Organic Molecules in Organisms

 

Atoms, Bonds, and Molecules in Biology

Molecules, polarity, and hydrogen bonds. Examples: Water and carboxylic acid.

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  • Watch video clip from Lecture 2 (0:00 - 10:10)

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Hydrophobic, Hydrophilic, and Amphipathic Molecules

Hydrophobicity (dislike of water) of non-polar long carbon chains and hydrophilicity (like of water) of polar molecules. Behavior of amphipathic molecules such as phospholipid bilayer, micelle, and vesicles.

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  • Watch video clip from Lecture 2 (10:10 - 18:45)

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Interactions Between Biological Molecules

Hydrogen bond and electrostatic interactions between carboxylic (COO-) and amine (NH2) groups. Van der Waals interaction between uncharged, non-polar molecules.

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  • Watch video clip from Lecture 2 (18:45 - 23:17)

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Phospholipid Bilayer

Synthesis and properties of lipid. Permeability of phospholipid bilayer membranes to ions, water, gases, and amino acids. Membrane as a barrier to create concentration gradients on the outside and inside of the cell.

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  • Watch video clip from Lecture 2 (23:17 - 35:45)

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Carbohydrates–Overview

Name, composition, synthesis, and hydrolysis. Alternate structures and linkages of cyclic carbohydrates. Examples: Glucose, fructose, galactose, and lactose.

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General formula, 3D structure (linear and cyclic), linkage, and examples. Synthesis/polymerization and hydrolysis of disaccharides and polysaccharides.

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Description of carbohydrates and their chemistry.

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Polymerization of Macromolecules

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Synthesis of glycogen, cellulose, and polysaccharides from monomers.

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Synthesis of glycogen, cellulose, and polysaccharides as polymers from monomers. Storage of glucose and energy in long chains of glycogen.

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Transmembrane Proteins

Transmembrane portions of proteins consist of hydrophobic amino acids so they can interact with the hydrophobic tails of phospholipids in the membrane. All charged side chains must be neutralized by opposite charges.

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Properties of the phospholipid bilayer and transmembrane proteins. Tertiary and quaternary structures of proteins involving multiple subunits.

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Post-translational Modification

Chemical alterations are made to the protein after translation.

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Cell Composition

Atomic and molecular composition of cells. Four classes of macromolecules-proteins, DNA/RNA, carbohydrates, and lipids.

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  • Watch video clip from Lecture 2 (10:35 - 15:08)

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Covalent Bond

Description, length, strength, and examples. Forming and breaking of bonds; ability to rotate, stretch, and bend without breaking; single, double, and triple bonds and saturation.

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  • Watch video clip from Lecture 2 (16:35 - 23:05)

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Chirality

Carbon as a chiral center with four attached groups. Mirror images.

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Nucleic Acids–DNA and RNA

Nucleotide structure and components-sugar, phosphate group, and bases. Formation of DNA/RNA from monomeric nucleotides through phosphodiester bonds. Hydrogen bonds and base pairing results in the double helical structure of DNA.

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  • Watch video clip from Lecture 3 (0:00 - 7:26)

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Proteins and Amino Acids

Formation and properties of the peptide bond. Side chains of amino acid with unique properties-positive and negative charges, polar and non-polar, hydrophobic and hydrophilic. Special cases-glycine, cysteine, and proline.

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  • Watch video clip from Lecture 3 (7:26 - 18:03)

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Protein Primary and Secondary Structures

Primary (amino acid sequence) and secondary (alpha helix and beta sheets) structures. Hydrogen bonds are important in secondary structures.

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  • Watch video clip from Lecture 3 (18:03 - 30:42)
  • Watch video clip from Lecture 4 (4:17 - 11:07)

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Ionic Bond and van der Waals (VDW) Interaction

Transfer of electrons result in ionic bonds between positively and negatively charged atoms. Transient polarity in non polar bonds result in VDW interactions. VDW interactions are weak with short ranges. Example: geckos.

