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How many copies of a gene?

How many copies of a gene?


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I am studying mathematical models of transcription and translation and I am wondering:

In a particular genome, how many copies of a gene coding for one particular protein should one expect? Are they all transcribed at the same rate?

I know humans have two copies of each chromosome, so the answer would be at least 2 in humans. But I wonder if one particular gene coding for a protein we need in abundance might be present in many copies in the genome to increase expression.


Remi.b talked at great length in his answer about copy-number variation and the generation of new genes. However, I don't think he quite answered what I think is a pretty basic question:

How many copies of any particular gene are there in (a human) genome?

The answer to that question is also simple: two - one on the chromosome from the mother, and one from the father. The exception is genes on the X and Y chromosomes, but that's complicated so I'll ignore it :)

Now, that's not to say that there might be several versions of any particular gene, having arisen through such mutational events as Remi.b explained. So, in antiquity, gene ABC123 might have been duplicated, leading to today's genes ABC123a and ABC123b, which may or may not have different functions. But, for ABC123a, there are only two copies per (normal) cell, and the same is true for ABC123b and all the rest.

Are they all transcribed at the same rate?

But I wonder if one particular gene coding for a protein we need in abundance might be present in many copies in the genome to increase expression.

The regulation of gene expression is quite complex. However, the cell (I'm referring to eukaryotes here, I don't know how different prokaryotes and Archaea are) has mechanisms to ensure that the products of so-called housekeeping genes, which are needed in great abundance, are available to the cell. One method is to attract and keep the RNA polymerases (which transcribe the gene into messenger RNA (mRNA), which is the template for translation into a protein - the actual gene product) bound to the gene sequence through a variety of DNA "promoter" and "enhancer" sequences, which other proteins called transcription factors bind to and recruit the polymerase to the gene. These polymerases are kept active for as long as the cell needs the gene's protein product, churning out copy after copy of mRNA. There are many other mechanisms as well, ranging from how the core histone proteins that give chromosomes their shape bind near the gene, to the manner in which the translation machinery (ribosomes) bind to the mRNA and produce multiple protein molecules per mRNA copy. So, even though we may only have two copies of a particularly vital gene, the cell has evolved ways of meeting demand for its product.

Are they all transcribed at the same rate?

No, they are not. This all depends on the number, kind, and placement of transcription factor binding sequences in the DNA surrounding and within a gene, as well as the exact identity of the transcription factor(s) recruited. Some keep the polymerase machinery very tightly bound, ensuring quick and accurate transcription, while others don't bind tightly at all, allowing the polymerase to "fall off" the DNA and/or work more slowly. Each gene is uniquely and exquisitely regulated to be transcribed where, when, and in the quantity needed.


Cell cycle

Talking about physical copies of gene, we would indeed have at least 1 copy during the haploid phase, 2 copies during the diploid phase and 4 copies during the mitosis (and during the first phase of the meiosis). Of course, species having mitosis during the haploid phase would have 2 copies of the gene during the mitosis. I am not talking about polyploid species and am not talking about some fungi and other things that have all kind of crazy reproductions system. I am not talking about mtDNA either. Finally, I am not addressing the case of specialized cells that lose part of their genome or the case of tissues that are basically cells who merged together, so that the concept of cell does not even hold any more such as the Syncytiotrophoblast (in the placenta) (see also cell fusion and syncytium).

In short, the variation in the number of copies during the life-cycle is very dependent on the species of interest, the sequence of interest and may also fall under some semantic issue about what is a cell. Note another potential semantic issue result from the question "how similar two genes have to be to still be called copies?".

Mutations and polymorphism

Now, some genes can be found in several copies. When, in a given population the number of copies of a given gene varies from one individual to another, we talk about Copy-Number Variation (CNV). The increase in the number of copies is called gene duplication (or gene amplification or chromosomal duplication when a very big chunk of DNA gets duplicated). The decrease in the number of copies is called gene deletion. There are a diversity of processes that can cause deletions and duplications such as homologous recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.

