Biology 110: The Molecules of Cells Flashcards

Chapter 3 Big Ideas: The Molecules of Cells## Course Context- Course: BIO 110- Semester: Fall 2025- Primary Classification: Organic compounds, Lipids, Nucleic Acids, Proteins, and Carbohydrates.## Introduction to Biological Molecules - Case Study: Lactose Intolerance- Case Relevance: Many adults globally are unable to digest dairy products because they cannot break down lactose, which is a sugar found in milk.- Biological Mechanism: Lactose is broken down by a specific enzyme called lactase.- Evolutionary/Genetic Link: A genetic mutation involving nucleic acids allows for the production of the enzyme (a protein) required to digest the lactose (a carbohydrate).## Organic Compounds- Definition: Organic compounds are compounds primarily made of carbon.- Properties of Carbon:- Carbon possesses $4$ valence electrons.- It has the ability to bond with $4$ other atoms, enabling the creation of large, complex molecules.- Carbon chains serve as the backbone for $\text{most}$ organic molecules.- Bonding Types:- Single Bonds: Formed by sharing one electron.- Double Bonds: Formed by sharing two electrons.- Molecular Geometry: Different types of bonds and arrangements result in distinct molecule shapes.- Methane ($CH_4$): Represented as a model with four single bonds, resulting in a tetrahedral shape.- Carbon Skeleton Variations:- Hydrocarbons: Compounds containing exclusively carbon and hydrogen atoms (e.g., methane, ethane, propane, butane).- Isomers: Molecules that share the same molecular formula but possess different structures. This results in different shapes and properties (e.g., butane vs. isobutane).- Diversity: Isomers significantly increase the diversity of organic molecules.- Examples of Carbon Skeletons:- Ethane: $H-C-C-H$ with hydrogens filling valence spots.- Propane: $H-C-C-C-H$ with hydrogens filling valence spots.- 1-Butene: A four-carbon chain with a double bond between the first and second carbons.- 2-Butene: A four-carbon chain with a double bond between the second and third carbons.- Butane: A straight four-carbon alkane chain.- Isobutane: A branched isomer of butane.- Cyclohexane: A six-carbon ring structure.- Benzene: A six-carbon ring with alternating double bonds.## Important Chemical Groups- Concept: An organic compound's properties depend not only on the carbon skeleton but also on the atoms attached to it.- Functional Groups: Most are hydrophilic (water-loving) and increase a molecule's solubility in water.- Methyl Group: Specifically nonpolar and non-reactive.- Key Chemical Groups Detailed:- Hydroxyl Group ($-OH$): A hydrogen atom bonded to an oxygen atom. Compounds with this group are classified as alcohols.- Carbonyl Group ($C=O$): A carbon atom double-bonded to an oxygen atom.- Carboxyl Group ($-COOH$ or $HO-C=O$): A carbon atom double-bonded to an oxygen and also bonded to a hydroxyl group. Acts as a carboxylic acid; can exist in an ionized form ($-COO^- + H^+$).- Amino Group ($-NH_2$): A nitrogen atom bonded to two hydrogen atoms. Compounds are called amines. Can exist in an ionized form ($-NH_3^+$).- Phosphate Group ($-PO_4$ or $-OPO_3^{2-}$): A phosphorus atom bonded to four oxygen atoms. Found in organic phosphates such as ATP components.- Methyl Group ($-CH_3$): A carbon atom bonded to three hydrogen atoms. Found in methylated compounds.- Functional Differences Example: The sex hormones testosterone and estradiol differ only slightly in their attached chemical groups, illustrating how small structural changes drastically affect biological function.## Macromolecules: Making and Breaking Polymers- Definitions:- Macromolecules: Very large biological molecules.- Polymers: Large molecules made by stringing together smaller building blocks.- Monomers: The individual building blocks of polymers.- Chemical Reactions:- Dehydration Reaction: Links monomers to form polymers by removing a water molecule.- Hydrolysis: Breaks polymers apart into monomers by adding a water molecule.- Mediation: These reactions are facilitated by enzymes, which are specialized macromolecules (usually proteins) that speed up chemical reactions.## Carbohydrates- Monomers: Called monosaccharides.- Chemical Formula: Generally multiples of $CH_2O$.