Archive for February, 2013

Endocrine Glands Table

endocrine 1EndocrineSystem 2


Important Topics for annual exam :- Class XI (Biology)

Mechanism of Muscle Contraction,Hearing,Vision,Breathing.

Secondary growth in Dicot Stem/Root.

ETS, Glycolysis, Kreb’s Cycle, Calvin Cycle.

Nitrogen Fixation, ECG, Urine Formation, Counter Current Mechanism, Blood Circulation.


Diffusion and Osmosis


-the process by which molecules spread from areas of high concentratiion, to areas of low concentration. When the molecules are even throughout a space – it is called EQUILIBRIUM


Concentration gradient – a difference between concentrations in a space.

Molecules will always move down the concentration gradient, toward areas of lesser concentration. Think of food coloring that spreads out in a glass of water, or air freshener sprayed in a room.

Selectively Permeable – membranes that allow some things through, the cell membrane is selectively permeable, water and oxygen move freely across the cell’s membrane, by diffusion

Osmosis – the diffusion of water (across a membrane)

Water will move in the direction where there is a high concentration of solute (and hence a lower concentration of water.

A simple rule to remember is: salt sucks

Salt is a solute, when it is concentrated inside or outside the cell, it will draw the water in its direction. This is also why you get thirsty after eating something salty.


Type of Solutions

Isotonic Solutions

If the concentration of solute (salt) is equal on both sides, the water will move back in forth but it won’t have any result on the overall amount of water on either side.

ISO” means the same


Hypotonic Solutions

The word “HYPO” means less, in this case there are less solute (salt) molecules outside the cell, since salt sucks, water will move into the cell.

The cell will gain water and grow larger. In plant cells, the central vacuoles will fill and the plant becomes stiff and rigid, the cell wall keeps the plant from bursting

In animal cells, the cell may be in danger of bursting, organelles calledCONTRACTILE VACUOLES will pump water out of the cell to prevent this.


Hypertonic Solutions

The word “HYPER” means more, in this case there are more solute (salt) molecules outside the cell, which causes the water to be sucked in that direction.

In plant cells, the central vacuole loses water and the cells shrink, causing wilting.

In animal cells, the cells also shrink.

In both cases, the cell may die.

This is why it is dangerous to drink sea water – its a myth that drinking sea water will cause you to go insane, but people marooned at sea will speed up dehydration (and death) by drinking sea water.

This is also why “salting fields” was a common tactic during war, it would kill the crops in the field, thus causing food shortages.


Diffusion and Osmosis are both types of PASSIVE TRANSPORT – that is, no energy is required for the molecules to move into or out of the cell.

Sometimes, large molecules cannot cross the plasma membrane, and are “helped” across by carrier proteins – this process is called facilitated diffusion.


The Theory of Evolution

In science, theories are statements or models that have been tested and confirmed many times.

Theories have some important properties:

  • They explain a wide variety of data and observations
  • They can be used to make predictions
  • They are not absolute, they serve as a model of understanding the world and can be changed as the world view changes

In science, the term “Theory” does not express doubt.

In science, the term theory is used to represent ideas and explanations that have been confirmed through tests and observations

The theory of evolution remains one of the most useful theories in biology because it explains many questions and observations.

Some questions that can be answered by evolution.

  • Why do so many different animals have the same structures, the arm bones in a human are the same bones as a flipper in a whale?
  • Why do organisms have structures they no longer use, like the appendix in a human? Non functioning wings in penguins
  • Why are there bones and fossil evidence of creatures that no longer exist? What happened to these creatures?
  • Why do so many organisms’ morphology and anatomy follow the same plan?
  • Why is the sequence of DNA very similar in some groups of organisms but not in others?
  • Why do the embryos of animals look very similar at an early stage?
The Theory of Evolution is considered a Unifying Theory of Biology, because it answers many of these questions and offers and explanation for the data.

Lamarke’s Theory of Acquired Characteristics

Some thought that you would gain or lose features if you overused or didn’t use them, and you could pass these new traits onto your offspring.

This was known as the Inheritance of Acquired Characteristics

  • A lizard that didn’t use it legs would eventually not have legs and its offspring wouldn’t have legs
  • A giraffe stretched its neck to reach higher leaves, and this stretched neck would be a trait inherited by its offspring

Lamarke’s Theory was eventually discarded – PROVEN TO BE WRONG!

