DNA Illustrations
Over the last year I was working together with a publisher of a textbook on biology, to create a set of illustrations on genetics and gene expression. I was asked to make quite a few illustrations, which is why I selected only a few of the more interesting drawings to show here. The first illustrations explain the packaging of DNA, the second set of images is about DNA replication and the final illustrations show the process of translation from mRNA to polypeptide chains. All the drawings were designed and drawn in Illustrator.
DNA Packaging
Did you know that if you stretched out all of the DNA in one of your cells (about 3,2 billion base pairs), it would be about 2 meters long? That means all the DNA in all your cells together would reach about twice the diameter of the Solar System in length. To fit this 2 meter long sequence into a space as small as 6 microns (0,006 millimeters), the DNA is tightly packaged into chromosomes.
Basic Structure of DNA
The first step in chromosomal organization is the wrapping of DNA around specific proteins, called histones. There are five types of histones; H1, H2A, H2B, H3 and H4. Two pairs of histones H2A, H2B, H3 and H4 form a disk-shaped histone complex or octamer. The DNA wraps around the histone octamer approximately 1.7 times, which is then called a nucleosome. A series of nucleosomes strung together, with a piece of naked DNA or linker DNA in between them (like a string of pearls), has a diameter of 10‐nm and is called a 10-nm chromatin fiber.
First Steps in Chromosomal Organization
Histone H1 or linker histone, enables further packaging of the DNA. It is not part of the octamer but binds to the outside of a nucleosome. Histone H1 causes the DNA to be wound more tightly around the histone complex. This changes the structure of the chromatin fiber, and the nucleosomes are pulled much closer together. Consecutive nucleosomes arrange themselves in pairs and in this way form a 30‐nm chromatin fiber.
Full Overview of Chromosomal Organization
Further organizing occurs when the 30 nm chromatin fiber forms a series of large loops of 300 nm each. These then spiral further into a very dense structure with a total width of 700 nm. This structure gives the familiar appearance of chromosomes during cell division.
DNA Replication
DNA replication is the process by which a cell duplicates its DNA before cell division, ensuring that each daughter cell receives an identical copy of the genetic material. This process occurs during the S phase of the cell cycle and involves multiple enzymes and proteins. DNA replication follows a semi-conservative model, meaning that each new DNA molecule consists of one original (parental) strand and one newly synthesized strand. The replication process involves several key steps: initiation, elongation, and termination.
Initiation
DNA replication begins at specific locations on the DNA molecule called origins of replication (ORIs). In eukaryotic cells, which have large chromosomes, there are multiple ORIs to speed up the process. The key events in initiation include:
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Unwinding of DNA: The enzyme helicase binds to the ORI and unwinds the DNA double helix by breaking the hydrogen bonds between the complementary base pairs. This creates two single-stranded DNA templates.
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Formation of replication forks: As helicase unwinds the DNA, it forms Y-shaped structures called replication forks, where the two strands are separated.
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Binding of single-stranded binding proteins (SSBs): These proteins stabilize the unwound single strands and prevent them from re-annealing or being degraded by nucleases.
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Relieving tension: As the DNA unwinds, it creates tension and supercoiling in the remaining double-stranded DNA. Topoisomerase enzymes relieve this tension by making temporary cuts and then resealing the DNA.
Stages of DNA Replication
Elongation
Elongation is the process of synthesizing the new DNA strands. DNA synthesis occurs in both directions from the ORI, so two replication forks are active. However, DNA polymerase can only add nucleotides in the 5' to 3' direction, which creates the need for continuous and discontinuous synthesis:
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Primase synthesizes RNA primers: The enzyme primase creates short RNA primers (5-10 nucleotides long) on each DNA template strand. These primers provide a starting point for DNA polymerase, which can only add nucleotides to an existing 3' end.
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Leading strand synthesis: On the leading strand, DNA polymerase synthesizes the new DNA continuously in the 5' to 3' direction as the replication fork opens. This strand is synthesized toward the replication fork.
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Lagging strand synthesis: On the lagging strand, DNA polymerase synthesizes DNA in short fragments called Okazaki fragments, because it works away from the replication fork. Each fragment requires a new RNA primer, and the fragments are later joined together.
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DNA polymerase action: DNA polymerase adds complementary nucleotides (A pairs with T, C pairs with G) to the growing DNA chain, using the parental strand as a template.
Stages of DNA Replication
Termination
Once the entire DNA molecule has been replicated, the process is completed:
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Removal of RNA primers: The RNA primers are removed by an enzyme called RNase H, and the gaps are filled with DNA by DNA polymerase.
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Joining of Okazaki fragments: On the lagging strand, the enzyme DNA ligase seals the gaps between Okazaki fragments by forming phosphodiester bonds, creating a continuous DNA strand.
RNA Translation
Translation is the process by which ribosomes synthesize proteins from messenger RNA (mRNA), using the genetic code carried by the mRNA as a template to string together amino acids in the correct order. This process occurs in the cytoplasm of the cell and consists of three main stages: initiation, elongation, and termination.
Initiation
The first step in translation begins when the mRNA leaves the nucleus and enters the cytoplasm. There, it binds to a small subunit of the ribosome. The ribosome "reads" the mRNA in codons, which are sequences of three nucleotides that correspond to specific amino acids.
A special initiator transfer RNA (tRNA), carrying the amino acid methionine, recognizes the start codon (AUG) on the mRNA and binds to it. This is the signal for the large subunit of the ribosome to attach to the small subunit, forming a complete ribosome. This complex is now ready to start protein synthesis.
Stages of Translation
Elongation
In elongation, the ribosome moves along the mRNA, reading its codons one by one. Each codon matches a specific tRNA molecule, which carries the corresponding amino acid. The ribosome has three important sites:
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A site (Aminoacyl site): Where the incoming tRNA carrying an amino acid binds.
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P site (Peptidyl site): Where the growing polypeptide chain is held.
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E site (Exit site): Where the empty tRNA, after transferring its amino acid, exits the ribosome.
At each codon, the corresponding tRNA enters the A site, bringing in an amino acid. The ribosome catalyzes the formation of a peptide bond between the new amino acid and the growing polypeptide chain, which is held at the P site. The ribosome then shifts, moving the tRNA from the A site to the P site, and the tRNA in the P site moves to the E site, exiting the ribosome. This process repeats as the ribosome continues down the mRNA, extending the polypeptide chain.
Termination
Stages of Translation
The process continues until the ribosome encounters a stop codon (UAA, UAG, or UGA) on the mRNA. These codons do not correspond to any tRNA or amino acid. Instead, release factors bind to the stop codon, causing the ribosome to release the completed polypeptide chain. The ribosomal subunits then disassemble, freeing the mRNA and tRNA for future use.
The polypeptide chain released from the ribosome is the newly synthesized protein. It may undergo further folding and modifications to become fully functional within the cell.
This highly regulated process is crucial for translating genetic information from DNA, through mRNA, into proteins that perform a wide variety of functions in the cell.