Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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Why are some genes dominant over others? What is the mechanism behind it?

If I have a brown eye gene which encodes the protein that is responsible for the brown color and have a blue eye gene as well, what is the reason that my eye color is brown? How does one gene maintain ...
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4 votes
1 answer
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How does temperature influence the rate of protein degradation?

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on biochemical reactions. Question In particular, my question is: How does ...
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203 votes
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Why are so few foods blue?

Although blue foods exist, they're rare enough compared to other foods for food preparers to use blue plasters as a convention. The natural colour of a given food is due to pigments that have some ...
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13 votes
3 answers
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Does a man contain all the genes needed to make a woman?

This question is brought on by a Sci Fi novel I am thinking about writing. The plot device involves a colonist in charge of building a population on a new planet who loses his supply of embryos and so ...
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8 votes
2 answers
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Redundancy of the genetic code

One particular codon codes only for one amino acid, but an amino acid can be coded for by several different codons. Now according to the genetic code, the codon UUU ...
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34 votes
3 answers
58k views

Why is ATP the preferred choice for energy carriers?

Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?
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34 votes
4 answers
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How and where, in the human brain, are memories stored?

Background I am a computer programmer who is fascinated by artificial intelligence and artificial neural networks, and I am becoming more curious about how biological neural networks work. Context &...
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20 votes
3 answers
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Why is DNA antiparallel? Can it be parallel?

My biology textbook mentions that DNA is antiparallel and it got me wondering - can DNA be parallel? What would happen if it was parallel? Could DNA still replicate correctly?
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3 votes
1 answer
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Terminology of the sequences of promoters in relation to DNA strands

I'm studying molecular biology and I'm trying to understand an experiment which shows the importance of promoters in the relative transcription level (RT). The image below comes from Rolf Knippers' ...
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Why is uracil, rather than thymine, used in RNA?

This question was posed on SE Biology some time ago, but all the answers, including the accepted one, answered a different question instead: “Why is thymine, rather than uracil, used in DNA?”. I ...
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9 votes
2 answers
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How to find miRNA binding sites on a specific gene?

I am trying to find miRNAs that bind to the 3'UTR of a specific gene. What is the best way of doing that (that is, with a good scoring analysis that is most commonly used by researchers in this area)? ...
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12 votes
2 answers
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What is the function of the RNA primer in DNA replication?

During DNA replication, RNA primase puts an RNA primer in the lagging strand. What is the function of this RNA primer? Why can't the enzymes put DNA fragments directly?
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Influence of temperature on protein binding and decay rates

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on the dynamic of biochemical reactions. Question In particular, my ...
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7 votes
3 answers
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Crick’s Central Dogma — Counter Cases

I was recently reading about non-coding RNAs being a counter example to Central Dogma of Biology. Can someone add more cases which violate the Central Dogma? Thanks! UPDATE - Reference of lncRNAs ...
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11 votes
1 answer
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Why don't the heads of phospholipid bilayers repel hydrophobic molecules?

What I Think I Know: Hydrophilic and hydrophobic things repel each other. Since the cell membrane contains hydrophobic tails, it is difficult for hydrophilic molecules to pass through the cell ...
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1 answer
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A photosynthesizing mouse?

N. Shubin's Your Inner Fish makes the point several times that there is a lot of functional similarity between some seemingly remote gene cousins. If that needed reinforcing we have the spider-goat, ...
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2 votes
2 answers
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Was there originally a non-ribosomal way of synthesizing proteins?

Proteins are synthesized on ribosomes from mRNA copies of regions of the DNA. But ribosomes themselves are made up of proteins (and RNA). So how could the first ribosomes have arisen? Was there ...
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8 votes
2 answers
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How can E. coli proliferate so rapidly?

The E. coli has a genome with approximately 5×106 bp. The main DNA polymerase involved in its chromosome duplication (DNA pol III , the one with highest processivity) can polymerize ~103 nucleotides ...
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1 answer
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How is the rate of transcription influenced by temperature?

How is the rate of transcription influenced by temperature? More precisely, I am looking for an article who quantitatively measured the rate of transcription of an "average gene" and show how this ...
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27 votes
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How does RNA transcription determine which half of the DNA to use?

I feel that I might have a complete misunderstanding here. If DNA has two strands, how does the machinery of RNA transcription determine which one to transcribe?
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46 votes
6 answers
1k views

Why are amino acids in biology homochiral?

Why are nearly all amino acids in organisms left-handed (exception is glycine which has no isomer) when abiotic samples typical have an even mix of left- and right-handed molecules?
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28 votes
3 answers
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How, on a physical level, does ATP confer energy?

When ATP is used as the energy currency to make, say, reaction X + Y → Z happen, is what happens on a physical level down at the molecular scale that during the reaction ATP + H2O → ADP + Pi  &...
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10 votes
2 answers
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On which strand does the promoter sit?

My book keeps giving different indicators as to whether the promoters are on the coding or template strand. It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that ...
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4 votes
4 answers
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Photosynthesis: What Powers the Splitting of Water?

The splitting of water is an endergonic (non-spontaneous) reaction, and thus would require energy (chemical work to be done) in order to happen. In Photosystem II, an enzyme catalyzes this splitting, ...
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3 votes
1 answer
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How do DNA-binding proteins recognize the correct DNA base pairs?

My professor posed this question to the class today - "How do DNA binding proteins specifically bind to base pairs?" He alluded to the different arrangements of hydrogen-bond donor and acceptors in A-...
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1 vote
1 answer
133 views

Gene located on Which strand? Want reference. [duplicate]

Update: Initially my question (below) was appropriately marked as duplicate/overlapping with two other questions; This and this ; among them a specific part of an answer of the second duplicate/...
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15 votes
2 answers
11k views

Why is there more variation in proteins than genes?

