DNA Structure and Function

DNA structure

Two long strand twisted into double helix, made up of repeating nucleotides (deoxyribose sugar, phosphate group, nitrogenous base). The nitrogenous bases form specific pairs through hydrogen bonds. The two strands are antiparellel and held together by complementary base pairing rules

Function

1. Genetic information storage: stores genetic instructions in sequences of bases

2. Protein synthesis: genes transcribed into mRNA which carries instructions to ribosome for protein assembly. Group of 3 bases correspond to specific amino acids which are linked together to form proteins

3. Replication: during cell division to ensure each new cell receives identical copy. Each strand serves as a template.

4. Hereditary Transmission: Passed from parent to offspring during reproduction ensuring continuity of genetic information across generations

DNA significance

It encoded the instructions for making proteins

It’s ability to replicate and mustate as drives evolution and diversity

DNA replication enzymes

1. Helicase: unwinds and separates DNA strands

2. Primases: synthesises RNA primer

3. DNA polymerase: adds nucleotides to form new strand and proofreads for errors

4. Exonuclease: removes RNA primer

5. DNA ligase: joins gap in the sugar phosphate backbone

DNA replication

Ensures genetic continuity across generations of cells

DNA replication steps

1. Initiation: Helicase unwinds and unzips double strand of DNA by breaking hydrogen bonds between base pairs creating replication fork. Single strand proteins stabilize the separated strands preventing them for rejoining.

2. Elongation: each DNA strand serves as a template for new strand. Leading (synthesized continously in 5’-3’ end towards replication fork. A short RNA primer, created by primate, provides starting point for DNA polymerase to add complementary nucleotides). Lagging (synthesized discontinuously, Okazaki fragments, in 3’-5’ direction. Multiple RNA primers required and DNA polymerase synthesized fragments between primers. DNA ligate joins Okazaki fragments into a continuous strand)

3. Termination: RNA primers removed by exonuclease and gaps filled by DNA polymerase. DNA ligate seals nicks in sugar phosphate backbone forming 2 continous DNA molecules.

Mechanisms for maintaining genome integrity

1. Base pairing rule: complementary base pairing ensuring new strand is the same as parent strand

2. Proofreading by DNA polymerase: checks for mismatched pairs, if any they removed by exonuclease and replaced

3. Mismatch repair mechanism: detect erros after replication by identifying distortions in helix and fixing them

4. High fidelity of DNA polymerase: high fidelity and processivity

5. Semi conservative replication: each new molecule has parent strand and new strand helps preserve original genetic information

6. Chromatin maintenance: chromatin structures carefully regulated during replication to protect DNA from damage and ensure proper access to genetic material

Defects in DNA replication cause

1. Genetic mutations: errors during

2. Genomic instability: incomplete or inaccurate

   Therapeutic implications (understanding DNA replication and repair can provide insights into treating diseases caused by genetic instability i.e. targeting replication stress and DNA repair pathways offer potential strategies for cancer therapy)

Genetic mutations

Result from DNA replication errors and are changes in the DNA sequence that occur when mistakes are made during the replication process

1. Point mutations

2. Insertions

3. Deletions

4. Trinucleotide Repeat Expansions

Replication errors

•DNA polymerase mistakes: highly accurate but can still make a mistake these can be corrected by proofreading and editing

•Strand slippage: DNA strand loops out during replication, leading to insertions or deletions of nucleotides

•Wobble-induced errors: incorrect base pairing due to structural flexibility

Consequences: genetic diseases and contribute to cancer (errors at a fragile site in DNA can cause breaks and rearrangement potentially activating oncogenes)

Point mutations

Changes in DNA sequences that involve alterations of a single nucleotide. Can occure due to replication errors (DNA polymerase error) or environmental factors (exposure to radiation or chemicals)

Consequences: might be benign some can lead to genetic diseases or contribute to cancer development by altering gene expression or protein function

Types of point mutations

1. Transition: when purine is replaced by another purine or pyramidine is replaced by another pyramidine

2. Transverse: purine replaced by pyramidine and vice versea

3. Silent: mutation does not alter the amino acid sequence of the protein because the new codon still codes for the same amino acid

4. Missense: different amino acid being incorporated into protein (conservative and non conservative)

5. Nonsense: introduction of immature stop codon leading to early termination of protein synthesis and often resulting in a nonfunctional protein

Insertions

Genetic alterations where one or more nucleotide base pairs added into DNA sequence

1. Small scale: addition of one or a few nucleotides. Can cause framshift mutations

2. Large scale: larger segments or entire genes being inserted into chromosomes. May result from chromosomal rearrangement or transposable elements.

