Biology 112 Lecture Notes

Important Dates

  • Completed Assignment 2 is due on: Fri Sep 26, 11:59 p.m.

  • Reading Quiz 1 is on: Sep 26 - please bring your laptops.

Topics Covered

  • Review of Chemistry

  • Water and Organic Molecules Interaction in Cells

  • Macromolecules as Building Blocks of Cells: Carbohydrates, Lipids, Nucleic Acids, and Proteins

  • Structure and Function of Proteins in Cell Activities

  • The Role of Proteins as Enzymes in the Cell

Learning Objectives

After studying this lecture, students should be able to:

  • Describe the role of water in cells.

  • Define Macromolecules.

  • Distinguish between carbohydrates, lipids, nucleic acids, and proteins.

  • Correlate the structure and function of proteins in the activities of cells.

  • Describe the role of proteins as enzymes.

Textbook References

  • Chapter 2: pp. 50-61

  • Chapter 3: pp. 78-86

  • Chapter 4: pp. 89-93

  • Chapter 5: pp. 103-109

  • Chapter 6: pp. 116-119

  • Chapter 8: pp. 178-179

Note: Page numbers may vary depending on the textbook edition.

Atoms, Ions, and Molecules: The Building Blocks of Chemical Evolution

  • Atom: The smallest identifiable unit of matter that retains the chemical properties of an element. Each atom consists of a nucleus (containing positively charged protons and neutral neutrons) and negatively charged electrons orbiting the nucleus.

  • Four types of atoms (hydrogen, carbon, nitrogen, oxygen) make up 96% of all matter found in organisms today, largely due to their ability to form stable bonds and diverse molecules.

  • Early Earth had these atoms in simple substances like water (H2O) and carbon dioxide (CO2) – each containing only a few atoms but crucial for chemical evolution.

Atomic Structure of the First 18 Elements

  • Electrons move around atomic nuclei in specific regions called orbitals. Each orbital can hold up to two electrons.

  • Orbitals are grouped into levels called electron shells, numbered to indicate their distance from the nucleus (1 is closest). The first shell holds 2 electrons, the second holds 8, and the third holds 8.

  • Electrons fill the innermost shells first before going to outer shells.

  • Valence electrons are the electrons in the outermost shell. Unpaired electrons in unfilled shells are highly reactive and tend to form chemical bonds to achieve a stable electron configuration (typically a full outer shell).

Covalent Bonds

  • Result from electron sharing between atoms, causing both atoms to achieve a stable electron configuration (e.g., a full outer shell). This sharing leads to the formation of stable molecules.

  • Example: Two hydrogen atoms form a single molecule, denoted as H-H or H_2. Such bonds can be single, double, or triple, depending on the number of electron pairs shared.

Electron Sharing & Bond Polarity

  • Polar covalent bonds arise from unequal electron sharing due to differences in electronegativity (an atom's attraction for shared electrons). The atom with higher electronegativity pulls the electrons closer, acquiring a partial negative charge (\delta-), while the other atom acquires a partial positive charge (\delta+).

Ion Formation and Ionic Bonding

  • Ionic Bonds: Electrons are completely transferred from one atom to another, typically occurring when there is a large difference in electronegativity. This transfer results in the formation of ions, which are atoms or molecules with a net electrical charge.

  • Ions carry full charges: cations (positively charged, having lost electrons) and anions (negatively charged, having gained electrons). The strong electrostatic attraction between these oppositely charged ions forms the ionic bond.

  • Example: Sodium (Na) loses an electron to become Na^+ (a cation); Chlorine (Cl) gains an electron to become Cl^- (an anion). Sodium chloride (NaCl) consequently forms a strong ionic bond due to the attraction between Na^+ and Cl^-.

Covalent Bond Formation

  • The number of covalent bonds an atom can form is determined by its number of unpaired valence electrons, striving to complete its outer shell:

    • Carbon: C can form four covalent bonds (due to four unpaired electrons, needs four to complete its octet);

    • Nitrogen: N can form three bonds (needs three);

    • Oxygen: O can form two bonds (needs two);

    • Hydrogen: H can form one bond (needs one to complete its first shell duet).

Molecular Representation and Functionality

  • Molecules can be represented in different ways (e.g., structural formulas, ball-and-stick models) impacting function based on geometry. Molecular geometry is governed by bond positions and repulsive forces between electrons, which are critical for recognizing and interacting with other molecules.

  • Water molecules (H_2O), the most abundant in organisms, are polar due to their bent shape and the significant electronegativity difference between oxygen and hydrogen. This polarity allows them to participate extensively in hydrogen bonding (attraction between the partial positive charge on hydrogen and a partial negative charge on an electronegative atom like oxygen or nitrogen).

  • Water’s properties, derived from hydrogen bonding, include cohesion (attraction between like molecules) and adhesion (attraction between unlike molecules).

Unique Properties of Water

  • Cohesion and Adhesion: Hydrogen bonds allow water molecules to stick to each other (cohesion) and to other polar surfaces (adhesion). This is responsible for capillary action, where water moves up narrow tubes against gravity.

  • A meniscus forms in tubes due to both cohesive and adhesive forces.

  • Water has a high surface tension, allowing it to support small objects, caused by the strong cohesive forces between water molecules at the surface.

  • Ice's Lower Density: Hydrogen bonds between water molecules in ice form a crystalline lattice structure with more space between molecules than in liquid water, causing ice to be less dense and thus float. This insulates aquatic environments.

  • High Specific Heat: Water's hydrogen bonds require a large amount of energy to break before water molecules can move faster, leading to a high specific heat capacity. This property helps moderate climate by absorbing and releasing large amounts of heat with only slight temperature changes.

