Chapter 2 Notes/Flashcards

Chemical Composition of Cells

Living matter is dominated by carbon and hydrogen, with substantial enrichment relative to nonliving matter. The overall composition by weight is largely water (about $70.0\%$). Dry mass consists of organic molecules (mostly carbon–hydrogen bonds) and minerals. One widely cited breakdown (by weight) is: Water $70.0\%$; Inorganic ions $1.0\%$; Sugars $1.0\%$; Amino acids and precursors $0.4\%$; Nucleotides $0.4\%$; Fatty acids $1.0\%$; Macromolecules $26.0\%$. The takeaway is that the majority of the cell’s mass is water, while the remaining dry mass is built from organic molecules and minerals that form the biochemical machinery of life.

In addition to these bulk numbers, a common way to describe cellular composition is by the elements that make up the bulk (red), the ions and common elements (blue), and trace elements (green/yellow) that are often positioned in enzyme active sites or other functional sites of proteins. The principal bulk elements are hydrogen (H), carbon (C), nitrogen (N), and oxygen (O). Common ions include inorganic species such as calcium (Ca), sodium (Na), magnesium (Mg), potassium (K). Trace elements are essential but present in much smaller amounts; they frequently occupy catalytic or structural roles in biomolecules.

Bonding and Interactions in Biomolecules

Cells rely on various types of chemical interactions to build and stabilize macromolecules and complexes:

• Covalent bonds: sharing of electrons between atoms; electrons are shared to form a stable, low-energy state.
• Ionic bonds: transfer of electrons, resulting in positively and negatively charged ions that are attracted to each other.
• Hydrogen bonds: attractions between a hydrogen atom bound to a strongly electronegative atom (e.g., O, N) and another electronegative atom; important for structure and specificity.
• Van der Waals/dispersion forces: weak, short-range attractions arising from transient fluctuations in electron density that create small partial charges.
• Hydrophobic interactions: nonpolar regions tend to associate in water to minimize disruption of water’s extensive H-bond network. This is not a true bond, but a driving force that helps assemble nonpolar macromolecules and membranes.

These interactions vary in strength: covalent bonds are strong, ionic and hydrogen bonds are intermediate to weak, and hydrophobic/Van der Waals interactions are relatively weak but cumulatively significant in large systems. In water, ionic interactions can be screened and weakened, while covalent bonds remain robust.

Covalent Bonds and Carbon Chemistry

Covalent bonds typically have bond energies around $E<em>{bond} \approx 90\ \mathrm{kcal\,mol^{-1}}$, though the exact energy depends on the atoms involved; a broad range for carbon–hydrogen and carbon–carbon bonds is about $50\le E</em>{bond} \le 110\ \mathrm{kcal\,mol^{-1}}$. A classic simple example is molecular hydrogen, $\mathrm{H_2}$, where the two hydrogen atoms share a pair of electrons to form a single bond, creating a bonding molecular orbital with electrons delocalized over both nuclei. This high bond energy makes covalent bonds relatively stable under physiological conditions.

Covalent bonds can form between carbon and other atoms in diverse ways. Carbon has four unpaired outer electrons, enabling it to form up to four covalent bonds (e.g., methane, $\mathrm{CH_4}$). Electron sharing can produce polar or nonpolar covalent bonds depending on electronegativity differences. Carbon–carbon bonding enables carbon to link into chains and branched structures, forming the backbone of many biological macromolecules. In addition to C–C single bonds, carbon–carbon bonds can be single (C–C), double (C=C), or even triple (C≡C) bonds, though in biology, double bonds often introduce rigidity and can eliminate free rotation (as in unsaturated lipids and many rings).

Other elements in cells readily form covalent bonds as well: oxygen (O), hydrogen (H), nitrogen (N), and sulfur (S) are common partners for carbon in biomolecules. The presence of these elements gives rise to functional groups like –OH, –NH, and –SH, which strongly influence polarity and reactivity.