- Structure: Usually chains of $3$ to $7$ carbons. In aqueous (water-based) solutions, most $5$-carbon and $6$-carbon sugars (like glucose and fructose) form ring structures.- Disaccharides: Two monosaccharides linked via a dehydration reaction.- Maltose: Formed from two glucose molecules ($Glucose + Glucose \rightarrow Maltose + H_2O$).- Sucrose: The most common disaccharide (table sugar).- Health Note: The FDA recommends that added sugar should comprise no more than $10\%$ of daily caloric intake. High sugar intake is correlated with various adverse health effects.- Polysaccharides: Carbohydrate polymers made of hundreds to thousands of monosaccharides.- Energy Storage: Starch (in plants) and Glycogen (in animals).- Structural Support: Cellulose (plant cell walls) and Chitin (found in fungal cell walls and insect/crustacean exoskeletons).## Lipids- Definition: Diverse hydrophobic (water-fearing) compounds composed primarily of carbon and hydrogen.- Types of Lipids:- Fats (Triglycerides): Composed of one glycerol linked to three fatty acids. Primary function is long-term energy storage.- Unsaturated Fatty Acids: Contain one or more double bonds in the carbon chain. These create kinks that prevent solidification, making them liquid at room temperature (e.g., plant oils).- Saturated Fatty Acids: Contain the maximum number of hydrogen atoms (no double bonds). They are solid at room temperature (e.g., animal fats).- Trans Fats:- Origin: Created in the $1890s$ through hydrogenation (adding hydrogen to unsaturated fats) to create partially hydrogenated vegetable oils (PHOs).- Benefits to Industry: Do not spoil quickly and withstand frequent reheating (e.g., margarine).- Health Risks: Recent research indicates trans fats pose greater health risks than saturated fats.- Regulatory Timeline: In $2006$, the FDA required trans fat listing on labels. In $2015$, the FDA mandated PHO removal from foods within three years.- Phospholipids: Major structural components of cell membranes.- Steroids:- Cholesterol: Common in animal cell membranes and a precursor for other steroids like sex hormones.- Anabolic Steroids: Synthetic variants of testosterone.## Proteins- Definition: Polymers made of long chains of amino acids. They are involved in nearly every dynamic function of the body.- Structure-Function Relationship: Function depends on the specific three-dimensional shape of the protein.- Denaturation: The process where a protein unravels, losing its specific shape and, consequently, its function.- Amino Acids:- There are $20$ different types of amino acids.- Generic Structure: A central carbon atom bonded to an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a variable R group (side chain).- Peptide Bonds: Formed by a dehydration reaction linking the carboxyl group of one amino acid to the amino group of the next.- Polypeptide: A chain of amino acids.- Protein Functions:- Enzymes (catalysts).- Transport proteins (in membranes).- Defensive proteins (antibodies).- Signal proteins (hormones).- Receptor proteins.- Contractile proteins (muscle).- Structural proteins (collagen).- Storage proteins.- Four Levels of Protein Structure:- Primary Structure: The specific sequence of amino acids in the polypeptide chain.- Secondary Structure: Local coiling ($alpha helix$) or folding ($beta pleated sheet$) of the chain, stabilized by hydrogen bonds between backbone atoms.- Tertiary Structure: The overall $3$-dimensional shape resulting from interactions among R groups.- Quaternary Structure: Results when a protein consists of more than one polypeptide chain associated together.## Nucleic Acids- Definition: Molecules that store, transmit, and help express hereditary information.- Types:- DNA (Deoxyribonucleic Acid): The molecule of inheritance; contains directions for all cell components. Structure is a double helix.- RNA (Ribonucleic Acid): Usually a single polynucleotide chain.- Nucleotides: The monomers of nucleic acids. Each consists of:- A five-carbon sugar.- A phosphate group.- A nitrogenous base.- Nitrogenous Bases: Adenine ($A$), Guanine ($G$), Thymine ($T$), and Cytosine ($C$).- Flow of Genetic Information: The central dogma states that DNA is transcribed into RNA, which is then translated into Proteins ($DNA \rightarrow RNA \rightarrow Proteins$).