Exam Review (7) - PDF

UNIT 1 1.1 The fundamental Chemistry of Life Types of Chemical Bonds 1.​Ionic Bond ○​ Forms between two oppositely charged atoms or molecules. ○​ Cation: Positively charged ion. ○​ Anion: Negatively charged ion. 2.​Covalent Bond ○​ Forms when atoms s...

UNIT 1 1.1 The fundamental Chemistry of Life Types of Chemical Bonds 1.​Ionic Bond ○​ Forms between two oppositely charged atoms or molecules. ○​ Cation: Positively charged ion. ○​ Anion: Negatively charged ion. 2.​Covalent Bond ○​ Forms when atoms share electrons due to similar electronegativity. ○​ Electronegativity: An atom’s attraction to shared electrons. 3.​Polar Covalent Bond ○​ Unequal sharing of electrons between two atoms. ○​ Creates partial positive and negative charges within the molecule. Polarity and Intermolecular Forces ​ Polarity: Unequal charge distribution within a molecule, leading to intermolecular attractions. ​ Intermolecular Forces: Attractions between molecules, including: ○​ Van der Waals Forces: Weak attractions between molecules or molecular parts when close together.  ○​ Hydrogen Bonds: Attractions between a partially positively charged hydrogen atom and a partially negatively charged atom. Type Present in Molecular level Strength Dispersion All molecules and Low atoms Dipole-dipole Polar molecules To Hydrogen Molecules containing The bonding H bonded to F,O,or N Ion-dipole Mixtures of ionic Highest compounds and polar compounds Isotopes and Radioisotopes ​ Isotope: A form of an element differing in its number of neutrons. ​ Radioisotope: A radioactive isotope of an element. Applications of Radioisotopes ​ Dating organic materials, rocks, and fossils. ​ Using radioactive tracers to: ○​ Visualize internal structures in the body for diagnostics. ○​ Track chemical reactions to understand processes better. Common Chemical Reactions 1.​Dehydration Reaction: Removal of water to form bonds. 2.​Hydrolysis Reaction: Addition of water to break bonds. 1.2 Water’s Life’s solvent Water: Unique Properties and Importance Polar and Hydrophilic Nature ​ Hydrophilic Molecules: Polar or charged molecules strongly attracted to water. ​ Hydrophobic Molecules: Non-polar molecules not strongly attracted to water. Solvent Properties ​ Water is known as the universal solvent, capable of dissolving more substances than any other liquid. ​ This property enables water to: ○​ Distribute nutrients, minerals, and chemicals to cells. ○​ Facilitate the removal of waste products from the body. Thermal Properties 1.​High Specific Heat Capacity ○​ Hydrogen bonding allows water to absorb or release large amounts of thermal energy with minimal temperature change. ○​ This stabilizes environments and organisms, ensuring conditions necessary for life.  2.​High Heat of Vaporization ○​ Water absorbs significant thermal energy to transition from liquid to vapor. ○​ Evaporation cools surfaces, aiding in temperature regulation for plants and animals. 3.​Temperature Regulation ○​ Water’s thermal properties allow it to buffer temperature changes in organisms and environments. ○​ Evaporation provides an effective cooling mechanism. Cohesion and Adhesion ​ Cohesion: Water molecules form hydrogen bonds with each other, resulting in: ○​ High Surface Tension: Allows small organisms, like water striders, to walk on water surfaces. ​ Adhesion: Water molecules form hydrogen bonds with other polar substances, leading to: ○​ Capillary Action: Enables water to move up plant xylem tubes. ○​ Solubility of Polar Compounds: Polar substances, such as sugars, dissolve readily in water. ​ Significance of Cohesion and Adhesion: ○​ Facilitates water transport in plants. ○​ Supports water retention in soil. ○​ Provides lubrication in biological systems. Density of Solid Water ​ Ice is less dense than liquid water:  ○​ Ice floats, providing insulation for aquatic life in cold environments. Acids, Bases, and Buffers ​ Acids: Solutions with a higher concentration of hydronium ions (H₃O⁺) than hydroxide ions (OH⁻). ​ Bases: Solutions with a higher concentration of hydroxide ions than hydronium ions. ​ Neutralization Reactions: Acids and bases react to form water and a salt. ​ Buffers: ○​ Chemicals that stabilize pH by accepting or donating H⁺ ions. ○​ Essential for maintaining pH balance in biological systems. The Key to Water’s Unique Properties The word that gives water nearly all its unique properties is hydrogen bonding. These bonds are responsible for its high cohesion, adhesion, thermal properties, solvent capabilities, and the density anomaly of ice. 1.3 The Carbon Chemistry of Life Carbon: Uniqueness and Biological Importance Carbon’s Role in Life ​ Carbon is the foundation of many large and complex molecules essential for life. ​ Its unique structure allows it to form a vast diversity of molecules, making it central to biochemistry. The Structure and Flexibility of Carbon 1.