Polarity of Covalent Bonds and Water as a Solvent

C–H bonds are essentially nonpolar because carbon and hydrogen share electrons relatively evenly. By contrast, bonds involving more electronegative atoms (e.g., O, N, S) with hydrogen (such as C–O, C–N, N–H, O–H, S–H) tend to be polar, making the molecule overall polar when such groups are present. Water (H₂O) is a highly polar solvent because electrons are drawn closer to the oxygen nucleus, giving the molecule a partial positive charge on the hydrogens and a partial negative charge on the oxygen. Water can form up to four hydrogen bonds per molecule and creates a dynamic, three-dimensional hydrogen-bond network.

The polarity of water underlies many cellular properties:

• Water is a polar solvent that stabilizes charged and polar species.
• It supports capillary action in plant tissues due to surface tension.
• Water’s high boiling point and high heat capacities contribute to temperature regulation in cells and organisms.

Polarity also influences the behavior of functional groups: –OH, –NH, and –SH groups confer polarity to larger molecules, affecting solubility, interactions, and reactivity.

Ionic Bonds and Their Context in Biological Systems

Ionic bonds are weaker in most aqueous environments (roughly 1$–$3\ \mathrm{kcal\,mol^{-1}} in water) but can be very strong in solids or crystal forms (up to $\sim 80\ \mathrm{kcal\,mol^{-1}}$). The presence of other ions and polar molecules in solution reduces the effective strength by forming a solvation shell around the ions, which screens electrostatic attractions. Water is especially effective at screening ionic interactions.

In proteins, selective environments can stabilize otherwise unfavorable ionic interactions (e.g., iron bound to the heme group in hemoglobin is protected from free solvent). This illustrates how macromolecular context modulates bond strengths and functionality.

Water: Structure, Properties, and Biological Relevance

Water is a polar solvent with a well-defined hydrogen-bonding network. Consequences of polarity include:

• Each water molecule can form up to four hydrogen bonds, promoting extensive intermolecular interactions.
• A three-dimensional network emerges from H-bonding, contributing to water’s unique properties.

Key properties of water with biological relevance:

• High surface tension supports capillary rise in plant tissues.
• High boiling point helps maintain stable liquid water over biological temperature ranges.
• High specific heat provides a temperature buffer for metabolically active cells.
• High heat of vaporization makes evaporative cooling (e.g., sweating or panting) effective.

Macromolecules: Polymers of Life

Biomolecules that form the bulk of cellular macromolecules are polymers built from monomers:

• Carbohydrates are polymers of simple sugars (monosaccharides) with general formula $( ext{CH}<em>2 ext{O})</em>n \,, \ n \text{ between } 3 \text{ and } 6$ for the monomer unit.
• Lipids are built from fatty acids that have hydrophobic hydrocarbon chains and a hydrophilic portion, contributing to energy storage, membranes, and signaling.
• Proteins are polymers of amino acids with diverse 3D structures that underlie their functional roles.
• Nucleic acids (DNA and RNA) are polymers of nucleotides that store, transmit, and translate genetic information.

All these macromolecules are assembled by condensation (loss of water) and can be hydrolyzed back into monomer units.

Carbohydrates

Carbohydrates range from small monosaccharides to large polysaccharides. Monosaccharides (e.g., glucose) can polymerize to form polysaccharides such as glycogen and starch, which serve as glucose storage in animals and plants, respectively. Cellulose, another glucose polymer, is the principal structural component of plant cell walls. A general structural motif of polysaccharides is the repeated linkage of monosaccharide units via glycosidic bonds, formed in condensation reactions and cleaved by hydrolysis.

