Questions tagged [biochemistry]
The study of chemistry within the scope of biology: the compounds that occur and the reactions involving them in living organisms.
2,001
questions
0
votes
0
answers
31
views
Need help designing an enzyme immunoassay (EIA)
I have a FITC-labelled DNA sequence and an anti-FITC antibody, however this antibody is not conjugated with HRP or any other enzyme. I work in a lab with limited finances, so is there a way I could ...
- 35
-1
votes
1
answer
205
views
How to convert cell units (c.u.) to mole?
If one has values in terms of cell units (c.u.) how may it be converted to $\mu$M? Should I think a "cell unit" as
$1\;c.u.= \frac{1}{\text{cell volume}}$
and
$1\;c.u.=\frac{1}{\text{cell ...
- 3
1
vote
0
answers
56
views
VDJ sequencing in mice, DNA or RNA?
I am wondering if anyone who is well versed with VDJ sequencing for TCR repertoire analysis (specifically CDR3) would know if DNA or RNA is a better starting material? We are looking at the effects of ...
0
votes
2
answers
626
views
Numbering amino acid residues
While reading about primary structures of protein, I came across the following image.
What do the numberings $n-1, n, n+1$ in the below image refer to?
I thought about it : The amino acid residues are ...
- 21
0
votes
1
answer
1k
views
Exact average molecular weight of a dsDNA basepair
I am trying to calculate the exact weight of a given dsDNA.
On the Internet and the literature, different values for the av. molecular weight of one basepair are given :
660 g/mol (probably wrong),
...
- 231
1
vote
1
answer
384
views
Can fermentation and aerobic respiration occur at the same time?
In muscle cells during exercise, does lactic acid fermentation and aeorobic respiration occur at the same time, and does this mean the cell makes more or less ATP during this time?
The cell can't ...
- 115
1
vote
1
answer
96
views
When should I use cryofixation and chemical fixation?
We know that the technique used in TEM sample preparation involves multiple steps, one of the most important of them is fixation.
Fixation can be of two types:
Cryofixation, that suggests that the ...
- 113
4
votes
2
answers
229
views
CAM Photosynthesis Oxygen Generation?
I've been looking into CAM plants - notably the snake plant which is native to West Africa.
Upon researching the CAM photosynthesis cycle, I've found it fascinating that the plant stores CO2 at night ...
user63784
0
votes
1
answer
959
views
How do cellular conditions change the Gibbs free energy of a reaction?
How do cellular conditions change the Gibbs free energy of a reaction?
Taking glycolysis as an example, how exactly would cellular conditions affect the free energy released from this reaction?
- 115
0
votes
0
answers
67
views
Calvin cycle- combining three "turns"
In the common Calvin cycle diagram, it is commonly stated that "three cycles are combined to show the production of 1 molecule of G3P".
How does the G3P molecule escape from this cycle in ...
- 115
0
votes
1
answer
777
views
In which reactions of glycolysis is magnesium involved?
I am currently studying the metabolic pathways for biochemistry and I am not quite clear in which reactions of glycolysis magnesium is involved.
So I have now found out that magnesium is present in ...
1
vote
0
answers
77
views
Why protons flow back to the matrix through ATP synthase?
I am reading oxidative phosphorylation and I can't understand why the protons that are pumped out must go again into the matrix and finally produce ATP.
Suppose initially that the inside (Matrix-M) ...
- 113
-2
votes
1
answer
127
views
What favors the active transport in a membrane? [closed]
I was reading about active transport in membranes where ATP is used. ATP "reacts" with the protein pump and converts into ADP and also make a conformational change to the pump. Now this ...
- 113
0
votes
1
answer
78
views
Why are there 10 base pair steps, not 16?
In a biochemistry course I'm taking, the lecturer emphasised that there are 10 possible base pair steps; I've included a screenshot of a slide stating this. This confuses me, because I cannot work out ...
- 119
1
vote
1
answer
64
views
Does the fact cordyceps mostly affect insects have something to do with chitin being polysaccharide?
This is just a conjecture of mine based on those observations:
Fungus seems to be very good at attacking tough chains of sugars like cellulose and starch.
insects are covered by Chitin, a ...
- 181
2
votes
1
answer
99
views
Decreasing signals in assay measurements
I'm working with a calcium assay to study the effects of different virulence factors. The assay works, but from day to day the signals of cell lysis go down. Unfortunately, I haven't found an ...
- 401
0
votes
0
answers
72
views
Do all anabolic reactions involve condensation?
