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, 

Detailed Checklist for your Biomolecules test, 65 marks. Updated

1.  Know your illustration handouts: There will be 50 questions, multiple choice, short answer, or matching on these  booklets of drawing handouts.

     a. Examples of Biomolecules, Polymers are made of monomers, hydrolosysis and dehdydration
         synthesis, Water in, Water out, Biology Karaoke lyrics

     b. BONDS in biology - ionic, covalent, polar covalent, nonpolar covalent,
          name 7 properies of water,    
         Organic always contains CHO, Functional Groups (recognize all functional groups,
         Writing organic chemistry, drawing a glucose
         molecule

     c.  Carbohydrates: Monosaccharides, Disaccharides and Polysaccharides

     d.  Fat Facts: Be prepared to draw all parts of this illustrated booklet!  NOTE THAT THE DEFINITION OF SATURATED AND UNSATURATED TRIGLYCERIDES DIFFER FROM THE RAYCROFT NOTES.  Use the fact facts sheet as the definitive answer!!!

     e.  DNA is made of nucleotide letters, DNA structure:
         Be prepared to draw the ladder structure of DNA

2.  Review worksheets.  Be very familiar with all the answers of the  questions on the following worksheets:  They contain details from the illustrations above. The same 50 questions  mentioned above will be referencing these handouts.
      Fats,Carbohydrates and Nucleic acids. For the key, see the keywords and illustrations in
     the Biomolecule Summary Notes.  see note on fats above.

3.  In the Text be able to draw p. 54 and 55.

4.  Know the story of Watson Crick and Franklin.  There will be two questions on the discovery of DNA.
5.  There will be 15 marks on the labs and demos we did: You must choose ONLY three of the following four topics to write a paragraph about in detail
      a.  The Dry ice lab:  Summarize your observations during this lab.  What happens when you add solid carbon dioxide to water?  What acid is formed when Carbon dioxide is added to water?  
      b.  Drinking Milk: Lactose free milk is sweeter than regular milk.  Explain this demo in detail. 
      c.   Dropping food colouring in milk, and then adding soap, creates beautiful designs. 
     Describe what happens and explain how using your knowledge of polar and nonpolar interactions, 
     especially with soap.
      d.   You attended the Don Rix Distinguished Lecture or the DNA Fingerprint Lab.  
            Write a little summary of what you learned from these experiences.  I understand the science
      involved is university level thus I only need a description of your highlights of what you gathered 
      from these experiences rather than the university level vocab words. 
       e.  During the dry ice lab, an equation was written.  This equation was an equilibrium equation describing the carbonic acid buffer.  Describe how this equilibrium equation helps the body maintain homeostasis. 
6.  REVIEW SONGS: Know the lyrics of your songs especially a. and b.  and know what c. and d. are about.    
     a. DNA Replication Song
     b.  Water In and Water Out LYRICS from section 1a. above. sung to "Waterloo"
     c.   Take me to the Liver (a song about high density lipoprotein and their role to move 
          cholesterol back to the liver.) lyrics and mp3
     d.   Glucose song   
     

Poll for date of Biochemistry Test.

Fill out the poll here.  Bring completed worksheets on Carbohydrates, Fats, Nucleic acids next block.

Answers to worksheets in the Biomolecule summary notes

Today I'm actually here for half day (afternoon). I've just recovered from bronchitis.  Thanks for your patience.  Last period, you were given a worksheet on Fats, Carbohydrates and Nucleic acids. For the key, see the keywords in the Biomolecule Summary Notes.  The worksheet answers are in the sections starting on page 8. 
HW: Review the chapter and read the section on protein. Proteins and Acid/Base review will be our last topics before a comprehensive review and test coming up.  Our final lab will be on Potions, biological potions made from the buffer carbonic acid