Evolution of CNV

What mutation is likely to occur first

Gene duplication does not necessarily yield to an increase in the protein concentration (but it can as it is the case for the Pelizaeus-Merzbacher disease for example). If higher expression is selected for, it "feels more likely to me" that the first mutation(s) allowing for this increased expression will affect the regulatory sequences and will not increase the number of gene copies.

Consequences of gene duplications

Gene duplication (if not loss) can yield to subfunctionalization or neofunctionalization. From wikipedia:

Subfunctionalization [is a process] in which pairs of genes that originate from duplication, or paralogs, take on separate functions

… In others words, copies are free to accumulate mutations as long as the other copy is still doing its job

Neofunctionalization, one of the possible outcomes of functional divergence, occurs when one gene copy, or paralog, takes on a totally new function after a gene duplication event

… Basically, one copy gets a totally new function… that can yield to very interesting innovations such as anti-freeze proteins (ref) or snake venom (ref).


What is a gene?

A gene is the basic physical and functional unit of heredity. Genes are made up of DNA. Some genes act as instructions to make molecules called proteins. However, many genes do not code for proteins. In humans, genes vary in size from a few hundred DNA bases to more than 2 million bases. An international research effort called the Human Genome Project, which worked to determine the sequence of the human genome and identify the genes that it contains, estimated that humans have between 20,000 and 25,000 genes.

Every person has two copies of each gene, one inherited from each parent. Most genes are the same in all people, but a small number of genes (less than 1 percent of the total) are slightly different between people. Alleles are forms of the same gene with small differences in their sequence of DNA bases. These small differences contribute to each person’s unique physical features.

Scientists keep track of genes by giving them unique names. Because gene names can be long, genes are also assigned symbols, which are short combinations of letters (and sometimes numbers) that represent an abbreviated version of the gene name. For example, a gene on chromosome 7 that has been associated with cystic fibrosis is called the cystic fibrosis transmembrane conductance regulator its symbol is CFTR.

Genes are made up of DNA. Each chromosome contains many genes.


Gene Cloning

This describes the process of copying fragments of DNA which can then be used for many different purposes, such as creating GM crops, or finding a cure for disease. There are two types of gene cloning: in vivo, which involves the use of restriction enzymes and ligases using vectors and cloning the fragments into host cells (as can be seen in the image above). The other type is in vitro which is using the polymerase chain reaction (PCR) method to create copies of fragments of DNA.

For in vivo cloning a fragment of DNA, containing a single gene or a number of genes, is inserted into a vector that can be amplified within another host cell. A vector is a section of DNA that can incorporate another DNA fragment without losing the capacity for self-replication, and a vector containing an additional DNA fragment is known as a hybrid vector. If the fragment of DNA includes one or more genes the process is referred to as gene cloning.

Contributor: Genome Management Information System, Oak Ridge National Laboratory, U.S. Department of Energy Genome Programs http://genomics.energy.gov

There are 4 different type of vectors:

  • Plasmid vectors
  • Lamda (λ) phage vectors
  • Cosmids
  • Expression vectors

The host cell copies the cloned DNA using its own replication mechanisms. A variety of cell types are used as hosts, including bacteria, yeast cells and mammalian cells.


Elephants almost never get cancer thanks to multiple gene copies

It’s an elephant–sized mystery. Big animals like elephants live longer and their cells have to divide more, so you would expect them to be more susceptible to cancer. But that doesn’t seem to be the case – a phenomenon that has become known as Peto’s paradox.

Now there might be an explanation&colon elephants have extra copies of a gene that spots trouble in cells.

Joshua Schiffman, a paediatric oncologist at the University of Utah, and his team confirmed that Peto’s paradox is a real phenomenon in elephants by studying necropsy records from San Diego Zoo. Using more extensive data from an “Elephant Encyclopedia” that records the causes of death of captive elephants worldwide, Schiffman estimated that less than 5 per cent of elephants die of cancer, compared with 11 to 25 per cent of humans.

