Chapter 15

Mutation, DNA Repair, and Cancer

Mutation: Definition and Importance

Mutations are heritable changes in the genetic material and are essential for the continuity of life. They serve as the source of genetic variation, which is fundamental for natural selection. However, most new mutations are more likely to be harmful than beneficial. DNA repair systems exist to reverse DNA damage, and cancer is a disease caused by gene mutations.

Types of Gene Mutations and Their Effects

Gene mutations can affect the amino acid sequence of proteins, leading to various consequences:

• Silent Mutation: Does not alter the amino acid sequence due to the degeneracy of the genetic code.

• Missense Mutation: Changes a single amino acid in a polypeptide. The effect depends on the similarity of the substituted amino acid to the original. Example: Sickle-cell disease.

• Nonsense Mutation: Changes a normal codon to a stop codon, producing a truncated polypeptide.

• Frameshift Mutation: Addition or deletion of nucleotides (not multiples of 3), resulting in a completely different amino acid sequence downstream from the mutation.

Example: Sickle-cell Disease

Sickle-cell disease is caused by a missense mutation in the β-globin gene, resulting in abnormal hemoglobin and sickled red blood cells.

Mutations Outside Coding Sequences

Mutations can also occur outside coding regions, affecting gene regulation and expression:

• Promoter: May increase or decrease the rate of transcription.

• Transcriptional regulatory element/operator site: May alter regulation of transcription.

• Splice sites: May affect the ability of pre-mRNA to be properly spliced.

• Translational regulatory element: May affect the ability of mRNA to be translationally regulated.

• Intergenic region: Less likely to affect gene expression.

Germ-line vs. Somatic Cell Mutations

The time and location of a mutation determine its severity and heritability:

• Germ-line mutations: Occur in gametes or their progenitor cells and are heritable.

• Somatic mutations: Occur in other body cells and can result in genetic mosaics, but are not heritable.

Causes of Gene Mutations

Mutations can be spontaneous or induced:

• Spontaneous mutations: Result from errors in DNA replication, toxic metabolic products, changes in nucleotide structure, or transposons.

• Induced mutations: Caused by environmental agents (mutagens) such as chemicals or physical agents.

Mutagens and Their Effects

Mutagens are agents that alter DNA, leading to mutations:

• Chemical mutagens: Modify nucleotide structure, act as base analogues, or insert between bases.

• Physical mutagens: Include ionizing radiation (X-rays, gamma rays) and nonionizing radiation (UV light).

Nitrous Oxide as a Mutagen

Nitrous oxide deaminates cytosine, converting it to uracil, which pairs with adenine instead of guanine, leading to mutations.

UV Light and Thymine Dimers

UV light causes the formation of thymine dimers, which can disrupt DNA replication and lead to mutations.

DNA Repair Mechanisms

Organisms have evolved mechanisms to detect and repair DNA damage:

• Direct repair: Enzyme recognizes and corrects incorrect DNA structure.

• Nucleotide excision repair (NER): Removes and replaces a damaged DNA region using the undamaged strand as a template.

• Methyl-directed mismatch repair: Detects base pair mismatches and removes the surrounding DNA strand for replacement.

NER and Human Genetic Disease

Defects in NER are associated with genetic diseases such as Xeroderma pigmentosum, Cockayne’s syndrome, and PIBIDS, all characterized by photosensitivity due to inability to repair UV-induced lesions.

Cancer: General Information

Cancer is a disease of multicellular organisms characterized by uncontrolled cell division. It can originate from a single cell and progress from benign to malignant, invasive, and metastatic stages. Most cancers are not inherited, but exposure to carcinogens (mutagens) increases risk.

Oncogenes and Cell Division

Cell division is regulated by growth factors. Mutations in genes for cell growth signaling proteins can convert them into oncogenes, which promote cancer by keeping the cell division pathway permanently active.

Examples of Oncogenes

• erbB: Growth factor receptor for EGF

• ras: Intracellular signaling protein

• raf, src: Intracellular signaling proteins

• fos, jun: Transcription factors

Ras Protein and Cancer

Ras is an intracellular signaling protein that hydrolyzes GTP. Oncogenic mutations may decrease Ras's ability to hydrolyze GTP or increase GDP/GTP exchange, keeping the signaling pathway constantly active.

Proto-oncogenes and Genetic Changes

Proto-oncogenes are normal genes that can become oncogenes through:

• Missense mutations: Change amino acid sequence, potentially converting proto-oncogenes to oncogenes.

• Gene amplifications: Increase copy number, resulting in excess protein.

