Practice problems in Genetics and the topic of Sex Linkage

Here's a worksheet for Monohybrid crosses : http://www.biologycorner.com/worksheets/genetics_practice.html
And here is its answer key: http://www.biologycorner.com/worksheets/genetics_practice_key.html
try some sex linkage questions here: http://www.k-state.edu/biology/pob/genetics/intro.htm

SEX LINKED GENES

The sex chromosomes are XX and XY in humans. Some alleles are located on the X chromosome. But very few on the Y chromosome.  Remember that females have the genotype XX and males have XY.

The Y chromosome carries very little information, only enough to influence the embryo on the path towards male primary and secondary characteristics.

Meanwhile, many RECESSIVE ALLELES are located on the X chromosome, including
1. hemophilia, the inability to clot blood
2. colourblindness inability to tell the difference between red and green colour
3.  baldness

These characteristics are far more common in men than women because men have only one X. And if that X contains the recessive allele, they will show the phenotype.  Meanwhile, women may have the recessive and their "normal" dominant X will protect them.  For example

An example of using a punnet square to calculate probability is here:

Some things to note about sex linkage:  Signs of sex linked alleles are:
1. more males get the phenotype, but women can be carriers
2.  men can inherit from mother but not father (because men get their X from mom)
3.  Women have an extra X and this protects them.  Women must be homozygous to show the sex linked phenotype.
Further reading on sex linkage here http://learn.genetics.utah.edu/content/pigeons/sexlinkage/

FYI if you are a guy and you want to know if you're colourblind:  Test yourself here: Apparently most men find out they are colourblind from their science teacher...
http://colorvisiontesting.com/home.html

codominant alleles: Blood type

What if the heterozygous trait exhibited codominance?  in this case, two homologous alleles can code for co-dominant traits.  That is neither is dominant over the other.  Blood type is an example of this:
A is codominant to B
A is dominant over O
B is dominant over O

Possible genotypes:

heterozygous AB blood gives both type A and B on the erythrocytes
homozygous AA gives blood type A  protein on the erythrocytes
homozygous BB is blood type B protein on the erythrocytes
Heterozygous AO is gives blood type A
Heterozygous BO is blood type B

homozygous recessive OO gives blood type O or neither A or B on erythrocytes.

You have heard that blood type is important for blood transfusions. That is because the immune system will always attack an unknown protein.  Thus

type A person can receive  type A blood, and will reject type B blood
type B person can receive type B blood and will reject type A
type AB person can receive type A blood and Type B blood
Type O person can receive nobody's blood except from another type O

Everyone can receive type O, No-one can receive type AB

Blood type is heritable and that means you can sometimes deduce genotype by looking at phenotype. Here is a sample question:

Dominant, Recessive alleles and using Punnet Squares.

Alleles come in pairs and a GENOTYPE IS a pair of alleles which code for a PHENOTYPE.  Phenotype refers to the observed characteristic.
For example:

B= brown eyed allele   and    b = blue eyed allele
Genotype   Bb will give the PHENOTYPE of brown eyes because B is dominant over b.

GENOTYPE BB is homozygous dominant = brown eyes
GENOTYPE Bb is heterozygous = brown eyes
bb is homozygous recessive = blue eyes.

This is a case of COMPLETE DOMINANCE and it results in grandparents passing traits to grandchildren:

If a BB person mates with a bb person, we can calculate probability of their offspring traits using a punnet square:

When Baby grows up, she mates with this guy who happens to have the same GENOTYPE!

Note that a recessive allele can be hidden inside a HETEROZYGOUS genotype.

Introduction to Genetics

Gregor Mendel, monk, was the father of Genetics.

Last day we had an introduction to Genetics and we defined these terms:
Gene
Allele
Chromatin, Chromatid, Chromosome
Homologous pair of Chromosomes
diploid number vs haploid number or 2n vs n
Human diploid number = 46 chromosomes or 23 pairs, here they are below for a male human

Courtesy National Human Genome Institute http://www.genome.gov/glossary/resources/karyotype.pdf

Each of the HOMOLOGOUS CHROMOSOMES above  can contain many pairs of alleles.  To understand this, we considered an analogy of shoes...

