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Genetics

Here we go! The amazing cell and DNA size and scale app! website.

What is genetics?

Genetics is the science of studying how living things pass on characteristics (or traits) and its variations in their cell make-up from one generation to the other.

Simply, it is the study of how living things inherit features like eye-colour, nose shape, height and even behavior from their parents.
A scientist who studies genetics is called a geneticist.
{from eSchooltoday, “What is genetics (for kids)” }

Size and scale of cells and DNA

http://learn.genetics.utah.edu/content/cells/scale/

The discovery of DNA nucleotides

Today we know that genetics is based on chemicals: these chemicals transmit information from the parent to the offspring.

Back when Charles Darwin was developing the idea of evolution by natural selection, and when Gregor Mendel was first discovering the rules behind inheritance, they already knew that there must be some factor in the cells which stored information, but they didn’t know what this factor was. It took many teams of scientists many years to discover that this information was stored inside the chromosomes, and that these chromosomes were made of very long strands of DNA; it took many years for people to learn the genetic code.

We can read the history of how this was discovered in many books, and from these websites.

http://www.nobelprize.org/educational/medicine/dna_double_helix/readmore.html

http://www.dnaftb.org/

http://www.dnai.org/timeline/

Here is a cartoon history of how all this was discovered 🙂

//www.pixton.com/embed/xkovsb4g

What are the physical bits in our cells that store information?

DNA nucleotide

A type of chemical found in the nucleus of every cell. There are four types.
DNAbases

Gene

– A group of nucleotides strung together – instructions to build a protein.

Chromosome

– A wicked long string genes, wound up (with proteins to make it wind up neatly) into a big package.

The # of chromosomes in a cell.
The # of genes in a chromosome

Each organism has a characteristic number of chromosomes in a cell.

Humans have 46 chromosomes in almost every cell:

Half are from one’s mother, and half from one’s father.

Image from What's a Genome, courtesy of www.GenomeNews Network.org/J. Craig Venter Institute. http://www.expeditions.udel.edu/extreme08/genomics/

Image from What’s a Genome, courtesy of http://www.GenomeNews Network.org/J. Craig Venter Institute.
http://www.expeditions.udel.edu/extreme08/genomics/

Each chromosome contains many genes, so the total number of genes is huge.

 Image from What's a Genome, courtesy of www.GenomeNews Network.org/J. Craig Venter Institute. http://www.expeditions.udel.edu/extreme08/genomics/

Image from What’s a Genome, courtesy of http://www.GenomeNews Network.org/J. Craig Venter Institute.
http://www.expeditions.udel.edu/extreme08/genomics/

Homologous genes

You have 2 copies of every gene (one from each parent), so you must have 2 copies of every chromosome.
The pair of the mom one and the dad one are called homologous chromosomes

We can figure out where the genes are, on each chromosome

Here is a rough map of some genes, found on homologous chromosomes

Alleles are different versions of the same gene

Now consider: All people have hair…so we all have hair genes. But our hair varies in color, and texture.  So we must have different versions of the hair genes.
We all have eye color – but our eye color varies. So we must have different versions of our eye color genes.

Different versions of the same gene are called alleles.

Realistically, every pair of genes you have is an allele:
Look at one gene from your dad -> the corresponding gene from your mom will have always some tiny differences.
The only way that those two could be exactly the same, would be if your mom and your dad were identical twins… which obviously doesn’t happen.)

Nonetheless, as long as the two genes are almost the same, and do the same thing, we say that they’re the “same”, or they’re “identical”.

You may be homozygous for a certain gene:
You carry two copies of the same allele.

You may be heterozygous for a certain gene:
You carry two different alleles.

Dominant and Recessive genes

Different combinations of alleles produce different results.

Here is an example of gene for pea color, which can come in two forms:
Yellow (a dominant gene), and Green ( a recessive gene)

Dominant means that the gene always has a visible effect.

Recessive means that the gene doesn’t have any noticeable effect, if it exists alongside a Dominant gene.
Recessive genes only have visible effects if no dominant genes are around.

Here are the possible combinations, when both parents carry one dominant allele, and one recessive allele.

Many traits are controlled by 2 or more genes.

Here is a simplified Punnett square diagram for eye color
(This assumes that only 2 genes control eye color; really more genes are involved)
As you can see, doubling the number of genes has quadrupled (x4) the number of possible combinations!

Human hair texture is an example of incomplete dominance

Here is a key to the alleles:
ss = Straight   cc = Curly   sc = wavy

Genetic Apps

StarGenetics is a Mendelian genetics cross simulator developed at MIT by biology faculty, researched-trained scientists and technologists at MIT’s OEIT. StarGenetics allows students to simulate mating experiments between organisms that are genetically different across a range of traits to analyze the nature of the traits in question.

http://star.mit.edu/genetics/
VGL is a simulation of transmission genetics that approximates, as closely as possible, the hypothesis-testing environment of genetics research.  In this lab, students cross hypothetical creatures and examine the progeny in order to determine the mechanism of inheritance of a particular trait.  As in actual research, it is not possible to ‘see the answer’ – the student must decide for herself when she has collected enough data to be sure of her model. 

http://vgl.umb.edu/

Pigeon Breeding: Genetics At Work

http://learn.genetics.utah.edu/content/pigeons/

Many genes that influence skin color.