The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular). How do ...
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9 votes
2 answers
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Can forensic DNA analysis be used to generate a visual approximation of a suspect?

In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I ...
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5 votes
2 answers
186 views

Why mutations in genes involved in general processes like DNA repair increase the risk of developing specific types of cancer?

For example, mutation in MHS2, which encodes a protein involved in the repair of mismatches that occur during DNA replication, dramatically increases the risk of developing colon cancer. (There are ...
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4 votes
1 answer
102 views

Why do we need two markers to measure a recombination rate?

In calculating recombination, Why is it necessary to take into account pairs of loci where one marker is heterozygous? Why is it necessary to take into account pairs of loci where both markers are ...
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23 votes
1 answer
665 views

Can a human be made with ovum but without sperm?

This article says that scientists were successful in making a mouse using only a sperm and no egg (ovum). The article also states that this procedure could be applicable to humans. However, I want to ...
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11 votes
3 answers
41k views

Why do 60S & 40S ribosomal subunits make an 80S ribosome (not 100S)?

Why do 60S & 40S subunits make an 80S (not 100S) ribosome and, similarly, 50S & 30S make 70S? 60+40 is not equal to 80, nor is 50+30 equal to 70, so why are the subunits of the 80S and 70S ...
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10 votes
2 answers
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Do only one or both pairs of homologous chromatids exchange genetic material during the process of crossing over?

To be specific: Assume chromosomes A and B are homologous. They've both replicated into A1, A2 and B1, B2 and have formed a tetrad at the equator (synapsis). Most textbooks show either A1 and B1 OR A2 ...
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3 votes
2 answers
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Why is a magnesium ion essential for ATP activity in enzymic reactions?

The Wikipedia entry on Magnesium in Biology includes the following: ATP (adenosine triphosphate), the main source of energy in cells, must be bound to a magnesium ion in order to be biologically ...
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-1 votes
1 answer
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basic programming and bioinformatics [closed]

As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work ...
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12 votes
4 answers
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Why is AUG the initiation codon?

Is there any reason why AUG is the initiation codon? Can’t translation start with different codons?
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12 votes
3 answers
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Why does replication require primers while transcription does not?

In transcription, there is no need for any primer. I guess the basic mechanism of DNA polymerase & RNA polymerase is the same. So why does replication have the need for a primer?
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7 votes
1 answer
5k views

Role of calcium chloride during competent cell preparation

I am aware of the fact that $CaCl_2$ settles down on the cell wall making it less negative may be by forming bond with Teichoic acid. Also due to the positive charge it attracts DNA (DNA is negatively ...
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6 votes
1 answer
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What came first? The DNA or the DNA polymerases?

I know this sounds a lot like chicken and egg question and while the latter has an answer, I am intrigued about the former. A modified form of the question would be, in the course of abiogenesis, ...
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4 votes
1 answer
1k views

Reason behind formation of positive supercoils during DNA replication/ transcription

When a twist is unwound without cutting the DNA strands or is removed by cutting the strand(s) and resealing, negative supercoils are introduced in the DNA. From Cell and Molecular Biology -Karp But ...
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4 votes
1 answer
143 views

Can difference in the expression potential of alleles lead to dominance?

Several hour ago I was in thoughts what allele dominance really means on molecular level. As we know from basic genetics, if the organism had Aa type of some gene ...
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4 votes
1 answer
4k views

How do major and minor grooves arise in the DNA helix? [duplicate]

I understand that they arise due to the pairing of bases of two opposite stands and are sites through which important proteins needed for replication and transcription of DNA interact. But I don't get ...
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4 votes
1 answer
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Why are most mutations recessive? [duplicate]

Why are most of deleterious mutations recessive in nature? I understood that if it's recessive then one reason may be that the mutant gene doesn't code for a functional protein and so there is no ...
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3 votes
1 answer
225 views

Relationship between the ambiguity (wobble) at codon position 3 in elongation and codon position 1 in initiation

In prokaryotes the usual observed start codon frequency is AUG > GUG > UUG. An explanation for this is that AUG is the most common initiator codon because it forms the most stable interaction with ...
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3 votes
2 answers
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On which DNA strand is TATA box present?

My book (Snustard and Simmons) mentions that TATA box is present on the non-coding DNA strand but that was for the promoter of mouse thymidine kinase gene. I have tried to find out more information ...
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  • 8,754
13 votes
2 answers
509 views

Are codons that map to the same amino acids interchangeable?

From wikipedia, in the section on the RNA codon table, I see a mapping between codons and amino acids. There, Valine is related to GUU, GUA, GUG, GUC. Does it mean in the same context that these ...
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10 votes
1 answer
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How are there alternative initiation codons?

According to wikipedia and the original complete sequence of the K-12 genome, there are multiple non-AUG start codons such as GUG and UUG. How is this possible? I'm particularly curious about the ...
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7 votes
1 answer
432 views

How exactly can dsRNA be introduced to a cell?

Is it just by viruses or are there other means by which it gets into cells, such as plasmid uptake?
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4 votes
1 answer
349 views

How is the type of genetic manipulation determined in CRISPR-Cas9?

I've been reading up a bit on the CRISPR-Cas9 system for gene manipulation. From what I read, it introduces double-strand breaks at specific points determined by the choice of sgRNA. But how do you ...
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2 votes
1 answer
175 views

Why do oncogenes show genetic dominance?

As we know that tumor suppressor gene causes cancer only when both the alleles are recessive in nature.But in case of oncogenes if only one allele is dominant it can cause cancer.Why in case of ...
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