Episode 68 explores how does the structure of DNA influence the process of replication and transcription.
Episode 68 explores how does the structure of DNA influence the process of replication and transcription. Beginning with cell cycle placement (1:20), Melanie then distinguishes between quantity of synthesis (2:21). Zoom in further to draw 5’ to 3’ on a nucleotide (3:12). Lastly, the episode contrasts enzymes, cell types and Chargaff’s rules (5:55).
The Question of the Day asks (10:10) Which nitrogenous bases are classified as purines?
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Hi and welcome to the APsolute Recap: Biology Edition. Today’s episode will recap transcription vs. replication
Zoom out:
Unit 6 - Gene Expression and Regulation
Topic - 6.2 & 6.3
Big Idea: Information Storage and Transmission
Let’s think about this one. How does the structure of DNA influence the process of replication and transcription? DNA is an antiparallel double helix, with a sugar phosphate backbone and nitrogenous bases joined through hydrogen bonds. The “meat and potatoes” of DNA is with the sequence of the bases, the As, Ts, Cc and Gs. In order to replicate or transcribe the sequence, we will need to break the hydrogen bonds to access the code. Additionally, DNA has directionality - with enzymes interacting in a singular direction.
Let’s Zoom in:
When is all this happening? Recall that eukaryotic cells go through phases of the cell cycle - interphase with G1, S, and G2 before nuclear division through mitosis and cellular division of cytokinesis. Both processes of replication and transcription occur during interphase. DNA replication occurs once during the S phase in preparation for division. After all, the S of interphase stands for synthesis - the time when DNA, in loose chromatin form, will be copied with the assistance of enzymes within the nucleus. Transcription also occurs in the nucleus. However, it happens hundreds if not thousands of times throughout a cells life span during G1 and G2. Transcription is the process of reading a DNA strand and forming an mRNA transcript. It occurs every time the cell needs to synthesize proteins as it is the first step of the central dogma.
Quantity matters. DNA replication is a semiconservative process that copies an entire genome. After all, we want to make sure that we have identical information in the new daughter cells. Each original half of the parent strand serves as a template for new complementary nucleotides to be synthesized. In other words, half of the original strand is conserved or saved during replication. In transcription, very small portions of the genome are transcribed from one template strand (not both). This template strand of DNA is also known as the noncoding, minus, or antisense strand. We only need to have the sequence relevant to the gene being read. The mRNA transcript formed is single stranded and entirely new.
Directionality - It is so important! Just as English reads the left side of the paper to the right side of the paper, replication and transcription are direction specific processes. To understand why, let's look at a nucleotide more closely, the monomer of nucleic acids. A nucleotide is composed of a pentose sugar, phosphate group and nitrogenous base. The pentose sugar contains five carbons formed in a ring. Imagine the nucleotide like a kindergarten sketch. You have the house (which is the sugar) the sun above the house (which is a phosphate group) and a garage (the nitrogenous base). In DNA, this is a deoxyribose sugar and nitrogenous bases ATC and G whereas in RNA its a ribose sugar and bases AUC and G. Looking more closely at the pentose sugar we can identify the locations of the five carbons.
I’m going to stick with the house analogy for a few more minutes. Starting my view at the peak of the roof I see an oxygen, no carbon there. Moving my eyes down the roof line and to the right, I land at the one prime carbon. This first carbon forms a covalent bond with a nitrogenous base. Continuing around the pentose ring in a clockwise fashion I count my carbons - 2’ and 3’ along the bottom, 4’ at the left roof corner, and then up the chimney to carbon number 5. The five prime carbon connects to the phosphate group within a nucleotide while the three prime carbon connects to the phosphate group of the adjacent nucleotide, forming a sugar phosphate backbone.
Ok great, I can count carbons - how is that useful? Well, its important to be able to distinguish the orientation of the molecule. For reference, the 5’ carbon and the oxygen “roof’ of the pentose sugar point in the same direction. Second, DNA is antiparallel, with each strand running in opposite directions - 5’ to 3’ on one half and 3’ to 5’ on the other. Third, enzymes are direction specific. The enzymes responsible for synthesizing either the new DNA strand or the RNA transcript are called polymerases, literally polymer makers. Each reads the template strand in the 3 prime to 5 prime direction while it synthesizes complementary nucleotides in the 5 prime to 3 prime direction.
DNA polymerase binds to a short RNA primer and proofreads its own work as it synthesizes! On the leading strand, this synthesis is continuous in one piece as DNA polymerase follows the replication fork in the same direction that the enzyme helicase unwinds. But remember - DNA strands are antiparallel. So DNA polymerase synthesizes away from helicase on the lagging strand in short fragments. RNA polymerase and other transcription factors do not require primers but rather recognize a promoter sequence on the template strand (called the TATA box in eukaryotes) While the information is not proofread, there will be mRNA processing following transcription before translation in eukaryotes.
Since DNA is organized differently in prokaryotes and eukaryotes, it will have different strategies for replication and transcription. Prokaryotic DNA is organized in a singular, circular chromosome and has only one origin site of replication. Eukaryotic chromosomes are linear, contain multiple origin sites of replication and often lose the ends of their chromosomes, called telomeres, with each replication. Eukaryotic transcription is followed by mRNA processing while prokaryotic transcription overlaps with translation, so no RNA modification occurs.
Regardless of the process, Chargaff’s rules are still in effect.
Guanine is complementary to Cytosine and Adenine is complementary to Thymine or Uracil. Quick practice; if the DNA template was 3’-5’: TACGCA, what is the DNA complement and mRNA transcript? (pause). DNA complement is 5’ATGCGT3’ and mRNA transcript is 5’AUGCUT3’ - What! Those are so similar. Yup, the non-template strand of DNA is often referred to as the coding strand. Just swap Uracil for Thymine.
Time for unit connections. Unit 1: Chemistry of life with nucleic acids and protein structure, Unit 3: Cellular energetics with enzymes and even unit 4: because transcription and translation is often the result of cell signaling. Alright - what about the exam? Don’t get tripped up by directinalty, as that may be a feature in questions. It's unlikely that you will be asked to replicate or transcribe a sequence outright, but rather discuss cause and effect or disruption to a process. Also, you may need to distinguish between gene expression in prokaryotes and eukaryotes. Oh, and review the Lac Operon. We will review this in our next episode.
To recap……
DNA is all the rage during the processes of replication and transcription. Compare and contrast for timing, directionality, enzymes, nucleotides, cell types, and nitrogenous base pairings.
Coming up next on the Apsolute RecAP Biology Edition: crafting a gene
Today’s question of the day is about nitrogenous bases.
Question of the day: Which nitrogenous bases are classified as purines?