Chapter 7 (PART 2) : RNA to Protein

Initiator tRNA coupled to methionine is loaded into small ribosomal subunit along with ______ _____ ______.

*translation initiation factors*

What is the role of tRNA (clover-leaf shaped) in translation?

- Carries amino acids (aminoacyl-tRNA) - Matches amino acids with codons in mRNA

How many possible codons are there? amino acids?

64 codons and 20 amino acids

What is the start codon? What is its sequence?

Methionine = AUG = start of protein synthesis

One mRNA can code _____ proteins

One mRNA can code multiple proteins "Single mRNA can have multiple genes"

What are proteases?

Responsible for the break down of proteins

What translates the mRNA into proteins?

Ribosomes translate the mRNA into proteins

In step 4 of translation, the small subunit moves exactly how many nucleotides along the mRNA molecule?

THREE. (back to original position)

In step 2 of translation, a peptide bond is formed after the aminoacyl-tRNA binds to the vacant Acceptor (A) site (step 1). What peptide bond is actually forming?

The carboxyl end of polypeptide chain uncoupled from tRNA at P-site and joined by polypeptide bond to free amino group of amino acid linked to the tRNA at the A-site

Where does translation occur?

Translation occurs at the ribosome

Aminoacyl-tRNA synthetases covalently couples amino acids to __________ of tRNA and each amino acid to the appropriate set of tRNA molecules.

acceptor arm

[Translating an mRNA molecule] In Step 1 an aminoacyl-tRNA binds to ________.

the vacant Acceptor (A) site on the ribosome

What is a codon?

three consecutive nucleotides (triplet) specify an amino acid

During translation (the first step), what happens when A- and P-sites close together?

- two tRNAs forced to form base pairs with codons that are contiguous - no lost bases

How amino acids are loaded onto the tRNA?

-- *aminoacyl-tRNA synthetases* covalently couples amino acids to the *acceptor arm* of tRNA each amino acid to appropriate set of tRNA molecules -- Produces a high-energy bond between charged tRNA and the amino acid. -- The energy of this bond will be used later to link the amino acid covalently to the polypeptide chain

What are the "key players" in translation? (4)

1. Ribosomes 2. mRNA 3. tRNA 4. the product - Proteins!

Each ribosome binds __ mRNA and __ tRNAs

1; 3

How many synthetases are there in all?

20; one for each amino acid.

In tRNA, what end holds the amino acid that is corresponding with the mRNA code?

3' end holds aa corresponding with the mRNA code

There is a _-letter and _-letter code for amino acids. (hint: number of letters)

3; 1 For example: Methionine (start codon) 3-letter code: Met 1-letter code: M

5' of mRNA is recognized by what? Then, the small subunit looks for the first ___.

5' of mRNA recognized by 5' cap, then small subunit looks for first AUG.

The direction of translation is

5' → 3'

[Translating an mRNA molecule] In Step 2 (after the aminoacyl-tRNA binds to the vacant Acceptor (A) site), WHAT FORMS? and WHAT MOVES; to where?

A new peptide bond is formed and the ribosome moves to the next codon. The spent tRNA is moved to the Ejector (E) site

Describe the 3 binding sites of the ribosome.

A= aminoacyl-tRNA P = peptidly tRNA E = exit

At the 3' end of the tRNA, what is the sequence and amino acid?

ACC; (Phe)

After release, some proteins encounter _____ _____ that will aid them in folding.

After release, some proteins encounter molecular chaperones that will aid them in folding.

Gene expression is TIGHTLY regulated, by what means?

Altering the rate of transcription or translation (we can choose less or more of transcription/translation

What does the anti-codon of tRNA do?

Anti-codon recognizes the aa sequence on the mRNA

Some amino acids have SIX codons. Give three amino acid examples.

Arginine, leucine and serine.

Translation begins where?

Begins at AUG (Methionine) - initiator tRNA

During translation (the first step), what is retained?

Correct reading frame retained

The protein code is __________. (Important term!)

DEGENERATE

The 'language' of DNA & proteins are _____. Elaborate as to why.

DIFFERENT. DNA to RNA is transcription, their 'language' is through nucleotides, but during translation, RNA goes to proteins which are in the 'language' of amino acids, NOT nucleotides! Thus DNA and proteins have a completely different 'language' compared to DNA to RNA.

How are depurination, "open" reading frames, and mutations connected?

Depurination is the loss of a base. When that occurs, it can cause multiple reading frames, and completely change the sequence of bases thus codons would be read differently, creating different amino acids. Thus, it would lead to mutation.

There are multiple binding sites in ribosomes; what are they?

E & P & A (tRNA binding sites)

In step 4 of translation which site is left EMPTY?

Empty A-site allowing next aminoacyl tRNA to bind

In the anti-codon loop of the tRNA, it holds the anti-codon - what is its sequence?

GAA

What are the two protein subunits in ribosomes?

Large & small subunit

What does the large subunit do? How many large subunits make up the ribosome?

Large subunit - catalyzes the formation of the peptide bonds that link amino acids together ONE.

Describe poly-ribosomes

More protein molecules can be made in a given time

Most amino acids vary in the ______(____) position

Most vary in the third (wobble) position

Antibiotics that inhibit bacterial protein or RNA synthesis does ____ ____ eukaryotic.

