Molecular Genetics: Key Concepts and Mutation Effects

Posted on Nov 18, 2025 in Biology

Molecular Genetics Fundamentals

Cellular Transformation and Key Enzymes

Transformation studies demonstrate the ability to transition from non-disease-causing to disease-causing states, often involving the uptake of genetic material.

Enzyme Definitions

  • Enzyme that degrades DNA: DNase
  • Enzyme that degrades protein: Protease
  • Enzyme that degrades RNA: RNase

Cell Types and Ploidy

  • Somatic Cells: Non-reproductive cells (diploid).
  • Gametes: Reproductive cells (haploid), containing half the amount of DNA as somatic cells.

DNA and RNA Structure

DNA Composition and Base Pairing

  • DNA is composed of 4 nucleotides: A (Adenine), C (Cytosine), G (Guanine), T (Thymine).
  • Pyrimidines: Cytosine (C) and Thymine (T).
  • Purines: Guanine (G) and Adenine (A).
  • A nucleotide consists of a Base + Deoxyribose + Phosphate.
  • The G-C bond uses 3 hydrogen bonds, making it stronger than the A-T bond, which uses 2 hydrogen bonds.

Chargaff’s Rules

In double-stranded DNA:

  • The ratio A/T equals 1.0, and G/C equals 1.0.
  • The percentage of A is the same as T, and the percentage of G is the same as C.
  • However, the overall G-C content relative to the A-T content varies significantly among different organisms.

DNA Strand Orientation and Complexity

DNA consists of two anti-parallel strands, where the bottom strand is complementary to the top strand (and vice versa).

5' - AAACCTGTAGT - 3'
3' - TTTGGACATCA - 5'

The number of possible sequences is calculated as 4n, where n is the number of base pairs. For example, if n=1000, there are 41000 possible arrangements.

RNA Characteristics

RNA uses the bases A, C, G, and U (Uracil instead of Thymine). RNA often serves as the genetic material in some organisms, such as retroviruses (e.g., HIV). During transcription (DNA -> RNA), Adenine (A) pairs with Uracil (U).

Genetic Mutations and Phenotypic Impact

Mutation Basics and Heritability

Mutations (changes in DNA sequence) are the primary source of variation and the fuel for evolution, though most are deleterious. A change in the human population exceeding 1% frequency is classified as a Polymorphism.

Somatic vs. Germline Mutations

  • Somatic Cell Mutations: Occur in non-reproductive cells and are not passed to the next generation. Their effect may be masked by wild-type (WT) cells within the same tissue, but they have a greater effect if dominant or X-linked (recessive) in males.
  • Germline Cell Mutations: Occur in gametes and will be passed to the next generation.

Types of Point Mutations (Substitutions)

A substitution involves changing one nucleotide base:

  • Missense: Changes one amino acid to another.
  • Nonsense: Changes an amino acid codon to a premature stop codon. This usually causes a severe loss of function (e.g., when a tumor suppressor loses function, increasing cancer risk).
  • Silent: The nucleotide changes, but the resulting amino acid does not, due to code redundancy. This should have no effect on the protein.

Insertions, Deletions, and Frameshifts

  • Insertion/Deletion: If 3 letters (or multiples of 3) are inserted or deleted, the reading frame is maintained.
  • If 1 or 2 letters are inserted or deleted, it causes a frameshift.
  • A Frameshift mutation affects the entire protein-coding frame downstream, potentially ruining the entire protein, especially if it occurs early in the sequence.

Functional Consequences of Mutations

Loss-of-Function Mutations

Changes in DNA that result in the protein losing its function. Causes include insertion, deletion, premature stop (nonsense), or a missense mutation affecting a critical amino acid. Most loss-of-function mutations are recessive.

  • Null Mutation: Complete loss of protein function (e.g., complete gene deletion, early premature stop, or point mutation on a critical amino acid).
  • Partial Loss of Function: The mutant protein retains some function, but significantly less than the wild-type (WT).

Gain-of-Function Mutations

Results in too much functional protein being made, or the protein acquiring a new function. These are mostly dominant.

  • Causes: Deletion of a regulatory domain, or a missense mutation that changes an amino acid that normally acts as an “off switch,” leading to an “always on” state (e.g., an unregulated oncogene).

Dominant Negative Mutations (DN)

A loss-of-function mutation that acts dominantly. In a heterozygote, the mutant copy impairs the ability of the wild-type protein to function, resulting in a mutant phenotype even though only one copy is affected. Example: A distracting element actively interfering with a process.

Haplo-Insufficient Mutations

Loss of function in a gene highly sensitive to dosage. One copy of the wild-type gene is insufficient to produce the normal phenotype, making the mutation dominant (the heterozygote looks mutant).

Causes of DNA Sequence Changes

Spontaneous Mutations (Internal)

Changes in the nucleotide sequence occurring without external cause; accidental and typically at a very low rate, though this varies among organisms.

  • DNA Replication Errors: Occasional mistakes made by DNA polymerase.
  • DNA Replication Slippage: A portion of the template strand loops out during replication, often in repeat regions, leading to deletions in the new strand.
  • Tautomeric Shifts, Depurination, or Deamination: Changes in the chemical structure of a nucleotide that result in altered base pairing (e.g., U-A instead of C-G, or A-C instead of T-A).

Induced Mutations (External)

Mutations caused by external factors, which can be natural or artificial (e.g., exposure to carcinogens or radiation).