A review of Gene, Chromatin, Chromosome and inheritance

INHERITANCE is the ability to pass on traits from one generation to another.
The first experiments on inheritance was from farmers.  They made PUREBRED and HYBRID organisms to help them control the breeding of useful traits.  Every population has variation and by selecting certain traits to breed, one can get a purebred characteristic.  For example.  Suppose there is a population of bunnies:  white, brown, black, grey.  If you wanted to get only grey baby bunnies, you can SELECTIVELY BREED the grey ones.

The first experiments to look at the LAWS OF INHERITANCE was conducted by GREGOR MENDEL, a monk.  He called purebreds HOMOZYGOUS.  He called hybrids HETEROZYGOUS.

A Gene is a section of DNA which codes for a  protein. Note how it looks in Chromatin form and also Chromatid form.

A chromosome usually refers to a  duplicated chromatid.  It is a double copy of the DNA for the purpose of asexual or sexual reproduction.  Chromosomes become visible only during reproduction.

Chromatids are HOMOLOGOUS, that is, they come in pairs. In Eukaryotes, a PAIR OF GENES located on a PAIR OF CHROMATIDS  codes for one trait.

quiz next day: define the following words and download some summary notes

Adaptation
Fitness
Natural selection -
Transcription -
Translation -
mRNA
tRNA
rRNA -

CODON -
Anti CODON -

Promoter -

What are two forms of protection for the mRNA? -
What are the two parts of a ribosome -
How does the ribosome attach the amino acids? -
What is the start CODON and what amino acid does it code for? -
What are the stop CODONS?

If the DNA is this?  
Then what is the mRNA and what is the amino acid?

SUMMARY NOTES:
DNA and Protein Synthesis, a summary of DNA replication (a review), and the Central Dogma of DNA, RNA and protein synthesis
DNA and Protein Synthesis worksheet
Fun converting DNA to RNA and RNA to Amino Acids

our diagrams, note the correction in red

Codon song sung to the tune of YMCA

The Lyrics are here:from Biology Karaoke.  Put it on your playlist

t.R.N.A.

(to the tune of "Y.M.C.A.")

words by Frank Virzi

Codons - they've been looking for you;

anticodons - don't forget your delivery,

hold on, and remember to carry the

right a-mi-no acid

Details of DNA transcription and translation

Amino acids are made of a carboxyl group and amine group and an R group.  
they are the subunits for polypeptide chains which ultimately make a protein.

There are twenty one amino acids which correspond to a CODON. This forms the GENETIC CODE

Transcription: mRNA is made from the DNA strand
1.   DNA unwinds and a promoter region is exposed.  There is a SENSE STRAND (TEMPLATE STRAND) of DNA to make RNA.
2.  RNA polymerase synthesizes the mRNA from a 5' to 3' direction.  RNA nucleotides are attached only on the 3' end.
3.  When the mRNA is complete it undergoes processing
 a.EDITING THE mRNA STRAND:  INTRONS are removed and EXONS remain.
b.  A polyA tail and 5' cap are placed on the mRNA in order to protect the strand from exonuclease.  Exonucleases digest and recycle mRNA.  We want them to avoid digesting the mRNA while it is being read by the ribosome
4.  mRNA is now ready for the ribosome.  IN EUKARYOTES, it leaves the nucleus.  IN PROKARYOTES, protein synthesis starts right away

Translation:  mRNA gets read by the ribosome and a polypeptide chain is formed
 Initiation: 
1. METHIONINE is the first amino acid brought by a tRNA.  tRNA has an ANTICODON which is complementary to the mRNA CODON.  The START CODON IS ALWAYS AUG. Meanwhile, the small ribosomal subunit attaches to the strand.
2.  Next the large ribosomal subunit arrives with its P site and A site.

