Lecture10 Pre Class (Biomolecules)

Page 1: Objectives

• Biological Molecules:

  • Importance of carbon as the foundation for biological molecules.

  • Properties of common functional groups.

  • Differences between dehydration synthesis and hydrolysis.

  • Identification of subunits and structures of macromolecules including polar and non-polar regions.

  • Major functions of each macromolecule.

  • Basic structure of an amino acid.

  • Levels of protein structure and related bonds for each level.

Page 2: Cells & Cellular Macromolecules

• Cell Theory:

  • Contributions by Schleiden and Schwann in the mid-1800s.

  • The cell is the basic structural and functional unit of all life.

  • Living organisms are made of at least one cell.

  • Cells give rise to new cells.

• Cellular Components:

  • Classifications into four categories of molecules.

Page 3: Carbon: The Backbone of Life

• Carbon Compounds:

  • Living organisms are primarily composed of carbon-based compounds.

  • Carbon's unique ability to form complex and diverse molecules is unparalleled.

  • Proteins, DNA, carbohydrates, and other biological molecules are carbon compounds.

  • Organic Chemistry: The study of carbon-containing compounds.

Page 4: Carbon as an Atom

• Major Atomic Components:

  • Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N).

• Electron Configuration:

  • Carbon forms covalent bonds with many elements due to its electron configuration.

• Valences:

  • Building code for the architecture of living molecules determined by the valences of carbon and its partners (H, O, N).

Page 5: Carbon Bonding

• Carbon Bonds:

  • Carbon forms 4 covalent bonds.

  • Structural formula: Example of methane (CH4).

  • Different models: Ball-and-stick model, space-filling model.

Page 6: Carbon Structures

• Carbon Chains and Rings:

  • Carbon can form both chains and rings, with other atoms projecting from the carbon backbone.

Page 7: Common Functional Groups

• Definition:

  • Atoms or clusters of atoms covalently bonded to the carbon backbone.

• Behavior:

  • Functional groups behave similarly across different organic molecules.

Page 8: Chemical Groups and Function

• Influence on Molecules:

  • Estradiol and testosterone are steroids with a common carbon skeleton but differ in chemical groups attached.

Page 9: Types of Organic Molecules

• Basic Types:

  • Carbohydrates, Lipids, Proteins, Nucleic Acids.

  • Components: High-energy compounds: Polysaccharides, Triglycerides, Peptides, RNA, DNA, ATP.

• Composition:

  • Monosaccharides, Disaccharides, Fatty acids, Amino acids, Nucleotides.

Page 10: Macromolecule Formation

• Polymers:

  • Carbohydrates, proteins, and nucleic acids are polymers—long molecules made of similar building blocks (monomers).

• Synthesis:

  • Enzymes remove -OH from one and H from another molecule to form covalent bonds.

Page 11: Dehydration Synthesis & Hydrolysis

• Dehydration Reaction:

  • Forming a polymer by removing a water molecule.

• Hydrolysis:

  • Breaking a polymer by adding a water molecule.

Page 12: Organic Molecules Overview

• Key Types:

  • Carbohydrates, Nucleic Acids, Lipids, Proteins.

Page 13: Carbohydrates Overview

• Composition:

  • Carbohydrates are made from carbon and water; general formula: (CH2O)n.

• Types:

  • Monosaccharides: Basic building blocks, quick energy.

  • Disaccharides: Two carbon chains for transport.

  • Polysaccharides: More than two chains for structural support and energy storage.

Page 14: Structure of Sugars - Monosaccharides

• Chemical Formula:

  • Example: C6H12O6 (glucose).

• Models: Linear, ball-and-stick, and ring forms.

Page 15: Solubility of Sugars

• Interactions with Water:

  • Can sugars form hydrogen bonds with water?

  • Investigating the polarity of water and sugars.

Page 16: Formation of Disaccharides

• Examples:

  • Maltose: Assembled from two glucose molecules (α(1-4) linkage).

  • Sucrose: Composed of glucose and fructose (α(1-2) linkage).

  • Lactose: Formed from galactose and glucose (β(1-4) linkage).

Page 17: Polysaccharides

• Types:

  • Energy Storage:

    • Plants store starch; animals store glycogen.

  • Structural Support:

    • Plants use cellulose, animals use chitin.

Page 18: Storage Structures

• Starch in Plants:

  • Amylose (unbranched) and amylopectin (branched).

• Glycogen in Animals:

  • Stored in muscles and composed of branched chains.

Page 19: Cellulose Structure

• Cellulose:

  • Composed of glucose molecules, crucial for plant cell walls, forms fibers via hydrogen bonds.

Page 20: Chitin

• Structural Polysaccharide:

  • Found in exoskeletons of arthropods, formed from glucose molecules.

