Comprehensive Biology Unit 1 Study Guide: Cells, Chemistry, and Metabolism

Fundamental Cell Classification: Prokaryotes and Eukaryotes

Biological systems are categorized into two primary forms: Prokaryotes and Eukaryotes. Prokaryotes, which include bacteria and archaea, are characterized by the absence of a nucleus and membrane-bound organelles. They are generally smaller and simpler in their structural organization. In contrast, Eukaryotes, which encompass plants, animals, and fungi, possess a clearly defined nucleus and various membrane-bound organelles. Eukaryotic cells are larger and more complex. The definitive difference between these two categories is the presence of a membrane-bound nucleus in Eukaryotes.

Eukaryotic Cell Structure and Organelle Specialization

The eukaryotic cell is organized into specialized compartments to perform distinct functions. The cytoplasm refers to everything contained between the plasma membrane and the nucleus, while the cytosol is specifically the fluid inside the cell. The nucleus serves as the repository for genetic material, storing and protecting DNA; its nuclear envelope controls the transport of materials in and out. Within the nucleus, the nucleolus is responsible for the production of ribosomes.

The endomembrane system includes the Rough Endoplasmic Reticulum (Rough ER), which is studded with ribosomes and located near the nucleus to facilitate protein synthesis and the production of enzymes. The Smooth Endoplasmic Reticulum (Smooth ER) lacks ribosomes and is involved in lipid transport and the storage of calcium ions ($Ca^{2+}$). The Golgi Apparatus, often described as the "shipping center," is located closer to the cell membrane and is responsible for modifying and packaging proteins. For cellular maintenance and energy, lysosomes contain digestive enzymes for breaking down materials, while mitochondria are the sites of ATP production and cellular respiration. In plants, chloroplasts facilitate photosynthesis, and vacuoles serve as storage units, with large central vacuoles being particularly prominent in plant cells for storage.

Cytoskeleton and Tools for Cellular Study

The cytoskeleton is a critical network that controls cell shape, mobility, replication, secretion, and gene expression. It consists of three primary components: microfilaments, intermediate filaments, and microtubules. The discovery of cells is attributed to Robert Hooke. To visualize these structures, scientists use various forms of microscopy. The light microscope uses visible light and has lower resolution but allows for the observation of living cells. The confocal microscope utilizes lasers to generate 3D images. The electron microscope uses electron beams to achieve much higher resolution, though it can only be used to view dead cells.

To study individual cellular components, researchers employ differential cell fractionation. This process involves breaking cells open and using a centrifuge to separate organelles based on density. During centrifugation, larger and heavier components settle first, as a general rule that "big things fall faster."

Atomic Structure, Energy, and Electron Shells

Matter is defined as anything that possesses mass and occupies space. Elements are substances that cannot be broken down chemically into simpler forms. Compounds consist of two or more different elements in a fixed ratio; for example, $NaCl$ is a compound, whereas $O_2$ is a molecule but not a compound. Atoms represent the smallest unit of structure for an element and are composed of subatomic particles: protons (positive charge), neutrons (neutral), and electrons (negative charge).

Energy in biological systems is categorized into potential energy, which is stored energy due to position or structure, and kinetic energy, which is the energy of motion. In atoms, electrons contain potential energy. This energy is higher for electrons located further from the nucleus. Electron shells fill according to specific capacities: the first shell holds $2$ electrons ($e^-$), the second shell holds $8$ electrons ($e^-$), and the third shell holds $8$ electrons ($e^-$). Atoms strive to reach a full valence shell (the outer shell) for stability.

Chemical Bonding and Electronegativity

Chemical bonds are formed by interactions between valence electrons. Covalent bonds involve the sharing of electrons; a single bond involves $2$ shared electrons, and double or triple bonds are also possible. Covalent bonds are subdivided into two types based on electronegativity, which is an atom's attraction for electrons. Nonpolar covalent bonds feature equal sharing of electrons (e.g., $H-H$), typically occurring when the electronegativity difference ($EN \text{ DIF}$) is less than or equal to $0.4$. Polar covalent bonds involve unequal sharing (e.g., in water), occurring when the difference is between $0.4$ and $1.8$. If the difference is greater than $1.8$, the bond becomes ionic, characterized by electron transfer and the formation of ions.

