DNA Synthesis

DNA synthesis is the process of creating a new strand of DNA from an existing template strand. It is a crucial process for cell division and replication.

Steps of DNA Synthesis

1. Initiation: The process begins when an enzyme called helicase unwinds the double-stranded DNA molecule.

2. Priming: An enzyme called primase adds a short RNA primer to the template strand, which serves as a starting point for DNA synthesis.

3. Elongation: DNA polymerase III adds nucleotides to the 3' end of the RNA primer, creating a new strand of DNA that is complementary to the template strand.

4. Termination: The process ends when the DNA polymerase reaches the end of the template strand or encounters a termination signal.

Leading and Lagging Strands

During DNA synthesis, the two strands of DNA are replicated in different ways. The leading strand is synthesized continuously in the 5' to 3' direction, while the lagging strand is synthesized in short fragments called Okazaki fragments.

Proofreading and Repair

DNA polymerase has a proofreading function that checks for errors in the newly synthesized DNA strand. If an error is detected, the polymerase removes the incorrect nucleotide and replaces it with the correct one. Additionally, there are repair mechanisms that can fix errors that occur after DNA synthesis is complete.

Conclusion

DNA synthesis is a complex process that is essential for the replication and division of cells. Understanding the steps involved in DNA synthesis can help us better understand genetic diseases and develop new treatments.

Enzymes involved in DNA synthesis:

1. DNA polymerase: An enzyme that synthesizes new DNA strands by adding nucleotides to the 3' end of a growing DNA chain.

2. Helicase: An enzyme that unwinds the double helix structure of DNA, allowing other enzymes to access the individual strands.

3. Primase: An enzyme that synthesizes short RNA primers that provide a starting point for DNA synthesis.

4. Ligase: An enzyme that joins the Okazaki fragments on the lagging strand of DNA during replication.

5. Topoisomerase: An enzyme that relieves the tension caused by the unwinding of DNA during replication.

6. Exonuclease: An enzyme that removes nucleotides from the end of a DNA strand.

7. Endonuclease: An enzyme that cleaves DNA at specific sites.

8. Single-strand binding proteins: Proteins that bind to single-stranded DNA to prevent it from re-forming a double helix.

9. Sliding clamp: A protein that helps to hold DNA polymerase in place during replication.

10. Okazaki fragments: Short, discontinuous fragments of DNA synthesized on the lagging strand during replication.

There are three types of RNA: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).

Translation in genetics is the process by which the genetic information encoded in messenger RNA (mRNA) is decoded to produce a specific sequence of amino acids, which are the building blocks of proteins. This process occurs in ribosomes, where transfer RNA (tRNA) molecules bring the appropriate amino acids to the ribosome based on the sequence of codons in the mRNA. The amino acids are then linked together to form a polypeptide chain, which folds into a functional protein.

Book: Molecular Biology of the Cell, 6th Edition Chapter: 5 - DNA Replication, Repair, and Recombination

DNA polymerase 1 (Pol 1) and DNA polymerase 3 (Pol 3) are two enzymes involved in DNA replication in prokaryotes. Pol 1 is a multifunctional enzyme that plays a role in both replication and repair. It has 5' to 3' polymerase activity, 3' to 5' exonuclease activity, and 5' to 3' exonuclease activity. Pol 1 is involved in removing RNA primers during replication and replacing them with DNA. It also has a proofreading function, which allows it to correct errors in DNA synthesis.

On the other hand, Pol 3 is the main replicative polymerase in prokaryotes. It has high processivity, meaning it can add many nucleotides to a growing chain without dissociating from the template strand. Pol 3 has 5' to 3' polymerase activity and 3' to 5' exonuclease activity, which allows it to proofread and correct errors in DNA synthesis. It also has a clamp-loading function, which involves loading a sliding clamp onto the DNA template to increase processivity.

In summary, Pol 1 is a multifunctional enzyme involved in both replication and repair, while Pol 3 is the main replicative polymerase with high processivity and a clamp-loading function. Both enzymes have polymerase and exonuclease activities, but Pol 3 is specialized for replication and has a higher processivity than Pol 1.

DNA must be replicated in order for cells to divide and pass on genetic information to their daughter cells. This ensures that each new cell has a complete set of genetic instructions necessary for proper function and development.

• Translation: The process of converting a sequence of nucleotides in mRNA into a sequence of amino acids in a protein.

• mRNA: Messenger RNA, a single-stranded RNA molecule that carries genetic information from DNA to the ribosome.

• Ribosome: A complex molecular machine that reads the sequence of codons in mRNA and catalyzes the formation of peptide bonds between amino acids to form a protein.

• Codon: A sequence of three nucleotides in mRNA that specifies a particular amino acid or a stop signal during translation.

• tRNA: Transfer RNA, a small RNA molecule that carries a specific amino acid to the ribosome and matches it to the appropriate codon in mRNA.

• Anticodon: A sequence of three nucleotides in tRNA that is complementary to a codon in mRNA and allows the tRNA to recognize and bind to the correct codon.

• Amino acid: The building blocks of proteins, there are 20 different amino acids that can be combined in various sequences to form a protein.

• Initiation: The first step of translation, where the ribosome assembles on the mRNA and the first tRNA carrying the amino acid methionine binds to the start codon.

• Elongation: The second step of translation, where the ribosome moves along the mRNA and adds amino acids one by one to the growing protein chain.

