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(Source: Dr. Nilsson's old lecture notes, and Mader, S.S. 2010. Biology. Ed. 10. Used for educational purpose.Permission given in 2001 by McGraw-Hills then sales representative, Don Grainger, to use the pictures online on lecture notes.)



Genetics






Gregor Mendel. From S. S. Mader. 2010. Biology. McGraw-Hill.

--- Gregor Mendel and Mendel's Laws ---


Genetics is he branch of biology that deals with heredity (Especially the mechanisms of hereditary transmission and the variation of inherited characteristics among similar or related organisms. From Answers.com).

Science of genetics, which seeks to understand the process of inheritance, began with the work of Gregor Mendel in the mid-19th century. Mendel did not know the physical basis for heredity, but he observed that organisms inherit traits via discrete units of inheritance, which are now called genes (regions within DNA). (From Wikipedia).

Gregor Mendel, 1822 - 1884, is known as the "father of modern genetics", was an Austrian Augustinian monk and scientist, who studied the inheritance of certain traits in garden pea plants.

The importance of Mendel's work was not recognized until the turn of the 20th century, when independent rediscovery of these laws formed the foundation of the modern science of genetics. (By 1900, research aimed at finding a successful theory led to independent duplication of his work by Hugo de Vries and Carl Correns, and the rediscovery of Mendel's writings and laws. Both acknowledged Mendel's priority.)

Between 1856 and 1863 Gregor Mendel cultivated and tested some 29,000 pea plants (i.e., Pisum sativum). This study showed that one in four pea plants had purebred recessive alleles, two out of four were hybrid and one out of four were purebred dominant.


From S. S. Mader. 2010. Biology. McGraw-Hill.



Mendel showed that the inheritance of traits follows particular laws, which were later named after him.

Law of Segregation, states that each individual has two alleles (two alternative versions of a trait -- one from each parent), and they separate during gamete formation -- so that a gamete only have one of the alleles, and then randomly unite at fertilization when the new individual receives for the trait from both parents. Simplified: Eggs and sperms randomly receive only one allele of a trait.

Using pea plant color as the example, in the figure below the red chromosome has an allele noted with the capital letter "G" -- purple color version, while the blue chromosome has an allele noted with the small letter "g" -- white color version. Both are alleles for the same trait, pea flower color. They both occur on homologous chromosomes -- one received from the father, the other received from the mother.


From S. S. Mader. 2010. Biology. McGraw-Hill.




Law of Independent Assortment, states that each allele pair separate independently of other pairs during the formation of gametes. The inheritance pattern of one trait will not affect the inheritance pattern of another. Simplified example: An individual has blue eyes, the probability of his children having blue eyes does not depend on, for example, his hair color.






--- Simple Genetic Traits (Mendelian Genetics) ---



Simplified this is how genetics (inheritance) works...

The type of traits inherited is determined by:

Type of alleles received from your parents.
-- an allele is a different versions of the same trait.

e.g., Earlobe shape: Two (2) alleles, 1. Free Earlobes, 2. Attached earlobes


Interaction between these alleles.
-- one alleles is "dominant" and may mask the other allele.

e.g., Earlobe shape: If both earlobes alleles is inherited, the free earlobes will mask the attached earlobes.


Conditions the organism encounter.
-- the environment

e.g., Freckles is inherited, and it is affected by exposure to the sun.



Simple traits are controlled by two (2) alleles only.


Terminology.






Traits following “Simple Mendelian Rules” or “Mendelian Patterns of Inheritance”.

• 1. The type of alleles received from your parents

-- 'If your parents doesn't have a trait, you will not get it either'...


• Offspring receive two alleles for each trait, one from each parent

-- The chromosome with these allele separate (segregate) and sort independent of each other (independent assortment) during MEIOSIS when the gametes are produced.

-- At fertilization the zygote (fertilized egg) receives two alleles for a particular trait (one allele from each parent -- one allele from the sperm, one allele from the egg).




