Molecular Biology Essentials: DNA, RNA, and Gene Function

Posted on Jun 30, 2025 in Biology

Fundamentals of Molecular Biology

RNA Nucleotide Components

An RNA nucleotide consists of three main parts:

  • A ribose molecule
  • A phosphate group
  • A nitrogenous base

The Central Dogma of Molecular Biology

Information is transferred from DNA to RNA to protein.

Gene Expression and Regulation

Impact of Promoter Sequence Mutations

A mutation in the promoter sequence of a gene might prevent RNA polymerase from binding. As a result, the gene would not be transcribed.

DNA Preparation for RNA Synthesis

Before RNA polymerase can begin to assemble nucleotides into a new RNA strand, the DNA molecule must be separated into two strands.

Codon Structure and Amino Acid Specification

If codons consisted of two nucleotides instead of three, there would be only 16 possible combinations of nucleotides. This number is insufficient for all 20 amino acids to have a unique code, posing a significant problem for protein synthesis.

Location of Translation Within a Cell

Translation takes place on ribosomes in the cytoplasm.

Functions of RNA Types

The three main kinds of RNA perform distinct functions:

  • Messenger RNA (mRNA) carries copies of instructions for assembling proteins from DNA to the ribosomes, providing the code for translation.
  • Ribosomal RNA (rRNA) is a component of the ribosomes, where it helps read the code.
  • Transfer RNA (tRNA) molecules carry specific amino acids to the ribosomes for assembly into proteins, bringing the next amino acid specified by the code.

Understanding Polyploid Organisms

A polyploid organism possesses many sets of chromosomes.

Beneficial Human Mutations

Some beneficial mutations observed in humans include those that lead to stronger bones and better disease resistance.

Regulation of lac Genes in E. coli

It is beneficial for E. coli to regulate the expression of lac genes rather than expressing them constantly. This prevents the cell from wasting energy and resources building lac proteins when they are not needed, such as when lactose is absent from the environment.

How miRNA Blocks Gene Expression

A molecule of miRNA (microRNA) forms a small loop of RNA that combines with proteins to create a silencing complex. This complex binds to and destroys mRNA that matches the miRNA’s sequence, thereby blocking gene expression.

Similarity of Hox Genes Across Animals

Hox genes found in different animals are remarkably similar because they descended from the genes of common ancestors, highlighting evolutionary conservation.

Gene Regulation in Frog Metamorphosis

Internal and external factors work together to regulate gene expression during frog metamorphosis. For example, external forces like a drying pond can trigger internal factors, such as hormonal changes, which alter the rate of metamorphosis.

Pesticide Resistance: A Beneficial Mutation

Pesticide resistance is considered a beneficial mutation in mosquitoes. In environments where pesticides are present, mosquitoes with this mutation have a significant survival advantage over those without it. Resistant mosquitoes survive and reproduce, while non-resistant ones perish.

Effects of lac Repressor Gene Mutation

A mutation in the gene coding for the lac repressor in E. coli could have two main effects:

  • The lac repressor might be unable to bind with the operator, leading to permanent activation of the lac genes as RNA polymerase would not be prevented from initiating transcription.
  • Alternatively, the lac repressor might be unable to bind with lactose, causing it to permanently bind with the operator. This would prevent RNA polymerase from binding to the promoter, permanently turning off the lac genes.

Eukaryotic Gene Expression Regulation

Eukaryotic cells regulate gene expression through various mechanisms, including RNA interference. A Dicer enzyme cuts a small loop of miRNA into tiny pieces. These pieces then bind with proteins to form a silencing complex. When this complex encounters an mRNA molecule with a complementary code, it binds to the mRNA and effectively shuts down its expression.

Necessity of Gene Regulation in Multicellular Organisms

Gene regulation is crucial for the development of multicellular organisms. While every nucleated cell contains all the genes to build the organism, not every gene is needed in every cell. Therefore, unneeded genes must be switched off. For instance, nerve tissue requires flexibility, not the rigidity provided by bone-forming proteins. Thus, genes coding for bone structure must be turned off in nerve cells.

