Alleles and Genes (1 Viewer)

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Hello,
I am trying to get some clarity on the concept of allele. Please let me know if my concepts are correct:
  • Each human cell (almost, not all cells) has molecules of DNA, an acid, inside their nuclei. The DNA is 46 structures called chromosomes.
  • On each chromosome, DNA is arranged as two spiral and intertwined strands.
  • A small section of DNA strand is called a gene. Each gene is responsible for how a specific physical trait looks like (eye color, height, etc.). That is called phenotype.
  • For a certain specific physical trait, there are always and only two genes in a every human being that are specialized and determine that physical trait. In some cases, the gene for a particular trait comes in many variants, called alleles, in some cases only in two. Regardless, every human being always has only two alleles, i.e. two different types of a particular gene, correct?
  • Let's consider two different individuals and the gene that determines their hair color. Is that specific gene located in the same place (locus) on the DNA strand for both individuals?
  • What makes two genes similar so they are responsible for determining the same physical trait but different since they are different alleles? Is a certain gene responsible for determining a specific trait just because of its specific location on the DNA strand? Let's use this analogy: the genome is like a book. The chapters in the book are the chromosomes. Genes are the sentences inside the chapter. The words in the sentence are called codons. Each word (codon) is 3 letter long. The letters in this alphabet are just 4: A,C,G,T. Does that mean that the position (locus) of a sentence (gene) in the chapter (chromosome) attributes a specific task (determines a specific physical trait) to that sentence even if the words in that sentence are different (codons, allele)?
Thanks for any help!
 

jim mcnamara

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Please note these are direct answers without a lot of terminology, so they will not get you far unless your read the attached links. So the answers are not the best possible.

You have partially correct views of this subject. PLEASE read the links.

Each human cell (almost, not all cells) has molecules of DNA, an acid, inside their nuclei.
The DNA is 46 structures called chromosomes.
Normal mammal and human somatic cells have an even number of chromosomes. So they come in pairs. You can think of chromosomes like a special
package (like a suitcase) for internal handling of genetic blobs of code. Chromosomes have distinct parts that you can see during mitosis (when cells are dividing).

Chromosomes are primarily made of chromatin - protein, RNA, and DNA. They have other "sections" - e.g., arm, telomere, centromere.

http://www.biologydiscussion.com/chromosomes/6-main-parts-of-a-chromosome/35239

On each chromosome, DNA is arranged as two spiral and intertwined strands.
Sort of. DNA is extensively folded up (DNA Packaging) when chromosomes are visible. . So it is easy to handle during mitosis (or meiosis) when chromosomes are evident. Normally the DNA is unpacked. (See the suitcase analogy above)

If all of your DNA in all of your cells were placed into a loooong single strand it would reach from Earth to any of the inner planets. And beyond.
When your cells are doing most of their activities the DNA is unpacked (not arranged into chromosomes) and is generally inside the nucleus,
See:
https://www.nature.com/scitable/topicpage/dna-packaging-nucleosomes-and-chromatin-310

A small section of DNA strand is called a gene. Each gene is responsible for how a specific physical trait looks like (eye color,
height, etc.). That is called phenotype. For a certain specific physical trait, there are always and only two genes in a every human being
that are specialized and determine that physical trait. In some cases, the gene for a particular trait comes in many variants, called
alleles, in some cases only in two. Regardless, every human being always has only two alleles, i.e. two different types of a particular
gene, correct?
In general, no.
Allele - member of a single gene "family". For one trait there can be several sets of alleles, maybe all different, for a single trait.
Alleles are in a specific locus (place) on a specific chromosome. Human chromosomes have rather dull names, #1, #2,...#22, X, and Y
Multiple alleles for one trait can be found at separate places, on different chromosomes.

So humans do not always have only two alleles for a given trait. Some traits, yes. All traits, no.

Let's consider two different individuals and the gene that determines their hair color. Is that specific gene located in the same place (locus) on the DNA strand for both individuals?
If the gene only exists on one chromosome at one single locus, every human has that one gene in the same place.
In some cases a gene can be disabled (histones and methyl groups on the strand can do this). Sometimes having both alleles identical increases the expression of the gene.

This last question was the primary motivation for a colossal effort - The Human Genome Project, Mapping all of the DNA in a human cell. Turns out to be rather complex. For example not all DNA is active, some seems never to be used for anything. This could be ignorance on our part.
Terms you can look up - exon, intron.
https://en.wikipedia.org/wiki/Exon

It also deals with your last question: decoding DNA. DNA "remembers" how to make makes proteins - these proteins are mostly enzymes that make the actual functioning molecule or assists in a biochemical pathway. If you know Krebs Cycle, that is a biological pathway.
 

Ygggdrasil

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The human genome consists of 23 pairs of chromosomes (for a total of 46 chromosomes). Each chromosome is present in two copies, one inherited from the father and one inherited from the mother. Thus, each gene is also present in two copies. Different variants of a gene are called alleles. Thus, each individual has two alleles of every gene. These two alleles can be the same variant or different variants. The two alleles are able to influence the same trait because they are two copies of the same gene that encode the same protein within the cell.

It is important to note that each trait is not necessarily controlled by one gene and one gene does not necessarily control only one trait. Traits that are controlled by a single gene are called Mendelian traits (because they obey Mendel's laws of inheritance), and most introductory genetics courses focus on these traits because they are easiest to understand. There are many examples of Mendelian traits, including a variety of genetic diseases like cystic fibrosis, color blindness or sickle cell anemia. However, other traits, referred to as complex (or polygenic) traits, are influenced by a variety of genes in addition to the interactions of these genes with the environment. Examples of complex genes include height, intelligence and skin color. Efforts to identify the genes that influence these complex traits find many thousands of genes that each make a small contribution to the trait. Some geneticists have even made the argument that many complex traits are influenced by almost every gene in the body (https://www.physicsforums.com/threads/omnigenetic-model-for-complex-traits.922051/).

