Podcast
Questions and Answers
What is the primary focus of biochemistry?
What is the primary focus of biochemistry?
Which of the following best describes organic chemistry?
Which of the following best describes organic chemistry?
What distinguishes organic compounds from inorganic compounds?
What distinguishes organic compounds from inorganic compounds?
Which functional group is commonly associated with alcohols?
Which functional group is commonly associated with alcohols?
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Which statement about primary organic compounds is true?
Which statement about primary organic compounds is true?
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What is a characteristic of inorganic compounds compared to organic compounds?
What is a characteristic of inorganic compounds compared to organic compounds?
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Which of the following elements is NOT typically found in primary organic compounds?
Which of the following elements is NOT typically found in primary organic compounds?
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Which bond type is typically associated with organic chemistry?
Which bond type is typically associated with organic chemistry?
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What structures do biochemists primarily investigate within cells?
What structures do biochemists primarily investigate within cells?
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Study Notes
Refresher of Organic Chemistry
- Cora Rabe presented a refresher on organic chemistry.
- The course was GDNP 6510.
Presentation Objectives
- Explain the differences between biochemistry and organic chemistry.
- Recognize functional groups of organic chemistry.
- Recall an example of a compound containing a functional group.
- Describe primary chemical bonds.
The Sciences Explained
- Biochemistry: The study of chemical processes in the body, examining structures and functions of lipids, proteins, energy production, and DNA.
- Organic chemistry: The study of substances containing carbon; primary organic compounds include carbon, nitrogen, oxygen, halogens, silicon, phosphorus, and sulfur.
- Physics: The study of matter and its movement through space and its related energies; studying life, evolution and species interaction with the environment
Organic vs Inorganic
-
Organic:
- Covalent bonding
- Low melting points (<360°C) for gases, liquids, or solids
- Insoluble in water
- Soluble in organic compounds (e.g., diethyl ether, toluene, dichloromethane)
- Aqueous solutions do not conduct electricity
- Burn and decompose
- Slow reactions
-
Inorganic:
- Ionic bonds
- High melting points
- Soluble in water
- Insoluble in organic compounds
- Aqueous solutions for ions conduct electricity
- Fast reactions
Elements of the Periodic Table
- Hydrogen: 1 proton and 1 electron
- Helium: atomic number 2, 2 protons and 2 electrons
- Lithium: atomic number 3, 3 protons and electrons; 2 in the core and 1 valence, therefore reactive
The Atom
- Atoms consist of:
- Nucleus (neutrons, protons)
- Valence shell (electrons)
- Neutrons: neutral, weight of 1
- Protons: positive charge, weight of 1
- Electrons: negative charge, weight of 0
Octet Rule
- Atoms try to gain 8 valence electrons to become isoelectric with a noble gas.
- This maximizes attraction between electrons and nuclei while minimizing repulsions between electrons.
Matter
- Matter is anything with mass and occupies space.
- States of matter include:
- Ions: charged atoms
- Elements: single-kind atoms
- Molecules: chemically bonded atoms
- Compounds: multiple-kind atoms
- Mixtures: different elements or molecules that are not bonded
Valence Shell Electron Pair Repulsion (VSEPR)
- Compounds desire stable electron arrangements.
- 8 valence electrons in the outermost shell are needed for stability (octet rule).
Covalent vs Ionic Bonds
-
Covalent bonds: Shared electrons between atoms; typically between nonmetals.
- Lower energy to break
- Can be polar or nonpolar
- Poor conductors
-
Ionic bonds: Electrons are transferred between atoms; typically between metals and nonmetals.
- Higher energy to break
- Electrostatic attraction creates usually solid structures
- Conduct electricity
Types of Bonds
-
Types of chemical bonds (single, double, triple) shown in simple structural representations.
-
Examples of types of structures
- Branches
- Rings (Benzene)
Electronegativity
- Highly electronegative elements have a larger ratio of proton core to electron shells. Atoms with high electronegativity tend to "hog" electrons.
- Polarity is created when there are differences in electronegativity within a molecule.
- This is the basis for hydrogen bonding.
Intermolecular Forces
- Forces between chemical species.
- Hydrogen bonding allows molecules to be water-soluble.
- Oxygen is highly electronegative creating a slight positive charge on hydrogen.
- London forces < dipole-dipole < hydrogen bonding < ionic
Hydrogen, Nitrogen, and Oxygen
- Hydrogen: forms bonds by sharing or losing electrons.
- Nitrogen: typically forms three bonds and has a lone pair of electrons.
- Oxygen: typically forms two bonds and has two lone pairs; it is highly electronegative.
Carbon
- A foundation element for living organisms.
- Forms diverse compounds.
- Its four valence electrons allow it to form covalent bonds with other atoms in chains, branches, and rings.
Solubility
- The amount of solute that can dissolve in a solvent at a specific temperature.
- Saturated solutions contain the maximum dissolved solute.
- "Like dissolves like."
Functional Groups
- The chemically reactive part of a compound.
