A1.2 Nucleic Acidso

Definition and Function of DNA
- DNA stands for deoxyribonucleic acid.
- It functions as the storage molecule for hereditary or genetic information.
- This information is transmitted from parents to offspring across generations.
- All living organisms use DNA as their primary molecule for transmitting hereditary information.
Nucleic Acids in Viruses
- Some viruses use RNA (ribonucleic acid) as their genetic material instead of DNA.
- It is critical to note that viruses are categorized as non-living organisms; therefore, the rule that all living things use DNA remains consistent.
Molecular Classification
- Both DNA and RNA are polymers, which are long molecules composed of repeating subunits.
- The individual repeating units of nucleic acids are called nucleotides.

Core Components
- Every nucleotide, whether DNA or RNA, consists of three distinct parts:
  1. Pentose Sugar: A five-sided (five-carbon) sugar.
  2. Phosphate Group: Attached to a specific point on the pentose sugar.
  3. Nitrogenous Base: One of four possible bases attached to the opposite side of the pentose sugar.
Specific Sugars
- While "pentose sugar" is a general term, specific nucleic acids contain specific sugars:
  - DNA contains deoxyribose.
  - RNA contains ribose.
Visualizing the Structure
- In biological diagrams, the attachment points are highly specific and important.
- The phosphate group must be drawn attached to a specific carbon on the pentose sugar ring.
- The nitrogenous base is attached to a different specific carbon on the same sugar ring.

Base Options for DNA
- There are four nitrogenous bases found in DNA:
  - Adenine (A)
  - Thymine (T)
  - Cytosine (C)
  - Guanine (G)
- In written academic answers, the full names should be provided, though abbreviations (A, T, C, G) are acceptable in diagrams.
Base Options for RNA
- RNA also contains four bases, but the set differs slightly from DNA:
  - Adenine (A)
  - Cytosine (C)
  - Guanine (G)
  - Uracil (U): This replaces Thymine in the RNA structure.
Chemical Classification: Purines and Pyrimidines
- Nitrogenous bases are categorized based on their ring structure:
  - Purines: These have a double-ring structure. This group includes Adenine and Guanine.
  - Pyrimidines: These have a single-ring structure. This group includes Cytosine, Uracil, and Thymine.

The Phosphodiester Bond
- To form a polymer (DNA or RNA strand), nucleotides link together via covalent bonds.
- Specifically, a covalent bond forms between the phosphate group of one nucleotide and the pentose sugar of the next nucleotide.
- The technical name for this specific linkage is a phosphodiester bond.
- In diagrams, these are represented by solid lines to signify the strength of the covalent bond.
The Condensation Reaction Mechanism
- The formation of a phosphodiester bond occurs through a condensation reaction, which involves the removal of a water molecule ( $H_2O$ ) to create a covalent bond.
- Specifics of Water Removal:
  - An $-OH$ (hydroxyl) group is taken from the phosphate group of one nucleotide.
  - An $-OH$ group is targeted on the pentose sugar of the adjacent nucleotide.
  - Two hydrogen atoms ( $H_2$ ) and one oxygen atom ( $O$ ) are removed to form water.
  - One oxygen atom remains, which is shared between the phosphate and the sugar, creating the bond.
- Calculation Rule: To join $n$ nucleotides together, you must remove $n - 1$ water molecules. For example, joining 5 nucleotides requires the removal of 4 water molecules.

The DNA Backbone
- DNA consists of two strands that form a sugar-phosphate backbone.
- The nitrogenous bases point inward, toward the center of the molecule.
Anti-parallel Orientation
- The two strands in a DNA molecule are anti-parallel, meaning they run side-by-side but in opposite directions.
- If one strand is viewed as "right-side up," the other strand is a "mirror image" and "upside down."
Hydrogen Bonding
- The two strands are held together by hydrogen bonds between the nitrogenous bases.
- In diagrams, hydrogen bonds are represented by dashed or dotted lines to distinguish them from the solid lines of covalent bonds.
- Bond Counts:
  - Between Adenine and Thymine: 2 hydrogen bonds.
  - Between Guanine and Cytosine: 3 hydrogen bonds.
Complementary Base Pairing Rule
- The bases fit together like puzzle pieces following a strict rule:
  - Adenine (A) always pairs with Thymine (T).
  - Guanine (G) always pairs with Cytosine (C).

Structural Similarities
- Both are polymers made of repeating nucleotide subunits.
Structural Differences
- Stranding: DNA is double-stranded; RNA is single-stranded.
- Sugar Type: DNA contains deoxyribose; RNA contains ribose.
- Bases:
  - DNA uses Thymine (A pairs with T).
  - RNA uses Uracil (A pairs with U).
- Base Pairing Persistence: In both molecules, Guanine (G) always pairs with Cytosine (C).

Semiconservative Replication
- DNA replication is the process of making a copy of the molecule to pass genetic information to offspring.
- The process is semi-conservative:
  1. The two original (parent) strands separate.
  2. Each original strand acts as a template.
  3. New strands are synthesized using the rules of complementary base pairing.
- Result: Two identical DNA molecules, each containing one original (old) strand and one newly synthesized strand.
The Binary Code Metaphor
- The sequence of nitrogenous bases (A, T, G, C) acts similarly to the binary code (0s and 1s) used in computer science.
- Just as patterns of 0s and 1s determine computer functions, the specific sequence of A, T, G, and C determines the genetic traits of an organism, making a human different from an alligator or a neighbor.

Definition of Gene Expression
- Gene expression is the process where the code in DNA is used to synthesize functional proteins.
The Flow of Information
- Information flows from DNA to RNA to Protein:
  1. DNA is used as a template to create RNA.
  2. The RNA is then translated into a sequence of amino acids to form a protein.
- The entire process is governed by the rules of complementary base pairing.

Unity of Life
- All living organisms on Earth use DNA as their genetic material and utilize the same four nitrogenous bases.
- Universal Genetic Code: The codes on DNA and RNA are interpreted in an identical way across all organisms (e.g., humans, butterflies, trees).
- This conservation of the genetic code is strong evidence that all life on Earth evolved from a common ancestor.
Diversity of Life
- Diversity is driven by three main factors in the DNA molecules:
  1. Varying Lengths: DNA molecules can be very long or relatively short.
  2. Infinite Sequences: There are nearly infinite possible combinations of A, T, G, and C.
  3. Specific Patterns: The unique pattern of bases determines the unique traits of the organism.
Physical Properties and Storage
- A DNA molecule is incredibly thin, measuring only $2\,nm$ (two nanometers) in width.
- One nanometer is equivalent to one-billionth of a meter ( $10^{-9}\,m$ ).
- Because it is so thin, extremely long strands of DNA (holding billions of base pairs) can be tightly scrunched and packed to fit inside the tiny volume of a cell.