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What is the actual size of a nucleotide?

What is the actual size of a nucleotide?


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I found in this website that the dimension of a nucleotide is 0.34 nm. Is there any experimental paper confirming this statement?


If you want experimental papers, we should be precise about what we're measuring. "The dimension of a nucleotide" is rather imprecise, as a nucleotide is a rather oblong, knobbly thing.

0.34 nm is a relevant measurement related to nucleotides, but it's specifically the distance between consecutive bases in a standard B-form DNA helix - that is, what's the spacing between the "rungs" on a DNA ladder.

This measurement can be confirmed by several experiments, primarily those involving X-ray or neutron crystallography or scattering. For example, both the Wilkins and Franklin papers that were published back-to-back with the famous Watson & Crick DNA structure paper referrence the strong 0.34 nm reflections from X-ray fiber diffraction which Watson & Crick reference as the spacing of the bases in their model of DNA structure. Other papers have confirmed the measurement. This 1983 Biomed Biochim Acta paper uses wide-angle X-ray scattering to find it. Additionally, there are a large number of structures in the Protein Databank which contain DNA structures - these have been determined by a number of different approaches (X-ray crystallography, neutron diffraction, NMR, electron microscopy, etc.) and all of which are consistent with the 0.34 nm average spacing of base pairs. (Modulo minor structure-to-structure variations.)


O level biology Notes

1) Make a large diagram of a cell
Ans ) Draw a large diagram of any cell

  • First find the length of RBC in cell
  • Suppose x=3 cm
  • Find the actual size of RBC
  • find the length of drawn image
  • suppose it is 10 cm
  • If the magnification is not given ( x400 ) then leave the first step to find the actual size
  • x is necessary to use in the answer of magnification

16 comments:

when the question is being asked that draw a large diagram , the diagram should be drawn of a single cell or complete diadram .

The should be of one cell.

Can u please explain that if magnification is not given then how we will calculate the actual size or find out the magnificaion.


Abstract

A nucleotide repeat expansion (NRE) within the chromosome 9 open reading frame 72 (C9orf72) gene was the first of this type of mutation to be linked to multiple neurological conditions, including amyotrophic lateral sclerosis and frontotemporal dementia. The pathogenic mechanisms through which the C9orf72 NRE contributes to these disorders include loss of C9orf72 function and gain-of-function mechanisms of C9orf72 driven by toxic RNA and protein species encoded by the NRE. These mechanisms have been linked to several cellular defects — including nucleocytoplasmic trafficking deficits and nuclear stress — that have been observed in both patients and animal models.


Calculating actual size (CIE A-level Biology)

A Science teacher by trade, I've also been known to be found teaching Maths and PE! However, strange as it may seem, my real love is designing resources that can be used by other teachers to maximise the experience of the students. I am constantly thinking of new ways to engage a student with a topic and try to implement that in the design of the lessons.

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This lesson describes how to use the magnification formula to calculate the actual sizes of specimens in a range of units. The PowerPoint and accompanying resources have been designed to cover point 1.1 (e) of the CIE A-level Biology specification but can also be used as a revision tool on the content of the previous two lessons as prior knowledge checks are included along with current understanding checks.

The students are likely to have met the magnification formula at iGCSE so this lesson has been written to build on that knowledge and to support them with more difficult questions when they have to calculate actual size without directly being given the magnification. A step by step guide is used to walk the students through the methodology and useful tips are provided. The final quiz round of the competition that has run over the course of these 3 lessons will challenge them to convert between units so they are confident when challenged to present actual size in millimetres, micrometres or nanometres.

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Maths in A-level Biology (CIE A-level Biology)

Without doubt, the CIE A-level Biology specification contains a lot of maths calculations and every year, there are a large number of exam questions that require the application of a range of mathematical skills. Therefore, a clear understanding of how and when to apply these skills is closely related to success on this course and the following calculations are covered by the 7 lessons that are included in this bundle: * Using the eyepiece graticule and stage micrometer to measure cells and be familiar with units * Calculating actual sizes of specimens from drawings, photomicrographs and electron micrographs * Using the chi-squared test to determine significance between the observed and expected results of a genetic cross * Use the t-test to compare the variation of two populations * Using the Hardy Weinberg principle to calculate allele, genotype and phenotype frequencies in populations * Use Spearman's rank correlation to analyse relationships between the distribution and abundance of species and abiotic or biotic factors * Using Simpson’s index of diversity to calculate the biodiversity of a habitat All of the lessons contain step by step guides that walk the students through the application of the formulae and there are lots of worked examples and exam-style questions for the students to use to assess understanding