NOT INCLUDE (due to different shapes of their amino acids)

Only ______ ______ ______ can bind tightly to the P-site of the small ribosomal subunit.

Only charged initiator tRNA can bind tightly to the P-site of the small ribosomal subunit

What are ribosomes in translation?

Protein COMPLEXES responsible for protein translation, FULL of rRNA, which catalyses peptidyl-transfer reaction ( ie the joining of the AAs by peptide bonds )

*** Proteins coming together is what type of level of organization?

Quatenary

Ribosome releases _____ and dissociates into _ subunits

Ribosome releases mRNA and dissociates into 2 subunits

What catalyses peptidyl-transfer reactions?

Ribosomes

What is a large protein complex that makes polypeptides?

Ribosomes

What three main things work together to form proteins?

Ribosomes, tRNAs and mRNA work together to make proteins

What does the small subunit do? How many small subunits make up the ribosome?

Small subunit - matches tRNAs to the codons of the mRNA ONE

In step 3 of translation what is shifting, what does it move?

Step 3 - shift in large subunit relative to small subunit; moves two tRNAs into the E- and P-sites of the large subunit

In step 4 of translation what is moving?

Step 4 - small subunit moves exactly 3 nucleotides along the mRNA molecule - back to original position.

What are the stop codons? (list 3 sequence of codons)

Stop Codons signal end (UAA, UAG, UGA)

Subunits (large & small) are made up of what?

Subunits each made from more than 30 different proteins (ribosomal proteins) and several RNA molecules - ribosomal RNAs (rRNAs) *Do not concentrate on how many ribosomal proteins and rRNAs, but that subunits are made up of MANY DIFF PROTEINS*

[Translating an mRNA molecule] In Step 3 (after the peptide bond is formed & the ribosome moves to the (E) site), what happens to the tRNA and ribosome?

The spent tRNA is ejected and the ribosome is resetting for the next aminoacyl-tRNA entering the A site

How many stop codons are there?

Three

What are the translational stop codons?

Translational stop codons (UAA, UAG, UGA)

T/F: RNA can be translated in multiple reading frames. Elaborate as to how/why.

True, there are multiple "open" reading frames, BUT in reality, only ONE of these reading frames encodes the actual message.

T/F: You can have 1 or even 6 codons that represent ONE amino acid.

True; multiple codons can specify the same amino acid. It varies depending on what amino acid.

Besides the amino acid, Methionine, what other amino acid has only ONE codon?

Tryptophan = UGG

Ribosomes are made up of ____ protein subunits & ____ binding sites.

Two protein subunits & 3 binding sites

If we want to destroy the functional protein from our circulation, we use a post-translational modification, such as _______.

Ubiquitination

[Translating an mRNA molecule] Step 1 - 3 are repeated over and over until what is recognized?

Until a termination codon (UAA, UAG, or UGA) is recognized in the mRNA

We use to ________ view the ribosome to see where exactly the molecule is in space.

X-crystallography

tRNA is shaped as a _______

a clover leaf (three leafed clover)

tRNA carries what type of amino acids?

aminoacyl-tRNA

Aminoacyl-tRNA is...

an "activated" amino acid.

There is a high-energy bond between what?

charged tRNA and the amino acid

Later, amino acids are ______ linked to the __________ using the high energy bond between tRNA and the amino acid.

covalently; polypeptide chain

A fully functional protein is created after transcription or translation, but we can control if we have a fully functional protein by either _____ it or ____ it.

creating; destroying

Complementary base-pairing creates _____ regions

double helical regions

rRNAs are synthesized in the ___________.

nucleolus

Once a chain of ubiquitination is on the proteins, it can be recognized by what?

proteases

Many antibiotics block _____ _____.

protein synthesis

Ribosomes consist of?

rRNA and proteins

Release factors bind to any stop codon that....?

reaches the A-site on the ribosome

Ribosomes are contains...(what type of ribosome)

ribosomal RNAs (rRNA) and many proteins

Ribosome-binding sequences located a few nucleotides away from the _______ In contrast, eukaryotic mRNA usually carries the information for a _____ protein

start AUG; single

tRNA carrying amino acid binds to ____ site on the ribosome forming ____ ____ with the ____ ____.

tRNA carrying amino acid binds to 'A'-site on the ribosome forming 'base pairs' with the 'exposed codon'.

tRNA holds ______ and the corresponding_______

tRNA holds 'Anti-codon' and the corresponding 'amino-acid'

tRNA molecules carry ______ ______ to the _______ for incorporation into a _________

tRNA molecules carry AMINO ACIDS to the RIBOSOME for incorporation into a POLYPEPTIDE

[Translating an mRNA molecule] Each amino acid added to the growing end of the poly- peptide is selected by complementary base-pairing between what two things?

the anticodon of the tRNA and the next codon of the mRNA

Ribosomes start translating at the ?

the first AUG (start codon) that is closest to the 5' end of the mRNA

Binding of release factors on the A site alters the activity of the...?

the peptidyl transferase (P site), catalyzing the addition of a water molecule instead of an amino acid

What is the role of mRNA (mature messenger RNA) in translation?

the template for translation