- Several classes of functional groups have unique physical and chemical properties.
- Organic molecules contain a carbon backbone.
Alkanes, Cycloalkanes, Alkenes, Alkynes & Arenes
-
Hydrocarbons: Contain only carbon and hydrogen.
- Alkanes: Saturated hydrocarbons with single bonds in a chain.
- Cycloalkanes: Saturated hydrocarbons with single bonds in a ring.
- Alkenes: Unsaturated hydrocarbons with double bonds in chains.
- Alkynes: Unsaturated hydrocarbons with triple bonds in chains.
- Arenes: Contain benzene rings
Hydrocarbons
- Alkenes are more reactive than alkanes due to enhanced electron density in the double bonds. Alkenes serve as monomers for polymers like plastics.
Alkanes and Alkenes
- Aliphatic hydrocarbons have properties similar to long carbon chain molecules found in fats and oils.
Cycloalkanes
- Highly unstable, react quickly with oxygen, and produce large amounts of heat upon combustion.
Alcohols
- A compound containing an -OH (hydroxyl) group bonded to a tetrahedral carbon atom.
- Primary, secondary, or tertiary alcohols are categorized based on the number of carbons connected to the carbon with the hydroxyl group.
- Alcohols have unique properties because they are polar and able to hydrogen bond. This characteristic makes them hydrophilic and capable of mixing with or dissolving in water.
Alcohols - Phenyls
- Aromatic alcohols are known as phenols.
- Propofol has 12 carbon atoms.
- Phenols are insoluble in water (lipophilic).
Amines & Amides
-
Amines: Molecules containing carbon–nitrogen bonds (amino group).
-
Primary, secondary, tertiary, and quaternary amines: Classified by the number of carbons connected to the nitrogen atom in the amino group.
- Ammonia (unique) has no carbons attached
-
Amides: Contain carbon–nitrogen bonds.
Amines
- Neutral or uncharged amines cross barriers in the body. Charged amines usually don't.
Amides
- These form when carboxylic acids and amines bond.
Carboxylic Acids
- The structure is identified by the carboxyl group (-COOH).
- Fatty acids are long chains of carboxylic acids and serve as an energy storage component in organisms.
- Carboxylic acids are typically considered medium-strong acids, meaning they have moderate acidity.
Carboxylic Acids + Amines = Amides
- The reaction of amines with carboxylic acids creates amides, a critical process in protein synthesis.
Amino Acids
- Molecules with functional groups (amine and carboxylic acid).
- Peptide bonds form when carboxylic acid from one amino acid connects with the amine group of another amino acid.
Amino Acids to Proteins
- Amino acids form peptides, which further form proteins.
Aldehydes & Ketones
- Aldehydes: Carbonyl (C=O) in a hydrogen bond. Aldehydes have an "al" at the end of their name.
- Ketones: Two carbon atoms bonded to a carbonyl (C=O). Ketones have an "one" ending at the end of their name.
- Aldehydes and ketones are characterized by the carbonyl group, which makes them somewhat soluble in polar solvents.
Reactions of Aldehydes & Ketones
- Oxidation/reduction reactions and condensation can alter aldehyde and ketone structure..
Esters
- They are derivatives of carboxylic acids.
- Esters are formed when the hydrogen of a carboxylic acid is replaced with a carbon group.
Local Anesthetics
- Local anesthetics are either esters or amides, characterized by the presence of an intermediate bond.
Ethers
- Oxygen bonded to two carbon atoms.
- Ethers are generally considered polar.
- Ethers are used in general anesthetic procedures.
Halogenated Ethers
- These ethers do not easily burn or explode.
Thiols & Sulfides
- Thiols: Similar to alcohols, containing a sulfur atom.
- Sulfides: Compounds containing sulfur similar to ethers, with a specific smell.
Disulfide Bonds
- Important in protein structure.
- Created through the oxidation of sulfhydryl groups.
Capsaicin
- Organic compound that triggers pain response. Specifically, this is a chemical that triggers the receptors that cause hot and spicy sensations when eating it.
Isomers
- Compounds with the same number and kind of atoms but different arrangements.
- Constitutional Isomers: Differ in connectivity
- Stereoisomers: Same connectivity; differ in spatial arrangement
Stereocenter (Chiral Center)
- An atom with 4 different attachments.
- A molecule containing a chiral center is chiral.
Enantiomers
- Non-superimposable mirror images.
- They have the same atoms and groups, but their spatial arrangement differs; they are mirror-image structures.
- Chiral molecules have specific reactions with receptors in the body.
Enantiomers
- 50% of drugs are racemic mixtures (containing both enantiomers).
- Enantiomers can have different effects.
Enantiomers (cont.)
- Different reactions based on spatial arrangements (chirality).
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Description
This refresher course on organic chemistry focuses on the essential differences between organic and biochemistry. Participants will learn about functional groups, chemical bonds, and key organic compounds. Dive into the fundamentals that form the foundation of organic chemistry concepts.