Possible chromosome combinations with 3 pairs of chromosomes.

From S. S. Mader. 2010. Biology. McGraw-Hill.





• 2. The interaction between these alleles


• If the two alleles received from the parents are different there is a dominant/recessive relationship between them


Gregor Mendel used pea plants for his experiments. The figure below depicts some of the various pea plant traits...





From S. S. Mader. 2010. Biology. McGraw-Hill.





def. Allele: Alternative form of a gene. (Alleles occur on the same locus (location) on homologous chromosomes.


def. Homologous chromosomes: The pair of chromosomes that are alike, have the same traits, containing the same linear gene sequences (the genes controlling the same trait -- e.g., hair color) that are paired up during meiosis (one from mom and one from dad).



From S. S. Mader. 2010. Biology. McGraw-Hill.




From S. S. Mader. 2010. Biology. McGraw-Hill.







def. Dominant allele: an allele that expresses itself and masks the effects of the other allele for the trait (the homologous allele).
def. Recessive allele: an allele that does not express itself (does not show up) when the homologous allele is present. The other allele (the homologous allele) the dominant allele, mask the recessive allele.
- - -

Dominant allele vs. Recessive allele. In simple inheritance alternative versions of a trait occur as a pair, one of the alleles is the dominant allele -- so named because of its ability to mask the expression of the other allele, called the recessive allele. In the figure below the allele for purple pea flower is the dominant allele and the recessive allele is white.


Source: http://www.biology.iupui.edu/biocourses/N100/2k4ch10genetics.html. Used for educational purpose.


2. An allele that expresses itself and masks the effects of the other allele for the trait (this allele masks the homologous allele).

a. Homozygous trait
b. X-linked allele
c. Dominant allele
d. Recessive allele
e. A, C, and D





def. Genotype: the genetic constitution of an organism, distinguished from its physical appearance (the phenotype)
(= GENETIC CONSTITUTION)
def. Phenotype: the environmentally and genetically determined observable (outward) physical appearance of an organism, distinguished from its genetic constitution (the genotype)
(= PHYSICAL APPEARANCE)
- - -


Genotype vs. Phenotype. Two organisms with different allelic combination for a trait can have the same outward appearance (phenotype) but different genetic constitution (genotype). In the figure below, PP and Pp pea plants are both purple, even though one has both dominant alleles and the other only one of the alleles are dominant. The word genotype refers to the alleles an individual receives at fertilization. A genotype may be indicated by letters or short, descriptive phrases, e.g., PP, Pp, pp.

----- The word phenotype refers to the physical appearance of the individual.



http://bioserv.fiu.edu/~walterm/GenBio2004/new_chap13_inheritance/pics.htm



http://apps.cmsfq.edu.ec/biologyexploringlife/text/chapter10/concept10.2.html



3. The environmentally and genetically determined observable physical appearance of an organism.

a. Allele
b. Gene
c. Genotype
d. Phenotype
e. Homozygous trait







def. Homozygous trait: both alleles for the trait are identical (pure breeding, “pure”): PP, pp
def. Heterozygous trait: alleles of one of each kind – one dominant & one recessive allele for a trait (“hybrid”): Pp


 Homozygous trait vs. Heterozygous trait. A genotype may be indicated by letters.

--- Genotype PP is called a homozygous dominant individual.

--- Genotype pp is called homozygous recessive individual.

--- Genotype Pp is called heterozygous individual.


Both the homozygous dominant PP individual and the heterozygous Pp individual show the dominant phenotype and are purple, while the homozygous recessive pp individual shows the recessive phenotype and is white.

- - - Homozygous condition: When an organism has two identical alleles, e.g. PP or pp.