​Bonding Capacity ○​ Carbon can form bonds with up to four other atoms simultaneously. ○​ This enables the creation of a nearly infinite variety of molecules. 2.​Carbon Chains ○​ Carbon atoms bond with each other to form long chains, rings, or branched structures. ○​ Molecules made only of carbon and hydrogen are called hydrocarbons. ○​ Double or triple bonds between carbon atoms reduce available bonding sites, adding flexibility in molecular design. Functional Groups: Chemical Modifiers of Molecules ​ Definition: A functional group is a specific group of atoms that participates in chemical reactions and alters a molecule’s function. ​ Functional groups add polarity or ionic characteristics, influencing chemical and physical properties. Characteristics of Functional Groups 1.​Polarity and Solubility ○​ Ionic or polar functional groups create forces of attraction with other molecules. ○​ Polar groups dissolve in water and often act as handles for solubility in the cytosol of cells. 2.​Comparison Example ○​ Ethane: A hydrocarbon with no functional group, is non-polar, gaseous at room temperature, and insoluble in water. ○​ Ethanol: Contains an alcohol functional group (-OH), is polar, liquid at room temperature, and highly water-soluble. 3.​Ionic Functional Groups ○​ Carboxyl Group (COOH): Releases H⁺ to become COO⁻, acting as an acid. ○​ Amino Group (NH₂): Attracts H⁺ to become NH₃⁺, acting as a weak base. ○​ Phosphate Group: Loses H⁺ ions, becoming negatively charged, and contributes to the acidity of molecules like DNA. ○​ DNA’s overall negative charge is due to numerous phosphate groups. Dehydration and Hydrolysis Reactions 1.​Dehydration Reactions ○​ Components of water (H⁺ and OH⁻) are removed to assemble larger molecules from smaller subunits. ○​ Example: Combining sugar molecules to form starch.  2.​Hydrolysis Reactions ○​ The reverse process of dehydration, where water components (H⁺ and OH⁻) are added to break larger molecules into smaller subunits. ○​ Example: Breaking down starch into individual sugars via hydrolysis. Why Carbon is Unique ​ Carbon’s ability to form stable, covalent bonds with multiple elements, including itself, enables the creation of complex structures essential for life. ​ Functional groups attached to carbon backbones enhance reactivity, solubility, and biological functionality, making carbon indispensable in biochemistry. 1.4 Carbohydrates Carbohydrates: Structure, Types, and Uses Carbohydrates are essential biomolecules composed of carbon, hydrogen, and oxygen. They serve critical roles in energy storage, structural support, and cell communication. Additionally, carbohydrates are precursors for synthesizing other vital biomolecules like amino acids, lipids, and nucleic acids. Types of Carbohydrates 1.​Monosaccharides ○​ Simplest form of carbohydrates, consisting of a single sugar unit. ○​ Examples: Glucose, fructose, galactose. ○​ Glucose forms a ring structure due to interactions between functional groups. ○​ Isomers: Molecules with the same molecular formula but different structural arrangements (e.g., α-glucose and β-glucose). ○​ Monosaccharides are highly hydrophilic and soluble in water due to their polar functional groups, which contribute to their sweet taste. 2.​Disaccharides ○​ Formed by linking two monosaccharides via a glycosidic bond. ○​ Examples: ​ Maltose: Glucose + Glucose (α-linkage). ​ Sucrose: Glucose + Fructose. ​ Lactose: Glucose + Galactose (β-linkage). 3.​Polysaccharides ○​ Composed of hundreds to thousands of monosaccharide units linked through glycosidic bonds. ○​ Functions:  ​ Energy Storage: ​ Starch: Found in plants; consists of amylose (soluble component) and amylopectin. ​ Glycogen: Found in animals; stored in the liver and muscles for quick energy release. ​ Structural Support: ​ Cellulose: A primary component of plant cell walls; provides rigidity and strength. ​ Chitin: Found in the exoskeletons of insects and crustaceans, as well as fungal cell walls. Chitin contains nitrogen-functional groups, making it unique among carbohydrates. Glycosidic Bonds ​ Covalent bonds that link monosaccharides to form disaccharides and polysaccharides. ​ Example: A glycosidic bond between the 1-carbon of one glucose molecule and the 4-carbon of another forms maltose. Properties