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Comprehensive Biology Notes (Lecture Content)

Macromolecules: Carbohydrates (Pages 188–205)

Carbohydrates are a diverse group of organic compounds serving essential roles in living organisms, primarily as sources of energy, structural components, and recognition elements.

  • Roles and Functions:

    • Energy Storage and Supply: Monosaccharides like glucose are the primary immediate energy source for cellular respiration. Polysaccharides such as starch (in plants) and glycogen (in animals) serve as efficient, readily mobilizable energy reserves.

    • Structural Components: Cellulose is the main structural component of plant cell walls, providing rigidity and support. Chitin forms the exoskeletons of arthropods and the cell walls of fungi, offering protection and structural integrity.

    • Cell Identity and Recognition: Carbohydrates covalently linked to proteins (glycoproteins) or lipids (glycolipids) extend from the cell surface, acting as distinctive markers that enable cells to recognize each other and participate in cell-cell adhesion and signaling.

    • Precursors: Simple sugars can be metabolic precursors for the synthesis of other essential biomolecules, including nucleotides (components of DNA and RNA) and amino acids (building blocks of proteins).

  • Monomers: Monosaccharides (Simple Sugars):

    • These are the simplest form of carbohydrates, typically composed of a single sugar unit. Their chemical formula is generally a multiple of (CH2O)n. They are characterized by a carbonyl group (C=O) and multiple hydroxyl (-OH) groups.

    • Classification by Carbon Number:

    • Trioses (n=3): e.g., glyceraldehyde, dihydroxyacetone.

    • Pentoses (n=5): e.g., ribose (in RNA), deoxyribose (in DNA), xylose.

    • Hexoses (n=6): e.g., glucose, fructose, galactose. These are the most common and metabolically significant monosaccharides.

    • Linear and Ring Forms: In aqueous solutions, monosaccharides with five or more carbons typically cyclize, forming stable ring structures (pyranose for six-membered rings, furanose for five-membered rings). Glucose, for instance, primarily exists as \alpha-D-glucose and \beta-D-glucose anomers.

    • Isomers: Glucose, fructose, and galactose all share the chemical formula C6H{12}O_6 but differ in the arrangement of their atoms around asymmetric carbons (stereoisomers) or the position of their carbonyl group (structural isomers, e.g., glucose is an aldose, fructose is a ketose). These structural differences impact their reactivity and recognition by enzymes.

  • Disaccharides (Double Sugars):

    • Formed when two monosaccharide units are joined by a covalent bond called a glycosidic linkage, a bond formed through a dehydration synthesis reaction where a water molecule is removed.

    • Examples:

    • Maltose (Malt Sugar): Glucose + Glucose. Linked by an \alpha-1,4-glycosidic bond. Produced from the hydrolysis of starch.

    • Lactose (Milk Sugar): Galactose + Glucose. Linked by a \beta-1,4-glycosidic bond. Requires the enzyme lactase for digestion.

    • Sucrose (Table Sugar): Glucose + Fructose. Linked by an \alpha-1,2-\beta-2,1-glycosidic bond (anomeric carbons of both sugars involved).

  • Polysaccharides (Complex Carbohydrates):

    • Long polymers consisting of hundreds to thousands of monosaccharide units linked by glycosidic bonds. They can be linear or branched.

    • Energy Storage Polysaccharides:

    • Starch: The primary energy storage polysaccharide in plants. Composed of two types of glucose polymers:

      • Amylose: Unbranched chains of glucose monomers joined by \alpha-1,4-glycosidic linkages. Tends to form helixes.

      • Amylopectin: Branched chains of glucose monomers, with \alpha-1,4-linkages along the main chain and \alpha-1,6-linkages at branch points. More compact than amylose.

    • Glycogen: The main energy storage polysaccharide in animals (primarily in liver and muscle cells). Structurally similar to amylopectin but much more highly branched, allowing for rapid glucose mobilization.

    • Structural Polysaccharides:

    • Cellulose: The most abundant organic compound on Earth, forming the cell walls of plants. It is a linear polymer of glucose units linked by \beta-1,4-glycosidic bonds. The \beta-linkage allows cellulose chains to form straight, unbranched microfibrils that can aggregate through extensive hydrogen bonding between adjacent chains, creating extremely strong, insoluble fibers. Most animals cannot digest cellulose due to the lack of the necessary \beta-glucosidase enzymes.

