Understand steps of replication - AP Biology

Helicase, gyrase, and DNA polymerase are all used in the process of DNA replication, which takes place in the nucleus. Helicase is responsible for "unzipping" DNA, separating its two strands and unwinding the double-helix. Gyrase is responsible for relaxing the DNA strands and relieving tensions during unwinding. DNA polymerase synthesizes the the new DNA strands by recruiting nitrogenous bases.

Frameshift mutations involve the insertion or deletion of a nucleotide in a DNA sequence, changing the reading frame of the entire nucleotide sequence after the mutation. As a result, every subsequent codon is also affected, creating a change in the organism's phenotype.

Oftentimes, this results in a premature stop codon, which causes the protein product to be shorter than an unaffected polypeptide.

Point mutations replace a single nucleotide for a different one. This can change a certain codon to code for a different amino acid (missense), the same amino acid (silent), or lead to a stop codon (nonsense). Nonsense mutations are the most severe type of point mutation, as they will cause early termination of the protein.

This is really just a math equation. We need to double the amount of DNA each time it goes through a replication cycle.

Begin: 4

Cycle 1: 8

Cycle 2: 16

Cycle 3: 32

Cycle 4: 64

Cycle 5: 128

Cycle 6: 256

Cycle 7: 512

Cycle 8: 1024

Cycle 9: 2048

Cycle 10: 4096

After ten cycles, we would have 4096 copies from our original 4.

A shortcut calculation would be .

This is why PCR amplification is so effective.

The complementary strand will be going in the opposite direction (3'-5'). As a result, you will need to flip the direction in order for it to be complementary to the original strand. When pairing bases, remember that guanine (G) and cytosine (C) are paired with one another, and adenine (A) and thymine (T) are paired.

5'-ACTTGACT-3' Switch the direction.

3'-TCAGTTCA-5' Find the complement pairs.

5'-AGTCAAGT-3'

DNA polymerase always reads DNA strands in the 3'-to-5' direction, creating a complimentary 5'-to-3' strand. As a result, the parent strand oriented in the 3'-to-5' can be replicated seamlessly, but the strand that is unraveled in the 5'-to-3' direction will require multiple attachment points for DNA polymerase so that the whole strand can be replicated in the reverse direction.

These multiple segments of replication are called Okazaki fragments, and can only be found on the lagging strand, which is replicated more slowly.

Okazaki fragments are found on the lagging strand during replication. Because these fragments will not be attached together following strand synthesis, a protein is required to combine the fragments. DNA ligase will follow DNA polymerase on the lagging strand, and combine the fragments in order to create a complete strand.

DNA polymerase is responsible for recruiting and joining nucleotides in the 3'-to-5' direction, but cannot fuse Okazaki fragments on the lagging strand. Primase lays down an RNA primer to recruit DNA polymerase prior to replication. Helicase unwinds the DNA helix in order to expose the template strands. RNA polymerase is involved in transcription, and plays no active role in DNA replication.

Single-strand binding protein (SSB) binds the newly separated DNA strands to ensure that it does not reanneal during replication. This keeps the strands separate so that replication can occur.

All of the other answers describe the functions of other proteins. Primase synthesizes the RNA primers, which helps to recruit DNA polymerase. The structural basis for the replication of the leading and lagging strands ensures that replication follows the same rate on both strands.

DNA topoisomerases are the cell's solution to the "winding" problem. The double helical nature of DNA results in tension during the replication process that would interfere with the process. DNA topoisomerases cut the phosphate backbone to relieve this tension, and allow DNA to replicate properly.

The primary function of the ribosomes bound to the rough endoplasmic reticulum is to synthesize proteins for transport to the cell exterior or extracellular matrix. These ribosomes produce polypeptides that are packaged into vesicles by the Golgi apparatus and transported to the membrane. The vesicle then fuses with the membrane, either releasing proteins out of the cell or incorporating them into the cell membrane.

Nuclear ribosomes synthesize replication and transcription proteins into the nucleus, while cytoplasmic ribosomes produce cytoplasmic proteins.