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When they studied samples of elephant blood, they found that African elephants have at least 20 copies of the p53 gene from each parent.

P53 is an ancient gene found in all multicellular animals. It detects stress or damage in the cell, and stops the cell from dividing until the stress has passed or the DNA is repaired. Humans inherit one copy from each parent, and it has a crucial role in protecting us from cancer. People who have a defective version – a condition called Li-Fraumeni syndrome – usually get cancer in childhood, and their lifetime risk is close to 100 per cent.

Next, the team exposed elephant cells to radiation to see what happens when their DNA gets damaged. They expected elephant cells to be better at repairing DNA, but this wasn’t the case. Instead, the cells were twice as likely to die when they had faulty DNA.

Schiffman realised this made sense as an evolutionary adaptation. “If you just kill the cell, that’s the ultimate way of getting rid of the risk for cancer,” he says.

Cells from individuals with Li-Fraumeni syndrome were less likely to die when they were exposed to radiation, adding support to the idea that the number of working copies of p53 determines the response to DNA damage.

Another team led by Vincent Lynch at the University of Chicago reached the same conclusions and published the results this week on BioRxiv.

Genome studies in other large animals have uncovered different adaptations that could help keep cancer at bay. Earlier this year, researchers published the genome of the bowhead whale, which lives for more than 200 years and can weigh up to 100 tonnes. They found that it has mutations or duplications in several genes linked to DNA repair and ageing.

Naked mole rats are small but unusually long-lived and free of cancer. Research has shown they have unusual variants of molecules that regulate the cell cycle and how cells stick together.

“It wouldn’t be surprising if different long-lived or big animals came up with different solutions to the presumed extra risk of having more cells,” says Mel Greaves of the Institute of Cancer Research in London.

Schiffman says he hopes the findings will lead to new approaches to cancer prevention and early detection. “Evolution has had 55 million years to figure out how to avoid cancer,” he says. “Now I think it’s up to us to take a page out of nature’s playbook and learn how to take this information and apply it to those who need it most.”

His team plans to screen large numbers of compounds to look for molecules that might mimic the effect of extra copies of p53 in elephants, condemning damaged cells to death instead of trying to repair DNA. He also suggests that new technology such as nanoparticles might be able to deliver elephant p53 into human cells as a means for cancer prevention or treatment.

Greaves is more sceptical. “I think there are no obvious implications for treatment,” he says. “The interest for me in this is that it brings into focus the extraordinary risk that humans have in relation to other large, long-lived animals.”

Journal reference&colon Journal reference&colon Journal of the American Medical Association, DOI&colon 10.1001/jama.2015.13134


Explainer: How PCR works

A researcher at the National Cancer Institute adds materials to a test tube before copying some segment of DNA using the polymerase chain reaction, or PCR.

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January 30, 2017 at 7:09 am

Copy machines are handy in schools and offices because they can quickly duplicate pages from all types of sources. Similarly, biologists often need to make many, many copies of genetic material. They use a technology called PCR. It’s short for polymerase (Puh-LIM-er-ase) chain reaction. Within just a few hours, this process can make a billion or more copies.

The process starts with DNA, or deoxyribonucleic (Dee-OX-ee-ry-boh-nu-KLAY-ik) acid. It’s a playbook with instructions that tell each living cell what to do.

To understand how PCR works, it helps to understand the structure of DNA and its building blocks.

Each DNA molecule is shaped like a twisted ladder. Each rung of that ladder is made of two linked chemicals, known as nucleotides. Scientists tend to refer to each nucleotide as A, T, C or G. These letters stand for adenine (AD-uh-neen), thymine (THY-meen), cytosine (CY-toh-zeen) and guanine (GUAH-neen).

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One end of each nucleotide holds onto an outside strand — or edge — of the ladder. The other end of the nucleotide will pair up with a nucleotide holding onto the ladder’s other outside strand. The nucleotides are picky about who they link up with. All A’s, for instance, must pair with T’s. C’s will pair only with G’s. Each letter is therefore the complement of the other in its pair. Cells use this picky pairing pattern to make an exact copy of their DNA when they divide and reproduce.