Page 21: Polysaccharide Linkages

• Types of Linkages:

  • Different linkages (α(1-4) or β(1-4)) affect polysaccharide digestibility (e.g., glycogen, amylose, cellulose).

Page 22: Basic Kinds of Organic Molecules

• Overview Repeated:

  • Carbohydrates, Nucleic Acids, Lipids, Proteins.

Page 23: Nucleic Acids Composition

• Nucleotides:

  • Comprised of phosphate group(s), sugar, and nitrogenous base.

Page 24: ATP

• ATP:

  • Example of nucleotide; hydrolysis of the 3rd phosphate releases energy.

Page 25: DNA Structure

• DNA:

  • Made up of nucleotides consisting of sugar, phosphate, and nitrogenous bases.

Page 26: Kinds of Organic Molecules

• Recap:

  • Carbohydrates, Nucleic Acids, Lipids, Proteins.

Page 27: Lipids Overview

• Classes of Lipids:

  • Energy storage (triglycerides), structural (phospholipids), steroids (cholesterol, testosterone, estrogen), and waxes.

Page 28: Fat Synthesis

• Dehydration Reactions:

  • Formation of fats through reactions involving fatty acids and glycerol (ester linkage).

Page 29: Saturated vs Unsaturated Fats

• Structural Formulas:

  • Saturated fat (e.g., stearic acid) vs. unsaturated fat (e.g., oleic acid) and their properties regarding double bonds.

Page 30: Phospholipid Structure

• Components:

  • Polar head (phosphate group) and nonpolar tail (fatty acid chains).

Page 31: Phospholipid Arrangement in Water

• Membrane Formation:

  • Phospholipids assemble into bilayers in aqueous environments.

Page 32: Lipid Bilayer Barrier

• Composition:

  • The lipid bilayer forms a barrier to most substances based on head and tail interactions with water.

Page 33: Need for Water in Membrane Formation

• Hydrogen Bonds:

  • Membranes form due to water's capacity to form hydrogen bonds.

Page 34: Plasma Membrane Structure

• Components:

  • Fibers of extracellular matrix, glycoproteins, microfilaments, cholesterol, peripheral proteins, integral proteins.

Page 35: Cholesterol in Membranes

• Role in Membranes:

  • Cholesterol as a steroid is a natural component of cell membranes; examples include estrogen and testosterone.

Page 36: Organic Molecules Review

• Kinds of Organisms:

  • Carbohydrates, Nucleic Acids, Lipids, Proteins reiterated.

Page 37: Proteins Composition

• Amino Acids:

  • Proteins are made from 20 different amino acids, each with a unique side chain (R group).

Page 38: Nonpolar Amino Acids

• Examples:

  • List of nonpolar side chains: Glycine, Alanine, Valine, etc.

Page 39: Polar Amino Acids

• List of Polar Amino Acids:

  • Serine, Threonine, Cysteine, etc.

Page 40: Charged Side Chains

• Basic and Acidic:

  • Examples of basic (Lysine, Arginine) and acidic (Aspartic acid, Glutamic acid) amino acids.

Page 41: Peptide Bonds

• Protein Formation:

  • Amino acids linked by peptide bonds form polypeptides.

Page 42: Polypeptide Structure

• Polypeptides:

  • Peptide bonded backbone with N-terminus and C-terminus ends.

Page 43: Protein Folding

• Conformation:

  • Polypeptides fold into complex shapes to function as proteins.

Page 44: Levels of Protein Structure

• Primary Structure:

  • Unique sequence of amino acids.

• Secondary Structure:

  • Localized folding patterns.

• Tertiary Structure:

  • Three-dimensional shape formed by interactions among side chains.

• Quaternary Structure:

  • Protein with multiple polypeptide chains.

Page 45: Reinforcement of Protein Structure

• Recap of Structures:

  • All proteins have primary, secondary, and tertiary structures; only some possess quaternary structure.

Page 46: Amino Acid Bonding

• Primary Structure Explained:

  • Sequence and connections of amino acids through peptide bonds.

Page 47: Secondary Structure Characteristics

• Types of Structures:

  • Hydrogen bonds create β-pleated sheets and α-helixes.

Page 48: Tertiary Structure Details

• Overall 3D Shape:

  • Formed by sidechain interactions, including hydrogen bonds and disulfide bridges.

Page 49: Charm Bracelet Analogy

• Amino Acids and Function:

  • Unique side chains lead to diverse functions and characteristics in proteins.

Page 50: Quaternary Structures

• Complex Proteins:

  • Example of collagen and hemoglobin, both comprising multiple subunits.

Page 51: Review of Protein Structures

• Structural Levels:

  • Overview of primary, secondary, tertiary, and quaternary levels in proteins.