    • Chitin: A structural polysaccharide found in the exoskeletons of insects, crustaceans, and the cell walls of fungi. It is a polymer of N-acetylglucosamine (a glucose derivative) linked by \beta-1,4-glycosidic bonds, structurally similar to cellulose but with an amino-containing group, making it even stronger.

  • Glycosidic Linkages: \alpha vs. \beta:

    • The precise orientation of the glycosidic bond is crucial for the polysaccharide's structure and digestibility.

    • \alpha bonds (e.g., in starch, glycogen) create a curvilinear or helical structure, which is relatively open and easily accessible to digestive enzymes like amylase. This allows for efficient energy extraction.

    • \beta bonds (e.g., in cellulose, chitin) result in straight, extended chains. This linear conformation allows for strong intermolecular hydrogen bonding, forming tightly packed, insoluble fibers that are resistant to breakdown by most enzymes. This provides excellent structural stability.

  • Glycosidic Bond Formation and Hydrolysis:

    • Formation (Dehydration Synthesis): A water molecule is removed as a bond is formed between the anomeric carbon of one monosaccharide and a hydroxyl group of another. This is an anabolic, energy-requiring process.

    • Hydrolysis: A water molecule is added to break a glycosidic bond, releasing energy and individual monosaccharides. This is a catabolic, energy-releasing process, typically catalyzed by specific hydrolytic enzymes.

Macromolecules: Proteins (Pages 133–161, 161–162, 169–173)

Proteins are the most functionally and structurally diverse class of macromolecules, performing a vast array of essential tasks in all living cells. Their functions range from catalyzing biochemical reactions and transporting molecules to providing structural support and mediating cell communication.

  • Diverse Functions:

    • Enzymatic: Catalyze biochemical reactions, speeding up metabolic processes (e.g., digestive enzymes like amylase, pepsin).

    • Transport: Carry substances across cell membranes or throughout the body (e.g., hemoglobin transports oxygen, channel proteins transport ions).

    • Defensive: Protect against disease (e.g., antibodies).

    • Signaling and Receptors: Transmit signals between cells and receive chemical signals (e.g., insulin hormone, G protein-coupled receptors).

    • Regulation: Control gene expression and other cellular processes (e.g., transcription factors).

    • Movement/Contractile: Enable cell and organismal movement (e.g., actin and myosin in muscle contraction, proteins in cilia and flagella).

    • Structural: Provide support and shape to cells, tissues, and organs (e.g., collagen in connective tissue, keratin in hair and nails).

    • Storage: Store amino acids for later use (e.g., casein in milk, ovalbumin in egg whites).

  • Amino Acids: The Monomers:

    • Proteins are polymers of amino acids, of which there are 20 common types (canonical amino acids).

    • General Structure of an Amino Acid: Each amino acid has a central carbon atom (the \alpha-carbon) covalently bonded to four different groups:

    • An amino group (-NH2), which is basic and typically protonated (-NH3+) at physiological pH.

    • A carboxyl group (-COOH), which is acidic and typically deprotonated (-COO–) at physiological pH.

    • A hydrogen atom.

    • A unique side chain (R group), which varies among the 20 amino acids and confers its specific chemical properties.

    • R Groups and their Properties: The chemical nature of the R group determines whether an amino acid is:

    • Nonpolar/Hydrophobic: Tend to cluster away from water in the interior of folded proteins. Examples: Glycine (G), Alanine (A), Valine (V), Leucine (L), Isoleucine (I), Proline (P), Methionine (M), Phenylalanine (F), Tryptophan (W).

    • Polar/Hydrophilic: Have partial charges and can form hydrogen bonds with water and other polar molecules. Examples: Serine (S), Threonine (T), Cysteine (C), Tyrosine (Y), Asparagine (N), Glutamine (Q).

    • Electrically Charged/Hydrophilic:

      • Acidic (Negative charge): Have carboxyl groups in their R-chains that are deprotonated at physiological pH. Examples: Aspartate (D), Glutamate (E).

