amylopectin is branched)
Glycogen is highly branched
Cellulose is linear and forms microfibrils for structural support
Digesting cellulose (dietary relevance)
Some animals (e.g., cows) host cellulose-digesting bacteria that enable access to glucose from cellulose
Other animals (e.g., gorillas) may require dietary supplements for energy from cellulose-rich foods
Think About It (concept reinforcement)
What is the monomer for most polysaccharides?
Why can humans digest starch but not cellulose in the same way?
Concept 3.4: Lipids are a diverse group of hydrophobic molecules
Lipids are composed mainly of carbon, hydrogen, and oxygen (and sometimes phosphorus); they have more C–H bonds than carbohydrates and are generally hydrophobic.
Major categories
Fats and oils (triglycerides)
Phospholipids
Steroids (e.g., cholesterol, sex hormones)
Waxes
Not polymers
Lipids do not form long chain polymers like carbohydrates, proteins, or nucleic acids
Functions
1) Long-term energy storage2) Insulation against heat loss
3) Cushioning against physical shock
4) Protection against water loss
5) Chemical messengers (hormones)
6) Major components of membranes (phospholipids)
Triglycerides (fats & oils)
Structure: glycerol backbone + three fatty acids
Fatty acid: long hydrocarbon chain with a carboxyl head (–COOH)
Building triglycerides via dehydration synthesis
Formation: glycerol + 3 fatty acids → triacylglycerol + 3 H2O (ester linkages)
Example: palmitic acid as a representative fatty acid
Saturated vs. unsaturated fatty acids
Saturated: no double bonds; typically solid at room temperature
Unsaturated: one or more double bonds; typically liquid at room temperature
Phospholipids
Structure: glycerol + 2 fatty acids + phosphate group
Phosphate group is negatively charged; results in a hydrophilic (polar) head and hydrophobic (nonpolar) tails
In water: form micelles or bilayers; establish barriers in cell membranes
Steroids
Do not contain glycerol or fatty acids as building blocks
Four fused carbon rings; cholesterol is a key example and a precursor to many other steroids
Differences arise from attached functional groups
Why lipids matter in biology
Membranes: phospholipid bilayer forms basic barrier and matrix for membrane proteins
Signaling: steroid hormones regulate gene expression and cellular processes
Energy: high energy density per unit mass due to large hydrocarbon content
Concept 3.5: Proteins include a diversity of structures, resulting in a wide range of functions
Proteins are the most structurally and functionally diverse biomolecules
Composition: C, H, O, N, S
Functions include: enzymes, structural components (keratin, collagen), transport (membrane channels), receptors, defense, contraction (actin & myosin), signaling (hormones), storage (seed storage proteins)
Monomer and polymer
Monomer: amino acids (20 different kinds)
Polymer: polypeptide chains; a protein can be one or more polypeptides folded and bonded together
Proteins are large and highly folded into complex 3-D shapes
Amino acid structure
General structure: \text{H}_2\text{N} - \text{CH}(\text{R}) - \text{COOH}
The central carbon is the α-carbon; there is an amino group (–NH2), a carboxyl group (–COOH), a hydrogen, and a variable side chain (R)
At physiological pH, amino acids can be ionized to zwitterions: \text{NH}_3^+ \text{–} \text{CH}(\text{R}) \text{–} \text{COO}^-
Amino acid side chains (R-groups)
Nonpolar (hydrophobic) vs polar (hydrophilic) distinctions drive protein folding and interactions
Nonpolar: typically located in the interior of proteins
Polar: can be on surface interacting with water or forming hydrogen bonds
Joining amino acids: peptide bonds
Formed by dehydration synthesis between carboxyl of one amino acid and amino group of another
Result: a dipeptide, tripeptide, or longer polypeptide chain with repeating –N–C–C–O– backbone
General reaction: \text{Amino acid}1 + \text{Amino acid}2 \rightarrow \text{Dipeptide} + \text{H}_2\text{O}
Four levels of protein structure
Primary structure (1°): amino acid sequence determined by DNA; small changes can have major functional effects
Secondary structure (2°): local folding patterns stabilized by hydrogen bonds in the backbone; common forms: α-helix and β-pleated sheet
Tertiary structure (3°): overall 3-D shape stabilized by interactions among R-groups: hydrophobic interactions, disulfide bridges, hydrogen bonds, ionic interactions
Quaternary structure (4°): assembly of two or more polypeptide chains into a functional protein; stabilization often via hydrophobic interactions
Disulfide bridges
Formed between cysteine residues; create covalent links that stabilize the protein's 3-D structure
Hemoglobin as an example of quaternary structure
Composed of α and β subunits; each subunit carries a heme group to bind oxygen
Differences between normal and sickle-cell hemoglobin arise from single amino acid substitutions affecting quaternary interactions and overall shape
Denaturation
Environmental changes (pH, salt concentration, temperature) can disrupt 3° structure (and higher) by breaking hydrogen bonds, ionic bonds, and disulfide bridges
Some proteins can refold and regain function; others cannot
Molecular chaperonins
Help guide protein folding by providing a sheltered environment to avoid misfolding and aggregation
Think About It (protein structure)
If you eat green beans, what reactions convert dietary amino acids into body proteins?
How can a mutation disrupt a protein’s function?
Why does denaturation impair protein function?
