Cell Biology lecture 8

5’ Capping

Addition of a methylated Guanylate (G) at 5’end of a mRNA

3' poly(A) adenylation

addition of 100- 250 adenylates (A) at 3’end

codon

group of 3 consecutive nucleotides in the coding

region in mRNA

start codon

AUG, encodes methionine, is used to initiate protein synthesis

stop codons

codons that signal the termination of protein synthesis, UAA, UAG, UGA

Reading frames

three possible ways of reading the 3-nucleotide

codons in DNA or RNA

open reading frame

The reading frame that encodes a protein

How many amino acids, tRNAs, and codons are thier

20 amino acids, 30-40 tRNAs, and 64 codons

What is unique about bases in tRNA

They have non standard bases

tRNA synthetase

combines an

amino acid and its compatible tRNA

wobble position

The third base of a codon

can form a nonstandard

base pair with an anti-

codon.

Why are their 64 codons but only 30-40 tRNAs

Because the wobble position allows for one tRNA anticodon to bind to more than one type of codon

A site

binding site for Amino acid-tRNA

P site

binding site for peptidyl-tRNA

E site

tRNA exit site

Translation Processes

Initiation, Elongation, Termination

Initiation steps

1. Initiation factors cause small subunit of ribosome and met-tRNA to bind to mRNA at AUG

2. Large subunit connects to the top putting met-tRNA in the P site

3. Another tRNA binds to the A site and met binds to its amino acid with help of peptidyltransferase

Elongation steps

1. aminoacyl-tRNA is brought to A site

2. aa chain of the peptidyl-tRNA of the p site connects to the aminoacyl-tRNA of a site.

3. Ribosome scoots over placing the newly formed peptidyl-tRNA in the P site and the old peptidyl-tRNA (now just naked tRNA) to the E site where it is ejected

Termination steps

1. Stop codon is found under the A site

2. instead of tRNA, a release factor binds to the A site

3. Release factor causes translation complex to dissociate letting the newly formed protein free

How does each tRNA get the correct amino acid

Aminoacyl-tRNA synthetases recognize one amino acid, and

the tRNA(s) that correspond to that amino acid, and even proofreading sites.

What happens if wrong aa is bonded to the wrong tRNA

The ribosome doesn’t know the difference, because it only looks at the codons, so the incorrect amino acid will be injected into the protein being formed.

Polyribosomes (Polysomes)

The complex of several

ribosomes and a mRNA

engaged in translation

peptidyl-transferase

A ribozyme that is part of a ribosome, it catalyzes the formation of peptide bonds between amino acids during translation. And is special because it is an enzyme made of RNA instead of proteins.

Release factor

A protein that recognizes stop codons and signals the end of translation

What are the advantages of using RNA as an intermediate molecule during protein synthesis

DNA protection DNA stays safe in nucleus while mRNA is used temporarily

Regulation Cell controls when and how much protein to make

Amplification One gene → many mRNAs → many proteins

housekeeping genes

Genes such as cytoskeleton genes that all cells express for basic function.

At which level is the most effective step to turn off gene

expression based on the principles of feedback inhibition?

Reducing Transcription initiation

What affects transcriptional regulation

transcription factors that interact with the regulatory elements of a gene

What do transcription factors bind to

DNA regulatory sequences

How does the structure of the DNA effect expression

Tighter packed heterochromatin doesn’t transcribe while loosely packed euchromatin will

miRNA

are short, ~22–25 nucleotide-long RNA molecules that bind to complementary sequences on target mRNA molecules to either degrade the mRNA or inhibit its translation

small interference RNA

(siRNA)

RNA derived from pathogenic RNA and used to against pathogens

How is miRNA made

Pri miRNA is made in the nucleus, then is processed into miRNA

How is siRNA made

Outside viruses inject double standed RNA, that RNA is processed to be single stranded and the cell gets rid of half.

RNA-induced silencing complex (RISC)

is a protein complex that incorporates one strand of siRNA and uses it as a guide to bind complementary mRNA molecules, leading to their cleavage or translational inhibition.

Levels of gene control

1. transcriptional control

2. RNA processing control

3. RNA transport control

4. translation control

5. mRNA degradation control

6. protein activity control

Benefits of polyribosomes

significantly increases the efficiency of protein synthesis