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Structure of nucleic acids and replication of DNA (3)

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1.

Describe the structure of a DNA molecule as a double helix. In your answer, include a discussion of the importance of complementary base pairing between the 5′ to 3′ strand and the 3′ to 5′ strand (antiparallel strands), and explain the differences in hydrogen bonding between C–G and A–T base pairs.

DNA exists as a double helix, a spiral staircase-like structure. This structure is primarily due to two polynucleotide strands winding around each other. The two strands are antiparallel, meaning they run in opposite directions. One strand runs in the 5′ to 3′ direction, while the other runs in the 3′ to 5′ direction. This directionality is crucial for DNA replication and transcription.

Complementary base pairing is a fundamental aspect of DNA structure. Adenine (A) always pairs with Thymine (T), and Guanine (G) always pairs with Cytosine (C). This pairing is due to hydrogen bonds between the bases. The specific number of hydrogen bonds is different for each pair: two hydrogen bonds between A and T, and three hydrogen bonds between G and C. The difference in the number of hydrogen bonds contributes to the stability of the DNA double helix; G-C pairs are held together more strongly than A-T pairs.

The 5′ and 3′ designations refer to the carbon atoms in the deoxyribose sugar of the nucleotide. The 5′ end has a phosphate group attached to the 5′ carbon, while the 3′ end has a hydroxyl (-OH) group attached to the 3′ carbon. The antiparallel arrangement ensures that the sugar-phosphate backbone of one strand runs in the 5′ to 3′ direction, while the other runs in the opposite direction. This arrangement is essential for the correct sequence of base pairing during DNA replication and transcription.

2.

Question 2

Explain the process of DNA replication, detailing the roles of DNA polymerase and DNA ligase. Specifically, discuss how the 5' to 3' directionality of DNA polymerase influences the synthesis of the leading and lagging strands.

DNA replication is the process by which a cell duplicates its DNA before cell division. It's a semi-conservative process, ensuring each daughter cell receives a complete copy of the genetic information. The process begins with the unwinding of the DNA double helix at specific locations called origins of replication. This unwinding is facilitated by helicase, which separates the two strands.

DNA polymerase is the primary enzyme responsible for synthesizing the new DNA strands. It works by adding nucleotides to the 3' end of a pre-existing primer or DNA strand, following the base-pairing rules (A with T, and G with C). This means DNA polymerase can only add nucleotides in the 5' to 3' direction.

The 5' to 3' directionality has a significant impact on leading and lagging strand synthesis. The leading strand is synthesized continuously in the 5' to 3' direction, as the replication fork moves forward. Only one RNA primer is needed to initiate synthesis on the leading strand. As the fork progresses, DNA polymerase continuously adds nucleotides to the 3' end of the growing strand.

The lagging strand is synthesized discontinuously in short fragments called Okazaki fragments. Because DNA polymerase can only add nucleotides in the 5' to 3' direction, the lagging strand is synthesized in short, discontinuous segments moving away from the replication fork. Each Okazaki fragment requires a new RNA primer. After the synthesis of an Okazaki fragment, the RNA primer is removed and replaced with DNA by another DNA polymerase. Finally, DNA ligase seals the gaps between the Okazaki fragments by forming a phosphodiester bond between the 3'-OH of one fragment and the 5'-phosphate of the adjacent fragment, creating a continuous DNA strand.

3.

Describe the process of mRNA processing in eukaryotes, highlighting the roles of capping, splicing, and polyadenylation. Explain how these modifications are important for the correct translation of the mRNA.

In eukaryotes, mRNA undergoes several processing steps after transcription to become mature mRNA, which is ready for translation. These modifications are essential for mRNA stability, transport, and accurate translation.

Capping: A 5' cap, consisting of a modified guanine nucleotide, is added to the 5' end of the pre-mRNA molecule. This cap protects the mRNA from degradation by cellular enzymes and is also recognized by the ribosome during translation, ensuring the mRNA is correctly bound and translated.

Splicing: Eukaryotic genes contain non-coding regions called introns, which are removed by a process called splicing. Splicing is carried out by a complex called the spliceosome. This process joins together the coding regions (exons) of the pre-mRNA, creating a continuous coding sequence. Alternative splicing allows for different protein isoforms to be produced from a single gene.

Polyadenylation: A poly(A) tail, consisting of a string of adenine nucleotides, is added to the 3' end of the pre-mRNA molecule. This tail also protects the mRNA from degradation and enhances its export from the nucleus. The poly(A) tail also plays a role in translation initiation.

These modifications are crucial for ensuring that the mRNA is stable, correctly transported to the cytoplasm, and accurately translated into a protein. Without these modifications, the mRNA would be vulnerable to degradation, might not be correctly read by the ribosome, and could lead to the production of non-functional or incorrect proteins.