Weak bonds are also essential for biological structure. Hydrogen bonds occur when a hydrogen atom is attracted to an electronegative atom; while individually weak, they are strong in aggregate. Van der Waals interactions are weak, temporary attractions between molecules. These are vital for protein shape, enzyme-substrate binding, and antibody interactions. A notable example is the gecko, which uses many weak Van der Waals interactions to achieve strong adhesion to surfaces.

The Unique Properties of Water

Water is a polar molecule that forms up to four hydrogen bonds, leading to four essential properties. First is cohesion (water sticking to itself) and adhesion (water sticking to other surfaces). Second is temperature moderation; water has a high specific heat, meaning it resists temperature changes, and evaporation effectively removes heat. Third, ice is less dense than liquid water because water molecules in the solid state are further apart in an open crystal structure, allowing ice to float and insulate the water below. Fourth, water is an excellent solvent, capable of dissolving polar and charged substances due to its polarity and the formation of hydration shells. Substances that interact well with water are termed hydrophilic.

Water dissociation occurs when $2H_2O \rightleftharpoons H_3O^+ + OH^-$. In pure water, the concentrations are $[H^+] = 10^{-7}M$ and $[OH^-] = 10^{-7}M$, resulting in a neutral $pH$ of $7$. The $pH$ scale is defined by the formula $pH = -\text{log}[H^+]$. Acids increase the concentration of $H^+$ and lower the $pH$ (lower than $7$), while bases decrease the concentration of $H^+$ and raise the $pH$ (higher than $7$). Changes in $pH$ are critical because they alter the charge of molecules, which changes their structure and, consequently, their function.

Carbon Chemistry, Isomers, and Functional Groups

Carbon is the fundamental building block of life because it has $6$ protons and $4$ valence electrons, allowing it to form $4$ covalent bonds (single, double, or triple). Hydrocarbons are molecules consisting only of carbon and hydrogen; they are nonpolar and hydrophobic. Isomers are molecules with the same molecular formula but distinct arrangements of atoms. Structural isomers have different atom arrangements (e.g., $C_5H_{12}$ can exist in different forms). Geometric isomers differ around double bonds, identified as cis (same side) or trans (opposite sides). Enantiomers are mirror-image isomers. These structural differences can cause dramatic changes in biological function.

Functional groups are small groups attached to hydrocarbons that change their reactivity, polarity, solubility, and function. Key groups to know include Hydroxyl ($OH^-$), Carboxyl ($COOH$), Amino ($NH_2$), Sulfhydryl ($SH$), and Phosphate ($-O-PO_3^{2-}$).

Biological Macromolecules: Carbohydrates and Lipids

Life is composed of four main biological molecules: carbohydrates, lipids, proteins, and nucleic acids. These form macromolecules through polymer reactions. Dehydration synthesis builds polymers by removing a water molecule ($H_2O$) to form a covalent bond. Hydrolysis breaks polymers by adding a water molecule.

Carbohydrates function in energy storage, structure, recognition, and protection. Monosaccharides are single sugars, disaccharides are two sugars, oligosaccharides contain $3$ to $10$ sugars, and polysaccharides consist of many sugars. Glucose is a common monomer that exists in ring form as either $\text{α-glucose}$ or $\text{β-glucose}$. A glycosidic linkage is the covalent bond formed between sugars via dehydration synthesis; for example, maltose is formed from glucose plus glucose. Storage polysaccharides include starch (found in plant plastids) and glycogen (found in animal liver and muscle), both made of $\text{α-glucose}$. Structural polysaccharides include cellulose (plant cell walls, made of $\text{β-glucose}$) and chitin (fungal cell walls).

Lipids are hydrophobic molecules used for energy storage, membranes, hormones, and insulation. Fats are composed of fatty acids. Saturated fatty acids have no $C=C$ double bonds, resulting in straight chains that are solid at room temperature. Unsaturated fatty acids contain $C=C$ double bonds, causing a kinked chain that remains liquid at room temperature. Phospholipids are amphipathic, containing a hydrophilic (polar) head and a hydrophobic (nonpolar) tail, and they form the lipid bilayer of membranes. Steroids are lipids characterized by four fused carbon rings, such as cortisol and aldosterone.