That pattern also helps biologists copy DNA in the lab. And they might want to copy only part of the DNA in a sample. Scientists can tailor which bit they copy using PCR. Here’s how they do it.

Story continues below image.

An artist’s depiction of part of a DNA molecule. The nucleotides show up as colored half-rungs of the twisted-ladder, with A in green, T in blue, C in orange and G in yellow. Each nucleotide attaches to an outside strand of the molecule, and to its complement nucleotide. As a DNA molecule gets ready to reproduce, it splits down the middle of the ladder, with each nucleotide letting go of its complement. colematt / iStockphoto

Heat, cool and repeat

Step one: Insert DNA into a test tube. Add in short strings of other nucleotides, known as primers. Scientists choose a primer that will pair with — or complement — a specific series of nucleotides at the end of the DNA bit they want to find and copy. For instance, a string of A, T and C will only pair with a T, C and G. Each such series of nucleotides is known as a genetic sequence. Scientists also throw into the mix a few other ingredients, including single nucleotides, the building blocks needed to make more DNA.

Now place the test tube into a machine that heats and cools these test tubes over and over again.

A normal piece of DNA is described as double-stranded. But before it prepares to reproduce itself, DNA will split down the middle of the ladder. Now the rungs separate in half, with each nucleotide remaining with its adjacent strand. This is known as single-stranded DNA.

With PCR technology, after the sample cools down again, the primers seek out and bind to the sequences they complement. Single nucleotides in the mix then pair up with the rest of the open nucleotides along the targeted single strand portion of DNA. In this way, each original bit of target DNA becomes two new, identical ones.

Each time the heating and cooling cycle repeats, it’s like pressing “start” on a copy machine. The primers and extra nucleotides duplicate the selected portion of DNA again. PCR’s heating and cooling cycles repeat over and over and over.

With each cycle, the number of target DNA pieces doubles. In just a few hours, there can be a billion or more copies.

PCR acts like a genetic microphone

This researcher at the National Cancer Institute is preparing a rack of genetic samples and primers for the polymerase chain reaction, or PCR. Daniel Sone, NCI

Scientists describe this copying as amplifying the DNA. And that’s the real value of PCR. Think about walking into a crowded cafeteria. Your friend is sitting somewhere inside. If your friend saw you and said your name, you might not hear it above all the other students talking. But suppose the room had a microphone and sound system. If your friend announced your name over the mike, that voice would drown out all the rest. That’s because the sound system would have amplified your friend’s voice.

Similarly, after PCR has copied a selected bit of DNA in some sample, those over-represented copies will drown out everything else. The process will have copied the target snippets of DNA so many times that soon they vastly outnumber all of the rest of the genetic material. It’s like trying to pick out just the red M&Ms from a big bin. Picking out individual candies would take a really long time. But suppose you could double the red M&Ms over and over. Eventually, nearly every handful would contain just what you wanted.

Scientists use PCR for many types of work. For instance, scientists might want to see whether someone has a certain gene variation, or mutation. That altered gene might signal the person has a higher risk for a certain disease. PCR also can be used to amplify tiny bits of DNA from a crime scene. That lets forensic scientists work with the evidence and match it to other samples, such as DNA from a suspect. Environmental scientists might use PCR to see if any of the DNA taken from a river matches a particular species of fish. And the list goes on.

All in all, PCR is a really handy tool for genetics work. And who knows? Maybe one day you’ll find yet another use for this DNA copying machine.

