Introduction to Biomolecules and Chemical Reactions

Functional Groups and Polarity

• Carbon acts as the foundational chemical backbone of organic molecules.

• Functional groups function like household appliances (such as a dishwasher, HVAC system, or plumbing) by providing specific chemical functions to the organic molecule.

• Functional groups dictate two primary properties of organic molecules:

  • Chemical Reactivity: Determines how reactive a molecule will be, specifically whether it will remain intact or break apart during chemical processes.

  • Polarity: Determines the charge distribution across the molecule.

• Polarity is defined as an asymmetrical charge distribution across a molecule, resulting in one side possessing a positive charge and the opposite side possessing a negative charge.

• Water ($H_2O$) serves as a classic example of a polar molecule:

  • One side of the water molecule carries a negative charge, while the opposing side carries a positive charge.

• Opposite charges attract in polar interactions:

  • The negative side of a polar molecule attracts the positive region of an adjacent molecule.

  • The positive side of a polar molecule attracts the negative region of an adjacent molecule.

• Polarity enables molecules to cling together, facilitating the assembly of diverse and exceptionally large biological structures.

Isomers and Molecular Formulas

• Isomers are organic molecules that possess identical molecular formulas but feature different structural arrangements of their constituent atoms.

• A molecular formula represents the exact chemical count of each atom present in a molecule (for example, $C_3H_6O_3$).

• Isomer Structural Comparison ($C_3H_6O_3$):

  • Each isomer contains $3$ Carbon atoms, $6$ Hydrogen atoms, and $3$ Oxygen atoms ($C_3H_6O_3$).

  • One isomer contains a double bond situated at the end of the carbon chain.

  • A distinct isomer contains the double bond positioned in the middle of the carbon chain.

  • The precise placement of double and triple bonds significantly alters both the chemical reactivity and the polarity of the molecule.

• Furniture Analogy: Rearranging a bedroom by placing a bed near a window and moving a dresser changes the room's arrangement (structure), even though the room contains the exact same furniture inventory (molecular formula).

• Biological Importance: Isomers play a critical role in biomedical research.

Chemical Prefixes, Suffixes, and Mnemonic Tools

• Root words, prefixes, and suffixes allow for the identification and classification of organic compounds:

  • Prefix iso-: Means "same" or "similar".

  • Prefix mono-: Means one ($1$).

  • Prefix di-: Means two ($2$).

  • Prefix poly-: Means three or more ($3+$).

  • Suffix -ose: Indicates that the molecule is a sugar.

  • Root word saccharide: Means sugar.

• Classifications of Saccharides:

  • Monosaccharide: Consists of $1$ sugar unit.

  • Disaccharide: Consists of $2$ sugar units.

  • Polysaccharide: Consists of $3+$ sugar units.

• Mnemonic Device for Biomolecules: "Cows like peanuts" represents Carbohydrates, Lipids, Proteins, and Nucleic acids.

Major Biomolecules, Monomers, and Polymer Structures

• Monomer Definition: The basic repeating unit or building block that links together to form a polymer (analogous to standard Lego bricks used to build a complex structure like a car).

• Carbohydrates:

  • Monomer Subunit: Monosaccharide.

  • Polymer Structure: Polysaccharide (formed when $3+$ monosaccharide monomers join together).

• Lipids:

  • Subunits / Monomers: Glycerol and fatty acids (contains $2$ distinct subunit types).

  • Polymer Structure: None. Lipids do NOT form polymers.

  • Structural Exception: Lipids are not classified as polymers because they contain two different types of monomers (glycerol and fatty acids) and lack a repeating rhythmic pattern (for example, a sequence may run glycerol-glycerol-fatty acid-fatty acid-fatty acid-glycerol).

• Proteins:

  • Monomer Subunit: Amino acids.

  • Polymer Structure: Polypeptide (formed by linking $3+$ amino acids).

  • Chemical Bonding: Amino acids are joined together via peptide bonds.

  • Practical Application: Human hair is composed primarily of protein. Hair products (such as Pantene) incorporate amino acids into their formulas to assist in building and strengthening hair strands directly from the root.

• Nucleic Acids:

  • Monomer Subunit: Nucleotide.

  • Polymer Structure: Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA).

Dehydration Synthesis (Dehydration Reaction)

• Alternate Terminology: Dehydration reaction is commonly referred to as dehydration synthesis.

  • "Dehydration": Indicates the removal or loss of a water molecule ($H_2O$).