and Uses ​ Energy Source: Monosaccharides like glucose are quickly metabolized to provide energy. ​ Structural Role: Polysaccharides like cellulose and chitin provide strength and support to cell walls and exoskeletons. ​ Cell Communication: Carbohydrates on cell surfaces participate in recognition and signaling processes. ​ Precursor Molecules: Serve as raw materials for synthesizing other biomolecules, including nucleic acids and lipids. Summary Carbohydrates, ranging from simple monosaccharides to complex polysaccharides, play diverse roles in energy storage, structural integrity, and biochemical processes. Their versatility stems from the variety of glycosidic bonds and functional groups that influence their structure and function. Lipids Overview of Lipids ​ Definition: Lipids are nonpolar compounds made primarily of carbon and hydrogen, with lesser amounts of oxygen. ​ Characteristics: ○​ Nonpolar and insoluble in water. ○​ Smaller than complex carbohydrates and not typically classified as macromolecules. ○​ Not polymers with defined monomeric subunits. ​ Functions: Used for energy storage, as hormones, vitamins, and structural components. Types of Lipids Lipids in living organisms are classified into five main categories: 1.​Fatty Acids ○​ Structure: Composed of a carboxyl group attached to a long hydrocarbon chain. ○​ Types:  ​ Saturated Fatty Acids: Hydrocarbon chains contain only single bonds between carbon atoms and are saturated with hydrogen atoms (e.g., stearic acid). ​ Unsaturated Fatty Acids: Hydrocarbon chains contain one or more double bonds, allowing for fewer hydrogen atoms (e.g., oleic acid). 2.​Fats ○​ Structure: Made from glycerol and fatty acids. ○​ Formation: A triglyceride forms when one glycerol molecule binds to three fatty acid chains via dehydration synthesis. ○​ Types: ​ Saturated Fats: Composed of saturated fatty acids with only single bonds in their hydrocarbon chains. ​ Unsaturated Fats: Composed of unsaturated fatty acids with one or more double bonds in their hydrocarbon chains. ○​ Function: Serve as long-term energy storage molecules. 3.​Phospholipids ○​ Structure: Consist of two fatty acid chains, a glycerol molecule, and a phosphate group. ○​ Properties: ​ Hydrophilic Head: Attracted to water (phosphate group). ​ Hydrophobic Tails: Repel water (fatty acid chains). ○​ Function: Form the phospholipid bilayer, which is the fundamental structure of cell membranes. 4.​Steroids ○​ Structure: Composed of four interconnected carbon rings. ○​ Examples:  ​ Sex hormones such as testosterone and progesterone. ​ Cholesterol, a key structural component in cell membranes and a precursor to other steroids. 5.​Waxes ○​ Structure: Formed when long fatty acid chains bond with alcohols or carbon rings. ○​ Function: Provide waterproofing and protection in plants and animals. Importance of Lipids ​ Energy Storage: Lipids are dense energy sources, providing more energy per gram than carbohydrates. ​ Structural Role: Phospholipids and cholesterol are vital for maintaining cell membrane integrity and fluidity. ​ Hormonal Functions: Steroids regulate various biological processes. ​ Protection and Insulation: Waxes and fats serve as protective barriers and insulation in organisms. 1.5 Proteins and Nucleic Acids Summary: Proteins – Structure, Types, and Uses Proteins are large, complex biological molecules composed of amino acid subunits joined by peptide bonds. They fold into unique three-dimensional shapes, which determine their diverse and essential functions in living organisms. Functions of Proteins  1.​Enzymatic Function ○​ Act as enzymes to catalyze biochemical reactions without being consumed. ○​ Example: Amylase breaks down carbohydrates during digestion. 2.​Structural Support ○​ Provide structural integrity to cells and tissues. ○​ Examples: Collagen (connective tissues), Keratin (hair, skin, nails). 3.​Transport and Storage ○​ Transport molecules or store essential substances. ○​ Examples: ​ Hemoglobin: Transports oxygen in blood. ​ Ferritin: Stores iron. 4.​Defense ○​ Antibodies neutralize pathogens, aiding the immune system. 5.​Signaling and Communication ○​ Hormones (e.g., insulin) and receptors enable cell signaling and communication. 6.​Movement ○​ Proteins like actin and myosin are involved in muscle contraction and cellular movement. 7.​Regulation ○​ Control gene expression and other cellular processes. 8.