Nucleic Acids: Structure, Function, and Genetic Information Flow

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Nucleic Acids

Primary Structure of Polynucleotides

The primary structure of a polynucleotide refers to the linear sequence of nucleotides joined by phosphodiester bonds. Each nucleotide consists of a nitrogenous base (adenine, thymine, cytosine, or guanine in DNA), a deoxyribose sugar, and a phosphate group. The sequence is always read from the 5′ end to the 3′ end.

Phosphodiester Linkage: Connects the 3′-OH group of one nucleotide to the 5′-phosphate of the next.
Naming: The sequence CATG is read from the 5′ to 3′ direction.
Sugar-Phosphate Backbone: Provides structural stability to the nucleic acid strand.
Bases: Project from the backbone and encode genetic information.
Example: A DNA strand with the sequence 5′-CATG-3′.

Primary structure of a polynucleotide showing phosphodiester linkages and base sequence Sugar-phosphate backbone of a polynucleotide

The DNA Double Helix

The double helix model of DNA, proposed by Watson and Crick with contributions from Rosalind Franklin, describes DNA as two antiparallel polynucleotide strands coiled into a right-handed helix. The sugar-phosphate backbones are on the outside, while the nitrogenous bases are on the inside, paired through hydrogen bonds.

Antiparallel Strands: One strand runs 5′ to 3′, the other 3′ to 5′.
Base Pairing: Purines (adenine, guanine) pair with pyrimidines (thymine, cytosine).
Complementary Base Pairs: Adenine (A) pairs with Thymine (T) via two hydrogen bonds; Cytosine (C) pairs with Guanine (G) via three hydrogen bonds.
Stability: Hydrogen bonding and base stacking stabilize the helix.

Three-dimensional structure of DNA double helix Hydrogen bonding in the DNA double helix between base pairs

Flow of Genetic Information

Genetic information in DNA is used to direct protein synthesis through two key processes: transcription and translation. DNA replication ensures genetic continuity during cell division.

Replication: DNA makes a copy of itself before cell division.
Transcription: DNA is used as a template to synthesize RNA.
Translation: RNA directs the synthesis of proteins, determining the amino acid sequence.

Central dogma: DNA replication, transcription, and translation

DNA Replication

Mechanism of Replication

DNA replication is semiconservative: each new DNA molecule contains one parental and one newly synthesized strand. Replication begins at origins of replication, forming replication forks and bubbles.

Helicase: Unwinds the double helix at origins of replication.
Primase: Synthesizes short RNA primers to initiate DNA synthesis.
DNA Polymerase: Adds nucleotides to the 3′ end of the primer, synthesizing the new strand in the 5′ to 3′ direction.
Leading Strand: Synthesized continuously toward the replication fork.
Lagging Strand: Synthesized discontinuously as Okazaki fragments, later joined by DNA ligase.
Exonuclease: Removes RNA primers; DNA polymerase fills gaps.
DNA Ligase: Seals nicks in the sugar-phosphate backbone.

Semiconservative DNA replication: parent and daughter DNA Formation of replication fork and replication bubble Leading and lagging strand synthesis at the replication fork Bond formation in DNA replication: phosphodiester bond formation

Base Pairing in DNA

During replication, the identity of the bases on the template strand determines the order of bases on the new strand. A pairs with T, and G pairs with C, ensuring accurate copying of genetic information.

Base pairing in DNA: A-T and G-C pairs

RNA: Structure and Types

Differences Between DNA and RNA

RNA differs from DNA in several key aspects:

Sugar: RNA contains ribose; DNA contains deoxyribose.
Bases: RNA uses uracil (U) instead of thymine (T).
Structure: RNA is typically single-stranded and shorter than DNA.
Types: Three main types are ribosomal RNA (rRNA), messenger RNA (mRNA), and transfer RNA (tRNA).

Functions of RNA Types

rRNA: Forms the core of ribosomes, the site of protein synthesis.
mRNA: Carries genetic information from DNA to ribosomes.
tRNA: Brings specific amino acids to the ribosome during translation.