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  • Watch video clip from Lecture 3 (30:42 - 38:56)

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Hydrophobic Effects

Hydrophobic amino acids tend to congregate and stay away from water.

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Protein Tertiary Structure

Ionic, van der Waals, and hydrophobic interactions are responsible for the tertiary structure, the association between various parts of the protein.

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  • Watch video clip from Lecture 4 (11:07 - 16:50)

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Protein Quaternary Structure

Interactions between polypeptide subunits form the quaternary structure. Movie of a protein dimer.

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  • Watch video clip from Lecture 4 (16:50 - 20:31)

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Protein Functions

Proteins as enzymes/catalysts, structures, antibodies/immune responses, motors and machines. Movie on protein motors.

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  • Watch video clip from Lecture 4 (20:31 - 27:20)

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Lipids and Phospholipid Bilayer

Definition, structure and synthesis. Saturated versus unsaturated fat. Structure, formation, amphipathic properties, and permeability of phospholipid bilayers as the cell membrane and barrier. Movie of transmembrane protein.

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  • Watch video clip from Lecture 4 (27:20 - 38:20)

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Amino Acids and Proteins/Polypeptides

Charges and structure of amino acids with carboxyl, amino groups, and side chains. Formation of peptide bonds during protein synthesis.

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Amino Acid Side Chains and Disulfide Bonds

Side chains of each of the 20 amino acids unique biochemical properties-- polar versus non-polar, hydrophilic versus hydrophobic, and positive and negative charges. A brief list of individual amino acid and behavior

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Three-Dimensional Structure of Proteins

Primary, secondary, tertiary and quaternary structures of proteins. Hydrogen bonds as the main force in the secondary structure (alpha-helices and beta-sheets).

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Enzymatic and Structural Functions of Proteins

Overview of catalytic functions of proteins that speed up biochemical reactions and structural functions of proteins in the cell.

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Biological Conditions and Enzyme Activity

A brief exploration of the temperature-sensitive nature of biological processes.

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Introduction to Polymers and Bonds

Definition and description of macromolecules, polymers, bonds and bond types, condensation and hydrolysis reactions, and the four major types of macromolecules/polymers.

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Lipids

Description of lipids and their chemistry.

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Nucleic Acids

Introduction to nucleic acids, the four bases, and a brief look at their chemistry and importance.

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Molecular Interactions

Biochemical forces that drive all molecular interaction in biology.

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Strength of molecular interactions and boiling points.

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Carbohydrates–Structure and Nomenclature

Structures, linkages, and names of mono-, di-, and polysaccharides.

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Nucleic Acids–Sugars and Bases

Structures and names of the components of nucleotides-deoxyribose and ribose, and pyridimine and purine nitrogenous bases.

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Proteins–Structure and Polymerization

Structures of amino acids grouped based on side chain properties. Polymerization of amino acids to form peptide bonds and proteins.

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Lipids and Phospholipids

Structures and names of various lipids and phospholipids.

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Enzyme-Substrate Interaction–Practice I

Chemical interactions between an enzyme and a substrate in its binding pocket.

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Protein Structure and Interactions

Using hemoglobin as an example to illustrate different levels of protein structure and how mutations can affect each level.

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Chemical Bonds and Enzyme-Substrate Interactions

Various types of chemical interactions and their relevance in enzyme-substrate interactions. Uses substrate analogs to demonstrate the importance of chemical interactions.

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Macromolecules

Structure and functions of proteins and other macromolecules.

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Chemical Bonds

Chemical bonds and interactions in biological molecules.

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Protein-Substrate Interaction–Example

Chemical interactions between amino acids on a proteins and its substrate, GDP.

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Small Molecule-Protein Interaction

Small molecule-protein interaction based on amino acid residues in the protein binding pocket.

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Transmembrane Proteins and Ion Channels

Properties of the phospholipid bilayer and transmembrane proteins. Secondary, tertiary and quaternary structures of proteins involving multiple subunits.

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