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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1answer
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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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4answers
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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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3answers
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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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3answers
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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?
3
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1answer
467 views
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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3answers
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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 right?
9
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2answers
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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)? ...
182
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3answers
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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 ...
14
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2answers
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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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3answers
957 views
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 ...
12
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2answers
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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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2answers
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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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1answer
153 views
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 ...
45
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5answers
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?
27
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3answers
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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 &...
8
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2answers
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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 ...
3
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1answer
2k views
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-...
1
vote
1answer
78 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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2answers
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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 ...
9
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2answers
344 views
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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2answers
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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 ...
5
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2answers
543 views
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, ...
5
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2answers
143 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 ...
4
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1answer
85 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 ...
1
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1answer
603 views
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 ...
27
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2answers
6k views
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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1answer
529 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 ...
10
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3answers
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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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2answers
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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 ...
5
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4answers
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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, ...
10
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1answer
7k views
Difference in length of Okazaki fragments
The length of Okazaki fragments in the lagging strand is about 100-200 nucleotides in eukaryotes and about 1000-2000 nucleotides in prokaryotes.
What (molecular mechanism, enzyme type ) determines ...
-1
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1answer
1k views
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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3answers
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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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4answers
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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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1answer
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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 ...
6
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4answers
360 views
Do we see protocells forming in nature today?
I understand that the current theory of chemical evolution (aka origin-of-life, abiogenesis) involves lipid-based protocells that enclosed RNA and perhaps some other compounds as a first steps to life....
5
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1answer
121 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 ...
5
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1answer
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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 ...
4
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1answer
662 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 ...
4
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1answer
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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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2answers
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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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2answers
353 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 ...
7
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1answer
342 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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1answer
150 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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2answers
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Are eukaroytic promoters located in the 5' UTR region?
I was wondering if promoter sequences are located on 5'UTR region in eukaryotic organisms?
13
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1answer
935 views
How do ion channels transport only specific ions?
Ion channels, such as $Na^+$ channels and $K^+$ channels, are higly specific for ion permeability. But how do these channels achieve and maintain this specificity? Like how does a $K^+$ channel ...
9
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2answers
231 views
How do we find antibiotics?
So the last class of antibiotics were made in 1984 (I think), which makes it appear as though they are hard to find(/design maybe). How is it then they were discovered? Was it by chance? I know some ...
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1answer
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What causes the colors we see in eyes?
Genetics aside, what are the biochemical reasons for the different colours of human irises?
Also, related, how does eye colour change, particularly in childhood? (example: my eyes used to be blue,...
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2answers
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How can CI repressor both activate and repress $P_{RM}$ promoter found in $\lambda$ phage?
I'm reading a paper where the authors constructed a toggle switch that uses bidirectional $P_R/P_{RM}$ promoter found in the $\lambda$ phage. There are 3 binding sites - $O_{R1}$, $O_{R2}$, $O_{R3}$ - ...