  • Universal Solvent: Water's polarity makes it an excellent solvent, especially for other polar and ionic substances. It forms hydration shells around ions and dissolves many organic molecules.

  • Water facilitates osmosis: the passive movement of water across semipermeable membranes, driven by concentration gradients.

Osmosis

  • Osmosis is the diffusion of water across a selectively permeable membrane, aiming to equalize solute concentrations:

    • Hypertonic solution: Has a higher solute concentration than the cell. Water moves out of the cell, causing cell shrinkage (crenation in animal cells, plasmolysis in plant cells).

    • Hypotonic solution: Has a lower solute concentration than the cell. Water moves into the cell, causing cell swelling and potentially bursting (lysis in animal cells, turgor pressure in plant cells).

    • Isotonic solution: Has an equal solute concentration compared to the cell. No net water movement occurs, and cell volume remains stable.

Carbon and Molecular Shapes

  • Carbon's ability to form four stable covalent bonds makes it exceptionally versatile. It can form long chains, branched chains, or ring structures, allowing for the creation of large, diverse, and complex organic molecules (biomolecules).

  • Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. They attach to the carbon backbone and significantly influence the molecule's behavior, solubility, and reactivity. Common functional groups include hydroxyl (-OH), carbonyl (C=O), carboxyl (-COOH), amino (-NH2), sulfhydryl (-SH), phosphate (PO4), and methyl (-CH_3).

Macromolecules

Macromolecules are large, complex organic molecules essential for life, typically formed by the polymerization of smaller repeating units called monomers.

  1. Carbohydrates: Serve as primary energy sources and structural components.

    • Monomers: Monosaccharides (simple sugars like glucose, fructose).

    • Polymers: Disaccharides (e.g., sucrose, lactose) and Polysaccharides (complex carbohydrates like starch, glycogen for energy storage; cellulose, chitin for structural support).

    • General formula is often represented as (CH2O)n.

  2. Lipids: A diverse group of molecules characterized by their insolubility in water (hydrophobic nature) due to abundant nonpolar C-H bonds.

    • Not true polymers in the same way as other macromolecules but are critical for energy storage, membrane structure, and signaling.

    • Includes fats/triglycerides (long-term energy storage), phospholipids (main components of cell membranes), and steroids (e.g., cholesterol, hormones).

  3. Nucleic Acids: Polymers of nucleotides responsible for storing and transmitting genetic information.

    • Monomers: Nucleotides, each composed of a five-carbon sugar (deoxyribose in DNA, ribose in RNA), a phosphate group, and a nitrogenous base (Adenine, Guanine, Cytosine, Thymine in DNA; Uracil replaces Thymine in RNA).

    • Examples: DNA (Deoxyribonucleic Acid) carries genetic instructions, and RNA (Ribonucleic Acid) is involved in protein synthesis and gene regulation.

  4. Proteins: Polymers of amino acids forming polypeptides; perform a vast array of diverse functions in cells.

    • Monomers: Amino acids. There are 20 common types, and their specific sequence and interactions determine the protein's unique structure and function.

Proteins and Amino Acids

  • The building blocks of proteins are amino acids, each characterized by:

    • A central carbon atom (alpha-carbon),

    • An amino group (-NH_2),

    • A carboxyl group (-COOH),

    • A hydrogen atom, and

    • A distinctive side chain (R-group), which varies among the 20 amino acids and determines their specific chemical properties (e.g., polar, nonpolar, charged).

  • Peptide bonds form through a dehydration reaction (removal of a water molecule) between the carboxyl group of one amino acid and the amino group of another, linking amino acids into a polypeptide chain.

  • A protein’s function depends critically on its four levels of structure:

    • Primary structure: The unique, linear sequence of amino acids in the polypeptide chain. This sequence is determined by genetic information.

    • Secondary structure: Localized folding patterns, such as alpha-helices (a coiled structure) and beta-pleated sheets (a folded, zigzagging structure), stabilized by hydrogen bonds between the backbone components (not R-groups).

    • Tertiary structure: The overall three-dimensional shape of a single polypeptide chain, resulting from interactions between the R-groups, including hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges (-S-S-).

    • Quaternary structure: The arrangement of multiple polypeptide subunits (if a protein has more than one) to form a functional protein complex.

  • The specific sequence of amino acids (primary structure) dictates how the protein folds into its higher-order structures, ultimately determining its biological function. Any change in this sequence can lead to a misfolded protein and loss of function.

Protein Functions

  • Proteins are incredibly versatile and perform a wide range of essential functions, including:

    • Enzymatic: Act as enzymes, biological catalysts that greatly speed up biochemical reactions by lowering the activation energy without being consumed in the process. Enzymes exhibit high specificity for their substrates, typically interacting via an active site (the region where the substrate binds).

    • Structural: Provide support (e.g., collagen in connective tissues, keratin in hair and nails).

    • Transport: Carry substances (e.g., hemoglobin transports oxygen in blood, membrane channels transport ions).

    • Signaling: Act as hormones or receptors, facilitating communication within and between cells (e.g., insulin).

    • Defense: Serve as antibodies to protect the body from pathogens.

    • Movement: Are components of muscle fibers (e.g., actin, myosin).

Summary

  • Water is a polar molecule, acting as a universal solvent, and its unique properties (cohesion, adhesion, specific heat, density of ice) are vital for life, largely due to hydrogen bonding.

  • Four major macromolecules (Carbohydrates, Lipids, Nucleic Acids, and Proteins) exist, each built from specific monomers, possessing distinct chemical properties, and crucial for cellular structure and function, with their diverse roles arising from their intricate structures.