1. Anatomy and Physiology Genetic Unit

2. MENDEL'S GENETIC LAWS
Once upon a time (1860's), in an Austrian monastery, there lived a monk named Mendel, Gregor Mendel. Monks had a lot of time on their hands and Mendel spent his time crossing pea plants. As he did this over & over & over & over & over again, he noticed some patterns to the inheritance of traits from one set of pea plants to the next. By carefully analyzing his pea plant numbers (he was really good at mathematics), he discovered three laws of inheritance.
Mendel's Laws are as follows:
1. the Law of Dominance 2. the Law of Segregation 3. the Law of Independent Assortment
Now, notice in that very brief description of his work that the words "chromosomes" or "genes" are nowhere to be found.  That is because the role of these things in relation to inheritance & heredity had not been discovered yet. What makes Mendel's contributions so impressive is that he described the basic patterns of inheritance before the mechanism for inheritance (namely genes) was even discovered.

3. Section #1
GENOTYPE = the genes present in the DNA of an organism.  Use a pair of letters (ex: Tt or YY or ss, etc.) to represent genotypes for one particular trait.  There are always two letters in the genotype because (as a result of sexual reproduction) one code for the trait from mom & the other comes from dad, so every offspring gets two codes (two letters).
Now, turns out there are three possible GENOTYPES - two big letters (like "TT"), one of each ("Tt"), or two lowercase letters ("tt").
When we have two capital or two lowercase letters in the GENOTYPE (ex: TT or tt) it's called HOMOZYGOUS ("homo" means "the same").  Sometimes the term "PURE" is used.
When the GENOTYPE is made up of one capital letter & one lowercase letter (ex: Tt) it's called HETEROZYGOUS ("hetero" means "other").  A heterozygous genotype can also be referred to as HYBRID.

4. PHENOTYPE = how the trait physically shows-up in the organism
PHENOTYPE = how the trait physically shows-up in the organism.  What they look like! 
ALLELES = (WARNING - THIS WORD CONFUSES PEOPLE; READ SLOW) alternative forms of the same gene.  Alleles for a trait are located at corresponding positions on homologous chromosomes. Remember genotypes I said that "one code (letter) comes from ma & one code (letter) comes from pa"? Well "allele" is a fancy word for what I called codes.
For example, there is a gene for hair texture (whether hair is curly or straight).  One form of the hair texture gene codes for curly hair.  A different code for of the same gene makes hair straight.  So the gene for hair texture exists as two alleles --- one curly code, and one straight code.

5. The Law of Dominance
In a cross of parents that are pure for contrasting traits, only one form of the trait will appear in the next generation.  Offspring that are hybrid for a trait will have only the dominant trait in the phenotype.
Cross pure yellow and pure green, yellow is dominate to green?
Cross 2 heterozygous yellow plants?

6. Let's revisit the three possible genotypes for pea plant height
Genotype Symbol
Genotype Vocab
Phenotype TT
homozygous DOMINANT or pure tall
Tall Tt
heterozygous or hybrid tt
homozygous RECESSIVE  or pure short
Short

7. Note: the only way the recessive trait shows-up in the phenotype is if the geneotype has 2 lowercase letters (i.e. is homozygous recessive). Also note: hybrids always show the dominant trait in their phenotype (that, by the way,  is Mendel's Law of Dominance in a nutshell).
ANY TIME TWO PARENT ORGANISMS LOOK DIFFERENT FOR A TRAIT, AND ALL THEIR OFFSPRING RESEMBLE ONLY ONE OF THE PARENTS, YOU ARE DEALING WITH MEDEL'S LAW OF DOMINANCE.

8. Here are the basic steps to using a Punnett Square when solving a genetics question
BABY STEPS: 1. determine the genotypes of the parent organisms 2. write down your "cross" (mating) 3. draw a p-square 4. "split" the letters of the genotype for each parent & put them "outside" the p-square 5. determine the possible genotypes of the offspring by filling in the p-square 6. summarize results (genotypes & phenotypes of offspring)

9. Step #1: Determine the genotypes of the parent organisms.
"Cross a short pea plant with one that is heterozygous tall. Tall is dominant to short".   
T= tall
t= short
Parent 1 tt
Parent 2 Tt

