Leading and Lagging Strands

When DNA helicase unzips the DNA strand, two templates are exposed. Because DNA is antiparallel and DNA polymerase can only create DNA in the 5’ to 3’ direction, one strand becomes the leading strand, and the other strand becomes the lagging strand. The template DNA of the leading strand has its 5’ end at the replication fork (the place where the DNA is split by DNA helicase). This means that the new strand can be written with DNA polymerase constantly moving towards the replication fork and continuing to add nucleotides as the replication fork moves forward. This means nucleotides can be added on the leading strand without any breaks. The opposite is true on the lagging strand. The 3’ end of the template strand is at the replication fork, so this strand must be read in the direction moving away from the replication fork in order to write the new strand in the 5’ to 3’ direction. However, as the replication fork moves forward, DNA polymerase moves away from the newly exposed template strand rather than towards it. As a result, the lagging strand is written in sections called
Okazaki fragments. Many RNA primers are added and DNA polymerase constantly leaves the template strand so it can restart replication closer to the replication fork. The gaps between Okazaki fragments are filled in by DNA ligase which also corrects any errors.

DNA Replication in Prokaryotes vs. Eukaryotes

Since prokaryotes have circular DNA, replication begins at a replication “bubble” that opens on two ends. As replication progresses, the bubble grows at both ends. At the end, the two ends of the bubble meet on the other side of the DNA loop and the two strands come apart. Since replication proceeds in both directions, both strands become the leading and lagging strand, depending on where the replication fork is in relation to the DNA polymerase.

Since eukaryotes have linear DNA, replication starts from multiple places within the chromosome. This makes replication faster because it can be completed from multiple starting points at once which is important since most eukaryotes have a lot of genetic material. However, the lack of circular DNA results in a small amount of genetic material being lost each replication. To prevent important information from being lost, DNA ends have long excess strands called telomeres that allow primase to add RNA primers. Since primase cannot add primers to the very end of the telomeres, a few nucleotides are lost each replication.

Transcription

Protein synthesis contains two distinct sections: transcription and translation. Transcription is the writing and processing of RNA from DNA in the nucleus, and translation is using this RNA to construct proteins in ribosomes. Protein synthesis relies on 3 different types of RNA: mRNA (messengers) which carries genetic information from the nucleus to the ribosomes; tRNA (transfer) which carries individual amino acids to ribosomes, and rRNA which make up the ribosomes.

Transcription uses RNA polymerase to write an RNA strand based on the template DNA in the nucleus. First, RNA polymerase binds to the promoter region of the DNA strand in the initiation step. Next, in the elongation step, the RNA polymerase reads the template strands and adds nucleotides to the RNA strand based on the DNA template. This differs from DNA replication in that only one side of the DNA template is used, only a small portion of the chromosome is read, and the nitrogenous base uracil (U) is used instead of thymine (T). Like DNA replication, the RNA is written in the 5’ to 3’ direction. Finally, termination occurs when RNA polymerase reaches a terminator sequence on the DNA strand.

Transcription continues with RNA processing in the nucleus. Only eukaryotes undergo this process because only eukaryotes have a nucleus. First, a cap and tail are added to the RNA strand to protect its material while it is in transit. The 5’ cap is made up of a modified guanine nucleotide, and the 3’ tail is made up of 100-200 adenine nucleotides which helps it leave the nucleus while also protecting the 3’ end. Next, splicing occurs with the help of a spliceosome. Introns are cut out and they stay in the nucleus. The exons are spliced back together, and the mRNA molecule is ready to leave the nucleus. Splicing is important because it ensures that the correct proteins are created from a DNA sequence. It is also possible that splicing can occur differently given the same RNA sequence at different times, leading the same DNA to code for multiple different proteins.

Transcription continues with RNA processing in the nucleus. Only eukaryotes undergo this process because only eukaryotes have a nucleus. First, a cap and tail are added to the RNA strand to protect its material while it is in transit. The 5’ cap is made up of a modified guanine nucleotide, and the 3’ tail is made up of 100-200 adenine nucleotides which helps it leave the nucleus while also protecting the 3’ end. Next, splicing occurs with the help of a spliceosome. Introns are cut out and they stay in the nucleus. The exons are spliced back together, and the mRNA molecule is ready to leave the nucleus. Splicing is important because it ensures that the correct proteins are created from a DNA sequence. It is also possible that splicing can occur differently given the same RNA sequence at different times, leading the same DNA to code for multiple different proteins.