Why? Logically it doesn’t work. Imagine if you were in a car accident and had a leg amputed. This does not mean that your children will only have one leg. Features gained during life are not passed on to children.

Darwin’s Theory of Evolution by Natural Selection

Darwin was a naturalist who observed many species. He is famous for his trips to the Galapagos Islands, his observations of the finches (and other animals) and the book he wrote: “The Origin of Species:

1. Variation exists among individuals in a species.
2. Individuals of species will compete for resources (food and space)
3. Some competition would lead to the death of some individuals while others would survive
4. Individuals that had advantageous variations are more likely to survive and reproduce.

This process he describes came to be known as Natural Selection
The favorable variations are called Adaptations

Darwin’s Finches: 

Darwin noted that all the finches on the galapagos island looked about the same except for the shape of their beak. His observations lead to the conclusion that all the finches were descendents of the same original population. The shape of the beaks were adaptations for eating a particular type of food (Ex. long beaks were used for eating insects, short for seeds)

Evidence of Evolution

1. Fossil Evidence

  • If today’s species came from ancient species, the we should be able to find remains of those species that no longer exist.
  • We have tons of fossils of creatures that no longer exist but bear striking resemblance to creatures that do exist today.
  • Carbon dating–gives an age of a sample based on the amount of radioactive carbon is in a sample.
  • Fossil record-–creates a geologic time scale.

2. Evidence from Living Organism

  • Evidence of Common Ancestry –Hawaiin Honeycreeper
  • Homologous Structures–structures that are embryologically similar, but have different functions, the wing of a bird and the forearm of a human
  • Vestigial Organs–seemingly functionless parts, snakes have tiny pelvic and limb bones, humans have a tail bone
  • Biochemistry and DNA
  • Embryological development–Embryos of different species develop almost identically
  • Observation of species change (wolves/dogs, peppered moths)

Mendel’s Genetics

Mendel’s Genetics

photo of 3 domesticated horses pulling a plow

Hybridized domesticated horses

For thousands of years farmers and herders have been selectively breeding their plants and animals to produce more useful hybrids click this icon to hear the preceding term pronounced.   It was somewhat of a hit or miss process since the actual mechanisms governing inheritance were unknown.  Knowledge of these genetic mechanisms finally came as a result of careful laboratory breeding experiments carried out over the last century and a half.

photo of Gregor Mendel 

Gregor Mendel

By the 1890’s, the invention of better microscopes allowed biologists to discover the basic facts of cell division and sexual reproduction.  The focus ofgenetics click this icon to hear the preceding term pronounced research then shifted to understanding what really happens in the transmission of hereditary traits from parents to children.  A number of hypotheses were suggested to explain heredity, but Gregor Mendel click this icon to hear the name pronounced, a little known Central European monk, was the only one who got it more or less right.  His ideas had been published in 1866 but largely went unrecognized until 1900, which was long after his death.  His early adult life was spent in relative obscurity doing basic genetics research and teaching high school mathematics, physics, and Greek in Brno (now in the Czech Republic).  In his later years, he became the abbot of his monastery and put aside his scientific work.

photo of 3 pea pods and peas

Common edible peas

While Mendel’s research was with plants, the basic underlying principles of heredityclick this icon to hear the preceding term pronounced that he discovered also apply to people and other animals because the mechanisms of heredity are essentially the same for all complex life forms.

Through the selective cross-breeding of common pea plants (Pisum sativum) over many generations, Mendel discovered that certain traits show up in offspring without any blending of parent characteristics.  For instance, the pea flowers are either purple or white–intermediate colors do not appear in the offspring of cross-pollinated pea plants.  Mendel observed seven traits that are easily recognized and apparently only occur in one of two forms:

1.    flower color is purple or white 5.    seed color is yellow or green
2. flower position is axil or terminal        6. pod shape is inflated or constricted
3. stem length is long or short 7. pod color is yellow or green
4. seed shape is round or wrinkled

This observation that these traits do not show up in offspring plants with intermediate forms was critically important because the leading theory in biology at the time was that inherited traits blend from generation to generation.  Most of the leading scientists in the 19th century accepted this “blending theory.”  Charles Darwin proposed another equally wrong theory known as “pangenesis” click this icon to hear the name pronounced.  This held that hereditary “particles” in our bodies are affected by the things we do during our lifetime.  These modified particles were thought to migrate via blood to the reproductive cells and subsequently could be inherited by the next generation.  This was essentially a variation of Lamarck’s incorrect idea of the “inheritance of acquired characteristics.”

