DNA, RNA, and Proteins - Biology

Given the backbone of DNA, with the phosphate group attached to the deoxyribose via a phosphodiester bond, DNA is negatively charged. For this reason, histones - the proteins around which DNA molecules are wrapped in eukaryotes - have lots of positively charged amino acids on their DNA-binding sites. This produces a strong attractive force between DNA and histones.

RNA is the key molecule involved in protein synthesis. During translation, the mRNA binds to a ribosome carrying a sequence of codons. The tRNA then binds to the ribosome/mRNA complex with the matching anticodon. The anticodon contains the three complimentary nucleotides to the codon.

The enzyme helicase divides the two strands of the double helix; henceforth, single stranded binding (SSB) proteins stabilize the newly single strands, and prevent reannealing. The enzyme DNA gyrase ensures the double stranded areas beyond the replication bubbles do not supercoil, relieving the newly-added tension. Primase is a type of RNA polymerase that adds an RNA primer to the DNA to begin replication. DNA Polymerase III cannot begin replication without this primer. Ligase joins ends of Okazaki fragments that were produced on the lagging strand.

The correct name of the fragments is Okazaki fragments. The lagging strand aligns in the 5'-to-3' direction (away from the replication fork), but must be read in the 3'-to-5' direction (toward the replication fork) by DNA ploymerase. The result is non-continuous synthesis of the strand in small fragments, called Okazaki fragments. DNA ligase fuses these fragments together later in the replication process.

DNA replication involves the separation of the two original DNA strands. Both of these strands are then replicated using DNA polymerase. This results in two DNA double helices, each with a new strand and an original strand.

Consider this example, in which the parent strands are represented by "P" and the daughter strands are represented by "D."

Before replication there are two parent strands: PP

The parent strands are split: P P

Daughter strands are made for each parent strand: PDDP

The fully-replicated double strands separate: PD DP

Each final strand has one parent strand (old DNA) and one daughter strand (new DNA).

Messenger RNA, or mRNA, is the RNA strand that is transcribed from the gene found on DNA. It is responsible for being read by a ribosome in order to create a protein.

Ribosomal RNA (rRNA) forms a structural component of the ribosomes. Transfer RNA (tRNA) carries amino acid residues and provides an anticodon to add the amino acids to the growing protein at the ribosome. Small nuclear RNA (snRNA) are found in the nucleus and help regulate transcription and maintain telomere length.

O=Original strand, N=New strand

Before any replications: OO

After one round of replication, both new double-helices contain one strand from the original double-helix and one newly synthesized strand.

1 replication: ON1, N1O

After the second replication, there are now four double-helix molecules. Two contain original strands in combination with new strands, and two contain only new strands.

2 replications: ON2, N2N1, N1N2, N2O

After the thrid replication event there will be eight total molecules. Of these, six will contain only new strands and two will contain a combination of original and new strands.

3 replications: ON3, N3N2, N2N3, N3N1, N1N3, N3N2, N2N3, N3O

There must always be two double-helices that contain original strands, as there are always only two original strands and they do not disappear.

RNA primer is the correct answer. A protein called RNA primase reads the existing DNA strand and adds a short sequence of RNA nucleotides. DNA polymerase then builds onto the 3' end of the RNA primer. After replication, the RNA primer is removed and replaced with DNA nucleotides.

DNA nucleotides bond via hydrogen bonding to form the double helix structure. DNA is negatively charged due to the phosphates and binds to histones to form compact chromosomes in the nucleus.

Replication of DNA is both continuous and discontinuous, each form of replication occurring simultaneously. Continuous DNA synthesis occurs from the 3’ end to the 5’ end of the parent strand. This is often referred to as the leading strand with new nucleotides being added to the 3’ end. Discontinuous DNA synthesis occurs from the 5’ end to the 3’ end of the parent strand. This strand is often referred to as the lagging strand. It is completed in short sequences of nucleotides called Okazaki fragments. Replication on the lagging strand begins with the addition of an RNA primer by the enzyme primase. Primase adds the RNA primers ahead of the 5’ end of the lagging. This allows DNA polymerase III to add the Okazaki fragments to fill in the space between primers. This process repeats itself until the entire strand has been replicated. DNA polymerase I then comes to exchange the RNA primer with DNA nucleotides, then DNA ligase reinforces the bonding between the fragments and the DNA nucleotides that replaced the RNA primer. Once both the leading and lagging stranded have completed replication, the result is two identical strands of the original DNA molecule.