  • "Synthesis": Means to make, build, or create a compound (for example, photosynthesis is the process by which plants synthesize glucose sugars using light energy).

• Definition: A chemical reaction that joins individual monomer subunits together to construct larger polymers.

• Chemical Mechanism of Dehydration Synthesis:

  • Reacting molecules possess a positive Hydrogen atom ($-H$) and a negative Hydroxyl group ($-OH$).

  • The $-H$ from one monomer bonds with the $-OH$ of an adjacent monomer.

  • The combined $-H$ and $-OH$ detach from the molecules as a free water molecule ($H_2O$).

  • The resulting open bonding sites allow the two monomers to join directly together into a single, larger molecule.

• Biological Function: Used continuously by the body to synthesize new tissue, replace dead skin cells, repair damaged internal structures, and store fat cells for energy reserves.

Hydrolysis Reaction Mechanism

• Etymology: Hydro- means water; -lysis (or lice) means to break or split.

• Definition: A chemical reaction in which a water molecule ($H_2O$) is added to split a covalent bond, breaking a larger molecule down into smaller subunit monomers.

• Chemical Mechanism of Hydrolysis:

  • A water molecule ($H_2O$) is added to a single complex molecule at the covalent bond connecting two subunits.

  • The covalent bond is cleaved.

  • The water molecule breaks into $-H$ and $-OH$; the $-H$ attaches to one released subunit, while the $-OH$ attaches to the other released subunit, yielding $2$ separate smaller molecules.

• Role in Digestion:

  • Ingested dietary proteins are broken down via hydrolysis into individual amino acids.

  • Ingested carbohydrates are broken down into monosaccharides.

  • Ingested fats/lipids are broken down into glycerol and fatty acids.

Physiology of Cellular Construction, Sleep, and Repair

• Skin Exfoliation and Regeneration:

  • Surface skin cells are constantly sloughed off and replaced by new cells produced via dehydration synthesis.

  • Approximately $90\%$ of household dust is composed of shed dead skin cells.

  • Bathing cleanses the body by removing accumulated dead skin cells from the skin surface.

• Rest and Metabolic Repair:

  • During sleep, the human body functions as an active construction site, diverting adenosine triphosphate (ATP) energy away from physical activity toward tissue repair and growth.

  • Microscopic tissue tearing occurs daily; adequate sleep is required to rebuild damaged tissue.

  • Insomnia or lack of sleep prevents complete tissue repair, leading to systemic body aches and malaise.

  • Pubescent children and adolescent males undergo rapid physical growth, necessitating increased amounts of sleep to facilitate cellular construction.

Academic Logistics, Grading Policies, and Course Schedule

• Career Insights on Teaching:

  • Teaching is a rewarding profession centered on mastering learning strategies and transferring knowledge to students.

  • Entry-level salaries for educators right out of college (at age $23$) are strong and comparable to starting salaries in engineering, though base salary progression remains relatively flat without structural advancements (such as obtaining a Master's degree or taking on coaching roles).

  • Teaching offers strong community connections and occasional professional courtesies (such as expedited doctor's visits for Mrs. Howard).

• Course Schedule & Lecture Progress:

  • Current Day: Thursday.

  • Next Class Session: Tuesday (unaffected by "lazy day").

  • Resumption Point: Lecture will resume on Slide $28$, starting with the topic of Enzymes.

• Laboratory Grading System:

  • Initial lab grades are based on active in-person participation (students actively working receive a grade of $100$).

  • Assignments generated during the final $30$ minutes of a lab session have built-in timers that close at the end of class. These are designated as "in-person lab" grades.

  • Students should distinguish between in-person lab participation grades and virtual lab submissions.

• Assignments:

  • Scientific Method papers must be retained by students for upcoming review in the following week.

• Carbon is the main building block of organic molecules (molecules containing carbon).

• Functional groups are parts of molecules that determine their specific chemical reactions and properties.

• Two main properties affected by functional groups are:

  • Chemical Reactivity: How likely a molecule is to react with other substances.

  • Polarity: The uneven distribution of charges within a molecule, meaning one side has a positive charge and the other side has a negative charge.

• Water ($H_2O$) is a common example of a polar molecule because it has a positive side and a negative side.

• In polar interactions, opposite charges attract:

  • The negative part of one polar molecule attracts the positive part of another.

  • The positive part of one polar molecule attracts the negative part of another.

• Polarity helps molecules stick together, which is important for forming large biological structures.