Biology Chapter on Macromolecules and Reactions

Biological Molecules

• Biological molecules, such as nucleic acids, proteins, lipids, and carbohydrates, are the crucial players in the structural and functional organization of cells.
• These molecules exhibit distinct structures and biochemical properties.
• Many are composed of smaller repeating subunits called monomers, forming polymers.
• Lipids are an exception, not a polymer.

Condensation & Hydrolysis Reactions

• Polymers are composed of repeating monomer subunits.
• Polymers form through condensation/dehydration reactions, where monomers bond together with the removal of water.
• Polymers break down into monomers through hydrolysis reactions, which involve adding water to break covalent bonds.

Lipids

• Lipids are a diverse group of fatty, water-insoluble compounds primarily composed of carbon, hydrogen, and oxygen.
• They have various functions including energy storage, membrane components, and hormone production.
• There are four main classes: Acylglycerides (neutral fats), Phospholipids, Steroids, and Waxes.

Lipids: Triacylglycerides

• Fats (solids) and oils (liquids) are known as triacylglycerides.
• They consist of glycerol and three fatty acids.
• Fatty acid chains can vary in length (14-20 carbons).
• Fatty acids might be saturated (no double bonds), unsaturated (one double bond), or polyunsaturated (two or more double bonds).
• These differences affect the physical state (solid or liquid) of the fat.
• The functions include long-term energy storage, insulation, structural support, and cushioning.
• Lipolysis (hydrolysis) breaks down triacylglycerides into glycerol and free fatty acids, while lipogenesis (dehydration) builds them from glycerol and fatty acids.

Lipids: Phospholipids

• Phospholipids are modified triglycerides.
• They contain a diglyceride with a phosphate-containing group—a polar head—and two nonpolar fatty acid tails—the hydrophobic tails..
• In aqueous environments, phospholipids form lipid bilayers—a key component in cell membranes.

Lipids: Steroids

• Steroids are flat molecules with four interconnected hydrocarbon rings.
• Cholesterol is the fundamental backbone for all steroids, synthesized by the liver.
• Steroids are also obtained from dietary sources.
• Steroids are crucial components of cell membranes and act as hormones, vital for various bodily functions, including Vitamin D production.

Lipids: Eicosanoids

• Eicosanoids are a diverse group of 20-carbon fatty acids derived from arachidonic acid.
• They act as signaling molecules in the body.
• Four types of eicosanoids exist: prostaglandins, prostacyclins, thromboxanes, and leukotrienes.
• These molecules regulate various physiological responses including inflammation, blood clotting, and labor contractions.

Lipids: Waxes

• Waxes consist of a fatty acid and a long-chain alcohol.
• They form an ester bond formed from a condensation reaction .
• Waxes protect surfaces and function as protective barriers.

Carbohydrates

• Carbohydrates are composed of simple sugars and sugar polymers, broadly classified by size: monosaccharides, disaccharides, and polysaccharides.
• Monosaccharides contain C, H, and O in a fixed ratio (CH2O)n, often with 3 to 7 carbons.
• Monosaccharides linked together by covalent bonds form disaccharides (two sugars) and polysaccharides (many sugars).
• Carbohydrates are a primary energy source for cells.
• They also serve as structural components and identification tags.
• Polymerization occurs through condensation reactions, and breakdown through hydrolysis.

Nucleic Acids

• Nucleic acids are the largest molecules in the body.
• They contain genetic information and facilitate its transfer.
• The key classes are DNA and RNA.
• Nucleic acids are polymers composed of nucleotide monomers.
• Nucleotides each contain a pentose sugar, a phosphate group, and a nitrogenous base.
• DNA and RNA differ in their sugar type (deoxyribose and ribose, respectively) and one nitrogenous base (thymine in DNA replaced by uracil in RNA).
• DNA is double-stranded; RNA is single-stranded, although some RNA conformations display base pairs.