Power Words

amplify To increase in number, volume or other measure of responsiveness.

cell The smallest structural and functional unit of an organism. Typically too small to see with the naked eye, it consists of watery fluid surrounded by a membrane or wall. Animals are made of anywhere from thousands to trillions of cells, depending on their size. Some organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.

chemical A substance formed from two or more atoms that unite (become bonded together) in a fixed proportion and structure. For example, water is a chemical made of two hydrogen atoms bonded to one oxygen atom. Its chemical symbol is H2O. Chemical can also be an adjective that describes properties of materials that are the result of various reactions between different compounds.

complement To match or fit with something else to complete it. In genetics, a series of nucleotides that pairs exactly with another sequence of DNA or RNA is called the complement of that sequence.

DNA (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.

DNA sequencing The process of determining the exact order of the paired building blocks — called nucleotides — that form each rung of a ladder-like strand of DNA. There are only four nucleotides: adenine, cytosine, guanine and thymine (which are abbreviated A, C, G and T). And adenine always pairs up with thymine cytosine always pairs with guanine.

environmental science The study of ecosystems to help identify environmental problems and possible solutions. Environmental science can bring together many fields including physics, chemistry, biology and oceanography to understand how ecosystems function and how humans can coexist with them in harmony. People who work in this field are known as environmental scientists.

forensics The use of science and technology to investigate and solve crimes.

gene (adj. genetic) A segment of DNA that codes, or holds instructions, for producing a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.

genetic sequence A string of DNA bases, or nucleotides, that provide instructions for building molecules in a cell. They are represented by the letters A,C,T and G.

mutation Some change that occurs to a gene in an organism’s DNA. Some mutations occur naturally. Others can be triggered by outside factors, such as pollution, radiation, medicines or something in the diet. A gene with this change is described as a mutant.

nucleotides The four chemicals that, like rungs on a ladder, link up the two strands that make up DNA. They are: A (adenine), T (thymine), C (cytosine) and G (guanine). A links with T, and C links with G, to form DNA. In RNA, uracil takes the place of thymine.

polymerase chain reaction (PCR) A biochemical process that repeatedly copies a particular sequence of DNA. A related, but somewhat different technique, copies genes expressed by the DNA in a cell. This technique is called reverse transcriptase PCR. Like regular PCR, it copies genetic material so that other techniques can identify aspects of the genes or match them to known genes.

primer (in genetics) A sequence of nucleotides that is the complement for a short part of a strand of DNA that someone wants to find. In the polymerase chain reaction, or PCR, the primer finds the end of a targeted DNA length and starts the process of copying it over and over.

species A group of similar organisms capable of producing offspring that can survive and reproduce.

variant A version of something that may come in different forms. (in genetics) A gene having a slight mutation that may have left its host species somewhat better adapted for its environment.

About Kathiann Kowalski

Kathiann Kowalski reports on all sorts of cutting-edge science. Previously, she practiced law with a large firm. Kathi enjoys hiking, sewing and reading. She also enjoys travel, especially family adventures and beach trips.

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Gene copy number - how to find how many? (Jun/17/2008 )

Hello I have a doubt about gene copy number. How or where do I find out how many copies of a given gene are in the genome?

Even better, is beta-actin a single copy gene in mouse?

hi,
you could blast the beta-actin sequence against the whole mouse genome and see how many times you find it. about the second question i have no idea.

thanks toejam, should definitely have thought of that myself.
will see what I find.

Hi again toejam. So i did the blast, and it comes with about 38 hits, but only one is the exact match, in chromosome 5 (which i knew already). Now my question, does that mean there's 38 copies (polymorphisms or whatever), or that there's only one. sooooo confused.
here's the link to my results in case it helps any. http://blast.ncbi.nlm.nih.gov/Blast.cgi

did you check where your matches are aligning? just to make sure it is not the same region. in the blast results you should also sheck the identity percentage, for some of them might be polymorpisms while others might be just artifacts i think.
to me it would make sense if there's more than one copy since this is a housekeeping gene, in case a copy has a mutation there would be the "backup". also, not because it has many copies it means all of them have to be necesarily active. i hope this makes it clearer.

did you check where your matches are aligning? just to make sure it is not the same region. in the blast results you should also sheck the identity percentage, for some of them might be polymorpisms while others might be just artifacts i think.
to me it would make sense if there's more than one copy since this is a housekeeping gene, in case a copy has a mutation there would be the "backup". also, not because it has many copies it means all of them have to be necesarily active. i hope this makes it clearer.

