Gene? What is that? DNA or Chromosome?

Gene? What is that? DNA or Chromosome?

Gene(Greek genos "birth, race”) is basic unit of heredity found in the cells of all living organisms, from bacteria to humans. Genes determine the physical characteristics that an organism inherits, such as the shape of a tree’s leaf, the markings on a cat’s fur, and the color of a human hair etc. That is the gene which is responsible for right handed and left handed character of individuals.

Genes are composed of segments of deoxyribonucleic acid (DNA), a molecule that forms the long, thread like structures called chromosomes (if you are interested, please notify me, I’ll write you about composition, structure and function of DNA). The information encoded within the DNA structure of a gene directs the manufacture of proteins, molecular workhorses that carry out all life-supporting activities within a cell.

Chromosomes within a cell occur in matched pairs. These can be seen on dividing cells under light microscope. Each chromosome contains many genes, and each gene is located at a particular site on the chromosome, known as the locus. Like chromosomes, genes typically occur in pairs. A gene found on one chromosome in a pair usually has the same locus as another gene in the other chromosome of the pair, and these two genes are called alleles. Alleles are alternate forms of the same gene. For example, a pea plant has one gene that determines height, but that gene appears in more than one form—the gene that produces a short plant is an allele of the gene that produces a tall plant. The behavior of alleles and how they influence inherited traits follow predictable patterns. Austrian monk Gregor Mendel first identified these patterns in the 1860s.

In organisms that use sexual reproduction, offspring inherit one-half of their genes from each parent and then mix the two sets of genes together. This produces new combinations of genes, so that each individual is unique but still possesses the same genes as its parents. As a result, sexual reproduction ensures that the basic characteristics of a particular species remain largely the same for generations. However, mutations, or alterations in DNA, occur constantly. They create variations in the genes that are inherited. Some mutations may be neutral, or silent, and do not affect the function of a protein. Occasionally a mutation may benefit or harm an organism and over the course of evolutionary time, these mutations serve the crucial role of providing organisms with previously nonexistent proteins. In this way, mutations are a driving force behind genetic diversity and the rise of new or more competitive species that are better able to adapt to changes, such as climate variations, depletion of food sources, or the emergence of new types of disease.

Geneticists are scientists who study the function and behavior of genes. Since the 1970s geneticists have devised techniques, cumulatively known as genetic engineering, to alter or manipulate the DNA structure within genes. These techniques enable scientists to introduce one or more genes from one organism into a second organism. The second organism incorporates the new DNA into its own genetic material, thereby altering its own genetic characteristics by changing the types of proteins it can produce. In humans these techniques form the basis of gene therapy, a group of experimental procedures in which scientists try to substitute one or more healthy genes for defective ones in order to eliminate symptoms of disease.

Genetic engineering techniques have also enabled scientists to determine the chromosomal location and DNA structure of all the genes found within a variety of organisms. In April 2003 the Human Genome Project, a publicly funded syndicate of academic scientists from around the world, identified the chromosomal locations and structure of the estimated 20,000 to 25,000 genes found within human cells. The genetic makeup of other organisms has also been identified, including that of the bacterium Escherichia coli, the yeast Saccharomyces cerevisiae, the roundworm Caenorhabditis elegans, and the fruit fly Drosophila melanogaster. Scientists hope to use this genetic information to develop life-saving drugs for a variety of diseases, to improve agricultural crop yields, and to learn more about plant and animal physiology and evolutionary history.

Here are some pictures, these might helpful to understand undoubtedly.

1.Nucleotides,
2..DNA
3.Genes
4.Chromosome
5.Cell
6.Body

DNA Translation

DNA Translation

What is it?
DNA translation converts the mRNA sequence into amino acids that form protiens. This creates most of the protiens that make up cells. It creates the last step from DNA to a protien.
Wher does it occur?
Translation occurs outside the nucleas also known as in the cytoplasm. Eventhough this is true one article suggests that translation can occur inside the nucleas. Click here to see.
When does it occur?
Translation occurs right after transcription is done and the mRNA is transported out of the nucleas.
How does it Happen?
During DNA translation, messenger RNA, transfer RNA, and ribosomes work together to produce proteins. A ribosomal subunit attaches to a mRNA molecule. The Transfer-RNA transports the amino acid from the cytoplasm to the ribosome. The start codon attaches to Met this starts making the protein.