Structure of tRNA

tRNA molecules have a cloverleaf structure with an acceptor stem at the 3′ end (for amino acid attachment) and an anticodon loop (for codon recognition).

Cloverleaf structure of tRNA with acceptor stem and anticodon

Transcription: DNA to RNA

Mechanism of Transcription

Transcription is the synthesis of mRNA from a DNA template. RNA polymerase binds to a promoter region, unwinds the DNA, and synthesizes mRNA complementary to the template strand.

Template Strand: Used to synthesize mRNA.
Informational (Coding) Strand: Has the same sequence as mRNA (except T is replaced by U).
Direction: mRNA is synthesized from the 5′ to 3′ direction.
Termination: Occurs when RNA polymerase reaches a stop signal.

Transcription: synthesis of mRNA from DNA template Steps of transcription: control segment, triplets, and RNA polymerase

Processing of mRNA

In eukaryotes, the initial mRNA (heterogeneous nuclear RNA, hnRNA) contains both exons (coding regions) and introns (non-coding regions). Introns are removed by splicing before translation.

Exon: Codes for protein.
Intron: Non-coding, removed before translation.

Splicing of hnRNA: removal of introns to form mature mRNA

Example: Transcription

Template strand: 3′—C T A G G A T A C—5′
mRNA: 5′—G A U C C U A U G—3′
Informational strand: 5′—G A T C C T A T G—3′

The Genetic Code

Codons and Amino Acids

The genetic code consists of triplets of nucleotides (codons) in mRNA, each specifying a particular amino acid. The code is universal and redundant (multiple codons can code for the same amino acid).

Start Codon: AUG (methionine) initiates translation.
Stop Codons: UAA, UAG, UGA signal termination of translation.
Example: UAC codes for tyrosine, UGC for cysteine.

mRNA Codon	tRNA Anticodon	Amino Acid
ACA	UGU	Threonine
GCG	CGC	Alanine
AGA	UCU	Arginine
UCC	AGG	Serine

Translation and Protein Synthesis

Mechanism of Translation

Translation is the process by which the sequence of codons in mRNA directs the synthesis of a polypeptide chain. It occurs in three main stages: initiation, elongation, and termination.

Initiation: mRNA binds to the ribosome; the first tRNA (carrying methionine) binds to the start codon (AUG).
Elongation: tRNAs bring amino acids to the ribosome, where peptide bonds form between them, extending the polypeptide chain.
Termination: When a stop codon is reached, the completed protein is released.

mRNA codon, tRNA anticodon, and amino acid relationship Initiation of translation: ribosome assembly on mRNA Elongation: peptide bond formation during translation Termination: release of completed polypeptide Comparison of DNA, mRNA, tRNA, and polypeptide sequences

Mutations and Genetic Disease

Types of Mutations

A mutation is a change in the nucleotide sequence of DNA. Mutations can be spontaneous or induced by mutagens, and their effects vary depending on the type and location of the change.

Point Mutation: Substitution of one nucleotide for another.
Deletion Mutation: Loss of one or more nucleotides.
Insertion Mutation: Addition of one or more nucleotides.
Silent Mutation: No effect on the protein sequence due to redundancy in the genetic code.
Missense Mutation: Changes one amino acid in the protein; effect can be minor or severe (e.g., sickle cell anemia).
Genetic Disease: Mutations causing defective proteins that are inherited can lead to genetic diseases.

Disease	Characteristics
Tay-Sachs disease	Mental retardation; defective hexosaminidase A enzyme
Sickle cell anemia	Anemia; defective hemoglobin, capillary occlusion
Phenylketonuria	Mental retardation; deficiency of phenylalanine hydroxylase
Galactosemia	Mental retardation; deficiency of enzyme for galactose metabolism
Huntington's disease	Progressive disability; defect in Htt protein gene, neuronal degeneration