Comprehensive Study Guide on Nucleic Acids: Composition, Structure, and Function

Overview of Nucleic Acids

There are two primary types of nucleic acids: Ribonucleic Acid (RNA) and Deoxyribonucleic Acid (DNA).
Quantitative Measurement: Both DNA and RNA together make up from $5\% \text{ to } 15\%$ of the dry weight of cell components.
Location and Forms of DNA:
- In differentiated cells, almost all DNA is present in the nucleus as chromatin.
- Chromatin fills the entire nucleus of resting cells but becomes highly condensed into chromosomes as soon as the process of DNA replication is completed.
- A small amount of DNA is present in the mitochondrion and chloroplast; this DNA is generally free of proteins.
- Scientists agree that DNA is the pure genetic material and is naturally in the form of a double helix.
- Within the cell, DNA is not pure; it is conjugated with proteins and coiled into structures called chromosomes.
Characteristics of RNA:
- RNA is present in three different types depending on its specific function.
- It is found in both the nucleus and the cytoplasm of the cell.
- The types are:
  - Messenger RNA (mRNA)
  - Transfer RNA (tRNA)
  - Ribosomal RNA (rRNA)
Nucleoproteins:
- Nucleic acids are typically conjugated to simple proteins in eukaryotes to form nucleoproteins.
- The simple protein involved is usually a basic protein such as histone.

The Role of DNA and the Central Dogma of Molecular Biology

Carrier of Genetic Material: It is well established that DNA serves as the carrier of genetic materials in both prokaryotes and eukaryotes.
Control of Cell Function: DNA is recognized as a macromolecule that controls every aspect of cell function. This control is exerted through the process of protein synthesis.
The Central Dogma:
- Proposed by Francis Crick in 1958, it suggests that genetic information flows from nucleic acids to proteins.
- The sequence is: DNA $\rightarrow$ mRNA $\rightarrow$ Protein.
- The first step is Transcription: The process of copying a segment of DNA into RNA.
- The second step is Translation: The process of synthesis of proteins involves a change from nucleotide sequences to amino acid sequences.
Heredity and Replication:
- DNA plays an important role in heredity because it acts as a replicon (it can make copies of itself).
- This self-replication permits DNA to make copies as a cell divides.
- These copies are given to daughter cells, which can thus inherit each and every property and characteristic of the original cell.
Information Storage: DNA is a molecule of unusual capacity, able to encode a very large quantity of biological information.

Chemical Structure of Nucleic Acids

Polymeric Nature: DNA and RNA are polymeric molecules (polymers of nucleotides).
Monomeric Units:
- The monomers of DNA are called Deoxyribonucleotides.
- The monomers of RNA are called Ribonucleotides.
Hydrolysis of Nucleic Acids:
- Partial Hydrolysis: Results in nucleosides and nucleotides.
- Complete Hydrolysis: Results in three components: Purine and Pyrimidine bases + Sugar (Ribose or Deoxyribose) + Phosphoric acid ( $H_3PO_4$ ).

Nitrogenous Bases: Pyrimidines and Purines

These are nitrogenous heterocyclic bases. A heterocycle is a compound that has one or more atoms other than carbon in at least one of its rings.
Pyrimidine and its Derivatives:
- Pyrimidine is the parent compound.
- There are three derivatives of the pyrimidine base:
  - Uracil (U): Found only in RNA.
  - Thymine (T): Found only in DNA.
  - Cytosine (C): Found in both RNA and DNA.
- These bases bond with a ribose sugar at nitrogen number 1 ( $N_1$ ).
Purine and its Derivatives:
- Purine is the parent compound.
- There are two major derivatives of purine bases:
  - Adenine (A): Found in both RNA and DNA.
  - Guanine (G): Found in both RNA and DNA.
- These bases bond with a ribose sugar at nitrogen number 9 ( $N_9$ ).

DNA in Mitochondria and Chloroplasts

Genetic studies discovered that not all genetic information in eukaryotic cells is encoded by nuclear-chromosomal DNA; mitochondria and chloroplasts have their own nucleic acids.
Structure: Organelle DNA is relatively small, simple, a double helix, and circular.
Histone-Free: DNA molecules from the mitochondria and chloroplasts are free from histone proteins.
Genome Size: The size of the mitochondrial genome is much larger in plants than it is in animals.

Polynucleotide Formation and Bonds

Polynucleotides are formed by the polymerization of nucleotides through a condensation reaction.
Sugar-Phosphate Backbone:
- A covalent bond forms between Carbon-5 ( $C_5$ ) of one pentose sugar group and the phosphate of the next nucleotide.
- This results in a sugar-phosphate backbone with nitrogenous bases projecting outward from the backbone.
- The backbone has two distinct ends: the $5^{\prime}$ end and the $3^{\prime}$ end.
- The backbone is negatively charged because of the negative charges on each of the phosphate groups.
Specific Bonds:
- Sugar + Base = Nucleoside (joined by a Glycosidic bond).
- Nucleoside + Phosphate = Nucleotide.
- The linkage between nucleotides in the chain is a Phosphodiester bond.
Stability: DNA is very stable, largely due to the hydrogen bonds between strands.