Genetic Variations - Mutations

Genetic Variations - Mutations

This is a complicated topic and I want to keep a record of what I learnt in school (and various other programs, materials) and also from related research. By writing it down I believe I understand the concepts better and additionally it allows me to refresh the concepts quickly.

This is sixth of my series on the quest for "Theory of Convergence" and second topic on genetics. This topic speaks to convergence of multi-discipline such as - biology, life, economics, environmental science, human studies, nature, design thinking, physics, chemistry, etc.
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As you may recall, from my earlier blog (Dec 31st 2010)  - "Basics of genetics" I had introduced the topic of Genetic mutations (Please read that topic again as a refresher). Well here we are getting back to the grind after a long hiatus from this topic. Unlike my other blogs, mutation topic will mostly be academic in nature.
Genetic variation is fundamental to evolutionary change. There are 3 types of genetic variations - Mutations, gene flow and sex.

    We will be discussing mutation in greater detail below,
    Gene flow is movement of genes from one population to other,
    Sex introduces new gene combinations in to population.

Gene flow occurs due to an event such as pollen dust migrating through the air to another set of plants or you can think of gene flow as people migrating from one part of the world to another. With out gene flow - there is less evolution, therefore less diversity. Less diversity means less innovation/creation. Gene flow has been the center of USA's innovative capabilities. USA's population was created on the basis of acceptance of people of all color, creed, etc. This has turned out to be the greatest asset of USA and has resulted in the land of great creativity & innovation. Innovation is not limited to gadgets such as iPads and iPhones, but creativity is extended to all fields including social, legal, arts, science, public policies, etc.  That fits right in to the theory of convergence. Isn't this getting exciting !!! Well I am getting excited and possibly digressing from the subject a bit. Back on topic.....
Sex is an important source of genetic variation. Organisms reproduce through sex and parent genes mixes resulting in an offspring that has genes from both the parents. For example, an offspring may inherit blue eyes from mom and big nose from dad. This shuffling of genetic variation is important for evolution but as you may imagine it can render some characteristics obsolete.

Mutation
Mutation is a change in DNA, the hereditary material of life. As noted in earlier blog, DNA affects how an organism looks and functions. Mutations of DNA are widely believed to be random, at this time. Some day science may prove it otherwise, until then we will stick to what we know so far. The mutations in DNA is the result of such diversity of life on earth. Mutations over 4 billion years have created fantastic creatures such as parasites, elephants, lions, apple, jelly fish, octopus, shark, redwood trees, apples, etc. There you go - that is 4 billion years of experimental results for human to analyze.

In fact I believe mutations are a classic example that humans can use in all aspects of our lives - Note this important comment for future - We will discuss this detail in later topics. Mutations and exaptations are marvels of natures innovation. I guess it is now time to explain exaptation (courtesy - http://evolution.berkeley.edu/evosite/evo101/IIIE5cExaptations.shtml)

    Exaptation—a feature that performs a function but that was not produced by natural selection for its current use. Perhaps the feature was produced by natural selection for a function other than the one it currently performs and was then co-opted for its current function. For example, feathers might have originally arisen in the context of selection for insulation, and only later were they co-opted for flight. In this case, the general form of feathers is an adaptation for insulation and an exaptation for flight.

Darwin never knew this, he understood that species adapt and change, but he did not know understand the actual process. Thanks to the discovery of DNA we now know how evolution works.

First of all it is important to note that not all mutations matter to evolution. Some mutations are not passed on to the off-spring.  (courtesy -  http://evolution.berkeley.edu/evolibrary/
For example, the golden color on half of this Red, Delicious, apple was caused by a somatic mutation. The seeds of this apple do not carry the mutation.
The only mutations that matter to large-scale evolution are those that can be passed on to offspring. These occur in reproductive cells like eggs and sperm.

Some mutations are positive and some are negative - that is the beauty of nature - Nature is experimenting all the time. For example some mutations cause an organism to develop cancer and some may cause an organism to develop legs instead of fins (which is what is believed to have been the first land animal).
In early 2000's scientists were studying stickle back fish in a lake in British Columbia (West Canada). They were particularly interested in how they had evolved. Ocean stickle backs had spikes & the the fresh water ones did not have any spikes. This was a mystery they intended to solve. They noticed that the lake stickle back fish had a trace of bones ,one small and one big, where the spike would have been there. On further study (which we will talk about, later under the topic "Epigenome") they concluded that a particular gene had mutated.