Topics 1 & 2: Cell structure & Biological molecules (CIE A-level Biology)

It's no coincidence that cell structure and biological molecules find themselves as topics 1 and 2 of the CIE A-level Biology course, because a clear understanding of their content is absolutely critical to promote success with the 17 topics that follow. Hours and hours of intricate planning has gone into the 18 lessons included in this bundle to ensure that the detailed content is relevant and can be understood and that links are made to related sections of topics 3 - 19. The lesson PowerPoints and accompanying resources contain a wide range of activities that include: * differentiated exam-style questions with clear mark schemes * directed discussion points * quiz competitions to introduce key terms and values * current understanding and prior knowledge checks Due to the detail included in these lessons, it is estimated that it will take in excess of 2 months of allocated teaching time to cover the content of the resources A number of the resources have been shared for free so these can be downloaded in order to sample the quality of the lessons

Topic 1: Cell structure (CIE A-level Biology)

As Biology is the study of living organisms which are built out of cells, a clear understanding of the topic of cell structure is critical for a student's success in A-level Biology. Intricate planning has gone into all 7 of the lessons included in this bundle and the variety of tasks will engage and motivate the students whilst the details of the following specification points in topic 1 of the CIE A-level Biology course are covered: **Topic 1.1: The microscope in cell studies** * Use an eyepiece graticule and stage micrometer to measure cells * Use of the millimetre, micrometre and nanometre * Distinguish between resolution and magnification * The use of light and electron microscopes * Calculate the actual sizes of specimens **Topic 1.2: Cells as the basic units of living organisms** * Recognise eukaryotic cell structures and outline their functions * State that ATP is produced in the mitochondria and the chloroplast and the role of this molecule in cells * The structure of a typical prokaryotic cell * The differences between eukaryotic and prokaryotic cells * The key features of viruses If you would like to sample the quality of these lessons, download the magnification and resolution lesson, the eukaryotic cell structures lesson and the viruses lesson as these have been shared for free


Calculating magnification and sizes of specimens

Microscopes are used to study the cells of living things.

A light microscope – which uses visible light – can magnify images up to about 1,500 times actual size.

The microscope had a really bright light on it (light microscope).

An electron microscope uses electron beams in place of light and can magnify up to around two million times.

The electronic robots (electrons) check out the images provided by the electron microscope.

The magnification of a specimen can be calculated using the following equation:

A plant cell in the microscope image measures 12mm across. The actual size of the cell is 0.012mm. So, in this instance:

Which means the magnification is 1000 times.

The actual size of a biological specimen can be calculated using this equation:

The nucleus of a cell in a magnified image is 4mm across. The magnification of the image is 800 times, so in this case:

Which means the actual size is 0.005mm.

Actual sizes of specimens or parts of specimens are often measured in micrometres. You just need to remember that a micrometre is 1000 th of a millimetre (or a millionth of a metre).

So, an actual size of 0.012mm would be 12 micrometres (0.012 X 1000), and an actual size of 0.005mm would be 5 micrometres (0.005 X 1000).

If you need to work out the magnification of a specimen and one figure is in micrometres and the other in millimetres, simply convert one measurement to the unit you want your answer to be in.


What Do Nucleotides Do?

We've already gone over the nucleotide definition. But what exactly do nucleotides do? In other words, what is their purpose?

DNA and RNA

We know that RNA and DNA are made up of "strings" of nucleic acid, and carry out genetic coding. RNA and DNA are changing all the time, and the cells are constantly growing and dying in them, as well as in all the other parts of our bodies.

Nucleotides are a major part of this process in a few key ways. First, they form that bases for nucleic acid. Second, working outside of nucleic acid, they help trigger and even participate in cell function.

