2) The Flow of genetic information from RNA to Protein

When an amino acid is chemically linked to the ____' end of a tRNA, this process is known as _________________. Enzymes perform this chemical linking and they are known as ___________________________. It is believed there are ______ different ones, one to link each different amino acid to a tRNA.

- 3' carbon - charging - Aminoacyl tRNA synthetases - 20 different ones

Let's examine ribosomes. Note: there is no need for you to memorize the details of the ribosome components (i.e. numbers and sizes of the proteins and rRNAs). As always, answer the questions here for your guide of what to focus on. What two macromolecules make up ribosomes? How many subunits make up a ribosome?

- rRNA and proteins - 2 subunits make up a ribosome

Some proteins in eukaryotes will be secreted from the cell and these proteins are built on ribosomes that are associated with the __________________________.

Endoplasmic reticulum. The ribosomes typically have a tunnel in the larger subunit of the ribosome. Studies in Yeast show that newly synthesized polypeptide chains exit the ribosome through the tunnel, and a membrane channel (to the ER) is perfectly aligned with the end of the ribosomal tunnel

In the language of DNA, what is the start codon? ___ In the language of DNA, what are the three stop codons? ____ _____ and _____.

ATG, TAA, TAG, TGA

After unloading the amino acid, the tRNA relocates to the ___ site of the ribosome before it leaves the ribosome to get re-charged with another amino acid.

E

We can artificially break the dynamic process of translation into three phases:

Initiation, elongation, termination

We know that not all the DNA in the genome and not even all the genes in the genome code for protein. When we have sequence data, we can find protein coding genes by looking for ORFs. What's an ORF?

Open Reading Frames (ORF's) are sequences of triplet nucleotides that, after transcription and mRNA splicing, are translated into the amino acid sequence of a protein.

Once initiation is set, the reading frame is in place because the initial AUG start codon and the initial tRNA are in the ___ (A/P/E) site of the ribosome. (We won't be focusing on all the additional factors that help with initiation.)

P

tRNA contains a modified nucleotide, inosinic acid or inosine that will sometimes be part of the anticodon. Looking at Figure 13-2, is the nitrogenous base of inosine a purine or pyrimidine?

Purine

Termination. The process ends when one of the stop codons _____, _____ or _____ is encountered.

UAG, UAA, or UGA

What is meant by the 5' UTR and what is 3' UTR?

UTR = Untranslated region

Elongation. During elongation, amino acids are brought close together because they are bound to tRNAs in the P and A sites. What kind of bond forms between the two amino acids and what catalyzes this reaction?

a peptide bond forms between the two amino acids, and this is catalyzed by the rRNA that is present in the larger ribosomal subunit

Define annotation:

analysis of genomic nucleotide sequence data to identify the protein-coding genes, the nonprotein-coding genes, and the regulatory sequences and function(s) of each gene

There are two important sites on a tRNA, they are:

anti codon and the region that is covalently bonded to the corresponding amino acid

If UTRs are not translated, what do we need them for?

for post-transcriptional modifications as well as for translation efficiency (poly A tail at 3')

tRNAs and mRNA interact through what type of bond?

hydrogen bonds

What is the basis for recognition between the small ribosomal unit, the initiation factors, the charged tRNAMet molecule, and the mRNA (Fig 13-6)? In other words, what makes each component of the initiation complex bind to its partners?

the hydrogen bonds between the complementary base pairs

What is GenBank?

the largest publicly available database of DNA sequences

Is the code for the translation start site present in DNA?

yes

What are a few of the important applications of bioinformatics once we have loads to genomic sequence data?

Compare DNA sequences to identify genes, find gene-regulatory regions, and deduce evolutionary relationships between genes and organisms.

The ribosome moves down the mRNA and tRNAs enter and exit. The polypeptide grows. Use Fig 13-7 to follow the movement of the ribosome from the first AUG down the mRNA. Use this video to watch the dynamic process too: https://www.youtube.com/watch?v=Vu6LBOQSqiE Consider this scenario, at one point during elongation, the A site has the mRNA sequence CCG. What will the anticodon of the tRNA that binds to this sequence look like? _______ What amino acid will this tRNA be carrying? _____ (pg 222 has the codon chart).

GGC

See Figure 18.4 and draw it. This is an excellent summary of all the parts of a gene that you should now be familiar with:

LOOK AT PAGE 365 TO FIND THIS BULLSHIT; I'M NOT PAYING PREMIUM FOR PICTURES HELL NO (ALSO SAVED TO IPAD PICKS)

Is the promoter sequence present in the mature mRNA?

No

Is the transcription initiation site present in the mature mRNA? If so, where?

No, it is spliced out

In eukaryotes, how is the 5' cap on the mRNA related to translation?

The 5' cap on the mRNA increases the efficiency of translation in eukaryotes

What is the main function of the rRNA molecules that make up the ribosome and how do scientists know this?

The RNA molecules perform the all-important catalytic functions associated with translation. This was concluded by scientists because of experiments where catalytic functions in ribosomes still occurred in the "ribosomal protein-depleted" ribosomes.

Initiation. Keep in mind that the mRNA transcript begins at its 5' before the initial AUG start codon shown in Fig 13-6. In prokaryotes there is a sequence 5' (upstream) of the AUG that allows binding of what?

The small ribosomal subunit bonded with the IF1 (initiation factor 1) forms a complex, which is then allowed to bind to the mRNA. The sequence that is present upstream of the start codon contains only purines and is called the Shine-Dalgarno sequence. This sequence facilitates the initiation of translation by recruiting the ribosome to the messenger RNA (mRNA) to initiate protein synthesis and aligning the ribosome with the start codon.

What us the result of having mRNAs that exist longer in eukaryotes (not degraded) compared to prokaryotes that degrade within minutes?

They exist longer and are available much longer to orchestrate protein synthesis

The book state that ribosomes serve "as a nonspecific workbench for the translation process." What do you think this means?

This means that the ribosome isn't specialized for different types of proteins; it's compatible with producing all types of proteins, just as long as the mRNA translates for them.

Why would we use BLAST?

To compare a newly sequenced genomic DNA to a already known sequence.