Thanks tj, I'll definitely have a closer look. I also expect b-actin to have more than one copy, but really cant get my head round it on how to find out.

why don't you perform a southern blot? the probe should bind to all the copies of b-actin in the genome.

I agree with TJ.
In silico queries are a good starting point, but it's necessary to achieve experimental proofs performing Southern analysis.
I'm afriad, that no referee is going to agree that your gene is in single copy just on the base of blast searches.

I'm taking for granted that this b-actin gene has not been studied that much in the organism you are working on. If you can cite literature where someone already demostrated the conserved copy number of this gene, then things may be different.

you might find this interesting. looks like the functional b-actin gene in mouse is single copy after all.

Hello
why dont you try southern blotting.
It is an easy way to find how many
copies you have in the genome


How many copies of a gene? - Biology

1. DNA and RNA are polynucleotides, made up of long chains of nucleotides.

2. A nucleotide contains a pentose sugar, a phosphate group and a nitrogen-containing base. In RNA the sugar is ribose, and in DNA it is deoxyribose.

3. A DNA molecule consists of two polynucleotide chains, linked by hydrogen bonds between bases.
There are four bases – adenine always pairs with thymine, and cytosine with guanine. RNA, which
comes in several diff erent forms, has only one polynucleotide chain, although this may be twisted
back on itself, as in tRNA. In RNA, the base thymine is replaced by uracil.

4. DNA molecules replicate during interphase by semi-conservative replication. Th e hydrogen bonds
between the bases break, allowing free nucleotides to fall into position opposite their complementary
ones on each strand of the original DNA molecule. Adjacent nucleotides are then linked, through their phosphates and sugars, to form new strands. Two complete new molecules are thus formed from one old one, each new molecule containing one old strand and one new.

5. The sequence of nucleotide bases on a DNA molecule codes for the sequence of amino acids in a polypeptide. Each amino acid is coded for by three bases. A length of DNA coding for just one polypeptide is a gene.

6. A change in the nucleotide sequence of DNA is a mutation, producing a new allele of the gene.

7. The DNA sequences for the HbA (normal) and HbS (sickle cell) alleles of the gene for the β-globin
polypeptide diff er by only one base. Th e triplet CTT in HbA is replaced by CAT in HbS, changing
the amino acid glutamic acid to valine. This single diff erence in the polypeptide results in sickle cell
anaemia in individuals with two HbS alleles.

8. During protein synthesis, a complementary copy of the base sequence on a gene is made, by building a molecule of messenger RNA (mRNA) against one DNA strand. Th is stage is called transcription.

9. After transcription, the next stage is called translation. In this stage the mRNA moves to a ribosome in the cytoplasm. Transfer RNA (tRNA) molecules with complementary triplets of bases temporarily pair with base triplets on the mRNA, bringing appropriate amino acids. As two amino acids are held side by side, a peptide bond forms between them. The ribosome moves along the mRNA molecule, so that appropriate amino acids are gradually linked together, following the sequence laid down by the base sequence on the mRNA.

1 What is found in both DNA and messenger RNA (mRNA)?

A deoxyribose
B double helix
C sugar–phosphate chain
D thymine

2 In DNA extracted from rat bone marrow, 29% of the bases were found to be adenine.

What was the proportion of cytosine?

3 The diagram shows part of a nucleic acid.

A a base pair
B a nucleotide
C a polynucleotide
D a purine

4 Which statement about base pairing is not correct?

A Adenine can pair with either thymine or uracil.
B Thymine pairs only with adenine.
C Cytosine makes two hydrogen bonds with guanine.
D Purine bases only pair with pyrimidine bases.