10. Step 2 , 3 and 4
Step #2: Write down your "cross" (mating).  Write the genotypes of the parents in the form of letters (ex: Tt x tt).
Step #3: Draw a p-square. 
Step #4:"Split" the letters of the genotype for each parent & put them "outside" the p-square.
t t
T= Tall
t= short T t

11. Step #5: Determine the possible genotypes of the offspring by filling in the p-square.
T= Tall
t= short

12. Step #6: Summarize the results (genotypes & phenotypes of offspring).
Simply report what you came up with.  You should always have two letters in each of the four boxes.
Genotype (what the genes look like) 2=Tt and 2=tt
Phenotype (what the offspring look like) 2 tall and 2 short

13. You know how, in Step #4, when we "split" the letters of the genotype & put them outside the p-square?  What that step illustrates is the process of gametogenesis (the production of sex cells, egg & sperm). 
Gametogenesis is a cell division thing (also called meiosis) that divides an organism's chromosome number in half. 
For example, in humans, body cells have 46 chromosomes a piece.  However, when sperm or eggs are produced (by gametogenesis/meiosis) they get only 23 chromosomes each.  When the sperm & egg fuse at fertilization, the new cell formed (called a zygote) will have = 46 chromosomes. 

14. Section #2 The Law of Segregation
During the formation of gametes (eggs or sperm), the two alleles responsible for a trait separate from each other.  Alleles for a trait are then "recombined" at fertilization, producing the genotype for the traits of the offspring.

15. Now, when completing a Punnet Square, we model this "Law of Segregation" every time.  When you "split" the genotype letters & put one above each column & one in front of each row, you have SEGREGATED the alleles for a specific trait. In real life this happens during a process of cell division called "MEIOSIS". 
You can see from the p-square that any time you cross two hybrids, 3 of the 4 boxes will produce an organism with the dominant trait (in this example "TT", "Tt", & "Tt"), and 1 of the 4 boxes ends up homozygous recessive, producing an organism with the recessive phenotype ("tt" in this example).

16. Any time two parents have the same phenotype for a trait  but some of their offspring look different with respect to that trait,  the parents must be hybrid for that trait. 

17. The Law of Independent Assortment
Alleles for different traits are distributed to sex cells (& offspring) independently of one another.
OK. So far we've been dealing with one trait at a time.  For example,  height (tall or short), seed shape (round or wrinkled), pod color (green or yellow), etc.  Mendel noticed during all his work that the height of the plant and the shape of the seeds and the color of the pods had no impact on one another.  In other words, being tall didn't automatically mean the plants had to have green pods, nor did green pods have to be filled only with wrinkled seeds, the different traits seem to be inherited INDEPENDENTLY.
Please note my emphasis on the word "different".  Nine times out of ten, in a question involving two different traits, your answer will be "independent assortment".  There is a punnet square that illustrates this law. It involves what's known as a "dihybrid cross", meaning that the parents are hybrid for two different traits.

18. The genotypes of our parent pea plants will be:
RrGg x RrGg "R" = dominant allele for round seeds "r" = recessive allele for wrinkled seeds "G" = dominant allele for green pods "g" = recessive allele for yellow pods
Notice that we are dealing with two different traits: (1) seed texture (round or wrinkled) & (2) pod color (green or yellow).  Notice also that each parent is hybrid for each trait (one dominant & one recessive allele for each trait).
We need to "split" the genotype letters & come up with the possible gametes for each parent.  Keep in mind that a gamete (sex cell) should get half as many total letters (alleles) as the parent and only one of each letter. So each gamete should have one "are" and one "gee" for a total of two letters.  There are four possible letter combinations: RG, Rg, rG, and rg. These gametes are going "outside" the p-square, above 4 columns & in front of 4 rows.  We fill things in just like before --- "letters from the left, letters from the top". When we finish each box gets four letters total (two "are's" & two "gees").

19. The results from a dihybrid cross are always the same for 2 heterozygous parents: 9/16 boxes (offspring) show dominant phenotype for both traits (round & green), 3/16 show dominant phenotype for first trait & recessive for second (round & yellow), 3/16 show recessive phenotype for first trait & dominant form for second (wrinkled & green), & 1/16 show recessive form of both traits (wrinled & yellow).
So, as you can see from the results, a green pod can have round or wrinkled seeds, and the same is true of a yellow pod.  The different traits do not influence the inheritance of each other.  They are inherited INDEPENDENTLY.
Interesting to note is that if you consider one trait at a time, we get "the usual" 3:1 ratio of a single hybrid cross (like we did for the LAw of Segregation). For example, just compare the color trait in the offspring; 12 green & 4 yellow (3:1 dominant:recessive).  Same deal with the seed texture; 12 round & 4 wrinkled (3:1 ratio).  The traits are inherited INDEPENDENTLY of eachother --- Mendel's 3rd Law.  