Concept 3.6: Nucleic acids store, transmit and help express hereditary information
Nucleic acids store and transmit genetic information; DNA and RNA are the principal molecules
Components- Made of C, H, O, N, P
Monomers are nucleotides (composed of a sugar, a phosphate, and a nitrogenous base)
DNA vs RNA differences- DNA stores hereditary information; RNA is involved in its expression and translation
DNA sugar: deoxyribose; RNA sugar: ribose
DNA bases: adenine (A), thymine (T), cytosine (C), guanine (G)
RNA bases: adenine (A), uracil (U), cytosine (C), guanine (G)
- Strandedness: DNA is typically double-stranded; RNA is typically single-stranded
Structure of a nucleotide
Base (A, T/U, C, G), a sugar (deoxyribose or ribose), and a phosphate group
Example: Adenine, Guanine, Cytosine, Thymine (DNA); Adenine, Guanine, Cytosine, Uracil (RNA)
Nucleotide example depiction: base attached to a sugar-phosphate backbone via phosphodiester bonds
Building nucleic acids
Sugar–phosphate backbone: alternating sugar and phosphate units linked by phosphodiester bonds
Directionality: 5' to 3' ends (in DNA and RNA synthesis)
Condensation reactions form the phosphodiester linkage; hydrolysis breaks it
DNA vs RNA recap
DNA: deoxyribose, thymine, double-stranded
RNA: ribose, uracil, typically single-stranded
Both use a phosphate-sugar backbone with nitrogenous bases projecting inward or outward for base pairing and function
Practice Questions (Unit 1: The Chemistry of Life) — Selected from slides 75–101
1. Identify the following molecule: H2N … ofofofo … O– (structure shown in slides)
2. Identify the following molecule: CH3 … (structure shown in slides)
3. Identify the following molecule: (structure shown in slides with functional groups)
4. Identify the following molecule: (structure shown in slides with glycerol and other groups)
5. Identify the following molecule: (molecule with polar head and nonpolar tail)
6. Identify the following molecule: (long chain with carboxyl and COOH groups)
7. Which type of bond is associated with molecules that are soluble in water? Options: ionic bond, polar covalent bond, nonpolar covalent bond, hydrophobic interaction, double bonds
8. All lipids: options about glycerol cores, nitrogen content, energy content, acidity with water, water solubility
9. Where in a protein would you expect to find glutamic acid? Options: exterior surface, interior away from water, active site, heme-binding site, site binding to negatively charged protein
Which is not a function of proteins? Options: membrane components, carry genetic code for translation, bind hormone receptors, can be hormones, catalyze reactions
How does RNA differ from DNA? Options: DNA encodes hereditary info; RNA does not; DNA duplexes; RNA single-stranded; DNA has thymine; RNA has uracil; DNA has five bases; RNA has four; all of the above
If you located a single-stranded piece of nucleic acid, what would it be made of? Options: nucleotides, amino acids, fatty acids, sugars, glycerol
If given a polysaccharide with glucose as the sole subunit, what would you have? Options: glycogen, starch, cellulose, amylopectin, or cannot determine
Which sugar is most important for making RNA? Options: glucose, ribose, frostose, glyceraldehyde, sucrose
Which is not a lipid? Options: estrogen, cholesterol, glucose, triacylglyceride, trans fat
Which provides the most compact energy storage? Options: proteins, carbohydrates, lipids, nucleic acids, all similar
For an acidic molecule, which functional group would you include? Options: hydroxyl, amino, carboxyl, carbonyl, none
If given glycine’s structure, which functional groups would you expect? Options: hydroxyl + amino; amino + carbonyl; carboxyl + amino; carbonyl + hydroxyl; carbonyl + sulfhydryl
What functional group is most critical to energy metabolism? Options: hydroxyl, amino, carboxyl, phosphate, carbonyl
For what is water most needed when digesting food? Options: dehydration reactions, temperature reduction, solubility, hydrolysis reactions, none
Which is not a general kind of macromolecule? Options: protein, cholesterol, nucleic acid, lipid, carbohydrate
When observing the synthesis of a biological macromolecule, what should you see more of? Options: water, amino acids, alcohol, ions, fatty acids
From what are polysaccharides made? Options: monosaccharides, glucose, disaccharides, sucrose
If asked to choose a lipid subunit, which would it be? Options: fatty acid, steroid, cholesterol, unsaturated side chain, none
Which is the least metabolically active kind of protein? Options: receptor, contractile, enzymatic, hormonal, structural
Which level of protein structure is most immediately encoded in DNA? Options: primary, secondary, tertiary, quaternary, or none of the above
Note: Answers are provided in the original slide deck; use these questions to practice applying the concepts above.
Quick Reference: Key Formulas and Concepts (Biology Unit 1)
Empirical formula for carbohydrates: \text{CH}2\text{O} per unit; common carbohydrate: \text{C}6\text{H}{12}\text{O}6
Dehydration synthesis (condensation) general form:- \text{Monomer}1 + \text{Monomer}2 \rightarrow \text{Polymer} + \text{H}_2\text{O}
Hydrolysis general form:- \text{Polymer} + \text{H}2\text{O} \rightarrow \text{Monomer}1 + \text{Monomer}_2 + \text{…}
ATP hydrolysis (energy release): \text{ATP} + \text{H}2\text{O} \rightarrow \text{ADP} + \text{P}i + \text{energy}
Peptide bond formation (between amino acids): \text{Amino acid}1 + \text{Amino acid}2 \rightarrow \text{Dipeptide} + \text{H}_2\text{O}
Nucleic acids: nucleotides as monomers; phosphodiester bonds link nucleotides to form the sugar–phosphate backbone; DNA uses deoxyribose and thymine; RNA uses ribose and uracil.
Carbohydrate bonding: glycosidic bonds join monosaccharides; digestion by hydrolysis yields monosaccharides.
Lipid structure: triglycerides = glycerol + 3 fatty acids via ester linkages; phospholipids = glycerol + 2 fatty acids + phosphate; steroids have four fused rings.
Protein structure: primary (sequence); secondary (a-helix, β-pleated sheet); tertiary (3-D folding); quaternary (multiple polypeptides).
Nucleic acid backbone: sugar–phosphate, polarity 5' to 3'.