Biochemistry vs. Organic Chemistry Quiz

Organic Chemistry Refresher

• The presentation is a refresher on organic chemistry, given by Cora Rabe (GDNP 6510).
• The objectives of the presentation are to explain the differences between biochemistry and organic chemistry, recognize functional groups of organic chemistry, recall examples of compounds containing those groups, and describe primary chemical bonds.

The Sciences Explained

• Biochemistry is the study of chemical processes in the body, focusing on structures and functions of lipids, proteins, energy production, and DNA.
• Organic chemistry is the study of compounds containing carbon, including compounds like carbon, nitrogen, oxygen, halogens, silicon, phosphorus, and sulfur.
• Physics is the study of matter and its movement, including related energies.

Organic vs. Inorganic Chemistry

• Organic: Primarily covalent bonds, low melting points (<360°C), insoluble in water, soluble in organic compounds (examples: diethyl ether, toluene, dichloromethane), aqueous solutions do not conduct electricity, burn and decompose, and reactions are slow.
• Inorganic: Ionic bonds, high melting points, soluble in water, insoluble in organic compounds, aqueous solutions of ions conduct electricity, and reactions are fast.

The Periodic Table of the Elements

• Elements: Hydrogen has 1 proton and 1 electron; Helium has atomic number 2 and 2 protons/electrons, and Lithium has atomic number 3 with 3 protons and 3 electrons.
• The presentation includes a full periodic table, with various elements.

The Atom

• An atom consists of a nucleus containing neutrons (neutral, weight of 1) and protons (positive charge, weight of 1), with electrons in the valence shell (negative charge, weight 0).

Octet Rule

• Atoms tend to gain or lose valence electrons to achieve eight valence electrons, similar to a noble gas configuration, to minimize repulsions between electrons.

Matter

• Matter is anything with mass and volume, existing in various states including ions, elements, molecules, compounds, and mixtures.
• Ions are charged atomic particles bonded together having an electrical charge.
• Elements are made up of only one kind of atom, such as carbon, hydrogen, etc.
• Molecules are a group of atoms bonded together. Molecules are electrically neutral.
• Compounds are made up of two or more different kinds of atoms.
• Mixtures are a physical combination of two or more different elements or compounds, not chemically bonded together.

Alkanes, Cycloalkanes, Alkenes, Alkynes & Arenes

• Hydrocarbons are compounds containing only carbon and hydrogen.
• Alkanes are saturated hydrocarbons with single bonds in a chain. Cycloalkanes are saturated hydrocarbons in a ring.
• Alkenes are unsaturated hydrocarbons with a double bond in a chain.
• Alkynes have a triple bond in a chain.
• Arenes contain a benzene ring (double bonded).

Hydrocarbons

• Alkenes are more reactive than alkanes due to extra electron density in the double bond, often acting as monomers for polymers.
• Aromatics are stable and common in molecules.
• Benzene is a fundamental structure for many aromatic molecules, with a specific ring structure.

Alkanes and Alkenes

• The presentation explains that the physical properties of long hydrocarbon chains are similar to fats and oils.
• Alkanes and alkenes exhibit a lack of polarity (nonpolar), meaning they are not soluble in water.

Cycloalkanes

• Cycloalkanes, like cyclopropane, are highly reactive when exposed to oxygen.
• Reactions produce products of carbon dioxide, water, and significant amounts of heat.

Alcohols

• Alcohols are compounds containing a hydroxyl group (-OH) bonded to a tetrahedral carbon atom.
• Alcohols are classified as primary, secondary, or tertiary based on the number of carbons attached to the carbon with the –OH.
• Alcohols (e.g., ethanol) are polar and hydrophilic, soluble in water.

Alcohols - Phenyls

• Aromatic alcohols are called phenols.
• Propofol is an example of an aromatic alcohol with 12 carbon atoms; it is insoluble in water and lipophilic.