• Polysaccharides are formed by enzyme-catalyzed condensation reactions that release water: $ext{Monomer} + ext{Monomer} <br /> ightarrow ext{Polymer} + \mathrm{H_2O}$
• Conversely, hydrolysis consumes water to break the bonds: $ext{Polymer} + \mathrm{H_2O} <br /> ightarrow ext{Monomer} + ext{Monomer}$

Enzymes involved in carbohydrate digestion include sucrase, lactase, and maltase, which are located on the outer surfaces of epithelial cells lining the small intestine. They hydrolyze disaccharides into monosaccharides for absorption.

Beta-1,4 linkages are characteristic of cellulose, a linkage that most animals cannot hydrolyze because they do not produce cellulases. In contrast, ruminant animals host microbial communities in their stomachs that produce cellulases, enabling the release of glucose from cellulose for metabolism. This difference highlights how different enzymes catalyze specific linkages and dictate metabolic capabilities.

Lipids, Fatty Acids, and Their Derivatives

Lipids perform energy storage, form cell membranes, and participate in signaling. The simplest lipid form is the fatty acid, a hydrocarbon chain with a terminal carboxyl group. The hydrocarbon tail is hydrophobic, whereas the carboxyl head is hydrophilic and reactive. Two important themes:

• Saturated fatty acids have no C=C bonds; all carbon–carbon bonds are single. Unsaturated fatty acids contain one or more C=C bonds, which introduce kinks into the chain and disrupt tight packing.
• Fatty acids store energy efficiently: they provide about six times as much usable energy per unit weight as glucose.
  Stored in cells as triacylglycerols (triglycerides), three fatty acids are esterified to a glycerol backbone.

A major role of fatty acids is in constructing membranes. Phospholipids, the primary membrane components, consist of two fatty acids and a polar head group bound to glycerol via a phosphate. The head group can be choline, serine, ethanolamine, or another polar moiety, giving the molecule an amphipathic character (both hydrophilic and hydrophobic parts).

Examples of fatty acids include a hydrophilic carboxylic head and a hydrophobic hydrocarbon tail, illustrated as: a head that attracts water and a tail that excludes water. Amphipathic molecules like phospholipids and soaps exploit this dual polarity to form membranes and micelles, respectively.

Lipids overview:

• 1) Triacylglycerols (fats): three fatty acids linked to glycerol via ester bonds.
• 2) Phospholipids: two fatty acids + a polar head group + phosphate, forming the bilayer of membranes.

Proteins and Amino Acids

Amino acids are the building blocks of proteins. There are about 20 standard amino acids incorporated into proteins. Each amino acid contains:

• An amino group (–NH2)
• A carboxyl group (–COOH)
• A central carbon (the α-carbon) with a hydrogen atom and a variable side chain (R).
  The basic structure can be represented as: $\mathrm{NH_2-CH(R)-COOH}$

Amino acids polymerize via peptide bonds through a condensation reaction:
$\text{amino\,acid}<em>1 + \text{amino\,acid}</em>2 \rightarrow \text{dipeptide} + \mathrm{H_2O}$
Proteins are long polymers of amino acids that fold into specific three-dimensional shapes to perform their diverse functions. In cells, proteins are synthesized by ribosomes and transferred RNA (tRNA) using messenger RNA (mRNA) as a template, integrating genetic information into functional polypeptides.

Nucleotides, Nucleic Acids, and Nucleotide-Derived Molecules

Nucleotides are the monomers of nucleic acids. A nucleotide comprises:

• A nucleoside: a purine or pyrimidine base linked to a five-carbon sugar (ribose in RNA or deoxyribose in DNA).
• A phosphate group(s) attached to the sugar.

DNA and RNA are polymers of nucleotides. RNA includes ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA), each playing distinct roles in protein synthesis and gene expression.

Nucleotides have important roles beyond information storage:
1) Energy carriers: nucleoside triphosphates such as ATP store chemical energy in their phosphoanhydride bonds. For example, hydrolysis of the terminal phosphate releases energy used in myriad cellular processes. ATP is a representative molecule of this class.
2) Cofactors/Coenzymes: nucleotides participate in enzyme catalysis as cofactors; examples include coenzyme A (CoA).
3) Small intracellular signaling molecules: cyclic AMP (cAMP) acts as a second messenger in signaling pathways.