• Termination: The final step of translation, where the ribosome reaches a stop codon and the protein is released from the ribosome.

RNA polymerase is an enzyme responsible for the synthesis of RNA from a DNA template during transcription. It catalyzes the formation of phosphodiester bonds between ribonucleotides, creating a complementary RNA strand that is antiparallel to the DNA template strand. The RNA polymerase also recognizes the promoter region of the DNA, which signals the start of a gene, and initiates transcription. Overall, the function of RNA polymerase is to transcribe DNA into RNA, which is then used to synthesize proteins.

There are three stages of transcription: initiation, elongation, and termination. During initiation, RNA polymerase binds to the promoter region of DNA and begins to unwind the double helix. In elongation, RNA polymerase moves along the DNA strand, adding complementary RNA nucleotides to the growing RNA strand. Finally, in termination, RNA polymerase reaches the end of the gene and the RNA transcript is released.

There are three stages of translation: initiation, elongation, and termination. During initiation, the ribosome binds to the mRNA and the first tRNA carrying the amino acid methionine binds to the start codon. In elongation, the ribosome moves along the mRNA, adding amino acids to the growing polypeptide chain. Finally, in termination, the ribosome reaches a stop codon and the polypeptide chain is released.

RNA splicing is the process of removing introns (non-coding regions) from pre-mRNA and joining together the exons (coding regions) to form mature mRNA. The purpose of RNA splicing is to increase the diversity of proteins that can be produced from a single gene by allowing different combinations of exons to be joined together. This process also allows for the removal of non-coding regions that may interfere with protein synthesis.

• Histone acetylation: addition of acetyl groups to lysine residues on histone proteins

• Acetylation neutralizes the positive charge on lysine, loosening the interaction between histones and DNA

• This allows for increased accessibility of DNA to transcription factors and RNA polymerase, leading to gene expression

• Histone acetylation is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs)

• Dysregulation of histone acetylation has been linked to various diseases, including cancer and neurological disorders.

During transcription, a pre-mRNA molecule is synthesized and then modified to form a mature mRNA molecule. One of the modifications involves the addition of a 5' cap and a 3' poly(A) tail to the ends of the mRNA molecule. The 5' cap is a modified guanine nucleotide that protects the mRNA from degradation and helps it bind to ribosomes for translation. The poly(A) tail is a string of adenine nucleotides that also protects the mRNA from degradation and helps regulate its stability and translation efficiency.

DNA methylation is a process by which a methyl group is added to the DNA molecule, usually to the cytosine base in a CpG dinucleotide. This modification can affect gene expression by altering the accessibility of the DNA to transcription factors and other proteins involved in gene regulation. It is an epigenetic mechanism that can be heritable and can play a role in development, aging, and disease.

The large ribosomal subunit is responsible for peptide bond formation during protein synthesis, while the small ribosomal subunit helps to position the mRNA molecule correctly on the ribosome.

tRNA (transfer RNA) plays a crucial role in building the polypeptide chain by carrying amino acids to the ribosome. Each tRNA molecule has an anticodon that matches a specific codon on the mRNA (messenger RNA) strand. As the ribosome moves along the mRNA, tRNA brings the corresponding amino acid to the ribosome, where it is added to the growing polypeptide chain.

An operon is a unit of genetic material that consists of a cluster of genes under the control of a single promoter. It includes the structural genes that code for proteins, as well as the regulatory elements that control their expression. The operon concept was first proposed by François Jacob and Jacques Monod in 1961 to explain the coordinated regulation of gene expression in bacteria.

Independent assortment : the random distribution of homologous chromosomes during meiosis.

How does independent assortment result in genetic diversity? It allows for unique combinations of genes from both parents

Crossing over is the exchange of genetic material between homologous chromosomes during meiosis. This process results in the creation of new combinations of alleles on the chromosomes, increasing genetic diversity.

Random fertilization is a process in sexual reproduction where any sperm can fertilize any egg, resulting in a genetically unique offspring. This process increases genetic diversity within a species.

Mendel proposed two principles of heredity: the Law of Segregation and the Law of Independent Assortment. The Law of Segregation states that an individual inherits one allele from each parent for each trait, and these alleles segregate during gamete formation. The Law of Independent Assortment states that the inheritance of one trait is independent of the inheritance of another trait.

A restriction enzyme is a type of enzyme that cuts DNA molecules at specific sequences, known as restriction sites. These enzymes are commonly used in molecular biology to create DNA fragments with specific ends that can be used in various applications, such as cloning and genetic engineering.

The steps of gel electrophoresis are as follows:

1. Preparation of the gel

2. Loading of the DNA sample onto the gel

3. Running the gel with an electric current

4. Staining the gel to visualize the DNA bands

5. Analysis of the DNA band pattern.

DNA markers are important in gel electrophoresis because they provide a reference for the size of DNA fragments being analyzed. By running a known size marker alongside the sample DNA, scientists can determine the size of the fragments in the sample. This information is crucial for a variety of applications, including genetic research, forensic analysis, and medical diagnostics.

Recombinant DNA is made by combining DNA from two or more different sources. This is typically done by using enzymes to cut the DNA at specific locations, and then joining the pieces together to create a new DNA molecule. The resulting recombinant DNA can be used for a variety of purposes, including gene therapy, genetic engineering, and the production of recombinant proteins.