Mendel picked common garden pea plants for the focus of his research because they can be grown easily in large numbers and their reproduction can be manipulated.  Pea plants have both male and female reproductive organs.  As a result, they can either self-pollinate themselves or cross-pollinate with another plant.  In his experiments, Mendel was able to selectively cross-pollinatepurebred click this icon to hear the preceding term pronounced plants with particular traits and observe the outcome over many generations.  This was the basis for his conclusions about the nature of genetic inheritance.

structures of
drawing of a flower cross-section showing both male and female sexual structures

In cross-pollinating plants that either produce yellow or green pea seeds exclusively, Mendel found that the first offspring generation (f1) always has yellow seeds.   However, the following generation (f2) consistently has a 3:1 ratio of yellow to green.

diagram showing the result of cross-pollination in the first 2 offspring generations--in generation f1 all are yellow peas but in generation f2 the ratio of yellow to green peas is 3 to 1

This 3:1 ratio occurs in later generations as well.   Mendel realized that this was the key to understanding the basic mechanisms of inheritance.

diagram showing the result of cross-pollination in the 3rd offspring generation--the offspring of the 2nd generation green peas are all green, the offspring of one third of the 2nd generation yellow peas are all yellow, the offspring of the other 2nd generation yellow peas are green or yellow in a 3 to 1 ratio

He came to three important conclusions from these experimental results:

1.   that the inheritance of each trait is determined by “units” or “factors” that are passed on to descendents unchanged      (these units are now called genes click this icon to hear the preceding term pronounced)
2. that an individual inherits one such unit from each parent for each trait
3. that a trait may not show up in an individual but can still be passed on to the next generation.

It is important to realize that, in this experiment, the starting parent plants were homozygous click this icon to hear the preceding term pronounced for pea seed color.  That is to say, they each had two identical forms (or alleles click this icon to hear the preceding term pronounced) of the gene for this trait–2 yellows or 2 greens.  The plants in the f1 generation were all heterozygous click this icon to hear the preceding term pronounced.   In other words, they each had inherited two different alleles–one from each parent plant.  It becomes clearer when we look at the actual genetic makeup, or genotype click this icon to hear the preceding term pronounced, of the pea plants instead of only the phenotype click this icon to hear the preceding term pronounced, or observable physical characteristics.

diagram of genotypes of pea plants in 3 generations after cross-pollination

Note that each of the f1 generation plants (shown above) inherited a Y allele from one parent and a G allele from the other.  When the f1 plants breed, each has an equal chance of passing on either Y or G alleles to each offspring.

With all of the seven pea plant traits that Mendel examined, one form appeared dominant over the other, which is to say it masked the presence of the other allele.  For example, when the genotype for pea seed color is YG (heterozygous), the phenotype is yellow.  However, the dominant yellow allele does not alter the recessive green one in any way.   Both alleles can be passed on to the next generation unchanged.

Mendel’s observations from these experiments can be summarized in two principles:

1.   the principle of segregation
2. the principle of independent assortment

According to the principle of segregation, for any particular trait, the pair of alleles of each parent separate and only one allele passes from each parent on to an offspring.  Which allele in a parent’s pair of alleles is inherited is a matter of chance.  We now know that this segregation of alleles occurs during the process of sex cell formation (i.e., meiosis click this icon to hear the preceding term pronounced).

illustration of the segregation of alleles in the production of sex cells

Segregation of alleles in the production of sex cells

According to the principle of independent assortment, different pairs of alleles are passed to offspring independently of each other.  The result is that new combinations of genes present in neither parent are possible.  For example, a pea plant’s inheritance of the ability to produce purple flowers instead of white ones does not make it more likely that it will also inherit the ability to produce yellow pea seeds in contrast to green ones.  Likewise, the principle of independent assortment explains why the human inheritance of a particular eye color does not increase or decrease the likelihood of having 6 fingers on each hand.  Today, we know this is due to the fact that the genes for independently assorted traits are located on different chromosomes click this icon to hear the preceding term pronounced.