AMINO ACYL T-RNA is the name of the tRNA attached to the amino acid.

the following is excerpted from this website as a quote:
 and is attributed to mrsdaintreysonlineclassroom. retrieved
january 20, 2016:  

Elongation
more amino acids are added and connected together to form a polypeptide, as specified by the mRNA sequence.
i. an incoming amino-acyl-tRNA (lets call this AA2-tRNA2) recognizes the codon in the A site and binds there.
ii. a peptide bond is formed through dehydration synthesis between the new amino acid and the growing polypeptide chain.
iii. the amino acid is removed from tRNA1 (bond breaks between aa1 and tRNA1)
iv. the tRNA1 that was in the P site is released, and the tRNA in the A site is translocated to the P site.
v. the ribosome moves over one codon along the mRNA (to the right in our diagram, or more specifically in the 5' ----> 3' direction.)
vi. This movement shifts the tRNA2 (which is attached to the growing amino acid chain) to the P site.
vii. tRNA3 with aa3 can now move into A site and bind with the next codon on mRNA.
viii. THIS PROCESS REPEATS, and the CHAIN ELONGATES as long as there are new codons to read on the mRNA. 

Termination
The process above repeats until a special codon, called a STOP CODON, is reached. There are 3 Stop codons: UAA, UAG, UGA.
i. the stop codons do not code for amino acids but instead act as signals to stop translation.
ii. a protein called release factor binds directly to the stop codon in the A site. The release factor causes a water molecule to be added to the end of the polypeptide chain, and the chain then separates from the last tRNA.

3. the protein is now complete. The mRNA is now usually broken down by exonuclease  and the ribosome splits into its large and small subunits.
   
4. the new protein is sent for final processing into the endoplasmic reticulum and golgi apparatus 
   

DNA, RNA and Protein Synthesis

Last period we discussed how DNA relates to the ADAPTATIONS in any organism and how these adaptations influence FITNESS.  We learned that your elderly granny has demonstrated more fitness in her youth than you presently have and we explored how DNA TRANSCRIPTION and TRANSLATION turns a one dimensional genomic "sentence" into a three dimensional protein or POLYPEPTIDE CHAIN.

We learned that DNA is a code with an alphabet of only four nucleotide letters: ATCG  and RNA differs only in the pyrimidine Uracil for AUCG.  RNA is like DNA in another coding language. Also, The "words" that these nucleotides form are called CODONS and a group of CODONS  can be translated  into a strand of molecular pearls called a polypeptide chain made out of little "pearls" the AMINO ACIDS.  The actors who orchestrate all this:  The RIBOSOMES who read the RNA, AND THE tRNA who fetch the correct amino acid.

These AMINO ACIDS are polar and thus their positive and negative poles cause the strand of pearls to bend and fold into a meaningful SHAPE.  This is the shape, colour and texture of life:  The feathers, the colours, the textures, spider silk, eye lash, the retina of an elephant, blood protein.  The shape of the protein is critical for its function, especially if that protein is an ENZYME.

An ENZYME is a biochemical catalyst and its SHAPE allows it to catalyze chemical reactions.  If an enzyme changes shape it ceases to function.  If all of our enzymes did that....it is a death sentence.

IN SUMMARY
DNA to RNA: TRANSCRIPTION
RNA to polypeptide chain: TRANSLATION
polypeptide chain folds into a correct 3D shape:  PROTEIN SYNTHESIS
The Environment selects some organisms to live and some to die in an elimination game: NATURAL SELECTION

Next period:  The Details of transcription , translation and protein synthesis
In addition to our Cartooon notes distributed in class, Here are some review materials for you.
DNA and Protein Synthesis, a summary of DNA replication (a review), and the Central Dogma of DNA, RNA and protein synthesis
DNA and Protein Synthesis worksheet
Fun converting DNA to RNA and RNA to Amino Acids

VGH David F. Hardwick Pathology Centre Field trip January 6

Please meet at Starbucks at the corner of Oak and 12th 

MORNING CLASS at 9:15AM

AFTERNOON CLASS at 12:15 NOON

We will then take attendance and proceed to 2775 Laurel St to the 

David F. Hardwick Pathology Centre to listen to a talk on pathology.  Please take the time to sign the card I will prepare for our host who is so generous with her time and expertise.


Our contact is Helen Dyck at
Diamond Health Care Centere, second floor near washrooms, Room 2201, 2775 Laurel Street,