In order to form nucleic acid, two triphosphate nucleotides must bond via hydrogen atoms in a process known as "base pairing." Each base is formed by complementary nucleotides, one purine and one pyrimidine:

  • Purines: Adenine, Guanine
  • Pyrimidines: Cytosine, Thymine, Uracil

In terms of our nucleic bases, here are the triphosphates that make up DNA:

    dATP:Deoxyadenosine triphosphate, a nucleotide that is made up of deoxyribose sugar, an adenine base, and three phosphate groups

The nucleotides that make up RNA are as follows:

    ATP:Adenosine triphosphate, a nucleotide that is made up of ribose sugar, an adenine base, and three phosphate groups

For example, dCTP and dGTP bonded together would form a nucleic acid.

An adenosine diphosphate molecule

Free Nucleotides

Di and mono phosphate nucleotides cannot bond to become nucleic acid. Nevertheless, these nucleotides still have important cellular functions.

Nucleotides can act as co-enzymes. An enzyme is a substance that's produced by living organisms and that acts as a catalyst to bring about a specific biochemical reaction. They can help speed along chemical processes when bound with an enzyme.

The function of the co-enzyme depends on several factors, including what the nucleotide bonds with. ATP in particular serves as a co-enzyme frequently and is considered the main energy currency in living cells. Since ATP is so stable, it stays in a cell until it's ready to be used and then releases energy to trigger a chemical reaction.

Nucleotides also play an important part in cellular metabolism. This is a process that takes place in cells, in which the cells are degraded due to chemical reactions in the nucleotide.

This process is especially important in RNA and DNA, as it's happening within our cells at all times, meaning that it's extremely important it goes right. If not, it can result in a variety of diseases.

This reaction is triggered in the nucleotide, and the cellular degradation begins. When this occurs in RNA and DNA, sometimes parts of the nucleotide can be salvaged to create new nucleotides.


Nucleotide vs Nucleoside

A nucleoside is said to be a nucleotide without a phosphate group?

Just revising and trying to figure out the difference.

However, a nucleotide with one phosphate group (naturally?), is then called a nucleoside monophosphate? Are these not the same thing in that case?

Not what you're looking for? Try&hellip

(Original post by Newbie2019)
A little confused here 🥴

A nucleoside is said to be a nucleotide without a phosphate group?

Just revising and trying to figure out the difference.

However, a nucleotide with one phosphate group (naturally?), is then called a nucleoside monophosphate? Are these not the same thing in that case?

(Original post by Newbie2019)
A little confused here 🥴

A nucleoside is said to be a nucleotide without a phosphate group?

Just revising and trying to figure out the difference.

However, a nucleotide with one phosphate group (naturally?), is then called a nucleoside monophosphate? Are these not the same thing in that case?

&ldquoNucleotide&rdquo you could say is the trivial name for &ldquoNucleoside monophosohate&rdquo however, as you said, they are exactly the same however you wish to say it and I&rsquom sure marks will be given for either expression. The term Nucleoside monophosphate is stating the molecule is a Nucleoside WITH a single phosphate, hence a nucleotide and can no longer be termed as a nucleoside.


PCR product size - (Mar/30/2011 )

I have a forward primer started from nucleotide no. 79 till 99 and a reverse primer located at nucleotide no. 114 till 391. From there, how can I predict my RT-PCR product size (from cDNA)?
I have designed my primer gDNA sequence where there is an intron within my primer design. Should I exclude or include the intron sequence in order to count my PCR producr size?

From your explanation it seems to me that predicting your RT-PCR product should be pretty straight forward: just count the number of bases from the start of your forward primer to the end of your reserve primer using the cDNA sequence of your gene. You should definitely the intron sequence.

you didn't finish your sentences. Definitely include or exclude intron sequence??

I got the bands for my gel electrophoresis but I didnt know whether they are the right bands or not. Can I have your email so that i can show to you the picture?

ifhmn on Wed Mar 30 13:59:44 2011 said:

Is your reverse primer really going from 114 to 391? I mean, no way you have a primer that's 277nt long, do you? I guess that's in the gDNA, so what's the actual location in the cDNA, ie WITHOUT the intron.

To calculate the size of your RT-PCR product you have to substract the start position of your forward primer, to the start position of your reverse. BUT, you need to look at the size in cDNA, by definition cDNA will not have introns, as is the copy of your mRNA.

I'm guessing the intron in between nucleotides 114 - 391, remove that, and calculate the actual size.

Sorry,my mistake. From my cDNA sequence, the forward sequence start at base no. 69 till 89 and reverse sequence start at base no. 395 till no. 414. From the gDNA seq., there is an inton between the primer with 188bp.

ifhmn on Thu Mar 31 10:07:10 2011 said:

Do you mean there's an intron between your forward and your reverse primer?

