lecture 8 translation and proteins

DNA to RNA review slide

nucleotide sequence of an mRNA is translated into

amino acid sequence of a protein via genetic code

_ is called a codon

each group of three consecutive nucleotides in RNA

each codon specifies ___

one amino acid

there how many combinations of 3 nucleotides possible

4×4×4=64

by convention codons are always written with 5’ terminal nucleotide to what direction

to the left

most amino acids are represented by _ codons

more than one (*most*)

codons for the same amino acid tend to contain the same nucleotides at the —- positions and vary at the —

codons for the same amino acid tend to contain the same nucleotides at the first and second positions and vary at the third position

codons for the same amino acid tend to contain the same nucleotides at the first and second positions and vary at the third position

this is called

wobble effect

how many codons act as stop codons

three

what are teh three stop codons

UAA UAG UGA

what do stop codons signal

the end of the protein

_ is an initiation codon

AUG

AUG codes for what amino acid

Met

AUG is an initiation codon signaling

the start of a protein-coding message, and as the codon that specifies methionine

codons are always written in what direction

5’ - 3’

do stop codons code for a specific amino acid

no

codons slide one

how many possible reading frames can mRNA molecule be translated in

three

In principle the same RNA sequence can specify three completely different amino acid sequences depending on reading frame. However,

only one of these reading frames encodes the actual message

reading frame slide

__ are molecular adaptors linking amino acids to codons

tRNA

tRNA stands for

transfer RNA

is transfer RNA a relatively stable RNA structure in our cells

yes

what part the tRNA lines up with and base pairs with the codon of the mRNA

the anticodon

what tRNA sequence end with

CCA

genetic code is translated by _ adaptors

2

genetic code is translated by two adaptors

the first adaptor is

the aminoacyl-tRNA synthetase

what does the aminoacyl-tRNA synthetase do

couples a particular amino acid

tRNA slide

the process of aminoacyl-tRNA synthetase couples a particular amino acid to its corresponding tRNA is called

charging

the second adaptor is

the tRNA molecule itself

the anticodon of the tRNA does what

baes pairs with the appropriate codon on mRNA

a tRNA coupled with its amino acid is called a

charged tRNA

an ACC on the anticodon base pair with what sequence of mRNA

UGG

what does aminoacyl tRNA synthetase do

looks at tRNA, looks at anticodon, puts on correct amino acid

is the anticodon the nucleotide code that tells which amino acid to add

no, the codon is

an error in either step, charging or binding of charged tRNA to its codon will cause

wrong amino acid to be incorporated into a protein

where are ribosomes found in eukaryotic cells

free in the cytosol and bound to the ER

aminoacyl tRNA synthetase slide and tRNA

ribosome slide

a ribosome is a large complex of __

four RNAs and more than 80 proteins

although ribosomal proteins greatly outnumber ribosomal RNAs, RNAs account for __ the mass of the ribosome

more than half

what is the most important component of a ribosome

the RNA

how many subunits in RNA

two, large subunit and small subunit

RNA components slide

_ give the ribosome its overall shape

ribosomal RNAs

ribosomal components are commonly designated by their _ values

S

what does a ribosomes S value refer to

their rate of sedimentation in an ultracentrifuge

ribosome shape slide

ribosome has binding site for __ and three binding sites for _

mRNA, tRNA

what are the three binding sites for tRNA that a ribosome has

E site (exit site), P site (peptidyl), A site (aminoacyl)

e site is

exit site

p site is

peptidyl site

A site is

aminoacyl site

where does new tRNA come in

binds

ribosome binding points slide

what are the three important stpes of transcription

iniation, elongation, termination

in eukaryotes, intiator tRNA, coupled to methionine is first _

loaded onto a small ribosomal subunit, along with additional proteins called translation initiation factors

initiator tRNA is distinct from

tRNA that normally carries methionine

of all charged tRNAs in cell, only the charged ___can bind tightly to P-site of the small ribosomal subunit

initiator tRNA

where does the loaded ribosomal subunit binds where

to the 5’end of an mRNA molecule, which is signaled by the cap of eukaryotic mRNA

small ribosomal subunit then moves __

forward (5’ to 3’) along the mRNA searching for the first AUG. When this AUG is encountered, several initiation factors dissociate from small ribosomal subunit to make way for the large ribosomal subunit to assemble and complete the ribosome