I know that condensation is one example of an anabolic reaction (building macromolecules from monomers), but do all anabolic reactions involve condensation? Or is there an example of an anabolic ...
- 111
1
vote
0
answers
60
views
Why do GPCRs pass exactly 7 times through the cell membrane?
7-transmembrane domain receptors or GPCRs are one of the most common receptors in biology.
They can be found in eukaryotic cells.
What is the significance of the number 7 here: why does it pass ...
- 119
1
vote
1
answer
235
views
How does glucose uptake happen in the various tissues of the body?
I know that the GLUT4 transporter allows for insulin-dependent uptake of glucose in skeletal muscle, liver and adipocytes. I also know that GLUT2 transporters are present in the liver and allow it to ...
0
votes
1
answer
55
views
Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain?
I have come across an online ppt slide of the bioinformatic algorithm where it is said that first and the last amino acid Ramachandran angle is not necessary to tell all its internal coordinates. Is ...
0
votes
1
answer
149
views
Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software
I am trying to compute Cartesian coordinates of backbone atoms and side-chain atoms (C beta alone) for a given set of internal coordinates (bond lengths, bond angles and dihedral angles) I have ...
1
vote
0
answers
39
views
Measuring the protein content using UV Vis
The experiment is to determine the protein content of the solution. I followed the procedure of the Bradford assay but the reagent needed is unavailable and so we use an alternative by using cold pure ...
- 11
4
votes
1
answer
1k
views
Why don't weak detergents lyse the nuclear membrane?
A low concentration of a non-ionic detergent lyses the cell membrane, but leaves the nuclear membrane intact. Both are phospholipid bilayers, so why is only the cell membrane lysed?
Under these ...
- 41
3
votes
2
answers
173
views
Average masses of atoms / amino acids
I recognized that there is some controversy about the average mass of amino acid masses in different online sources.
Expasy and Wikipedia report the same masses, but UWPR and Mascot report different ...
- 84
2
votes
1
answer
609
views
Why does ionizing radiation cause only DNA double strand breaks?
It's known that ionizing radiation such as X-ray and $\gamma$-ray, cause DNA damage, specifically double strand break. Why is it so? I mean, why not single strand break, why not pyrimidine dimer?
- 617
4
votes
1
answer
60
views
Why is this oxoglutarate dehydrogenase and not oxoglutarate decarboxylase?
I was looking at the oxoglutarate dehydrogenase complex and saw the reaction mechanism for its E1-TPP mechanism, which results in the formation of a stabilized carbanion intermediate.
The mechanism ...
- 155
1
vote
0
answers
11
views
What are the interaction energies/chemical potential values for the cytoplasm - protein interactions within the cytoplasm?
I'm trying to simulate phase separation in a biological based system using a Cahn Hilliard model. I have 3 components, they are 2 theoretical enzymes and the cytoplasm. I have found plenty of sources ...
2
votes
1
answer
121
views
Are the y-axis values informative when performing biolayer interferometry?
I am currently reading an this article by Alexandra C. Walls et. al.
I would like to ask a question about a graph that is being used in the article and I wanted to know if my analysis was correct.
I ...
- 149
1
vote
1
answer
140
views
Meaning of some unit of measurement of kinase activity
I need help knowing what $cpm \times 10^3$ means in Figure 4(C) of this paper (https://www.sciencedirect.com/science/article/pii/S0022202X15323149#f0010). It appears to be a unit of kinase activity.
- 229
1
vote
0
answers
705
views
What property of water explains how sweating helps the runner continue running?
My question I have to answer is: A runner picks up pace on a warm day and starts sweating profusely. What property of water explains how sweating helps the runner continue running?
The following are ...
- 13
-3
votes
1
answer
100
views
Question About Molecular Weight [closed]
In Lehninger's Principle of Biochemistry Pg. $14$, this is the definition for molecular weight (relative molecular mass):
The molecular weight of a substance is defined as the ratio of the
mass of a ...
-2
votes
1
answer
98
views
What is a metabolite? [closed]
I am a mathematician and work on metabolic networks as networks. But I could not find a proper definition for a metabolite? Are they organic molecules? can a gene or a protein also be a metabolite?
- 13
2
votes
0
answers
226
views
Does glycerol in E.coli culture media somehow inhibit the lac-operon?
I have have been taught that one should induce protein expression with IPTG at an OD of about 1.0 - 2.0 when E.coli grows it TB media (terrific broth). As a reference point, one typically induces ...
- 842
-5
votes
2
answers
967
views
Proinsulin is an 84 residue polypeptide with six cysteines. How many different disulfide combinations are possible?