- - - Heterozygous condition: When an organism has two different alleles, Pp.




http://cikgurozaini.blogspot.com/2010/06/genetic-1.html



4. An example of a heterozygous condition is

a. aa
b. AA
c. Aa
d. all of the above
e. none of the above




5. Both alleles for the trait are identical.

a. Homozygous trait
b. Allele
c. Dominant allele
d. Recessive allele
e. Heterozygous trait






• 3. Conditions the organism encounter (the environment)


• The phenotype is also sometimes influenced by the environment (this is the 3rd thing that determines a genetic characteristic -- discussed more later).








IN REVIEW: The type of characteristics (traits) inherited is determined by:

1. Type of alleles (different versions of a trait) received from your parents.
-- chromosomes segregate (separate) during meiosis.

2. Interaction between these alleles.
-- one alleles is "dominant" and may mask the other allele.

3. Conditions the organism encounter.
-- the environment








--- Predicting offspring ---

def. Punnett square: A method used to determine the probability of allele combinations in a zygote.
def. Monohybrid cross: A monohybrid cross is a breeding experiment between P generation (parental generation) organisms that differ in one trait.
def. Dihybrid cross: A monohybrid cross is a breeding experiment between P generation (parental generation) organisms that differ in two traits.


Punnett square. Geneticists use a diagram called a Punnett square to calculate the chances (probability) of genotypes and phenotypes of offspring. Punnett square diagrams can be used to calculate the probability of offspring receiving genetic disorders. The Punnett squares for one of Gregor Mendel's pea plant experiments with purple pea plant flowers is shown in the video below. (If you wish to see how a Punnett square diagram is done view the Khan Academy YouTube further down the page.)




6. The probability of parents w. genotypes Ss x Ss having an offspring w. the genotype ss is

a. zero
b. 25%
c. 50%
d. 75%
e. 100%






• Genetic disorders following Mendel's Laws.

Many disorders, like the traits above for pea flower color, follow Mendel's Laws.

def. Autosomal recessive disorders: The disorder is caused by the recessive allele.
def. Autosomal dominant disorders: The disorder is caused by the recessive allele.
Autosomal disorders are controlled by a single pair of alleles on the autosomal chromosomes (any chromosome other than the sex chromosomes).

--- Autosomal recessive disorders are disorders where the disorder is caused by the recessive allele, and both alleles are necessary in order to get the disorder (example cystic fibrosis). A person with only one of the recessive disorder alleles will NOT have the disorder, but have the potential to pass on the allele to the offspring.

--- Autosomal dominant disorders are disorders where the disorder is caused by the dominant allele, and only one allele is necessary in order to get the disorder (examples mentioned in your book are osteogenesis imperfects. A person with only one of the recessive disorder alleles will have the disorder, and a dominant disorder is therefore easier to pass on to the offspring.



• Natural characteristics

-- Simple genetic traits are controlled by two (2) alleles only.



EXAMPLE: 1. Pea plant colors
(P - Purple flower, p - white flower) PP, Pp, pp

EXAMPLE: 2. Interlacing of fingers when clasping
(I - Left thumb over right, i - right thumb over left) II, Ii, ii

EXAMPLE: 3. Tongue rolling
(T - Rolled tongue, t - flat tongue) TT, Tt, tt


EXAMPLE: 4. PTC taste
(TT - taste, Tt - Intermediate taste, tt no taste)

EXAMPLE: 5. Ear lobe shapes
(E - Free earlobes, e - attached earlobes) EE, Ee, ee







EARLOBE TRAIT (Free vs. Attached earlobe)


Genotypes --- Phenotypes

EE --- Free ear lobes Homozygous dominant (“pure”)
Ee --- Free ear lobes Heterozygous (“hybrid”)
ee --- Attached ear lobes Homozygous recessive (“pure”)




Cross I: male , Free ear lobes EE X female , Attached ear lobes ee


-------------------------------------------------------------------------------------------------
Cross II: male, free earlobes Ee X female, attached earlobes ee


-------------------------------------------------------------------------------------------------
Cross III: male, free earlobes Ee X female, free earlobes Ee


-------------------------------------------------------------------------------------------------
Cross IV: male, attached earlobes ee X female, attached earlobes ee








In the Virtual Exercise below, you can practice some genetic problems. They are not about the ear lobe trait, but if they were they might look someting like this:

Free earlobes (E) in humans is dominant over attached earlobes (e). Find the probabilities of offspring in the cross: BB x Bb.

