Comprehensive Study Notes on Macromolecules: Proteins, Nucleic Acids, and Polysaccharides

Macromolecules are characterized as polymers composed of smaller individual units known as monomers.
Chemistry and biochemistry define the connection of these monomers through covalent bonds.
Key macromolecule classes include proteins, nucleic acids, and polysaccharides.

Monomers: Proteins are polymers of amino acids. There are exactly $20$ different amino acids that serve as building blocks.
Linkages: Individual amino acids are linked by covalent peptide bonds. This bond forms specifically between the carboxylic group of one amino acid and the amino group of another.
Hierarchical Complexity: Proteins possess a unique complexity compared to other macromolecules due to their multiple levels of organization: * Primary Structure: This refers to the linear polypeptides mediated by covalent peptide bonds. * Secondary Structure: These are higher-level organizations such as alpha helices and beta sheets. They are primarily mediated by hydrogen bonds occurring between the carboxy groups and the amino groups. * Tertiary and Quaternary Structures: These levels define the three-dimensional folding and assembly of proteins. They are largely determined by the R groups (the unique side chains for each amino acid) which allow proteins to fold into diverse shapes and sizes.
Structural Determination: The specific sequence of amino acids (the order) is the primary factor determining the final structure and uniqueness of a protein.
Bonding Roles: While covalent bonds form the backbone, noncovalent bonds (especially hydrogen bonds and electrostatic interactions involving carboxyl and amino groups) play a more critical role in determining higher-level (secondary, tertiary, and quaternary) structures.

Functional Role: Nucleic acids are characterized as information carriers. Their primary roles involve: * Storing genetic information. * Transmitting information from one type of molecule to another. * Determining how molecules are expressed within the cell.
Types of Nucleic Acids: * DNA (Deoxyribonucleic Acid). * RNA (Ribonucleic Acid).
The distinct difference between DNA and RNA is the presence or absence of an oxygen atom on the sugar molecule.
Structural Form: DNA and RNA are linear polymers of subunits called nucleotides. They are organized in a one-dimensional, head-to-tail sequence with no outward branching.

Standard Components: Every nucleotide consists of three distinct parts: 1. A Base: An organic molecule connected to the sugar. 2. A Pentose Sugar (referred to as "plentils" in transcript): A five-member ring sugar molecule. 3. A Phosphate Group: Attached to the sugar.
Carbon Numbering System: * Carbon $1$ : The position where the base is always connected. * Carbon $2$ : Determines the type of nucleic acid. If a hydroxyl group ( $OH$ ) is present, it is RNA. If only a hydrogen atom is present, it is DNA. * Carbon $3$ : Involved in linking neighboring nucleotides. * Carbon $4$ : Part of the sugar ring structure. * Carbon $5$ : The position where the phosphate group is attached.
Bases: The transcript identifies five different bases, specifically mentioning $A$ , $P$ , $C$ , and $G$ as found in DNA (note: $P$ is likely a transcription for $T$ /Thymine).
Acidity: The acidic nature of "Euclid acids" (nucleic acids) is derived from the phosphate group, which originates from phosphorus acid. At physiological $pH$, this group remains as phosphate, influencing the molecule's properties.

Nucleoside: This term denotes a structure consisting of only the base and the sugar (ribose), such as Adenosine.
Nucleophile/Nucleotide: Often used to denote the full unit of base, sugar, and phosphate groups (one or more).
Chemical Bonds: * Phosphodiester Bond: The bond between the phosphate group and the sugar. * Phosphoanhydride Bonds: These occur between the phosphate groups themselves, identified as alpha, beta, and gamma phosphates. * Three-Five ( $3$ - $5$ ) Phosphodiester Bridge: The specific linkage that connects neighboring nucleotides in a polymer. A phosphate group connects the $3$ prime hydroxyl group of one nucleotide to the $5$ prime hydroxyl group of the next, removing two phosphates in the process to form the bridge.

Classification by Size: * Oligosaccharides: Sugars ranging from $3$ to $10$ units in length. These can attach to other macromolecules on the cell surface.
Glucose Structure: A six-carbon sugar ( $C_6$ ). * Linear Form: A straight-chain representation of the six carbons (numbered $1$ through $6$ ). * Cyclic Form: In the body, glucose exists in a stable six-member ring (cyclorized). * Ring Geometry: Carbons $1$ through $5$ are part of the ring structure, while carbon $6$ is not in the ring and projects upwards.
Functional Carbon Positions: * Carbon $1$ and Carbon $4$ are considered the most important positions for bonding and structure. * Carbon $2$ is identified as a site that can be modified.