      • Basic (Positive charge): Have amino groups in their R-chains that are protonated at physiological pH. Examples: Lysine (K), Arginine (R), Histidine (H).

  • Protein Structure Levels:
    The complex three-dimensional shape of a functional protein is crucial for its activity and arises from a hierarchical organization:

    • Primary Structure: The unique, linear sequence of amino acids in a polypeptide chain, read from the N-terminus (amino end) to the C-terminus (carboxyl end). This sequence is determined by the genetic code (DNA) and is stabilized by peptide bonds (covalent bonds formed between the carboxyl group of one amino acid and the amino group of another via dehydration synthesis).

    • Secondary Structure: Refers to localized, regularly repeating structural patterns formed by hydrogen bonds between atoms of the polypeptide backbone (the N-H and C=O groups of different peptide bonds), not the R groups. The two main types are:

    • \alpha-helix: A coiled structure, like a spiral staircase, held by hydrogen bonds between every fourth amino acid.

    • \beta-pleated sheet: A folded, zig-zagging structure formed by hydrogen bonds between parallel or antiparallel segments of the polypeptide chain.

    • Tertiary Structure: The overall, three-dimensional shape of a single polypeptide chain, determined by various interactions between the amino acid R groups and between R groups and the polypeptide backbone. These interactions stabilize the intricate folding patterns:

    • Hydrophobic interactions: Nonpolar R groups tend to cluster in the protein's interior, away from the aqueous environment.

    • Hydrogen bonds: Form between polar R groups.

    • Ionic bonds: Attractions between positively and negatively charged R groups (acidic and basic amino acids).

    • Disulfide bridges: Strong covalent bonds formed between the sulfhydryl (-SH) groups of two cysteine residues (oxidative reaction of: -SH + HS- \rightarrow -S-S- + H_2O). These are crucial for stabilizing many protein structures.

    • Quaternary Structure: The arrangement and association of multiple polypeptide chains (subunits) to form a single, functional protein complex. This level is present only in proteins composed of two or more polypeptide chains (e.g., hemoglobin, which has four subunits, or collagen, a triple helix of three polypeptides).

  • Protein Chemistry:

    • Peptide Bond Formation: Formed via dehydration synthesis, where a water molecule is removed as the carboxyl group of one amino acid and the amino group of another join. This forms a rigid C-N bond (peptide bond) with partial double-bond character.

    • Denaturation: The process by which a protein loses its native, functional three-dimensional structure (secondary, tertiary, and quaternary structures) due to disruptions by external factors such as extreme heat, changes in pH, high salt concentrations, or strong chemicals. Denaturation results in the loss of biological activity. While sometimes irreversible, renaturation (restoration of structure and function) can occur if the disrupting conditions are mild and the primary sequence (which contains all the information for folding) remains intact.

  • Relationship of Structure to Function:

    • The specific three-dimensional structure of a protein is paramount to its function. Even a slight alteration in shape can compromise or abolish its biological activity. For example, the precise active site structure of an enzyme is essential for binding its specific substrate and catalyzing a reaction.

Macromolecules: Nucleic Acids (Pages 162–181, 183–187, 190–177)

Nucleic acids are macromolecules that store and transmit hereditary information, playing a central role in gene expression and the continuity of life. They exist primarily as deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

  • Functions:

    • Storage of Genetic Information: DNA serves as the long-term repository of genetic instructions for all cellular processes and the inherited characteristics of an organism.

    • Transmission of Genetic Information: DNA is replicated faithfully to pass genetic information from one generation to the next.

    • Expression of Genetic Information: The information in DNA is transcribed into RNA, which then directs the synthesis of proteins (translation), thereby controlling cell structure and function.

  • Monomers: Nucleotides:

    • Nucleic acids are polymers of nucleotides. Each nucleotide is composed of three covalently linked components:

    1. A five-carbon sugar (pentose):

      • Deoxyribose in DNA (lacks an oxygen at the 2' carbon).

      • Ribose in RNA (has an oxygen at the 2' carbon).

    2. A phosphate group (-\text{PO}_4^{2-}).

    3. A nitrogenous base (N-containing ring structure).

    • Nitrogenous Bases:

    • Purines: Double-ring structures.