You can use a punnett square to figure out the probability (0%, 25%, 50%, 75%, 100%). For an example how to use the Punnett Square, look at the video in the Virtual Exercise * box.




VIRTUAL EXERCISE *.




Read the text in this box and view the video. Then click on the link below and do the genetic (Punnett Square) quiz on the page you land on (looks like the figure above). (If you are in a F-2-F class and doing this in the biology computer lab, the instructor will show the video, since the computers in the lab have no speakers...)




Source: mahalodotcom
The presenter does a good job explaining a Punnett Square, with one exception, she used human eye color -- which is NOT a simple trait that can be explained with a simple Punnett Square as illustrated. Human eye color is a complex trait (Polygenic inheritance). However, lt's overlook that "simplification" (?) in this otherwise very good video...





Punnett Square and Probability exercise. Read the page you land on and follow the instructions to start the quiz. You will navigate to a genetic problem dealing with fur color in guinea pigs. In guinea pigs black fur(B) is dominant over white fur(b).

There will be six (6) problems, all dealing with different parental genotypes (different alleles of the fur color trait). Your job is to figure out the probability of two guinea pigs with certain fur color traits, receiving a certain kind of offspring. You must solve all 6 problems correctly. If you get one wrong you must start over. The problems will load in a different order each time you restart.

Note: You might want to have a paper in front of you and DRAW the punnet squares before answering. Some are not that easy to do in your head, and guessing the answers is of no educational value.

In some of the genetic problems you are given the genotypes directly, e.g. Bb x Bb, in others you must know some terminology in order to figure out the parental allele genotype (BB, Bb or bb), and/or the phenoptype. All the terms have been covered in the Learning Resource (above).

Dominant trait, recessive trait, heterozygous trait, homozygous trait, homozygous dominant trait, homozygous recessive trait, hybrid trait, phenotype, genotype.


Some of you might be in an online class and doing this on your own, but if you are in a F-2-F class with the instructor in the classroom when doing this, you must show the instructor the text box (the result box illustrated below). When all 6 problems are correct, show the result box to the instructor...





Here is the link:

http://www.quia.com/quiz/220564.html



When finished sign the participation roster (provided by the instructor). Next, navigate to the DNA Learning Resources (Resource 12). A link to the Learning Resources page is provided HERE for your convenience. Click on Learning Resources 12 (DNA). Scroll down the page to the section discussing DNA Replication. Find Virtual Exercise **.










Several other traits, including some genetic disorders, do not follow the simple Mendelian laws, and are discussed below.












--- Complex Genetic Traits ---




Traits that are controlled by more than two (2) alleles.




Multiple allele traits (Codominance), are traits with more than the two alleles discussed above for simple Mendelian genetics is affecting a characteristic. When characteristics (traits) are determined by three or more alleles, but only two are present in each individual, the trait is called a multiple allele trait. An example of this type of trait would be the ABO blood types. While a persons ABO blood type is controlled by only two alleles, there are three possible alleles that determine the blood type, which cause a red blood cell to have or not have certain antigens on the plasma membrane.





IA, IB, and i. (Sometimes this is simply written A, B, i.

Both IA, IB are dominant alleles, so the trait is also called codominance. The small letter i is a recessive trait. See your textbook for the phenotype and the genotype, and other details.


Source: http://www.mhhe.com/cgi-bin/. Used for educational purpose.