Types of mutations

There are many ways a DNA can change. As you may know in human body - DNA is made of base pairs A, C, G & T. There are six billion base pairs in human genome.  These are being constantly copied and replicated during a human's life time. Hence mathematically the possibility of error is large. However the nature has been kind to life and such mutations (or errors if you want to call them that) are rare.

Some of the main types of mutation are substitution, insertion and deletion. Substitution occurs when one letter in DNA is substituted with another (for example A is replaced by G - may occur during copying). Insertion occurs when extra base pairs are inserted in to the chain. Deletion is just that deletions - deletion of base pairs.

Causes of mutations

Mutations occur mostly when cells divide and DNA makes a copy of itself. Sometime the DNA fails to copy and there is small difference in DNA sequence. We are talking really small changes here. Human genome has 6 billion base pairs, and any base pair letter can change during copying.

Another main reason for mutation is the external factors such as environment. For example exposure to chemicals such as DDT, can cause DNA to breakdown and when cells repair themselves it might not be perfect. I have friends who were running behind trucks (when they were kids) that was spewing DDT to kill mosquitoes in cities - Sad isn't it - At that time we did not know the ill effects of DDT. Thanks to genetic research, DDT is now banned all over the world.
From: http://evolution.berkeley.edu/evolibrary/article/0_0_0/mutations_04Following cell division, the copied DNA is imperfect

Effects of mutations
Mutations usually has negative connotation. However mutuations have both positive and negative effects.
From http://evolution.berkeley.edu/evolibrary/article/0_0_0/mutations_05
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Some regions of DNA control other genes, determining when and where other genes are turned "on". Mutations in these parts of the genome can substantially change the way the organism is built. The difference between a mutation to a "control gene" and a mutation to a less powerful gene is a bit like the difference between whispering an instruction to the trumpet player in an orchestra versus whispering it to the orchestra's conductor. The impact of changing the conductor's behavior is much bigger and more coordinated than changing the behavior of an individual orchestra member. Similarly, a mutation in a gene "conductor" can cause a cascade of effects in the behavior of genes under its control.---------------------

Let us know talk about some negative effects

In 1910, Herrick (hope I spelled it right) provides the first description of sickle cell anemia - when he reports that blood smear of a student at Chicago college had pear shaped and elongated forms. Since then several scientists have researched this disease. We now know that this disease is caused by a mutated version of the gene that helps make hemoglobin — a protein that carries oxygen in red blood cells. When red blood cells carrying mutant hemoglobin is deprived of oxygen the red blood cells becomes sickle shaped. These sickle shapes can restrict the flow of blood in the body, causing death. Pittsburgh Steelers (Foot ball team) safety (whose name I do not remember) has sickle cell disease and when he visits Denver Broncos (Denver's foot ball team) he does not play. Due to Denver's elevation ( one mile above sea level) there is less oxygen to go around and this can cause his red blood cells to sickle up. Although he is depressed about not playing, he is doing the smart thing.
Here is another weird fact: Scientists have been studying flies carrying Hox mutations (We will leave Hox mutation alone for now - let us just say it is a type of gene) sprout legs on their foreheads instead of antennae







Now on to some positive effects:

Courtesy:www.tiktaalik.us


Scientist, Neil Shubin has devoted his life to finding the transitional forms. Transitional form is the evolution by which a species transforms itself to a completely different form providing a platform for evolutionary change. (Sort of like conductor gene changes). He started his research on Elsmers island (a remote island near north pole). He set up camps there and started digging through the fossil records. The conditions were harsh - the island was accessible for only a few months of the year. He made 4 trips to the island and was almost giving up on his quest mainly due to high cost of conducting the research. On his last trip, he got lucky - he found a snout of a fish on a rock that was 375 million years old. It was the transitional form he was looking for - The first land fish which had limbs that it used to push itself around - It is now called "Tectalic". it had an arm like fin which is the basic bone structure of every land animal today. Tectalic had evolved to survive from big fishes. Well if it were not for Tectalic we humans would not be here today. Such is the power of evolution - rather mutation.

Mutation is such an important topic and we will revisit this topic through out our Genetic journey blogs.