April 11th, Friday

...So we picked up having last talked about Codons -  which are the code of three nulcleotides form 1 amino acid

Looking at the Table on slide (Graphic LE 17-5)

GGU  -   GGC  -  GGA  -  GGG      :  all code for glycine.

Those two first bases (GG)  are the most important.

The third base (the last letter of the triplet) in the codon is called the wobble base, which is the less important, varying member.

Of the 64 available, 61 codons code for a specific amino acid. 

There are Four Special Codons:

You will need to know this for the exam.

Codon	Purpose
AUG	START CODON as well as coding for Methiomine (Met.) It's classified as both a "Special" codon (for its start properties) -&- a "Regular" within our 64 group because it's really Met.
UAA UAG UGA	STOP CODONS: as soon as you come to one of these, you've reached the end of your polypeptide

mRNA sequence = codons do not overlap and are read continuously

ex: AUG  UAC CCG AAA  UAG

(They're read as one right after another) - we read this as:

AUG = START - Met.

UAC = tyrosine

CCG = prolene

AAA = lysine

UAG = STOP

However, given a sequence, AUG may not always be the first item of a given sequence.

Below is a charted verion showing Reading frames.

In easy to understand terms:

If I were to give a sequence, and told you to break it into Groups of three (from left to right) here's the first three ways I could do it.:

A C C U A U G G G C U U
A C C U A U G G G C U U
A C C U A U G G G CU U
A C C U A U G G G C UU

The Greyed is the original thing we're asked to group.

The first variation (RED) is if we started with the first term on the left, and just went down grouping 3's as we saw them (we get 4 complete codons)

The second variation (PURPLE) is if we start with the second term (C) and started our groupings (we get 3 complete codons and some extra singles)

The last variation (GREEN) is if we started at the Second Term (the other C) and started groupings (we get 3 complete codons, and extra singles)

The correct reading frame is the one where you can see our Start Sequence (AUG)

- so in our example above, the only break-down whichshows the AUG is in the 2nd example (PURPLE).

 THAT's our correct Reading Frame!

Genetic code is universal- all organisms use the same triplet code

• Evidence that all organisms are related
• At some time in the past they had common ancestor
• Biotechnology easier - genes from one organism wlll work in another (as far as protein translation)
• BT Plants (bacterial protein put in plants which produces a toxin that discourages pests)
• Picture - Firefly genes into a plant ---Pretty.

Mechanism of Transcription:

• Transcription Unit: A stretch of DNA that holds all the information necessary for the formation of one transcript.
• Enzyme - RNA Polymerase.
• Bulding blocks for RNA: ATP, CTP, UTP, GTP nucleotides
• (the sugar is ribose - did you catch that? If they weren't it would be DNA and the nucleotides would have a little 'd' in the front of them)

1. Transcription Initiation:

   • a.) promoter - DNA Sequence that regulate the expression of the gene. It's an on/off switch, upstream of the gene.
   • ~100 nt long
   • this is where RNA polymerase binds at the start of transcription.
   • Transcription factors - other proteins that bind at the promoter to turn on transcription - they are necessary for transcription of the gene at the proper time and in the proper cell.
2. Transcription Elongation:

•  RNA poly opens up DNA & transcribes the Template DNA to make RNA.

 3. Transcription Termination

•  special termination sequence that signals RNA polymerase to release from the DNA & to release the MRNA

RNA Processing - eukaryotes only

• occurs in the nucleus.
• pre-mRNA - just after transcription.

1. Cap added to the  5' end of the mRNA
2. There's a poly-A tail added to the 3' end (quite long ~ 200 nt of nothing but Adenine's)

What is the function of this?

1. Facilitate mRNA transport out of the nucleus.
2. Protects the mRNA from degradation once it gets to the cytosol. (messenger Rna is very easily degraded, so its a big help)

3. The cap & tail act as recognition sites to help bind mRNA to ribosome.

   
   

3.) Splicing: exons = sequence that will be part of proteins. (exons = EXpressed regiONS)

                  introns = sequences that will not be part of proteins ( introns = INTeRvening regiONS)

     removal of the introns & splicing (joining) the exons together into one continuous sequence.

mature mRNA --> move into the cytosol

UTR = untranslated region.

Evolutionary significance of exons & introns:

Exon Codes for a protein domain = particular function.

• break down ATP
• active site for enzyme
• seq that makes it attach to a particular membrane in the cell

(Slide LE 17-12 )

Mechanism of Translation:   mRNA ---> Protein

Transfer RNA (tRNA) translated mRNA codon to the amino acid sequence

-single stranded, folds back on itself & parts are double stranded

-anti-codon = 3nt sequence that is complementary to the codon of mRna

-amino acid binding site

tRNA - amino acid linkages are specific based on the anti-codon

mRNA 5 ' UCA 3'  = codon

  tRNA 3 ' AGU 5' = anti-codon (serine = amino acid linked to tRNA)

Overview of translation:

1.) mRNA binds to the ribosome

2.) each tRNA is "loaded" with it's appropriate amino acid (amino acid activation) and moves to the ribosome.

3.) Complementary anti-codon of tRNA (with its amino acid) recognizes the corresponding codon of mRNA.

4.) Ribosomal enzymes (probably RNA not protein) connect the new amino acid to the polypeptide chain.