For simplicity the I is ignored:

AA -- A blood
Ai -- A blood
BB -- B blood
Bi -- B blood
AB -- AB blood
ii -- 0 blood


Incomplete dominance, are traits where the heterozygote has an intermediate phenotype (appearance intermediate between the two parents) -- unlike the simple pattern followed by pea plants where the heterozygote had the same color as the homozygous dominant flower (see the figure above and compare it with the figure below).

Hair shape -- curly hair, wavy hair, and straight hair, is an example of incomplete dominans in humans, where curly is dominant, wavy is the heterozygote, and straight hair is recessive. Sickle cell anemia is yet another example (Sickle cell-disease is also an example of pleotropic effects).


From S. S. Mader. 2010. Biology. McGraw-Hill.




Pleiotropic effects occurs when a single gene affects two or more unrelated traits -- have one or more effect on the body, e.g., Sickle-cell disease. (more about this when we get to the evolution chapters.)


http://geneed.nlm.nih.gov/topic_subtopic.php?tid=142&sid=149




Polygenic inheritance, also called multifactorial traits, is when characteristics (traits) are determined by three or more alleles, and these are (unlike multiple allele traits) all present in each individual. Human skin color, and human eye color are examples.








X linked inheritance (Sex-linked trait). The X and Y chromosomes in all mammals -- including humans, determine the gender of an individual. Females are XX and males are XY.


XX = girl
XY = boy

 Q1: Probability of having a boy or a girl. (Do the Punnett Square?)



Source: Wikipedia (Karyotype)



The term X-linked is used for genes that are carried on the X chromosome and are absent on the much smaller Y chromosome.

Because the allele is absent on the Y chromosome, in males a recessive trait will be expressed even if only one allele is present; in females a recessive trait required both X chromosome to carry a recessive trait in order for it to be expressed. (Examples: Red/Green color blindness, Muscular dystrophy, and Hemophilia).



http://science.halleyhosting.com/sci/soph/genetics/notes/sexlinked.htm





7. Number of chromosomes in human somatic (body) cells?

a. 1
b. 2
c. 22
d. 23
e. 46

8. Number of chromosomes in human sex cells?

a. 1
b. 2
c. 22
d. 23
e. 46

9. Number of X chromosomes in a human female?

a. 1
b. 2
c. 22
d. 23
e. 46

10. Number of X chromosomes in a human male?

a. 1
b. 2
c. 22
d. 23
e. 46




Alleles in sex cells (XX= female; XY male)

XA = Red/Green Colorblind allele
XN = Red/Green Normal allele
Y0 = Red/Green color allele MISSING

http://primaryimmune.org/about-primary-immunodeficiencies/relevant-info/inheritance/



Offspring:

XAXA: Red/Green colorblind female
XAXN: Normal colorvision female (carrier)
XNXN>: Normal colorvision female
XNY0>: Normal colorvision male
XAY0 Red/Green colorblind female

Q2: If you are a colorblind boy, who should you "blame" for your colorblindness? Mom or dad?

Q3: Who have the highest chance of inhereting red/green colorblindness? Females or males?




Dihybrid Cross exercise:

(This is a F2F activity. Further information will be given in the classroom.)








- Punnett square fun (Khan Academy You Tube) -

COMMENT ON THE YOUTUBE: Reginald Crundall Punnett FRS (20 June 1875 ­ 3 January 1967) was a British geneticist who co-founded, with William Bateson, the Journal of Genetics in 1910. Punnett is probably best remembered today as the creator of the Punnett square, a tool still used by biologists to predict the probability of possible genotypes of offspring. There is where the Punnett came from.

If you have problems understanding the concept of the "Punnett square" here is an excellent YouTube video from Khan Academy, which will help you understand -- even though some of the information is beyond what is required for this class. It is 25 minutes long; I don't recommend that you try to view it from home unless you are connected via broadband. It takes too long to download via telephone modem. View it at STC instead...





Including good explanation of mutations, and a short review of meiosis and also transcription and translation -- which will be part of the NEXT topic.