Structural note: Phosphodiester bonds link nucleotides in nucleic acids, forming the backbone of DNA and RNA via connections between the sugar of one nucleotide and the phosphate of the next. Interaction involves the hydroxyl group of the sugar and the phosphate group in a condensation-type linkage, resulting in a repeating sugar–phosphate backbone with nitrogenous bases projecting outward.

Summary of Relationships and Relevance

• The cell is predominantly water; the dry mass comprises organic polymers and minerals that carry out metabolic, structural, and regulatory roles.
• The key interaction types—covalent, ionic, hydrogen bonding, van der Waals, and hydrophobic effects—underpin the formation, stability, and specificity of biomolecules.
• Carbon’s tetravalence enables complex architectures: linear, branched, cyclic, and unsaturated structures with varying rigidity and functionality.
• Macromolecules assemble through dehydration condensation and can be disassembled via hydrolysis; enzymatic control ensures directionality and regulation in metabolism.
• Carbohydrates serve as energy sources (glycogen, starch) and structural components (cellulose in plants); digestion involves specific enzymes on intestinal surfaces that hydrolyze disaccharides into monosaccharides for absorption.
• Lipids, particularly fatty acids and phospholipids, provide energy and form membranes; amphipathic lipid molecules underpin the formation of membranes and other organized structures.
• Proteins, built from 20 amino acids, perform the vast majority of catalytic, structural, signaling, and regulatory functions. Their properties are dictated by amino acid composition and higher-order folding.
• Nucleotides furnish energy, coenzymes, and signaling molecules, as well as forming DNA and RNA, which store and transmit genetic information.

Practical and Real-World Connections

• Water as solvent and temperature buffer is central to all cellular chemistry and organismal physiology (e.g., sweating, panting, and maintaining stable intracellular environments).
• Dietary fiber (cellulose) is not digested by most animals but supports gut microbiota in ruminants and other herbivores; this illustrates how enzyme availability and ecological context shape metabolism.
• The amphipathic nature of phospholipids is fundamental to membrane structure, selective permeability, and signaling platforms in cells.
• ATP, CoA, cAMP, and other nucleotide-based molecules are fundamental to energy transfer, metabolism, and signaling—linking chemistry to physiology and behavior.

Notation and Key Formulas (for quick reference)

• Monomer polymerization (condensation):$\text{Monomer} + \text{Monomer} \rightarrow \text{Polymer} + \mathrm{H_2O}$
• Polymer hydrolysis:$\text{Polymer} + \mathrm{H_2O} \rightarrow \text{Monomer} + \text{Monomer}$
• General carbohydrate monomer:$(\mathrm{CH<em>2O})</em>n,\quad 3 \le n \le 6$
• Covalent bond energy (typical):$E<em>{bond} \approx 90\ \mathrm{kcal\,mol^{-1}},\quad 50 \le E</em>{bond} \le 110\ \mathrm{kcal\,mol^{-1}}$
• Water energy units:$1\ \mathrm{kcal} = 1\ \mathrm{L\,H_2O^{\circ}C}$
• Amino acid general structure:$\mathrm{NH_2-CH(R)-COOH}$
• Peptide bond formation:$\text{Amino\,acid}<em>1 + \text{Amino\,acid}</em>2 \rightarrow \text{Dipeptide} + \mathrm{H_2O}$
• Nucleoside vs nucleotide: nucleoside = base + sugar; nucleotide = nucleoside + phosphate(s); sugars: ribose (RNA) or deoxyribose (DNA)
• Nucleic acid backbone: phosphodiester bonds link sugars and phosphates along the polymer
• Energy carriers and signaling: examples include ATP, CoA, and cyclic AMP (cAMP)