Translation

Translation always follows transcription. Translation turns the message carried in the nucleotide language from the mRNA to the amino acid language to make a protein. Transcription occurs at ribosomes which are made of two subunits, one large and one small. The large subunit contains 3 openings for tRNAs to enter, add the amino acid they carry to the polypeptide chain, and exit the ribosome. mRNA slides into the ribosome between the two subunits.

When the mRNA enters the ribosome, it is read in sections of three nucleotides called a codon. As shown in the table, each codon codes for a specific amino acid. Since there are 22 amino acids, the codons are redundant but not ambiguous. This means that multiple codons can code for a single amino acid, but a single codon cannot code for multiple amino acids. Each tRNA molecule contains a set of three nucleotides called an anticodon. Each tRNA carries a specific amino acid, and its anticodons match with codons in the mRNA strand. Within the ribosome, a tRNA matches with the complementary mRNA strand, attaches to the ribosome, adds its amino acid to the chain, and then leaves the ribosome.

The three steps of translation are the same as the three steps of transcription: initiation, elongation, and termination. Initiation begins with the start codon, AUG, which also codes for the amino acid methionine. Once the start codon is read, tRNAs begin to bring amino acids to the ribosome in the elongation step. The tRNA enters the “A” position for attachment. Then, the ribosome moves the polypeptide chain onto the tRNA in the A position where a peptide bond binds the new amino acid to the chain. Next, the tRNA in the “P” position (for polypeptide elongation) which just gave the polypeptide chain to the tRNA in the A position, enters the “E” position to exit the ribosome. Then, the tRNA in the A position with the amino acid chain shifts over to the P position, and the princess begins again. The mRNA stops being read when a stop codon is identified. These three codons (UAA, UAG, and UGA) do not code for amino acids; rather, they end the translation process.

In prokaryotes, because they have no nucleus, there is no RNA processing in transcription. As a result, translation can occur while translation is still happening with ribosomes attached to RNA as it is still being synthesized by RNA polymerase.

Mutation

Mutations occur when there is a change in the DNA or RNA sequence. This can change the entire structure of a protein by rendering different codons during translation. There are three main types of mutations which can result in three different effects.

A point mutation occurs at a single nucleotide. This is usually a substitution when one nucleotide is switched out for another.

A deletion mutation occurs when one nucleotide is deleted. This causes a frameshift mutation as the first nucleotide from the next codon after the deletion is read with the two nucleotides that lost their third part of the codon which can change the rest of the protein structure.

An addition mutation occurs when one nucleotide is added. Similarly to a deletion mutation, this also causes a frameshift as the codons are read improperly due to the additional nucleotide added.

The effects of mutations include missense, silent, and nonsense mutations. A missense mutation occurs when a different amino acid is added to the polypeptide when a nucleotide is changed. A silent mutation occurs when a change in an amino acid has no change on the polypeptide (because of the redundancy of the amino acids). A nonsense mutation occurs when an amino acid is changed into a stop codon which ends translation.

Operons

Operons are responsible for control of transcription and translation in many prokaryotes. Operons are controlled by a repressor protein that blocks DNA polymerase from transcribing the genes. There are two types of operons: inducible and repressible. Inducible operons are typically turned off with an active repressor protein, meaning that the genes are not being transcribed. One example of an inducible operon is the lac operon. The lac operon includes the gene that codes or the lactase enzyme which breaks down lactose. This operon is typically off, meaning that the enzyme and other proteins in the pathway are not being synthesized. However, when allolactose (a derivative of lactose) is present, the operon is induced and transcription begins. Contrastingly, a repressible operon is typically switched on with an inactive repressor protein. One example of a repressible operon is the trp operon which codes for all the genes needed to make tryptophan. Typically these genes are transcribed, but when lots of tryptophan is present, the operon turns off. Repressible operons act like negative feedback loops by regulating the amount of a protein present. Operons are beneficial because they allow the transcription and translation of multiple proteins that are part of the same cellular pathway to be synthesized together.

Lytic and Lysogenic Cycles

The lytic and lysogenic cycles are processes through which a virus can live and reproduce within a host. In the lytic cycle, a phage inserts its DNA into a cell. Then, its DNA is read and replicated. This DNA codes for the creation of new virus parts, and the cell follows the instructions of this DNA thinking it is part of its own DNA. When enough virus parts are created, the virus assembles then causes the cell to lyse or burst, thus releasing many new phages into the surroundings.

In the lysogenic cycle, the phage inserts its DNA into a cell and the DNA is integrated into the host’s genome. As the cell replicates, the virus’s DNA replicates as well. Under stressful conditions, the DNA separates itself from the host’s genome and switches into the lytic cycle in an effort to avoid dying within its host.