20. In a dihybrid cross…If two heterozygous round, yellow plants are crossed…yellow is dominate to green and round is dominate to wrinkled what are the genotype & phenotype?
1st write your letters…
Y= yellow
y= green
S= spherical/round
s= wrinkled
2nd write your parents…
YySs

21. Pair up the letters 1st pairs with 3rd , 1st with 4th, then 2nd letter with 3rd, 2nd with 4th

23. Next drop in your letters bring both letters down separate them by letter S or Y and always put the capitol letter first…

24. Now count up the genotype (letter combination square by square)
Genotypes:
SSYY :1
SSYy :2 SsYY :2 SsYy :4
SSyy :1 Ssyy :2
ssYY:1 ssYy :2
ssyy :1

25. Then do the Phenotype what they look like
9 yellow, round
3 yellow, wrinkled
3 green, round
1 green, wrinkled

26. Summarize Mendel's Laws by listing the cross that illustrates each.
PARENT CROSS
OFFSPRING
DOMINANCE
TT x tt tall x short
100% Tt tall
SEGREGATION
Tt x Tt tall x tall
75% tall 25% short
INDEPENDENT ASSORTMENT
RrGg x RrGg round & green x round & green
9/16 round seeds & green pods 3/16 round seeds & yellow pods 3/16 wrinkled seeds & green pods 1/16 wrinkled seeds & yellow pods

27. Mendel’s work has stood the test of time, even as the discovery & understanding of chromosomes & genes has developed in the 140 years after he published his findings.  New discoveries have found "exceptions" to Mendel's basic laws, but none of Mendel's things have been proven to be flat-out wrong.

28. Section #3 IncOMpleTe & COdominANce
In many ways Gregor Mendel was quite lucky in discovering his genetic laws.  He happened to use pea plants, which happened to have a number of easily observable traits that were determined by just two alleles.  And for the traits he studied in his peas, one allele happened to be dominant for the trait & the other was a recessive form.  Things aren't always so clear-cut & "simple" in the world of genetics, but luckily for Mendel (& the science world) he happened to work with an organism whose genetic make-up was fairly clear-cut & simple.
INCOMPLETE DOMINANCE
If Mendel were given a mommy black mouse & a daddy white mouse & asked what their offspring would look like, he would've said that a certain percent would be black & the others would be white.  He would never have even considered that a white mouse & a black mouse could produce a GREY mouse!  For Mendel, the phenotype of the offspring from parents with different phenotypes always resembled the phenotype of at least one of the parents.  In other words, Mendel was unaware of the phenomenon of INCOMPLETE DOMINANCE.  

29. I remember Incomplete Dominance in the form of an example like so: RED Flower x WHITE Flower ---> PINK Flower 
With incomplete dominance, a cross between organisms with two different phenotypes produces offspring with a third phenotype that is a blending of the parental traits.  It's like mixing paints, red + white will make pink.  Red doesn't totally block (dominate) the white, instead there is incomplete dominance, and we end up with something in-between.
We can still use the Punnett Square to solve problems involving incomplete dominance.  The only difference is that instead of using a capital letter for the dominant trait & a lowercase letter for the recessive trait, the letters we use are both going to be capital (because neither trait dominates the other).  So the cross I used up above would look like this:

30. INCOMPLETE DOMINANCE
R = allele for red flowers W = allele for white flowers
red x white ---> pink RR x WW ---> 100% RW

31. The trick is to recognize when you are dealing with a question involving incomplete dominance.  There are two steps to this: 1) Notice that the offspring is showing a 3rd phenotype.  The parents each have one, and the offspring are different from the parents. 2) Notice that the trait in the offspring is a blend (mixing) of the parental traits.

