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44 votes

How do proteins 'know' where to go?

Even though this animation is very well-known and the narrator says it is "... an accurate representation of the actual DNA replication machine ...", be very careful of its visual appeal. It ...
Domen's user avatar
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11 votes

How do proteins 'know' where to go?

This answer is specific to the "two-legged" proteins from the end of the video (motor proteins). The animation shows identical proteins moving in perfect lockstep, but really there is wide ...
benrg's user avatar
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10 votes

Does gene orientation relative to origin of replication matter on small plasmids?

I like this question, and I had a similar thought when reading that "Forward or Reverse Strand" post. I've since found a 2005 publication by Mirkin and Mirkin1, which investigates the ...
acvill's user avatar
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10 votes
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Can genetic recombination occur between DNA viruses?

Summary Certainly DNA viruses do recombine — some of them encode proteins specifically for this purpose. And this is unsurprising if one reflects on the fact that recombination is a fundamental ...
David's user avatar
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9 votes

How do proteins 'know' where to go?

There have been some suggestions that biological molecules may 'know where to go'. Barry Honig's group at Columbia analyzed the electrical charge arrangements in protein and proposed that by placing ...
shigeta's user avatar
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7 votes
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DNA & mRNA During Transcription

Transcription occurs in a special structure known as transcription bubble. Inside the bubble are present the mRNA, template DNA being transcribed and the RNA Polymerase. Upstream of bubble is the DNA ...
another 'Homo sapien''s user avatar
7 votes

Do mitochondria contain the genes to specify themselves?

The answer is a bit more complicated than that. Mitochondria contain their own genome called mitochondrial DNA (mtDNA), encoding 13 proteins that are part of respiratory complexes I, III, IV, and V, ...
MattDMo's user avatar
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7 votes
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Thermodynamically, how did the first cell arise?

The first amino acids For how life arose from no life, the Miller-Urey Experiment demonstrates how in primordial Earth conditions, a spark in the atmosphere (analogous to lightning) could have ...
Fuzzy Bee's user avatar
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6 votes
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Can mitochondria become cancerous?

Interesting question. As a prelude, I should probably mention that single celled organisms cannot get cancer as we understand and define it. Mitochondria are not, of course, single celled organisms, ...
De Novo's user avatar
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6 votes

Why is DNA replication so much faster in prokaryotes than eukaryotes?

The difference in DNA replication rate between prokaryotes and eukaryotes is still under current research, but the basics are understood. It is very much a matter of complexity, as eukaryotes are more ...
pascal's user avatar
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5 votes
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DNA replication: How many DNA polymerase molecules work in parallel?

In the (beautifully rendered) video you linked to, the green molecules are DNA polymerases. So you can already see that there are more than two DNA polymerases at work! At each replication fork, ...
leekaiinthesky's user avatar
5 votes

Chemistry of phosphodiester bond formation by DNA polymerase

I found this paper, which goes very deep into the molecular details of the individual steps of this reaction and also discusses how this is coupled to nucleotide selectivity. The 'basic' details ...
Nicolai's user avatar
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5 votes
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Typical DNA replication times

A mammalian cell takes about 8 hours to replicate all of its DNA in its S phase; a yeast cell would take about 40 minutes. Some other information that you seem to not have quite the right information ...
Leo's user avatar
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4 votes
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Role of dam methylase in bacteria

The dam methylase has three different functions: Correction replication errors, since the new DNA molecule is only hemimethylated (the old strand is methylated, the newly synthesized is not). Since ...
Chris's user avatar
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4 votes
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When does histone synthesis occur in relation to DNA replication?

Yes, they have to. But that is just half of the story. The (canonical) histones which are used in DNA replication are synthesized at the beginning of the S phase, and subsequently transported into ...
adjan's user avatar
  • 2,106
4 votes

Typical DNA replication times

I think your view of DNA replication is a little off-target in relation to strand separation (which produces what you call “single helix structure”). The strands of the DNA are separated continually ...
David's user avatar
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4 votes

Why does the structure of RNA change?

Summary Most nucleic acid species have specific structures (or a limited number of alternative structures) which may involve a greater or lesser amount of double helix through complementary base ...
David's user avatar
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4 votes
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Time required for DNA replication in E. coli

Remember that E. coli has a single circular chromosome, and that chromosome is replicated bidirectionally. Hence, your calculated value (90 minutes) is exactly twice that of the correct answer.
acvill's user avatar
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4 votes

Why do eubacterial DNA Ligases use NAD whereas eukaryotic and archaeal DNA Ligases use ATP?

This difference is certainly intriguing, but, like many other general ‘why?’ questions, can be approached on different levels. Because they evolved differently. is one answer, and not a trivial one ...
David's user avatar
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4 votes

Can DNA replicate without polymerase?

Nope. Not happening. The high temperature (90 °C) needed to separate a DNA strand also makes an association of free floating bases to a template strand much too unstable. Even if the bases associated ...
markur's user avatar
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3 votes
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How is a portion of DNA selected and unwound from nucleosome?

This answer will be a very broad overview and is based largely on information from the textbook "Molecular Biology of the Gene" by Watson et al. (which I highly recommend). Nucleosomes are dynamic ...
canadianer's user avatar
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3 votes

Don't understand how multiple replication bubbles work

You mistake replication direction with polymerase synthesis direction. Indeed, the polymerase synthesizes new strands 5' -> 3' but if the replication of each strand was continuous, there would be no ...
Krzysztof Czarnecki's user avatar
3 votes
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How do point mutations arise from mistakes in DNA replication?

Source of your misunderstanding Your misunderstanding is very comprehensible as the figure is misleading. The figure only shows a single event of replication. What you see as a second replication ...
Remi.b's user avatar
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3 votes

When does histone synthesis occur in relation to DNA replication?

In Molecular Biology of the Cell (Chapter 4), it is written that The major histones are synthesized primarily during the S phase of the cell cycle and assembled into nucleosomes on the daughter DNA ...
gc5's user avatar
  • 820
3 votes

After the primer is removed from the leading strand, how does DNA polymerase I add dNTPs without a 3'-OH?

The leading strand post-initiation First consider the DNA replication fork after initiation has occurred. The 3′-OH primer on the leading strand is the 3′-end of the strand of DNA being synthesized in ...
David's user avatar
  • 26.2k
3 votes

Molecular animations of, say, protein synthesis, are simplified, but how exactly?

tldr: Making these things accurate representations is really hard Accurate representations can be hard to look at anyway, so aren't always good to convey understanding Molecular dynamics ...
JEngleback's user avatar
3 votes
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Why does inbreeding cause genetic defects, but cell division in one's own body does not?

I suspect your problem is grasping what is a deleterious recessive allele. Wikipedia and textbooks explain it much better but I will try to illustrate with respect to your question. I have to merge ...
BagiM's user avatar
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3 votes

Why does inbreeding cause genetic defects, but cell division in one's own body does not?

You say cells basically create copies of DNA all the time in our body. There may be a few mutations/errors, but it works out fine. and Why does merging two similar things cause more problems ...
rumtscho's user avatar
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3 votes
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How can DNA replication result in hair pin structures?

DNA Hairpins are formed when two regions in same single stranded DNA are complementary in nucleotide sequence but in the opposite directions (as represented in image below). These two sets of ...
Twinkle Sheen's user avatar
3 votes

Why is a solution of cesium chloride used in Meselson & Stahl's DNA replication experiment?

In saline solution all the DNA ends up at the very bottom. Under centrifugation, the Caesium Chloride solution forms a density gradient, each DNA rises or sinks to the equivalent density. The same ...
Polypipe Wrangler's user avatar

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