• Chromosomal translocations: Create chimeric genes associated with certain tumors.

• Retroviral insertions: Viral DNA inserts near proto-oncogenes, enhancing expression.

Chromosomal Translocation Example

Translocation between chromosomes 9 and 22 creates a fused gene (bcr-abl), causing chronic myelogenous leukemia.

Viruses That Cause Cancer

Virus	Description
Rous sarcoma virus	Causes sarcomas in chickens
Simian sarcoma virus	Causes sarcomas in monkeys
Abelson leukemia virus	Causes leukemia in mice
Hardy-Zuckerman 4 feline sarcoma virus	Causes sarcomas in cats
Hepatitis B	Causes liver cancer in several species, including humans

Tumor-Suppressor Genes

Tumor-suppressor genes prevent cancerous growth by maintaining genome integrity and inhibiting cell division. Checkpoint proteins, such as p53, halt cell cycle progression if DNA damage is detected.

p53 Protein

• Acts at the G1 checkpoint to prevent progression to S phase if DNA is damaged.

• If DNA cannot be repaired, p53 activates genes promoting apoptosis (programmed cell death).

Rb Protein and Retinoblastoma

Rb protein inhibits the transcription factor E2F, preventing cell division. Loss of both Rb gene copies results in uncontrolled cell division and retinoblastoma.

Loss of Tumor-Suppressor Gene Function

• Mutation within the gene inactivates its function.

• Chromosome loss removes tumor-suppressor genes.

• Abnormal methylation of CpG islands near promoter regions silences gene expression.

Cancer as a Series of Genetic Changes

Cancer typically requires multiple genetic changes, beginning with benign alterations and progressing to malignancy. Additional mutations can make cancer more difficult to treat.

Summary Table: Consequences of Point Mutations

Mutation in the DNA	Effect on polypeptide	Example
None	No change	Normal sequence
Base substitution	Silent—causes no change	Same amino acid sequence
Base substitution	Missense—changes one amino acid	Sickle-cell disease
Base substitution	Nonsense—changes normal codon to stop codon	Truncated polypeptide
Addition or deletion	Frameshift—produces different amino acid sequence	Altered sequence downstream

Summary Table: Effects of Mutations Outside Coding Sequence

Sequence	Effect of mutation
Promoter	May increase or decrease transcription rate
Transcriptional regulatory element/operator site	May alter regulation of transcription
Splice sites	May affect pre-mRNA splicing
Translational regulatory element	May affect mRNA translation
Intergenic region	Less likely to affect gene expression

Summary Table: Common Causes of Gene Mutations

Common causes	Description
Errors in DNA replication	DNA polymerase mistakes
Toxic metabolic products	Reactive chemicals from metabolism
Changes in nucleotide structure	Spontaneous base linkage breakage
Transposons	Mobile DNA segments
Chemical agents	Mutagens like benzopyrene
Physical agents	UV light, X-rays

Summary Table: Examples of Mutagens

Mutagen	Effect(s) on DNA structure
Nitrous acid	Deaminates bases
5-Bromouracil	Acts as base analogue
2-Aminopurine	Acts as base analogue
Nitrogen mustard	Alkylates bases
Ethyl methanesulfonate (EMS)	Alkylates bases
Benzo(a)pyrene	Inserts between bases, causes additions/deletions
X-rays	Causes base deletions, nicks, crosslinking, breaks
UV light	Promotes pyrimidine dimer formation

Summary Table: Genes That Encode Signal Transduction Proteins

Gene	Cellular function
erbB	Growth factor receptor for EGF
ras	Intracellular signaling protein
raf	Intracellular signaling protein
src	Intracellular signaling protein
fos	Transcription factor
jun	Transcription factor

Summary Table: Examples of Viruses That Cause Cancer

Virus	Description
Rous sarcoma virus	Causes sarcomas in chickens
Simian sarcoma virus	Causes sarcomas in monkeys
Abelson leukemia virus	Causes leukemia in mice
Hardy-Zuckerman 4 feline sarcoma virus	Causes sarcomas in cats
Hepatitis B	Causes liver cancer in several species, including humans

Summary Table: Cell Cycle Checkpoints

Checkpoint	Function
G1 checkpoint	Halts cell division if DNA damage is detected
G2 checkpoint	Ensures DNA is fully replicated and undamaged
Metaphase checkpoint	Ensures chromosomes are properly aligned

Summary Table: Genetic Changes in Cancer Progression

Stage	Genetic change
Benign	Initial genetic alteration
Malignant	Additional mutations
Metastatic	Further genetic changes, invasion, migration