      • Adenine (A)

      • Guanine (G)

    • Pyrimidines: Single-ring structures.

      • Cytosine (C)

      • Thymine (T) (found only in DNA)

      • Uracil (U) (found only in RNA, replaces thymine)

  • Nucleotide Polymerization: Sugar-Phosphate Backbone:

    • Nucleotides are linked to form a polynucleotide chain by phosphodiester bonds. These are covalent bonds formed between the phosphate group of one nucleotide (attached to its 5' carbon) and the hydroxyl group on the 3' carbon of the adjacent nucleotide's sugar.

    • This creates a repeating sugar-phosphate backbone with directional polarity:

    • 5' end: Has a free phosphate group attached to the 5' carbon of the sugar.

    • 3' end: Has a free hydroxyl group attached to the 3' carbon of the sugar. Genetic information is always synthesized and read in the 5' to 3' direction.

  • DNA Structure (Deoxyribonucleic Acid):

    • Double Helix: DNA typically exists as a double helix, proposed by Watson and Crick, resembling a twisted ladder. It consists of two long polynucleotide strands wound around a common axis.

    • Antiparallel Strands: The two strands run in opposite 5' to 3' directions (one is 5' to 3', the other is 3' to 5'), which is essential for replication and transcription.

    • Base Pairing (Chargaff's Rules): The two strands are held together by specific hydrogen bonds between complementary nitrogenous bases:

    • Adenine (A) always pairs with Thymine (T) via two hydrogen bonds (A=T).

    • Guanine (G) always pairs with Cytosine (C) via three hydrogen bonds (G\equiv C).

    • Stability: The large number of hydrogen bonds and the stacking interactions between bases contribute to the high stability of the DNA double helix.

    • Information Storage: The sequence of nucleotides along the DNA helix constitutes the genetic code, encoding instructions for protein synthesis and cellular functions. In eukaryotes, DNA is found primarily in the nucleus, organized into chromatin with histone proteins.

  • RNA Structure (Ribonucleic Acid):

    • Single-Stranded: RNA molecules are typically single-stranded, unlike the double-stranded DNA. However, they can fold back on themselves to form localized double-helical regions, creating complex 3D structures.

    • Ribose Sugar: Contains ribose sugar instead of deoxyribose.

    • Uracil (U) instead of Thymine (T): Uracil pairs with Adenine in RNA (A=U).

    • Diverse Forms and Functions:

    • Messenger RNA (mRNA): Carries genetic information from DNA in the nucleus to the ribosomes in the cytoplasm for protein synthesis.

    • Transfer RNA (tRNA): Acts as an adaptor molecule, carrying specific amino acids to the ribosome during translation, matching them to codons on the mRNA.

    • Ribosomal RNA (rRNA): A major component of ribosomes, catalyzing peptide bond formation during protein synthesis.

    • Other types: Small nuclear RNA (snRNA), microRNA (miRNA), etc., involved in gene regulation and processing.

  • Gene Expression Flow (The Central Dogma):
    The fundamental process by which genetic information is converted into a functional product (protein):

    \text{DNA} \xrightarrow{\text{Transcription}} \text{RNA} \xrightarrow{\text{Translation}} \text{Protein}

    • Transcription (DNA to RNA): Occurs in the nucleus of eukaryotic cells (and cytoplasm of prokaryotes). The genetic information in a DNA segment (gene) is copied into an RNA molecule.

    • Translation (RNA to Protein): Occurs on ribosomes in the cytoplasm. The nucleotide sequence of mRNA is decoded to synthesize a specific protein with its unique amino acid sequence.

  • Nucleic Acid Terminology:

    • Nucleoside: Consists of a nitrogenous base covalently linked to a pentose sugar (e.g., adenosine, guanosine, deoxycytidine).

    • Nucleotide: A nucleoside with one or more phosphate groups attached (e.g., ATP - adenosine triphosphate, dCTP - deoxycytidine triphosphate).

    • Directionality (5' to 3'): The inherent polarity of nucleic acid strands is crucial for enzymes involved in synthesis and reading, always proceeding from the 5' phosphate end to the 3' hydroxyl end.