​Energy Source ○​ Serve as an energy source during fasting or starvation. Amino Acids: Protein Building Blocks ​ Structure: Each amino acid consists of:  ○​ A central carbon atom. ○​ A carboxyl group (-COOH). ○​ An amino group (-NH2). ○​ A variable R group (side chain). ​ Diversity: There are 20 amino acids, including essential ones that must be obtained through diet. Protein Structure Levels 1.​Primary Structure ○​ The unique linear sequence of amino acids in a polypeptide chain. 2.​Secondary Structure ○​ Local folding into alpha-helices (spirals) or beta-pleated sheets. 3.​Tertiary Structure ○​ The overall three-dimensional folding of the polypeptide, influenced by side chain interactions. 4.​Quaternary Structure ○​ Multiple polypeptide chains combine to form a functional protein. Peptides and Polypeptides ​ Peptide: A short chain of amino acids linked by peptide bonds. ​ Polypeptide: A chain with more than 50 amino acids. Prosthetic Groups  ​ Some proteins require non-protein components, called prosthetic groups, for their function (e.g., the heme group in hemoglobin). Structure-Function Relationship ​ Linear proteins: Provide strength and form fibers (e.g., silk, collagen, keratin). ​ Globular proteins: Compact shapes suited for transport (e.g., hemoglobin). Proteins’ intricate structures and vast functional versatility are crucial to nearly every biological process, from catalysis and structural support to movement and immune defense. Nucleic Acids Summary: Nucleic Acids (RNA vs. DNA, Structure of DNA and Nucleotides, Purines vs. Pyrimidines) Nucleic Acids Overview ​ Nucleic acids serve as the assembly instructions for all proteins in living organisms. ​ Two main types: DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid). Nucleotides: Building Blocks of Nucleic Acids  ​ Components: 1.​Phosphate group 2.​Sugar: ​ DNA: Deoxyribose. ​ RNA: Ribose. 3.​Nitrogenous base: A molecule with high nitrogen content. Nitrogenous Bases ​ Two Types: 1.​Pyrimidines (Single-ring structure): ​ Cytosine (C) ​ Thymine (T) (in DNA only). ​ Uracil (U) (in RNA only). 2.​Purines (Double-ring structure): ​ Adenine (A) ​ Guanine (G) DNA vs. RNA Feature DNA RNA Strans Double-stranded Single-stranded Sugar Deoxyribose Ribose Bases A, T, C, G A, U, C, G Function Stores genetic Transmits genetic information, information protein synthesis Structure Double helix, Single linear strand antiparallel strands Structure of DNA ​ Double Helix: Two strands wound around each other. ​ Antiparallel: Strands run in opposite directions. ​ Base Pairing: Hydrogen bonds between complementary bases: ○​ Adenine (A) pairs with Thymine (T) using 2 hydrogen bonds. ○​ Guanine (G) pairs with Cytosine (C) using 3 hydrogen bonds. ​ Phosphodiester Bonds: ○​ Link nucleotides through a phosphate bridge. ○​ Formed by dehydration synthesis. Other Roles of Nucleotides ​ ATP (Adenosine Triphosphate): A nucleotide that serves as the main energy currency in cells. Nucleic acids, composed of nucleotide subunits, are vital to genetic information storage, transmission, and energy transfer, enabling cellular processes and life itself. 1.7 Enzymes Enzymes are biological catalysts, typically proteins, that accelerate chemical reactions. They bind to substrates at their active sites, forming an enzyme-substrate complex. The induced-fit model describes how enzymes adjust their shape to better bind the substrate. Enzymes often require cofactors (non-protein molecules) or coenzymes (organic molecules) for catalytic activity. Enzyme inhibitors can affect enzyme function: ​ Competitive inhibition: A substance competes with the substrate for the active site. ​ Noncompetitive inhibition: A molecule binds to a site other than the active site, altering the enzyme's function. ​ Allosteric regulation: Involves binding to an allosteric site, which regulates enzyme activity. ​ Feedback inhibition: When the product of a pathway accumulates, it inhibits an early enzyme in the pathway, regulating production. Enzyme activity is influenced by factors like pH and temperature: ​ Enzymes typically function best around pH 7, though some, like pepsin and trypsin, have optimal pH outside this range. ​ Temperature increases enzyme reaction rates until the enzyme denatures, reducing activity. Applications of enzymes: ​ Lactose intolerance: Lactase supplements aid digestion by breaking down lactose in dairy. ​ Cheese production: Chymosin coagulates milk for cheese curds. ​ Flavor enhancement: Fat-hydrolyzing enzymes are used to develop stronger cheese flavors. ​ Starch industry: Enzymes convert starch into glucose syrup, a common sweetener. ​ Cleaning industry: Enzymes in detergents break down stains like blood and grass, improving cleaning efficiency at lower temperatures.