Generally cysteine residues form disulfide linkages - so how many combinations are possible out of (say) six residues. Also can cysteine form bonds with all the residues?
- 1
2
votes
1
answer
58
views
Which modern methods of antibiotic production are there?
For my seminar paper in the field of biology, I have to collect modern methods of antibiotic production. The topic is a little overwhelming, but the work should also be quite extensive (approx. 18 ...
- 29
0
votes
0
answers
151
views
What is "KK1 enzyme"?
In the book "The Kaizen Way" by Robert Maurer, I've read the following:
When we’re sitting, our muscles go into a form of hibernation, causing
our bodies to shut down the enzyme (called KK1)...
- 17
1
vote
0
answers
92
views
Can I use dATP instead of ATP (vice versa) for in vitro assay? [closed]
For example, polynucleotide synthesis reaction requires dATP which gives H on 3'end and synthesizes polynucleotide. For this reaction can I use ATP because I knew that ddNTPs are used so that ATP ...
- 21
2
votes
1
answer
104
views
Question in gel chromatography experiment
Here I am trying to do
gel chromatography to separate vitamin B12 and Bovine Serum Albumin (BSA)
in this experiment, I am using sephacryl s-100 HR gel column
my question is can I use Phosphate ...
- 21
1
vote
1
answer
37
views
Question on thick filaments
In this photo, I know that the arrows pointing towards the M-line of sarcomere on actin filaments are due to the power strokes of myosin heads. However, what I don't understand are the arrows on the ...
- 153
3
votes
1
answer
48
views
How is silica transported to the leaves of genus Dendrocnide trees to form stinging needles for toxin delivery?
I just read the NYTimes' This Tree’s Leaves Look Soft and Inviting. Please Don’t Touch Them. which mentions the genus Dendrocnide and that Wikipedia section begins with:
Contact with the leaves or ...
- 5,094
2
votes
0
answers
80
views
What are the carbohydrates that are found in white rice?
From this Wikipedia page on rice, it is mentioned that 100g of rice contains 80 g of carbohydrates, of which 0.12 g is "sugar" and 1.3 g is "fibre". I believe the "fibre" ...
- 131
1
vote
1
answer
15
views
Natural Toxins and Medicine
How are natural venoms and toxins (e.g. spider and snake venoms) used to make antidotes? In other words, what is in that venom that is part of a harmful substance but, when used correctly, can ...
- 317
0
votes
0
answers
33
views
Transcription of two different factors from the same transcription factor - seeking a relation between concentrations
Let's assume that:
Factor $X$ enters nucleus and results in the transcription of two different factors, $A$, and $B$.
$X$ $\to$ $A$
$X$ $\to$ $B$
Can it be expressed as
$[A]=\alpha [X]$ or $[A]=\...
- 3
4
votes
1
answer
64
views
How do organophosphates affect kidney function?
Many organophosphates, besides inhibiting acetylcholinesterase, can also permanently inhibit the enzyme neuropathy target esterase, leading to nerve damage. NTE also happens to be found in the kidneys,...
- 409
16
votes
2
answers
2k
views
How is it thought that phosphine is synthesized by living organisms on Earth?
The recent (Sept. 2020) report of “Phosphine gas in the cloud decks of Venus” states that phosphine (PH3) is only known to occur on Earth due to anaerobic life. Quoting from a report in the New York ...
- 279
4
votes
1
answer
102
views
Who discovered DNase?
I was recently studying genetics in which DNase had a crucial role in proving DNA to be the genetic material and I tried to find who discovered DNase (like the discoverer of DNA) but in vain.
Who ...
- 53
-1
votes
1
answer
63
views
Is there an enzyme that functions without being associated with a complex?
I'm looking for an enzyme that does not function as part of a complex in its active state. Preferably it also is not part of a kinase or other kind of activating cascade as well though I would ...
- 101
2
votes
3
answers
695
views
Is a virus a poison?
I've understood that a virus is not a living organism (like e.g. a bacterium). From Wikipedia I get that a poison is a substance that reacts physically or chemically with molecules in the human body. ...
- 153
29
votes
1
answer
3k
views
Killing enveloped viruses with soap
Unlike non-enveloped viruses, enveloped viruses can be killed with soap, alcohol, etc. Why?
Why does just having an envelope make it susceptible to soap and alcohol?
- 415
0
votes
2
answers
134
views
What specific markers does a Covid-19 PCR test look for?
I've done a search and can't find anything as to what specifically makes a Covid-19 positive that identifies it as unique. I would expect to see something like this:
https://madridge.org/journals-...
- 1