DNA and RNA: Nucleotide Structure

• DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are essential nucleic acids that play critical roles in storing and expressing genetic information.

Nucleotide Structure

• Nucleotides are the building blocks of DNA and RNA.
• A nucleotide consists of a nitrogenous base, a pentose sugar, and one to three phosphate groups.
• The nitrogenous base is a heterocyclic ring structure containing nitrogen atoms.
• There are two classes of nitrogenous bases: purines and pyrimidines.
• Purines (adenine and guanine) have a double-ring structure.
• Pyrimidines (cytosine, thymine, and uracil) have a single-ring structure.
• DNA contains the bases adenine (A), guanine (G), cytosine (C), and thymine (T).
• RNA contains the bases adenine (A), guanine (G), cytosine (C), and uracil (U).
• The pentose sugar is a five-carbon sugar.
• In DNA, the sugar is deoxyribose (lacking an oxygen atom on the 2' carbon).
• In RNA, the sugar is ribose (containing an oxygen atom on the 2' carbon).
• The phosphate group is attached to the 5' carbon of the sugar.
• Nucleotides are linked together by phosphodiester bonds between the 3' carbon of one nucleotide and the 5' carbon of the next nucleotide.
• This creates a sugar-phosphate backbone with the nitrogenous bases extending from it.

DNA Structure

• DNA is a double-stranded helix.
• The two strands run antiparallel to each other (one strand runs 5' to 3', and the other runs 3' to 5').
• The sugar-phosphate backbone is on the outside of the helix, and the nitrogenous bases are on the inside.
• The two strands are held together by hydrogen bonds between complementary base pairs.

Base Pairing Rules

• Adenine (A) always pairs with thymine (T) via two hydrogen bonds (A=T).
• Guanine (G) always pairs with cytosine (C) via three hydrogen bonds (G≡C).
• These base pairing rules ensure that the sequence of one strand dictates the sequence of the other strand.
• The consistent base pairing results in a uniform width of the DNA helix.

RNA Structure

• RNA is typically single-stranded but can fold into complex secondary and tertiary structures.
• RNA contains ribose as its sugar and uracil (U) in place of thymine (T).
• RNA molecules can have various lengths and sequences, allowing them to perform diverse functions.
• RNA structures are stabilized by base pairing within the same strand (e.g., stem-loop structures).

Transcription Process

• Transcription is the process by which RNA is synthesized from a DNA template.
• It involves three main stages: initiation, elongation, and termination.

Initiation

• RNA polymerase binds to a specific region of the DNA called the promoter.
• The promoter contains specific DNA sequences that allow RNA polymerase to recognize and bind to the DNA.
• In eukaryotes, transcription factors are required to help RNA polymerase bind to the promoter.
• RNA polymerase unwinds the DNA double helix, creating a transcription bubble.

Elongation

• RNA polymerase moves along the DNA template strand, reading the sequence and synthesizing a complementary RNA molecule.
• RNA polymerase adds RNA nucleotides to the 3' end of the growing RNA molecule.
• The RNA molecule is synthesized in the 5' to 3' direction.
• The template strand is read in the 3' to 5' direction.

Termination

• Transcription continues until RNA polymerase reaches a termination signal in the DNA sequence.
• In bacteria, the termination signal can be a specific DNA sequence that forms a hairpin loop in the RNA, causing RNA polymerase to detach.
• In eukaryotes, the termination signal involves specific sequences and proteins that cleave the RNA transcript and release RNA polymerase.
• The resulting RNA molecule is called the primary transcript or pre-mRNA.
• In eukaryotes, the pre-mRNA undergoes processing to become mature mRNA.

RNA Processing (Eukaryotes)

• RNA processing includes capping, splicing, and polyadenylation.

Capping

• A modified guanine nucleotide (7-methylguanosine) is added to the 5' end of the pre-mRNA.
• The 5' cap protects the mRNA from degradation and helps in ribosome binding during translation.

Splicing

• Introns (non-coding regions) are removed from the pre-mRNA, and exons (coding regions) are joined together.
• Splicing is carried out by a complex called the spliceosome, which consists of small nuclear RNAs (snRNAs) and proteins.
• Alternative splicing allows different combinations of exons to be included in the mature mRNA, resulting in different protein isoforms.

Polyadenylation

• A poly(A) tail (a string of adenine nucleotides) is added to the 3' end of the mRNA.
• The poly(A) tail protects the mRNA from degradation and enhances translation.

Translation Process

• Translation is the process by which the genetic information encoded in mRNA is used to synthesize a protein.
• Translation takes place on ribosomes, which are made up of ribosomal RNA (rRNA) and proteins.
• Translation involves three main stages: initiation, elongation, and termination.

Initiation

• The small ribosomal subunit binds to the mRNA.
• An initiator tRNA (carrying methionine) binds to the start codon (AUG) on the mRNA.
• The large ribosomal subunit joins the complex, forming the initiation complex.

Elongation

• The ribosome moves along the mRNA, one codon at a time.
• For each codon, a tRNA molecule with a complementary anticodon binds to the mRNA.
• The tRNA carries the corresponding amino acid.
• A peptide bond is formed between the amino acid on the incoming tRNA and the growing polypeptide chain.
• The ribosome translocates to the next codon, and the process is repeated.

Termination

• The Ribosome continues to move along the mRNA until it encounters a stop codon (UAA, UAG, or UGA).
• Stop codons do not have corresponding tRNAs.
• Instead, release factors bind to the stop codon, causing the ribosome to release the polypeptide chain and dissociate from the mRNA.
• The polypeptide chain folds into its functional three-dimensional structure.

Genetic Code

• The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells.
• Each codon (a sequence of three nucleotides) specifies a particular amino acid or a stop signal.
• The genetic code is degenerate, meaning that multiple codons can specify the same amino acid.
• There are 64 possible codons: 61 codons specify amino acids, and 3 codons are stop signals.
• The start codon (AUG) also codes for methionine.
• The genetic code is nearly universal, meaning that it is used by almost all organisms.