32. CODOMINANCE
First let me point out that the meaning of the prefix "co-" is "together". Cooperate = work together.  Coexist = exist together.  Cohabitat = habitat together.
The genetic gist to codominance is similar to incomplete dominance.  A hybrid organism shows a third phenotype --- not the usual "dominant" one & not the "recessive" one ... but a third, different phenotype.  With incomplete dominance we get a blending of the dominant & recessive traits so that the third phenotype is something in the middle (red x white = pink).
In COdominance, the "recessive" & "dominant" traits appear together in the phenotype of hybrid organisms.

33. I remember codominance in the form of an example like so:
red x white ---> red & white spotted
With codominance, a cross between organisms with two different phenotypes produces offspring with a third phenotype in which both of the parental traits appear together. 
When it comes to punnett squares & symbols, it's the same as incomplete dominance.  Use capital letters for the allele symbols.  My example cross from above would look like so:

34. CODOMINANCE R = allele for red flowers W = allele for white flowers
red x white ---> red & white spotted RR x WW ---> 100% RW

35. The symbols you choose to use don't matter, in the end you end up with hybrid organisms, and rather than one trait (allele) dominating the other, both traits appear together in the phenotype.  codominance.
A very very very common phenotype used in questions about codominance is roan fur in cattle.  Cattle can be red (RR = all red hairs), white (WW = all white hairs), or roan (RW = red & white hairs together).  A good example of codominance.
Another example of codominance is human blood type AB, in which two types of protein ("A" & "B") appear together on the surface of blood cells.

36. MULTIPLE ALLELES
It makes absolutely no sense whatsoever to continue if we don't know what the word "allele" means.
allele = (n) a form of a gene which codes for one possible outcome of a phenotype
For example, in Mendel's pea investigations, he found that there was a gene that determined the color of the pea pod.  One form of it (one allele) creates yellow pods, & the other form (allele) creates green pods.
Get it? Two possible phenotypes of one trait (pod color) are determined by two alleles (forms) of the one "color" gene.

37. Y = the dominant allele for yellow
y = the recessive allele for green
Genotypes
RESULTING PHENOTYPE
Homozygous Dominant (YY) Heterozygous (Yy) Homozygous Recessive (yy)
Yellow
Green

38. If there are only two alleles involved in determining the phenotype of a certain trait, but there are three possible phenotypes, then the inheritance of the trait illustrates either incomplete dominance or codominance.
In these situations a heterozygous (hybrid) genotype produces a 3rd phenotype that is either a blend of the other two phenotypes (incomplete dominance) or a mixing of the other phenotypes with both appearing at the same time (codominance).

39. THE DEALS ON MULTIPLE ALLELES
Now, if there are 4 or more possible phenotypes for a particular trait, then more than 2 alleles for that trait must exist in the population.  We call this "MULTIPLE ALLELES".
Let me stress something.  There may be multiple alleles within the population, but individuals have only two of those alleles.
Why?
Because individuals have only two biological parents.  We inherit half of our genes (alleles) from ma, & the other half from pa, so we end up with two alleles for every trait in our phenotype.
An excellent example of multiple allele inheritance is human blood type. Blood type exists as four possible phenotypes: A, B, AB, & O.
There are 3 alleles for the gene that determines blood type. (Remember: You have just 2 of the 3 in your genotype from mom & 1 from dad).

40. ALLELE IA IB i
CODES FOR Type "A" Blood Type "B" Blood Type "O" Blood
GENOTYPES IAIA IAi
IBIB
IBi
IAIB ii
RESULTING PHENOTYPES Type A Type A Type B Type B
Type AB
Type O

41. As you can count, there are 6 different genotypes & 4 different phenotypes for blood type.
Note that there are two genotypes for both "A" & "B" blood --- either homozygous (IAIA or IBIB) or heterozygous with one recessive allele for "O" (IAi or IBi).
Note too that the only genotype for "O" blood is homozygous recessive (ii).
And lastly, what's the deal with "AB" blood?  What is this an example of?  The "A" trait & the "B" trait appear together in the phenotype.  Think think think ....

42. Lubey, Steve. Lubey's Biohelp. - Mendel's Genetic Laws. Aug
Lubey, Steve. Lubey's Biohelp! – Incomplete & Codominance. Aug. 26, 2005 <
Lubey, Steve. Lubey's Biohelp! – Multiple Alleles. Aug. 26, 2005 <
Mendel Image.