The Watson-Crick Model of DNA Structure

Discovery History:
- Maurice Wilkins and Rosalind Franklin used X-ray diffraction to obtain accurate information about the position of atoms in the DNA macro-molecule. Their work showed that DNA was a double helix.
- Erwin Chargaff used paper chromatography to analyze DNA from various organisms.
Chargaff’s Rules:
- The amount of each nucleotide in DNA is the same for individuals of the same species but different between species.
- The number of nucleotides containing purines ( $A + G$ ) always equals the number of nucleotides containing pyrimidines ( $C + T$ ).
- Numerical Relationships: $A = T$ and $G = C$ .
- Equation: $A + G = T + C$ .
- Calculation Example: If Adenine is $20\%$ , then Thymine is $20\%$ . This leaves $60\%$ for Guanine and Cytosine, meaning Guanine is $30\%$ and Cytosine is $30\%$ .
The Watson and Crick Model (1951/1953):
- They built metal models based on X-ray diffraction and Chargaff's results.
- Structure: Two polynucleotide chains wrapped helically around each other.
- External/Internal distribution: Sugar-phosphate chain on the outside; Purines and Pyrimidines on the inside.
- Dimensions:
  - Width: $2\,nm$ (or $20\, \text{\AA}$ ).
  - Base Pair Spacing: $0.34\,nm$ (or $3.4\, \text{\AA}$ ).
  - Full Turn of Helix: $3.4\,nm$ (or $34\, \text{\AA}$ ), containing 10 base pairs.
Complementary Base Pairing:
- Adenine (A) bonds only to Thymine (T) by 2 hydrogen bonds ( $A=T$ ).
- Guanine (G) bonds only to Cytosine (C) by 3 hydrogen bonds ( $G \equiv C$ ).
- A purine paired with a pyrimidine provides a perfect fit for the $2\,nm$ width; pairing two purines ( $3\,nm$ ) or two pyrimidines ( $2\,nm$ ) would not fit correctly.
Antiparallel Nature: The two strands run in opposite directions. One runs $5^{\prime}$ to $3^{\prime}$ while the other runs $3^{\prime}$ to $5^{\prime}$ .
Grooves: The helix has two external grooves:
- Major groove: Deep and wide.
- Minor groove: Shallow and narrow.
- Both are large enough to allow protein (Histone) to contact the bases.

Ribonucleic Acid (RNA)

Definition: RNA is a single-stranded polynucleotide. It often folds, forming small areas that are double-stranded.
Components: Contains ribose sugar and the bases A, C, G, and U (Uracil replaces Thymine).
General Features:
1. Usually single-stranded with a flexible sugar-phosphate backbone that can fold.
2. Complementary base pairs can form between A-U and C-G.
3. Short length: While a human chromosome DNA molecule can contain $300 \times 10^6$ nucleotide residues, an RNA molecule is usually only about $75\text{--}8000$ nucleotides long.
4. Stability: RNA is much less stable than DNA. It acts as a short-term functional molecule, whereas DNA needs to be extremely stable to store genetic information.
Types of RNA:
- Messenger RNA (mRNA): Serves as a copy of the information stored in DNA. It is transcribed using DNA as a template. The template determines the order of ribonucleotide residues. It carries information from the nucleus to the cytoplasm to associate with ribosomes for protein synthesis.
- Transfer RNA (tRNA): Transfers amino acids to the ribosome during translation to form proteins. Its structure includes several key regions: Acceptor arm, D-arm, T-loop, and Anti-codon arm.
- Ribosomal RNA (rRNA): Facilitates the alignment of mRNA with ribosomes.

Comparison and Key Definitions

DNA vs. RNA Summary:
- DNA: Double-stranded, contains Deoxyribose, Pyrimidines are C and T, highly stable, longer than RNA, stores genetic information.
- RNA: Single-stranded, contains Ribose, Pyrimidines are C and U, less stable, shorter than DNA, transfers genetic material.
Additional Definitions:
- Codon: A sequence of three adjacent nucleotides which encode for a specific amino acid during protein synthesis or translation.
- Stop Codons: Three special codons that signal protein synthesis to terminate.
- Template: A physical object whose shape is used as a guide to make other objects. In biology, it is a macromolecule providing a pattern for the synthesis of another molecule.
DNA Replication Requirements:
- DNA template
- Enzymes (e.g., DNA polymerase, and enzymes to break hydrogen bonds)
- Nucleotides
- Primers

I can't provide diagrams directly, but I can help describe the components or structures related to nucleic acids, such as the double helix structure of DNA or the types of RNA. Let me know if you need a specific description or explanation!