- - - Connecting the Concepts - - -

A good experimental design (with garden peas that have many generations in a short time period, and visible characteristics to observe) and luck (since garden pea traits are controlled by two alleles only) allowed Mendel to discover the laws of inheritance. In the next chapter we will discuss how genes on chromosomes direct the production of proteins in the cytoplasm of cells, via an RNA intermediate. It is the activity (or inactivity) of these proteins that leads to the phenotypes discussed in this chapter -- some of which were genetic disorders.

(Source: Mader, S.S. 2010. Biology. Ed. 10. Used for educational purpose.)












pdf





1. Widow's Peak

Widows peak (dominant): W
Straight hairline (recessive): w



Ww (male) X Ww (female)
Genotypes?

Phenotypes?









Ww



W



w



Genotypes: ____________________________________________________

Phenotypes: ___________________________________________________




2. Bent Little Finger

Bent little finger (dominant): B
Straight little finger (recessive): b



BB (male) X bb (female)
Genotypes?

Phenotypes?









BB



b



b



Genotypes: ____________________________________________________

Phenotypes: ___________________________________________________




3. Albinism

Melanin production (dominant): A
Albino -- no melanin (recessive): a



aa (male) X Aa (female)
Genotypes?

Phenotypes?









aa



A



a



Genotypes: ____________________________________________________

Phenotypes: ___________________________________________________




4. Pigmented Iris

This is a Polygenic inheritance trait -- not a simple trait. The trait is controlled by three alleles.

Green, Brown, "Black" ("dominant"): P
Blue or Gray eyes ("recessive"): p





No cross...








5. Earlobes

Free earlobes (dominant): E
Attached earlobes (recessive): e






Carrier of recessive trait (male) X Carrier of recessive trait (female)
Genotypes?

Phenotypes?









Ee



E



e



Genotypes: ____________________________________________________

Phenotypes: ___________________________________________________




6. Hitchhiker's Thumb

Straight Thumb (dominant): H
Hitchhiker's Thumb (recessive): h



Homozygous dominant (male) X Homozygous recessive (female)
Genotypes?

Phenotypes?









HH



h



h



Genotypes: ____________________________________________________

Phenotypes: ___________________________________________________




7. Interlacing Fingers

Left thumb over right (dominant): C
Right thumb over left (recessive): c



Left thumb over right with homozygous dominant parents for the trait (male) X Right thumb over left (female)
Genotypes?

Phenotypes?









CC



c



c



Genotypes: ____________________________________________________

Phenotypes: ___________________________________________________





8. PTC Tasting

This is an Incompleye Dominance inheritance trait -- not a simple trait. The trait is controlled by two alleles, both are incompletely dominant, so a carrier will be an itermediate "mix". Also affected by the environment (e,g., smoking).

Taste ("dominant"): T
No taste ("recessive"): t




No cross...






9. Middigital Hair

Middigital hair (dominant): M
No hair (recessive): m



Heterozygous (male) X Heterozygous (female)
Genotypes?

Phenotypes?









Mm



M



m



Genotypes: ____________________________________________________

Phenotypes: ___________________________________________________




10. Dimpled Chin

Dimple (dominant): D
No dimple (recessive): d



DD (male) X no dimples (female)
Genotypes?

Phenotypes?









DD



d



d



Genotypes: ____________________________________________________

Phenotypes: ___________________________________________________




11. Six Fingers (Polydactyly)

Six fingers (dominant): S
Five fingers (recessive): s



Ss (male) X Ss (female)
Genotypes?

Phenotypes?









Ss



S



s



Genotypes: ____________________________________________________

Phenotypes: ___________________________________________________





12. Tongue Rolling

Rolled tongue (dominant): T
Flat tongue (recessive): t



Homozygous dominant tongue roller (male) X heterozygous tongue roller (female)
Genotypes?

Phenotypes?









TT



T



t



Genotypes: ____________________________________________________

Phenotypes: ___________________________________________________