If so, your expected product from cDNA should be 414-69 = 345bp you add the intron to that 345 + 188 = 533bp which will indicate that you have gDNA contamination.

Fo a primer to "expand and intron" it should bind to the end of one exon and the begining of the next one, wihout binding to the intron. That way, those primers will not be able to amplify from gDNA as the intron wont allow the primer to bind.


Background

Differences in human skin pigmentation have been attributed to genetic variation in several different genes [1–3]. Among these, the melanocortin 1 receptor gene (MC1R, MIM#155555), a member of the G protein-coupled receptors superfamily, is the major contributor to normal pigment variation in humans. It is a small, highly polymorphic gene consisting of one exon with 951 coding nucleotides on chromosome 16q24.3.

Numerous studies have demonstrated associations between specific MC1R variants and red hair, light skin, poor tanning ability and heavy freckling [4–9]. A recent genome-wide association scan confirmed the role of MC1R SNPs in hair, eye, and skin pigmentation[3]. The functional role of many of these variants has been described [10–13]. Several MC1R variants are also associated with increased risk of malignant melanoma in a variety of populations [14–22] The effect of MC1R polymorphisms in melanoma risk appears to extend beyond its effect on pigmentation in most of these investigations, and to be linked to melanomas harboring mutations in the BRAF oncogene[23].

Several hypotheses have been generated in an effort to understand the evolutionary history of skin pigmentation in humans. It has been suggested that as humans migrated out of Africa to climates with more limited exposure to sunlight, relaxation of functional constraints in pigmentation genes, including MC1R, or selection for functionally relevant variants that led to lighter skin pigmentation occurred[24]. This could result in an improved ability to synthesize vitamin D in the presence of limited sunlight exposures [25–27]. It has also been suggested that darker skin is favored in regions closer to the equator for protection against ultraviolet radiation[24]. In addition, differences in skin pigmentation could protect against pathogens and cold injury, and may have also been important in sexual selection[28].

Genetic variation of MC1R, in the form of single nucleotide polymorphisms (SNPs), is significantly different across populations from different geographic regions [29, 30]. In most regions of the genome, there is a higher degree of genetic variation in individuals of African descent than in other populations, most likely due to evolutionary history [31, 32]. MC1R is an exception to this observation. It has been shown to be more polymorphic in individuals of European descent than in those from Africa [29, 30]. A comprehensive study of SNP allele frequencies in MC1R from populations around the world, further quantified the large differences in the distribution of variants across populations, with a prominent difference between light and dark-pigmented individuals [29]. The goal of the current study was to expand on that study of MC1R genetic variation by characterizing nucleotide diversity, population specific differentiation (FST), and to study measures of selection.


Facts about the Cell Nucleus

Can you believe the cell nucleus is the largest organelle of the cell and holds approximately 2 meters of DNA? Read this BiologyWise article for more such interesting facts about this structure.

Can you believe the cell nucleus is the largest organelle of the cell and holds approximately 2 meters of DNA? Read this BiologyWise article for more such interesting facts about this structure.

The cell nucleus is a compact organelle found in every eukaryotic cell. In fact, its presence is used as a differentiating point between eukaryotes and prokaryotes. As the nucleus houses the primary components of a eukaryotic cell, you can imagine its importance in the overall functioning of the cell. Functionally, one of the interesting cell nucleus activities is its active participation in protein synthesis. Continue reading to know some of the most interesting facts about this structure.

Interesting Facts About Cell Nuclei

Would you like to write for us? Well, we're looking for good writers who want to spread the word. Get in touch with us and we'll talk.

Discovery

Location

Structure

Composition

Functions

So, aren’t these facts interesting to note? As far as synthesis of proteins is concerned, the transcription phase is carried out in the cell nucleus, while the later translation phase occurs outside the nucleus, in the cell cytoplasm. Other than this structure, some amount of the hereditary material is present in the mitochondrion organelle.

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Watch the video: Electron Microscope Video - SEM 10,000,000x - DNA replication u0026 Protein synthesis. SEM animation (May 2022).


Comments:

  1. Roy

    What a funny question

  2. Merla

    Thanks to whoever is doing this blog!

  3. Gillespie

    What a sentence ... great, the idea excellent



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