Amines & Amides

• Amines are compounds with carbon-nitrogen bonds, called an amino group. Amides contain carbon-nitrogen bonds, often part of a longer chain of atoms.
• Primary amines have one carbon attached to nitrogen, secondary have two, and tertiary, three. A Quaternary amine has four carbons on the nitrogen molecule.
• Amides are condensation products formed between carboxylic acids and alcohols.

Amines

• Neutral amines cross biological barriers like the blood brain barrier.
• Charged amines do not easily cross biological barriers.

Amides

• Amides are molecules containing nitrogen atoms connected to carbonyl groups.
• The carbonyl group involves a carbon that is doubly bonded to an oxygen atom.

Carboxylic Acids

• A carboxylic acid contains a carboxyl group (-COOH), which is a combination of carbonyl and hydroxyl groups.
• Fatty acids are long-chained carboxylic acids, used for energy storage.
• Carboxylic acids are medium-strong acids with pKa values between 4 and 5.

Carboxylic Acids + Amines = Amides

• Amides are formed through a reaction between carboxylic acids and amines.
• This reaction is important in biological systems for protein formation.

Amino Acids

• Amino acids have both amine and carboxyl groups in their structure.
• Peptide bonds form between amino acids to create chains.

Amino Acids to Proteins

• Amino acids form long chains (proteins).
• The R-group of amino acids provides their unique properties.
• Different structures (e.g., primary, secondary, tertiary, quaternary) result from the order and interactions of amino acids in a protein.

Aldehydes & Ketones

• Aldehydes and ketones contain carbonyl groups (C=O) with different structures.
• Aldehydes have a carbonyl group bonded to a hydrogen, while ketones have a carbonyl group bonded to two carbons.
• Aldehydes sometimes have the suffix "al"; Ketones have the suffix "one".

Reactions of Aldehydes & Ketones

• Aldehydes and ketones can be oxidized or reduced, leading to various reaction products.
• Condensation reactions are also possible involving hemiacetal and acetal formations.

Esters

• Esters are derivatives of carboxylic acids, with hydroxyl (-OH) of the carboxylic acid replaced with a carbon group.
• Ester functional groups are often associated with the phrase (-COOR).
• Hydrolysis of esters is reversible.

Local Anesthetics

• Local anesthetics are esters or amides.
• Each group of local anesthetics has specific characteristics depending on the type of bond.

Ethers

• Ethers contain an oxygen atom bonded to two carbons.
• Ether molecules have a structure of R-O-R'
• Diethyl ether is a commonly used anesthetic.

Halogenated Ethers

• Halogenated ethers which contain fluorine, chlorine, bromine, and iodine are present in anesthetics.

Thiols & Sulfides

• Thiols are similar to alcohols, but contain a sulfur atom instead of oxygen.
• Disulfide bonds are important in protein structure and folding.

Disulfide Bonds

• Disulfide bonds form between cysteine amino acid residues; important for protein folding and stability.
• This reaction is an example of oxidized sulfur that produces disulfide bridges.

Capsaicin

• Capsaicin structure displayed.
• Shows an aromatic/phenol group, an amide group and an alkene.

Isomers

• Isomers have the same kinds of atoms, same number of kinds of atoms in a compound, but differ based on spatial arrangement.

Structural VS Stereoisomers

• Constitutional isomers have the same molecular formula, but different bonding arrangements.
• Stereoisomers have identical molecules with identical formulas, but differ based on the molecules' spatial arrangement.

Stereocenter (Chiral Center)

• A stereocenter is an atom with three or four different attachments.
• The mirror image of a chiral molecule is another molecule, not identical to the original molecule.

Enantiomers

• Enantiomers are a type of stereoisomer; they are not superimposable.
• They contain a chiral carbon, and their mirror images are different.

Enantiomers

• Racemic mixtures contain an equal amount of each chiral molecule (enantiomers) of a specific molecule.
• Enantiomers are crucial as the different molecules of an enantiomer have various different reactions within the body.

Test your knowledge on the distinctions between biochemistry and organic chemistry. This quiz covers key concepts such as functional groups, bonding types, and the properties of organic compounds. Challenge yourself with questions that highlight the fundamental differences and similarities in these two fields of science.