Molecular Processes in Detail

Transcription Versus DNA Replication

Transcription and DNA replication differ in several key aspects:

  • Enzyme Involved: RNA polymerase is involved in transcription, whereas DNA polymerase is involved in DNA replication.
  • Template Strands: During transcription, free nucleotides base pair with nucleotides on only one strand of a DNA molecule. In DNA replication, both strands serve as templates.
  • Nucleotide Type: In transcription, the free nucleotides are RNA nucleotides (containing uracil), not DNA nucleotides (containing thymine).
  • Process Duration: Transcription continues until a stop signal is reached on the DNA strand. DNA replication continues until the entire chromosome is replicated.
  • Product: At the end of transcription, one single-stranded RNA molecule is formed. DNA replication yields two double-stranded DNA molecules.
  • Product Location: The newly formed RNA molecule typically leaves the nucleus, while the newly formed DNA molecules remain in the nucleus.

Pre-mRNA to Final mRNA Conversion

After transcription from DNA, a pre-mRNA molecule undergoes significant processing to become a final mRNA molecule:

  1. Portions of the pre-mRNA molecule, called introns, are cut out.
  2. The remaining pieces, called exons, are then spliced together.
  3. Finally, a cap is added to one end and a tail to the opposite end of the mRNA molecule, forming the mature mRNA.

The Process of Translation

Translation is the process by which genetic information in mRNA is used to synthesize proteins:

  1. After an mRNA molecule is transcribed in the nucleus, it moves to the cytoplasm.
  2. A ribosome positions itself at the start codon on the mRNA molecule.
  3. As each successive codon passes the ribosome, a tRNA molecule brings a specific amino acid to the ribosome. Only a tRNA molecule with an anticodon complementary to the mRNA codon can attach. The codons and anticodons have complementary nitrogenous bases, allowing them to base pair. This base pairing brings a specific sequence of amino acids to the ribosomes. For example, a codon like GCU specifies the amino acid alanine, and the start codon specifies methionine.
  4. The ribosome attaches each new amino acid to the growing polypeptide chain, and the bond holding the tRNA to its amino acid is broken. The tRNA then moves away from the ribosome, allowing it to bind with another amino acid.
  5. The ribosome moves to the next codon, and the process repeats until the entire mRNA molecule is translated, forming a complete protein.

Point Mutations and Protein Changes

Point mutations, which include substitutions, insertions, and deletions of single nucleotides in DNA, can have varying effects on proteins. Insertions and deletions generally have a greater impact than substitutions because they can affect every amino acid specified by the nucleotides following the mutation point. This is known as a frameshift mutation. For instance, the deletion of a single nucleotide can shift the reading frame of all subsequent codons during translation, potentially changing the entire amino acid sequence. In contrast, a substitution typically affects only a single amino acid. A change in multiple amino acids is more likely to alter the protein’s normal function than a change in just one.

Substitution Mutations with No Effect

Some substitution mutations have no effect on the final protein assembled by the ribosome. This is possible because most amino acids can be specified by more than one codon (degeneracy of the genetic code). If a substitution mutation results in a new codon that still specifies the same amino acid, the mutation will be silent. For example, if a ‘C’ in a ‘CUG’ codon is substituted with a ‘U’, the resulting codon ‘UUG’ still codes for the amino acid Leucine (Leu). Similarly, if ‘UUG’ is changed to ‘UUA’, it would also still specify Leu.

Chromosomal Mutations

General Types of Chromosomal Mutations

The general type of mutation involving large-scale changes to chromosomes is a chromosomal mutation.

Chromosomal Processes Involving Two Chromosomes

Certain chromosomal processes, such as translocation, involve two chromosomes.

Deletion Versus Duplication Processes

In chromosomal mutations, deletion results in the loss of a segment of a chromosome, while duplication results in the repetition of a segment of a chromosome.

Chromosomal Inversion Process

A segment of a chromosome becomes oriented in the reverse direction during the process of inversion.

Chromosomal Translocation Process

Translocation is a chromosomal process where a segment of one chromosome breaks off and attaches to another non-homologous chromosome.