The enzyme primase adds sequences of RNA to the DNA strand to begin replication. Primase is a type of RNA polymerase, and thus, it does not need a free 3' hydroxyl group as a substrate. The nucleotides it lays down act as a substrate for DNA polymerase. Okazaki fragments from the lagging strand are joined by ligase, and helicase is responsible for unzipping the DNA to prepare for replication.

DNA polymerase I is the only polymerase that has 5' 3' exonuclease activity. This means that it can remove nucleotides in the 5' 3' direction. It also has 3' 5' exonuclease activity, as does DNA polymerase III; this is like a "backspace" for nucleotides that have just been added and need to be removed. DNA polymerase II's functions are largely unknown, DNA polymerase V plays a complex role in DNA repair, not replication.

During DNA replication, the parent strand is used as a template that the new strand uses to add the correct nucleotides (via complementary base pairing). The entire parent strand (template) is conserved, while the daughter strand is completely synthetic, meaning the nucleotides came from free nucleoside triphosphates (ATP, TTP, GTP, and CTP). Thus, DNA replication is said to be semi-conservative. The Meselson-Stahl experiment illustrated this principle through the use of different isotopes of nitrogen.

Primase, like all RNA polymerases, can lay down nucleotides with their only substrate being the template strand. Even though the nucleotides are RNA, not DNA, they still have the substrate that DNA polymerase needs in order to add nucleotides—a free 3' . Since the difference between deoxyribose and ribose occurs at the 2' position, DNA polymerase can use either RNA or DNA as a substrate. Helicase and gyrase help with formation and maintenance of the replication bubble, however they indirectly help DNA polymerase add new nucleotides.

The enzyme helicase unzips the two strands of the double helix. Once unzipped, single stranded binding (SSB) proteins stabilize the newly single strands. The enzyme DNA gyrase ensure the double stranded areas beyond the replication fork do not supercoil onto one another. After stabilization of the replication fork, an enzyme complex known as DNA polymerase III commences the addition of nucleotides to the new strand. Proteins such as the beta clamp and clamp loader assist in keeping DNA polymerase III in its place on the strand of DNA, The enzyme primase adds sequences of RNA primers to the DNA strand to begin replication. DNA Polymerase III cannot begin replication without this primer. DNA ligase reinforces the bonding between the Okazaki fragments and the DNA nucleotides that replace the RNA primer.

Replication of DNA is both continuous and discontinuous, each form of replication occurring simultaneously. Continuous DNA synthesis occurs in the 3’ 5’ direction on the parent strand. This is often referred to as the leading strand with new nucleotides being added to the 3’ end. Discontinuous DNA synthesis occurs in the 5’ 3’ direction on the parent strand. This strand is often referred to as the lagging strand. It is completed in short sequences of nucleotides called Okazaki fragments. Replication on the lagging strand begins with the addition of an RNA primer by the enzyme primase. Primase adds the RNA primers ahead of the 5’ end of the lagging. This allows DNA polymerase III to add the Okazaki fragments to fill in the space between primers. This process repeats itself until the entire strand has been replicated. DNA polymerase I then comes to exchange the RNA primer with DNA nucleotides, then DNA ligase reinforces the bonding between the fragments and the DNA nucleotides that replaced the RNA primer. Note that in both leading and lagging strand synthesis, nucleotides are added to the 3' end of the growing chain, thus synthesis always occurs in the 5' 3' direction of the growing strand.

DNA ligase catalyzes the formation of bonds between the Okazaki fragments and the DNA that has replaced the RNA primers on the lagging strand.

DNA synthesis always occurs in the 5' to 3' direction, so one new strand is synthesized continuously towards the replication fork, producing the leading strand. The other strand, known as the lagging strand, forms away from the replication fork in small fragments.

DNA replication occurs both continuously and discontinuously at the same time. Nucleotides can only be added to a new strand of DNA on the 3' end, so the process has to start with the 5' end. As DNA continues to be split apart, the leading strand (growing in the direction towards the replication fork) can continuously add new nucleotides. However, for the lagging strand, the 5' to 3' direction is away from the replication fork, so new nucleotides are added in small chunks called Okazaki fragments as the DNA strand continues to separate.

The enzyme helicase opens the double helix of DNA at points called replication forks.

The unwinding of the double helix of DNA is caused by an enzyme called helicase, which breaks the hydrogen bonds holding the complementary base pairs together, creating two template strands of DNA ready to begin the next step of replication. The place where this enzyme 'unzips' the DNA is called the replication fork.

DNA helicase unwinds the double helix, separating the two strands so they may be replicated by DNA polymerase.

Primase adds an RNA primer to help initiate DNA replication. DNA ligase is responsible for joining Okazaki fragments on the lagging strand during replication.