Proteins and Nucleic Acids

Proteins consist of one or more polypeptides folded into a specific 3D structure. A polypeptide is a linear sequence of amino acids joined by covalent peptide bonds. Amino acids consist of an amino group, a carboxyl group, a central carbon, and a variable R group that determines polarity, charge, and size. Special amino acids include cysteine, which forms disulfide bonds; glycine, which is the smallest; and proline, which has a ring structure.

Protein structure is organized into four levels:

1. Primary structure: The linear amino acid sequence held by covalent peptide bonds.
2. Secondary structure: Patterns such as $\text{α-helices}$ and $\text{β-sheets}$ held by hydrogen bonds.
3. Tertiary structure: The overall 3D shape resulting from R-group interactions (ionic, hydrophobic, hydrogen bonds, and disulfide bridges).
4. Quaternary structure: The interaction between multiple polypeptide subunits.

Misfolded proteins are associated with diseases such as Alzheimer's, Parkinson's, and Cystic Fibrosis. Denaturing an enzyme alters its active-site shape and destroys its function.

Nucleic acids (DNA and RNA) are made of nucleotides, each containing a nitrogenous base, a pentose sugar (deoxyribose for DNA, ribose for RNA), and a phosphate group. Nitrogenous bases are divided into Purines (Adenine, Guanine) and Pyrimidines (Cytosine, Thymine in DNA, Uracil in RNA). Nucleotides are joined by phosphodiester bonds to create a sugar-phosphate backbone. DNA is typically double-stranded, while RNA is single-stranded.

Thermodynamics and Enzyme Kinetics

Metabolism includes all biochemical reactions in a cell, divided into catabolism (breaking down molecules and releasing energy) and anabolism (building molecules and requiring energy). The First Law of Thermodynamics states that energy cannot be created or destroyed. The Second Law states that every energy transfer increases entropy (disorder). Free energy ($G$) is the energy available to do work, calculated as $\text{Δ}G = \text{Δ}H - T\text{Δ}S$.

Exergonic reactions have a negative $\text{Δ}G$ ($\text{Δ}G < 0$) and release free energy, meaning they are spontaneous. Endergonic reactions have a positive $\text{Δ}G$ ($\text{Δ}G > 0$) and require energy. Equilibrium occurs when $\text{Δ}G = 0$. ATP (adenosine triphosphate) is an unstable molecule with three repelling phosphate groups. ATP hydrolysis ($ATP + H_2O \rightarrow ADP + P_i$) is highly exergonic and acts as an energy coupler, driving endergonic reactions forward.

Enzymes are biological catalysts (usually proteins) that accelerate reactions without being consumed. They work by lowering the activation energy ($E_A$), which is the energy required to reach the transition state. Enzymes do not change $\text{Δ}G$ or the equilibrium of a reaction; they only affect the speed. Substrates bind to the enzyme's active site, forming an enzyme-substrate complex. This often involves an induced fit, where the active site changes shape slightly upon binding. Enzyme activity can be regulated by allosteric regulation, coenzymes, or inhibitors. Irreversible inhibitors (toxins/poisons) permanently disable enzymes, while endpoint inhibition provides normal feedback regulation.

Summary Relationships and Final Exam Review

• Primary structure: Peptide bonds.
• Secondary structure: Hydrogen bonds.
• Tertiary/Quaternary structure: Ionic, hydrophobic, hydrogen bonds, disulfide bonds (R-group interactions).
• Electronegativity values ($EN$): $C=2.6$, $H=2.2$, $N=3.0$, $O=3.4$, $P=2.2$, $S=0.9$. For example, $C-H$ ($2.6-2.2=0.4$) is nonpolar, whereas $O-S$ ($3.4-0.9=2.5$) is ionic.
• Membrane Fluidity: Membranes are more fluid with unsaturated fatty acid tails (more kinks, loose packing) and less fluid with saturated tails (straight tails, tight packing).
• Thermodynamics: $\text{Δ}G$ tells if a reaction can happen; $E_A$ tells how fast it will happen. Enzymes affect speed, not spontaneity.