Gene Regulation Mechanisms

Operon Systems

  • Inducible System: Enzymes are only produced when the substrate is present (induced by the substrate). This often involves a Double Negative mechanism (e.g., the Lac Operon, where the inducer blocks the repressor).
  • Repressible System: An operon that blocks transcription of a gene in the presence of a specific end-product, resulting in no enzyme production. The end-product activates repressor proteins. Enzymes are only made when the end-product is absent.

Allosteric Regulation Example

In the Lac Operon, Lactose acts as an allosteric effector, causing a conformational change in the LacI repressor so that it can no longer bind to the operator sequence.

Regulatory Elements

  • Cis-Acting Element: A DNA sequence that regulates the expression of a gene located nearby. Examples include the promoter, operator, and enhancer.
  • Trans-Acting Element: Factors (usually proteins) that control gene expression by binding to a cis-acting element. Examples include Transcription Factor Activators and Repressors. These proteins can move around the cell and often provide more complex regulation than the promoter alone.

Cancer Genetics and Cell Control

Characteristics of Cancer

Cancer encompasses a large number of complex diseases characterized by uncontrolled cell growth and spread. Most cancers are caused by somatic cell mutations, although germline mutations account for a small percentage but confer a high lifetime risk. Genetic changes associated with cancer include translocations, deletions, and aneuploidy (abnormal number of chromosomes).

Clonal Origin

Cancer typically originates from a single common cell. Evidence includes: all cancer cells having the same pattern of X-inactivation, and patients with chromosomal abnormalities having the same translocation across all tumor cells.

Age and Mutation Accumulation

Cancer is often age-related because it takes time to accumulate the necessary multiple mutations (estimated rate of 1 in 106 cell divisions). This delay reflects the time required for exposure to carcinogens and subsequent development (e.g., cancer cases observed following Hiroshima/Nagasaki).

Defects in DNA repair mechanisms significantly increase the risk of cancer.

Cell Proliferation and Apoptosis

  • Cancer cells lose control over cell proliferation, unlike most adult animal cells which cease growth and division.
  • Many cancer-causing viruses are RNA viruses (retroviruses).
  • Apoptosis: Programmed cell death, a mechanism to limit cancer cells. It is also a normal process in development (e.g., forming gaps between fingers and toes).

Oncogenes and Tumor Suppressors

  • Tumor Suppressors: Loss of function of both alleles is typically required for cancer development.
  • Proto-Oncogene to Oncogene: This transition is a Gain of Function mutation (e.g., the c-myc gene being moved next to a strong enhancer).

Quantitative Genetics and Heritability

Trait Classification

  • Qualitative Traits: Monogenic (specified by single genes), often discontinuous (discrete categories like Tall/Dwarf), and mostly unaffected by environmental factors. Note: Monogenic traits can sometimes be continuous (e.g., incomplete dominance).
  • Quantitative Traits: Polygenic (controlled by multiple genes), significantly affected by the environment (e.g., nutrition), and typically continuous (following a distribution curve). Example: Human height.

Polygenic Calculations

  • Ratio of F2 individuals expressing one of the extreme phenotypes: 1/4n (where n is the number of genes involved).
  • Number of distinct phenotypes: 2n + 1 (where n is the number of genes).
  • Additive Alleles: Phenotype is determined by counting the number of capital letters (dominant alleles).

Defining Heritability

Heritability is not a fixed trait; it is context-specific. It represents the portion of phenotypic variation that can be attributed to genetic variation within a specific population in a particular environment.

Example: A heritability estimate of 0.65 means that 65% of the variation in height within that population and environment can be explained by genotypic differences among individuals.

Variance Components

Phenotypic Variance (VP) = Genotypic Variance (VG) + Environmental Variance (VE) + Gene-Environment Interaction Variance (VGXE)

In twin studies:

  • VG is typically greater in Dizygotic (DZ) twins than in Monozygotic (MZ) twins (due to greater genetic difference).
  • VE is generally similar for DZ and MZ twins.

Twin Studies and Concordance

  • Monozygotic (MZ) Twins: Share 100% genetic information, resulting from the splitting of a single fertilized egg.
  • Dizygotic (DZ) Twins: Share 50% of genetic material (like siblings), resulting from separate fertilization events.

Interpreting Concordance:

  • If concordance is much higher in MZ twins than in DZ twins, a strong genetic component is suspected.
  • If concordance is the same in MZ and DZ twins, a strong environmental component is suspected.

Calculating Variance

Variance is the average of the squared differences from the mean (sometimes calculated using n-1 in the denominator). Example calculation: (206² + 76² + (-224)² + 36² + (-94)²) / 5 = 21,704. The Standard Deviation is the square root of the variance.

Molecular Tools and Repair

Nucleotides in Sequencing

  • dNTP (Deoxynucleotide Triphosphate): Allows DNA synthesis to continue (“GO”).
  • ddNTP (Dideoxynucleotide Triphosphate): Causes chain termination (“STOP”).

RNA Interference (RNAi)

Small RNAs inhibit gene expression primarily by degrading mRNA.

  • siRNAs (Small Interfering RNAs): Often originate from an outside source (like a virus) but can also come from within the cell.
  • microRNAs (miRNAs): Originate from the cell of interest itself.

DNA Repair: Mismatch Repair

In mismatch repair, the incorrect nucleotide is removed. The old strand is marked (e.g., methylated), while the new strand (which is more likely to contain the error) is not marked, allowing the repair machinery to identify and correct the mistake on the new strand.