5 Which statements describe RNA?

1 composed of phosphate, deoxyribose, adenine, cytosine, guanine and thymine
2 backbone is a ribose–phosphate chain
3 each molecule consists of two chains
4 consists of a chain of nucleotides linked through phosphates and sugars

A 1, 2 and 3 only
B 1 and 2 only
C 2 and 3 only
D 2 and 4 only

6 The diagram shows part of a DNA molecule before replication.

Which diagram shows a daughter molecule?

7 A single base substitution in the gene coding for the β-globin polypeptide results in a change in the amino acid sequence.

Which statements describe what happens when haemoglobin containing polypeptides coded from the sickle cell allele, HbS, is not combined with oxygen?

1 The haemoglobin molecules are much less soluble.
2 The haemoglobin molecules form long fibres.
3 Red cells become distorted in shape.
4 Red cells become stuck in small capillaries.

A 1, 2, 3 and 4
B 1, 2 and 3 only
C 2 and 4 only
D 3 and 4 only

8 What is synthesised during transcription?

A DNA
B mRNA
C tRNA
D polypeptide

9 A mutation takes place in a DNA triplet coding for the amino acid tyrosine. The triplet ATA is changed to ATG.

The mRNA codons for tyrosine are UAU and UAC.

The mRNA codons signalling ‘stop’ are UAA, UAG and UGA.

What is the effect of the mutation?

A The mutated triplet codes for ‘stop’.
B The mutated triplet codes for a different amino acid.
C The mutated triplet is meaningless.
D The mutated triplet still codes for tyrosine.

10 In most organisms, the mRNA codons signalling ‘stop’ in translation are UAA, UAG and UGA. In the microorganism Methanosarcina barkeri, UAG codes for an amino acid.
Which tRNA carrying an amino acid will be found in M. barkeri but not in most organisms?

Answers for Multiple - choice Test

1 C
2 D
3 B
4 C
5 D
6 B
7 A
8 B
9 D
10 C

End-of-chapter questions

1. What can be found in both DNA and messenger RNA (mRNA)?

A double helix structure
B sugar-phosphate chain
C ribose
D thymine

2. Which statement about base pairing in nucleic acids is not correct?

A Adenine can pair with either thymine or uracil.
B Guanine only pairs with cytosine.
C Thymine can pair with either adenine or uracil.
D Uracil only pairs with adenine.

3. How many different arrangements of four bases into triplets can be made?

A 3+4
B 3 x 4
C 3 4

4. Look at the structures of nucleotides in Figure below:

Draw a nucleotide that could be found:
a in either DNA or RNA
b only in DNA
c only in RNA.

5. Distinguish berween a nucleotide and a nucleic acid.

6. Copy the drawing and annotate it to explain the replication of DNA.

7. Use Appendix 1 to find the sequence of amino acids that is coded by the following length of messenger RNA (mRNA):

The table shows all the possible triplets of bases in a DNA molecule and what each codes for. The three-letter abbreviation for each amino acid is, in most cases, the first three letters of its full name - see Appendix 2.

8. The table shows all the messenger RNA (mRNA) codons for the amino acid leucine.
Copy the table and write in, for each codon, the transfer RNA (tRNA) anticodon that would bind with it and the DNA triplet from which it was transcribed.


How to determine certain gene copy number? - (Jun/22/2009 )

I kow southern blotting is one of the techniques capable to determine the gene copy number but how? I am new for this technique. Do I need to set up a control to determine the interested gene copy number? Thanks in advance for your help!

zx0819 on Jun 22 2009, 01ᛣ AM said:

Copy number can be determined from a Southern pretty easily. Homologs can be detected too. And if you're working with transgenics, the southern will also identify multiple insertion sites in an animal.

Copy number is calculated by comparing the signal intensity of your unknown copy number to your known copy number. Your known will typically be the transgene in plasmid form, and it is blotted using picograms equal to 1 copy, 10 copies, 50 copies, etc.

eldon on Jun 23 2009, 08ᛚ AM said:

zx0819 on Jun 22 2009, 01ᛣ AM said:

Copy number can be determined from a Southern pretty easily. Homologs can be detected too. And if you're working with transgenics, the southern will also identify multiple insertion sites in an animal.