3. Trinucleotide repeat expansion: specific type of insertion mutation where repetitive sequences expand due to strand slippage

Causes of insertion mutations

DNA Replication errors: strand slippage during Replication

Transposable elements: mobile genetic elements, transports, can insert themselves into the genome causing mutation

Mutagens: exposure to mutagenic agents like UV radiation disrupt the DNA structure

Unequal crossover: during meiosis unequal crossing over between homologous chromosomes can result in large scale insertions

Consequences of insertion mutations

Frameshift mutations: alter the grouping of codons leading to nonfunctional proteins or premature stop codon

Gene disruption: insertions in regulatory regions can disrupt gene expression or protein function

Research application- insertional mutagenisis used to study gene function by intentionally inserting transposable elements into genome and observing phenotypic changes. Advanced tools like CRISPR/Cas9 and prime editing systems are also employed for precise gene insertions

Deletions

Genetic mutation where one or more nucleotides are removed from DNA sequence

Significance: contributors to genetic diversity and disease. Effect depend on size and location as well as genes affected.

Cystic fibrosis (in CFTR gene)

Duchenne muscular dystrophy (2/3 of cases cause of removal of dystrophy gene)

Spinal muscular atrophy (removal of SMN1 gene)

Types of deletion mutations

1. Small scale: loss of one or a few nucleotides. Often cause frameshift mutation

2. Large scale: remove larger segments of DNA parts of or entire genes. Can result in significant loss of genetic material and severe consequences.

3. Chromosomal: large sections of chromosomes removed.

4. Microdeletions: small specific regions of chromosomes removed

Causes of deletion mutation

1. DNA replication errors: skipping or misreading nucleotide

2. Chromosomal crossover error: unequal crossing over during meiosis can result in missing segment

3. DNA damage: radiation, oxidative stress and chemical exposure can break DNA strands

4. Spontaneous events: ransom error in cellular process may also cause deletions

Consequences of deletion mutations

1. Frameshift mutations: not in a multiple of 3 nucleotide, alters reading frame producing defective proteins

2. Loss of gene function: remove essential genes, leading to nonfunctional proteins and genetic disorders

3. Cancer development: inefficiency in tumor suppressors can contribute to cancer progression

Trinucleotide repeat expansion

Genetic mutation where sequences of 3 nucleotides are repeated multiple times in a gene characterized by:

•Threshold effect: Threshold number if repeats (~30-40) beyond which sequence becomes unstable and disease causing.

•Parental influence: sex of transmitting parent can influence the degree of expansion and disease severity, often results in larger expansion and earlier disease onset

•Disease severity: size of expansion correlates with disease severity and easier onset

Mechanism of Trinucleotide Repeat Expansion

1. DNA replication errors: strand slippage, this occurs when the repetive sequences form loop structures leading to addition or removal of repeats. If loop forms on daughter strand, repeat added, parent strands, repeats lost.

2. DNA repair: homologous recombination and mismatch repair, where strand slippage can occur during synthesis step

3. Hybrid RNA: DNA intermediates additional mechanism prise the involvement of RNA

DNA replication errors and disease

1. Protein malfunction: mutations can change the instructions for making proteins

2. Cancer: mutations in genes that regulate cell growth, tumor suppressor gene and oncogenes, leading to uncontrolled cell growth

3. Developmental disorders: mutations in essential developmental genes = severe defects

4. Inherited disorders: Germaine mutations (passed from parent to offspring) lead to inherited disease

5. Neurological disease:

6. Mosaicism: only some cells carry mutation

Inherited mutations

Present in every cell of the body and passed from parent to offspring via germline cell. Predispose individuals to certain conditions from birth

Acquired mutations

Occur during a person’s life time due to environmental factors or errors in replication. Limited to specific cells

Environmental factors

UV radiation: cause thymine dimers which distort DNA structure and lead to replication errors

Chemical exposure: mutations that alter DNA bases

Ionizing radiation: breaks DNA strands which may lead to chromosomal rearrangement

Mosaicism

Individual has 2 or more genetically distinct cell populations due to mutations arising after fertilization

Impact on disorders: severity depends on proportion and distribution of affected cells.

Polymorphism

Common genetic variations that do not typically cause disease but may influence susceptibility