Assuming something as simple as genes being only dominant or recessive:
* 2 genes create a total of 16 possibilities (see eye color chart above)
* 5 genes creates a 32×32 grid, for a total of 1024 possibilities.
* 10 genes creates a vast number of possibilities – a “spectrum” of skin colors.
* These possibilities cluster in groups that one can predict by evolutionary theory, and can be observed by looking at the genes (see gene “tree” image below)

“…Harrison and Owen predicted that a minimum of six to eight genes underlie the skin color differences between European and West African populations. More recently, researchers considering contemporary admixed populations, which had undergone admixture for many more generations, estimated that at least 10 genes contribute to population-level differences between European and West African populations”

“…Despite the many genes already implicated in human skin color variation, a substantial number of the differences among populations cannot be explained. There are more than 350 putative pigmentation loci identified in mouse models and cataloged in the IFPCS color genes database (http://www.espcr.org/micemut/); what, if any, role these genes play in the unexplained variation in human pigmentation remains unknown.”

The evolutionary genetic architecture of skin pigmentation in three populations. http://www.nature.com/milestones/skinbio4/full/skinbio20113a.html

The evolutionary genetic architecture of skin pigmentation in three populations.
http://www.nature.com/milestones/skinbio4/full/skinbio20113a.html

– Unpacking Human Evolution to Find the Genetic Determinants of Human Skin Pigmentation, Ellen E Quillen1 & Mark D Shriver, Milestones cutaneous Biology, 17 Nov 2011

Do races exist?

The answer depends on the definition of the word “race”.  Most people don’t have a specific, scientific definition of the word “race” to begin with. When we don’t ask a specific question then we can’t get a specific answer.  But when we ask precise questions we then can get precise answers. Human beings do have populations with genetic differences that arose through evolution through natural selection. See Genetic analysis of genes and “race”

Why do scientists care about genetics and skin color?

What Controls Variation in Human Skin Color?, Gregory S Barsh
PLoS Biol. 2003 Oct; 1(1): e27.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC212702/

From a clinical perspective, inadequate protection from sunlight has a major impact on human health (Armstrong et al. 1997; Diepgen and Mahler 2002).

In Australia, the lifetime cumulative incidence of skin cancer approaches 50%, yet the oxymoronic “smart tanning” industry continues to grow, and there is controversy over the extent to which different types of melanin can influence susceptibility to ultraviolet (UV) radiation (Schmitz et al. 1995; Wenczl et al. 1998).

At the other end of the spectrum, inadequate exposure to sunlight, leading to vitamin D deficiency and rickets, has been mostly cured by nutritional advances made in the early 1900s.

In both cases, understanding the genetic architecture of human skin color is likely to provide a greater appreciation of underlying biological mechanisms, much in the same way that mutational hotspots in the gene TP53 have helped to educate society about the risks of tobacco (Takahashi et al. 1989; Toyooka et al. 2003).

From a basic science perspective, variation in human skin color represents an unparalleled opportunity for cell biologists, geneticists, and anthropologists to learn more about:

* the biogenesis and movement of subcellular organelles,
* to better characterize the relationship between genotypic and phenotypic diversity
* to further investigate human origins
* and to understand how recent human evolution may have been shaped by natural selection.

Some great websites:

http://learn.genetics.utah.edu/

Learning Standards

HS-LS1-1. Construct a model of transcription and translation to explain the roles of DNA and RNA that code for proteins that regulate and carry out essential functions of life.

Clarification Statements: Proteins that regulate and carry out essential functions of life include enzymes (which speed up chemical reactions), structural proteins (which provide structure and enable movement), and hormones and receptors (which send and receive signals). The model should show the double-stranded structure of DNA, including genes as part of DNA’s transcribed strand, with complementary bases on the nontranscribed strand.

State Assessment Boundaries: Specific names of proteins or specific steps of transcription and translation are not expected in state assessment. Cell structures included in transcription and translation will be limited to nucleus, nuclear membrane, and ribosomes for state assessment.

HS-LS3-1. Develop and use a model to show how DNA in the form of chromosomes is passed from parents to offspring through the processes of meiosis and fertilization in sexual reproduction.

Clarification Statement: The model should demonstrate that an individual’s characteristics (phenotype) result, in part, from interactions among the various proteins expressed by one’s genes (genotype)

State Assessment Boundary: Identification of specific phases of meiosis or the biochemical mechanisms involved are not expected in state assessment.

HS-LS3-2. Make and defend a claim based on evidence that genetic variations (alleles) may result from (a) new genetic combinations via the processes of crossing over and random segregation of chromosomes during meiosis, (b) mutations that occur during replication, and/or (c) mutations caused by environmental factors. Recognize that mutations that occur in gametes can be passed to offspring.

Clarification Statement: Examples of evidence of genetic variation can include the work of McClintock in crossing over of maize chromosomes and the development of cancer due to DNA replication errors and UV ray exposure.

State Assessment Boundary: Specific phases of meiosis or identification of specific types of mutations are not expected in state assessment.

HS-LS3-3. Apply concepts of probability to represent possible genotype and phenotype combinations in offspring caused by different types of Mendelian inheritance patterns.

Clarification Statements: Representations can include Punnett squares, diagrams, pedigree charts, and simulations. Inheritance patterns include dominant-recessive, codominance, incomplete dominance, and sex-linked.

HS-LS3-4(MA). Use scientific information to illustrate that many traits of individuals, and the presence of specific alleles in a population, are due to interactions of genetic factors
and environmental factors.

Clarification Statements: Examples of genetic factors include the presence of multiple alleles for one gene and multiple genes influencing a trait.
An example of the role of the environment in expressed traits in an individual can include the likelihood of developing inherited diseases (e.g., heart disease, cancer) in relation to exposure to environmental toxins and lifestyle; an example in populations can include the maintenance of the allele for sickle-cell anemia in high frequency in malaria-affected regions because it confers partial resistance to malaria.

State Assessment Boundary: Hardy-Weinberg calculations are not expected in state assessment.

 

 

 

 

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