Because the initiator tRNA is bound to the P-site, protein synthesis is ready to begin with the addition of the next charged tRNA to the

A-site

initiator tRNA binds where

to small ribosomal subunit along with translation initiation factors

when new amino groups are added what bond forms between them

a peptide bond

translation initiation slide

translation takes place in a _ step cycle

four

first step of translation 4 step cycle

tRNA carrying next amino acid binds to vacant A-site on ribosome by forming base pairs
with exposed codon.

second step of translation 4 step cycle

Carboxyl end of polypeptide chain is uncoupled from tRNA at P-site and joined by a peptide bond to the amino group of the amino acid linked to the tRNA at the A-site. This reaction is catalyzed by the RNA-based peptidyl transferase, 23S rRNA, in large subunit. 23S rRNA is a ribozyme (catalytic properties)

third step of translation 4 step cycle

Shift of large subunit relative to small subunit moves two tRNAs into E- and P-sites of
large subunit.

fourth step of translation 4 step cycle

Small subunit moves exactly three nucleotides along mRNA molecule, bringing it
back to its original position relative to large subunit. This movement resets ribosome with an empty A-site so that the next aminoacyl-tRNA molecule can bind

translation four step cycle slide

in the final phase of protein synthesis binding of a __

release factor to an A-site bearing a stop codon terminates translation

the end of the protein-coding message in both prokaryotes and eukaryotes is signaled by presence of one of several codons called

stop codons

stop codons:

UAA, UAG, UGA

are stop codons recognized by a tRNA

no, and they do not specify an amino acid, but instead signal to ribosome: stop translation

release factors bind to

a stop codon that reaches A-site on ribosome, alters activity of peptidyl transferase, causing it to catalyze addition of water instead of an amino acid to peptidyl tRNA

when release factor binds what is added

instead of an amino acid a water is added

Release factors bind to a stop codon that reaches A-site on ribosome, alters activity of peptidyl transferase, causing it to catalyze addition of water instead of an amino acid to peptidyl-tRNA

This reaction does what

This reaction frees the carboxyl end of the polypeptide chain from its attachment to a tRNA molecule, and the completed protein chain is immediately released.

after the completed protein is released what happens

The ribosome releases the mRNA and dissociates into two separate subunits, which can assemble on another mRNA molecule to begin new round of protein synthesis.

translation termination slide

a single prokaryotic mRNA can encode for

several different proteins

in prokaryotes genes directing the different steps in a process are often organized into

clusters (operons) that are transcribed together into a single mRNA

unlike eukaryotic ribosomes which recognize a 5’ cap prokaryotic ribosomes initiate translation at

ribosome-binding sites which can be interior of an mRNA molecule

unlike eukaryotic ribosomes which recognize a 5’ cap prokaryotic ribosomes initiate translation at ribosome-binding sites which can be interior of an mRNA molecule

this feature enables prokaryotes to synthesize

several separate proteins from a single mRNA molecule

the amino sequence tells us

how the protein will fold

prokaryotic translation slide

proteins are translated by

polyribosomes

a series of ribosomes can simultaneously

translate the same mRNA molecule

polyribosomes slide

structure determines

function

proteins production in a eukaryotic cell requires many

steps

the final concentration of each protein depends on efficiency of

each step

even after a protein has been translated, its concentration can be regulated by

degradation and its activity regulated by binding of small molecules and other post translational modifications

protein production slide

many proteins require additional _ to become fully functional

modification

to be useful to the cell a complete polypeptide must

fold correctly into its three dimensional conformation, bind any cofactors required and assemble any protein partners

what type of bond formation drives proteins into their folded shapes

non-covalent bond formation

_ and - modifications are most common post translational modifications

phosphorylation, glycosylation