Nucleic Acids: Components

• Nucleotides: The monomers of nucleic acids, comprised of a pentose sugar, a phosphate group, and a nitrogenous base.
• Pentose Sugar: A five-carbon sugar (either ribose in RNA or deoxyribose in DNA) forms the backbone of the nucleotide.
• Phosphate Group: Attaches to the sugar's 5' carbon.
• Nitrogenous Base: A nitrogen-containing organic molecule. Purines (adenine and guanine) have a double ring structure; pyrimidines (cytosine, thymine, and uracil) have a single ring.

ATP: The Battery of the Cell

• ATP (adenosine triphosphate) is a crucial energy molecule in cells.
• Its structure comprises adenine, a ribose sugar, and three phosphate groups.
• The energy is stored in the high-energy phosphate bonds in the ATP molecule.
• The instability of ATP arises from the electrostatic repulsion between closely positioned phosphate groups.

DNA

• DNA is a long, double-stranded polymer.
• The DNA “backbone” consists of the sugars and phosphate groups, linked by phosphodiester bonds.
• The two strands run in opposite directions (antiparallel).
• DNA strands adhere via complementary base pairing (A with T, and C with G) held together by hydrogen bonds in a double helix.

RNA

• RNA is a single-stranded polymer of nucleotides.
• Different from DNA, RNA uses uracil (U) instead of thymine (T) as a base.
• RNA plays crucial roles in protein synthesis.
• The various forms of RNA exhibit different secondary and tertiary structures, contributing to their diverse functions..

Central Dogma of Genetics

• The central dogma of molecular biology describes the flow of genetic information from DNA to RNA to proteins.
• DNA encodes genetic information.
• RNA carries information from the DNA to the ribosome.
• Ribosomes synthesize proteins based on the RNA instructions.
• Transcription is the process of creating a temporary RNA copy of a gene from DNA.
• Translation is the process of converting RNA information into a protein.

Proteins

• Proteins are the fundamental structural and functional components of cells.
• They are composed of chains of amino acids.
• Proteins have diverse vital roles, including structure, catalysis (via enzymes), regulation (as hormones), and transport.

Amino Acids

• Amino acids are the building blocks of proteins.
• There are 20 common types of amino acids in proteins.
• Each amino acid has an amino group (-NH2), a carboxyl group (-COOH), and a unique side chain (R group) that distinguishes it.
• Amino acids are grouped based on their side chain properties (polar, non-polar, acidic, basic).

Peptide Bonds

• Peptide bonds link amino acids together to form polypeptide chains (proteins).
• The peptide bonds result from condensation reactions.
• The sequence of amino acids, determined by the DNA code, dictates protein structure and function.

Protein Folding

• Chaperone proteins assist in protein folding.
• They orchestrate the formation of the correct three-dimensional protein structure.
• This structure is crucial for protein function.

Protein Structure Levels

• Proteins have four structural levels: primary, secondary, tertiary, and quaternary.
• The primary structure is the linear sequence of amino acids.
• Secondary structure involves recurring patterns like α-helices and β-sheets stabilized by hydrogen bonds.
• Tertiary structure is the three-dimensional shape of the entire polypeptide chain, stabilized by various interactions including hydrogen bonds, hydrophobic interactions, ionic bonds, and van der Waals forces.
• Quaternary structure arises when multiple polypeptide chains interact to form a functional protein complex.
• All these levels are determined by the sequence of amino acids in the primary structure.

Denaturation

• Denaturation is a process that disrupts the three-dimensional structure of a protein.
• This disruption may be caused by changes in pH, high temperature, or the presence of certain chemicals.
• The loss of the three-dimensional shape is usually accompanied by resulting functional disruptions.

Enzymes

• Enzymes are biological catalysts that speed up chemical reactions in cells without being consumed.
• The substrates bind to a specific region called the active site of the enzyme to facilitate a chemical transformation.
• There's a specific relationship between the substrate's shape and the enzyme's active site—often described as an induced fit.
• Enzymes have specific characteristics.
• Enzyme activity is influenced by factors like substrate concentration, temperature, and pH.

Enzyme and Reaction Rates

• Enzyme activity depends on factors such as substrate concentration, temperature, and pH.
• Optimum conditions maintain the enzyme's 3D shape and hence its function.
• Enzymes facilitate rapid reactions, effectively lowering the energy needed to start a biological reaction.