Recombinant DNA technology involves combining genes from two sources, such as different species, into a single molecule.

Applying restriction enzymes to DNA will cleave the DNA into fragments, which can be isolated for specific genes. Ligase can then be used to fuse the fragments together into a full recombinant gene.

Topoisomerase is responsible for relieving tension in the winding of the DNA helix. DNA polymerase synthesizes new DNA from individual nucleotides, but would not be useful in fusing two types of DNA together.

Polymerase chain reaction, or PCR, is commonly used in laboratories to increase the amount of a small biological sample. Given a small sample of DNA, the process replicates the sample to make numerous identical copies. These copies can then be studied directly, used to make protein products, or incorporated into genetic modification.

Other laboratory techniques can be used to achieve the results given by the other answer options.

Helicases are enzymes that separate annealed strands of nucleic acids. This function provides the single-stranded template used in replication.

Primase is responsible for adding DNA primers, DNA polymerase I scans for mismatched nucleotides and mutations, and ligase repairs breaks in the DNA backbone.

Cohesin is a protein that is not involved in DNA replication. It has diverse functions, including regulating sister chromatids during mitosis.

During replication, helicase is responsible for unwinding DNA strands to expose the site for replication. DNA polymerase III functions primarily to add new nucleotides, while DNA polymerase II proofreads and corrects errors in replication. DNA ligase is responsible for joining breaks in the DNA backbone.

The lagging strand exists because DNA is antiparallel and replication always occurs in the 5' to 3' direction. One strand of DNA will be replicated in the 5' to 3' direction toward the replication fork, following in the same direction as the DNA is "unzipped." This is the leading strand, which can be replicated fluidly. The lagging strand is oriented in the 3' to 5' direction, and must be read backward (away from the replication fork).

Having a lagging strand does not help the cell conserve energy. DNA is a polyanion, but this is due to the phosphate groups in the backbone. If anything, having a lagging strand actually makes it more difficult to maintain a similar rate of replication between strands since they cannot be replicated in the same direction.

Primase is an enzyme that is essential for the process of DNA replication. It synthesizes RNA primers so that DNA polymerase may begin replicating DNA. Mutation to the gene that codes for primase would damage the protein. Without primase, a cell would not be able to go through the process of replication because DNA polymerase would not properly bind the DNA.

RNA polymerase is responsible for transcribing DNA and helicase is responsible for unwinding the DNA double stranded helix.

Okazaki fragments are the cell’s solution to replicating DNA in the opposite direction of the replication fork. They are small fragments of DNA synthesized on the lagging strand. While the leading strand can be continuously synthesized toward the replication fork, the lagging strand must be made in small pieces opposite from the replication fork.

Using small fragments of RNA to silence genes is a process known as RNA interference. DNA that has been cleaved by nucleases is not related to Okazaki fragments. Single-strand binding proteins are small proteins used to prevent DNA from reannealing during replication.

DNA ligase is an enzyme responsible for repairing nicks in the sugar-phosphate backbone of DNA and for fusing Okazaki fragments during DNA replication. It accomplishes this task by resynthesizing the phosphodiester bonds that hold the backbone together

The other answers describe the functions of other proteins involved in DNA replication or DNA transcription. Helicase is responsible for unwinding double-stranded nucleic acids and is essential for producing the replication fork during DNA synthesis. Primase synthesizes RNA primers as attachment points for DNA polymerase during replication. RNA polymerase is responsible for transcribing a DNA template into RNA products.

Heterochromatin is “dark” chromatin that represents DNA that is not active in transcription. The fact that it is “dark” implies that it is condensed and inaccessible by polymerases. Heterochromatin is created when DNA is tightly wound around histones. This tight winding prevents transcription proteins from interacting with the DNA. Heterochromatin is most common in the nucleus during mitosis, when no transcription is taking place. In contrast, euchromatin is capable of being transcribed and is most common during interphase, when most cellular growth and production occurs.

Translation occurs outside of the nucleus and uses mRNA as a template, not DNA.