Copy number is calculated by comparing the signal intensity of your unknown copy number to your known copy number. Your known will typically be the transgene in plasmid form, and it is blotted using picograms equal to 1 copy, 10 copies, 50 copies, etc.

zx0819 on Jun 22 2009, 06ᚴ PM said:

Same procedure applies. Have you cloned the cDNA or your gene? This will be your control.

If you know the haploid size of the plants genome, the gene size and a known amount of gDNA you can assess gene copy number.

Here is an example. just substitute your plant numbers into the haploid genome size:

Assumption: the Haploid content of a mammalian genome is 3 X 10^9 bp
Assumption: you have 2 micrograms of gDNA available

You want to determine the amount of your gene to assay by Southern. Since transgenic founder mice are hemizygous:

mass of transgene/1 ug of gDNA = N bp transgene DNA/3 X 10^9 bp gDNA


Now, for a 5,480 bp gene/transgene..re-arrange the equation to:

mass of transgene DNA = 3.66 picograms

Thus, to prepare a 1 copy standard: use 3.66 pg of gene DNA and compare signal intensity to 2 microgram of gDNA
0.1 copy 0.366 pg
1 copy 3.66 pg
10 copy 36.6 pg
50 copy 183 pg
100 copy 366 pg


Gene Drives

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Since the 1940s, researchers have thought of using gene drives to eradicate populations of pests and disease vectors, and to reduce or eliminate invasive species that wreak havoc on natural ecosystems. The idea of a gene drive stems from nature itself, where in sexually reproducing organisms a certain version of a gene is preferentially passed on to the next generation to over time become the dominant one in a population. Deployed willfully in human intervention efforts, a propagated dominant gene modification could, for example, by biassing the production of one sex over the other over many generations, force a deleterious disease vector to decline and lose its dangerous potential.

Wyss Institute researchers have leveraged the versatile RNA-guided genome editing tool CRISPR-Cas9, which they previously helped develop, as a part of synthetic DNA-modifying gene drives that in principle can swipe across large populations, potentially changing gender ratios or other biological traits in the process.

Our proposal represents a potentially powerful ecosystem management tool for global sustainability, but one that carries with it new concerns, as with any emerging technology.

These new types of synthetic gene drives could alter insect populations that spread diseases such as malaria, schistosomiasis, dengue and Lyme, protect at-risk ecosystems from the spread of destructive invasive species, or improve sustainability in agriculture by reducing the need for and toxicity of pesticides and herbicides. For more detailed information see our Frequently Asked Questions page.

On another venue, Wyss Institute researchers have also engineered gene drives that can be used to investigate pathogenic fungi and to identify new drug resistance mechanisms. A recent study showed, that the technology can be used to fast and efficiently delete both copies of a gene or of pairs of genes of the fungal pathogen Candida albicans, whose genome has been notoriously difficult to manipulate. This approach allowed the systematic analysis of fungal drug resistance and biofilm formation processes and can serve as a blueprint for also manipulating other pathogenic fungi.

In parallel to engineering gene drives that work effectively in different scenarios, the Wyss team has developed safeguarding methods that minimize potential risks associated with CRISPR-Cas9-based gene drives including unwanted genome editing at other places of the genome, that deploy secondary gene drives that are capable of overwriting the changes introduced by earlier gene drives, or that model the outcomes of drive release in nature.

In addition, because gene drive technology requires new ways to evaluate and regulate their potential and risks that differ from those put in place for other genetic modification technologies, the Wyss Institute and its leading gene drive researchers have engaged in a public discussion to help pave the way for these investigational tools and measures and to help define the essential ethical standards.

The environmental gene drive project initiated at the Wyss Institute is currently being continued by Kevin Esvelt at the Massachusetts Institute of Technology. Gene drives as tools to investigate drug resistance exhibited by pathogenic fungi such as C. albicans are further exploited and developed at the Wyss Institute.