These two principles of inheritance, along with the understanding of unit inheritance and dominance, were the beginnings of our modern science of genetics.  However, Mendel did not realize that there are exceptions to these rules.  Some of these exceptions will be explored in the third section of this tutorial and in the Synthetic Theory of Evolution tutorial.

By focusing on Mendel as the father of genetics, modern biology often forgets that his experimental results also disproved Lamarck’s theory of the inheritance of acquired characteristics described in the Early Theories of Evolution tutorial.  Mendel rarely gets credit for this because his work remained essentially unknown until long after Lamarck’s ideas were widely rejected as being improbable.


Gene Therapy

Gene Therapy.

Gene Therapy

What is gene therapy?

Genes, which are carried on chromosomes, are the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Although genes get a lot of attention, it’s the proteins that perform most life functions and even make up the majority of cellular structures. When genes are altered so that the encoded proteins are unable to carry out their normal functions, genetic disorders can result.

Gene therapy is a technique for correcting defective genes responsible for disease development. Researchers may use one of several approaches for correcting faulty genes:

  • A normal gene may be inserted into a nonspecific location within the genome to replace a nonfunctional gene. This approach is most common.
  • An abnormal gene could be swapped for a normal gene through homologous recombination.
  • The abnormal gene could be repaired through selective reverse mutation, which returns the gene to its normal function.
  • The regulation (the degree to which a gene is turned on or off) of a particular gene could be altered.

How does gene therapy work?

In most gene therapy studies, a “normal” gene is inserted into the genome to replace an “abnormal,” disease-causing gene. A carrier molecule called a vector must be used to deliver the therapeutic gene to the patient’s target cells. Currently, the most common vector is a virus that has been genetically altered to carry normal human DNA. Viruses have evolved a way of encapsulating and delivering their genes to human cells in a pathogenic manner. Scientists have tried to take advantage of this capability and manipulate the virus genome to remove disease-causing genes and insert therapeutic genes.

Target cells such as the patient’s liver or lung cells are infected with the viral vector. The vector then unloads its genetic material containing the therapeutic human gene into the target cell. The generation of a functional protein product from the therapeutic gene restores the target cell to a normal state. See a diagram depicting this process.

Some of the different types of viruses used as gene therapy vectors:

  • Retroviruses – A class of viruses that can create double-stranded DNA copies of their RNA genomes. These copies of its genome can be integrated into the chromosomes of host cells. Human immunodeficiency virus (HIV) is a retrovirus.
  • Adenoviruses – A class of viruses with double-stranded DNA genomes that cause respiratory, intestinal, and eye infections in humans. The virus that causes the common cold is an adenovirus.
  • Adeno-associated viruses – A class of small, single-stranded DNA viruses that can insert their genetic material at a specific site on chromosome 19.
  • Herpes simplex viruses – A class of double-stranded DNA viruses that infect a particular cell type, neurons. Herpes simplex virus type 1 is a common human pathogen that causes cold sores.

Besides virus-mediated gene-delivery systems, there are several nonviral options for gene delivery. The simplest method is the direct introduction of therapeutic DNA into target cells. This approach is limited in its application because it can be used only with certain tissues and requires large amounts of DNA.

Another nonviral approach involves the creation of an artificial lipid sphere with an aqueous core. This liposome, which carries the therapeutic DNA, is capable of passing the DNA through the target cell’s membrane.

Therapeutic DNA also can get inside target cells by chemically linking the DNA to a molecule that will bind to special cell receptors. Once bound to these receptors, the therapeutic DNA constructs are engulfed by the cell membrane and passed into the interior of the target cell. This delivery system tends to be less effective than other options.

Researchers also are experimenting with introducing a 47th (artificial human) chromosome into target cells. This chromosome would exist autonomously alongside the standard 46 –not affecting their workings or causing any mutations. It would be a large vector capable of carrying substantial amounts of genetic code, and scientists anticipate that, because of its construction and autonomy, the body’s immune systems would not attack it. A problem with this potential method is the difficulty in delivering such a large molecule to the nucleus of a target cell.