Similarly, there are also many genes that influence many traits. This can occur, for example, when the gene has different functions in different parts of the body. Situations where one gene affects many, seemingly unrelated traits is known as pleiotropy (https://www.nature.com/scitable/topicpage/pleiotropy-one-gene-can-affect-multiple-traits-569).
 
787
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Allele - member of a single gene "family". For one trait there can be several sets of alleles, maybe all different, for a single trait.
Alleles are in a specific locus (place) on a specific chromosome. Human chromosomes have rather dull names, #1, #2,...#22, X, and Y
Multiple alleles for one trait can be found at separate places, on different chromosomes.
Thanks jim. What I means is that some genes surely have multiple alleles and a physical trait can be determined by multiple genes...However, I thought I read that a human being receives only two specific alleles for a specific gene, among the several possible alleles. One allele comes from the mother and one from the father.
 
787
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Ok, thanks everyone. Let me try to summarize:
  • Genes are specific segments of DNA arranged along a chromosome. Different genes may have different length. The gene is a segment of chromosome, i.e. it includes both intertwined spirals of DNA (not just a single spiral).
  • Humans have 46 chromosomes in each cell and 44 of those chromosomes are called homologous while the last pair represents the sexual chromosomes. Hundreds or thousands of genes can be found on a single chromosome.
  • See figure below: Let's consider the specific chromosome pair #1. The two chromosomes (light orange and dark orange) have the same genes arranged in the same order. These "identical" genes are called identical because they have the same position on both chromosome and their base sequence (A,C,G,T) can be exactly the same or "about the same...The example below shows how allele A and allele B are (slightly) different versions of the same gene: the two sequences of bases A, C, T, G differ only in one base. The two sequence could be exactly the same but don't have to. Also, there could be many many different slightly different versions of these two sequences. However, as said previously, every human being gets one chromosome from the father and one chromosome from the mother so we all get just two alleles (identical or not) for the same gene.
Screen Shot 2019-03-09 at 7.44.31 PM.png


Thanks again.
 

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Ryan_m_b

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It's also important to note that the definition of a gene is not a sequence of DNA that codes for a physical trait. Many phenotypical traits aren't coded in a single gene, they are the emergent property of many genes acting together. There is no gene for having five fingers for example, signalling molecules called "morphogens" (which some genes code for) allow individual cells to adjust their behaviour based on where they are in relation to others.

Genes code for RNA which is used to synthesise proteins. So put simply a gene is just a sequence of DNA that codes for a protein. Proteins are biological, molecular machines that are responsible for much of the work that goes on within your cells.
 
787
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Thanks Ryan_m_b

I am glad I finally got these key concepts. In all this discussion about inheritance, what role does randomness have in all this process of genetic information being passed down to the offspring from the parents? Why aren't we exact copies of our parents? Where does our genetic originality and uniqueness reside? Does that originality derive from some randomness involved in the inheritance process?

Thanks
 

Ygggdrasil

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I am glad I finally got these key concepts. In all this discussion about inheritance, what role does randomness have in all this process of genetic information being passed down to the offspring from the parents? Why aren't we exact copies of our parents? Where does our genetic originality and uniqueness reside? Does that originality derive from some randomness involved in the inheritance process?
There are a few places where randomness and other non-genetic and non-deterministic processes play a role in inheritance and development :
1. We all contain two copies of each gene, but only pass one copy down to our offspring. Which copy gets passed from parent to child is random, so if a couple has multiple children, each child will have a unique combination of genes from their two parents. Based on the observed genetic variation present in human populations, the number of unique human genomes that can result just from the random assortment of these variants might be somewhere around ~10^480,000 (https://www.physicsforums.com/threads/how-many-possible-different-humans-are-there.678782/#post-4310122).

2. Mutations can randomly occur during cell division. This can cause children to have different versions of genes than either of their parents. So, even though all the cells in an individual's body derive from the same embryo and should have DNA identical to that original embryonic cell, random mutations will cause cells across an individual's body to have slight genetic differences: https://www.nytimes.com/2018/05/21/science/mosaicism-dna-genome-cancer.html

3. Some genetic processes occur randomly or stochastically. One example is the process of X-chromosome inactivation. Human females have two X chromosomes while males have only one X chromosome. To deal with this fact, female cells will inactive one X-chromosome during embryonic development. Which X-chromosome gets inactivated and which one stays active is essentially a random choice. If the X-chromosomes contain different alleles, this inactivation process will cause different alleles to be expressed in different cells across a female's body. The classic example of this process is the differently colored patches of fur on a calico cat (https://www.acsh.org/news/2016/07/27/calico-cats-are-a-walking-genetics-lesson). If one were to clone a specific calico cat, the clone would have a different pattern of fur coloration because the X-chromosome inactivation process is random and not genetically determined.

4. Even though identical twins share the exact same DNA, identical twins are not exactly identical. In addition to points #2 and 3, other non-genetic processes can cause differences between identical twins. For example, diet can affect many traits, like height and weight. Another important example is the wiring of neurons in the brain. While the large-scale organization of the brain is likely encoded in our genes, the exact pattern of what neurons connect to each other is not. Rather, the wiring of mammalian brains occurs in an experience-dependent manner. For example, researchers studied how neurons connect to muscles on mice's ears. Despite using nearly genetically identical mice from the same inbred colony, they found major anatomical differences in the wiring of the neurons between individuals and even between the left and right ears of the same individual mouse (https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000032). Thus, many important features of the human body are not determined completely by our genetics.
 
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