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12-5 Notes: Translation
Protein Synthesis
Original information DNA gets transcribed into mRNA
Next Step: to use the mRNA strand to build the polypeptide chain

mRNA carries the message as codons = 3 bases at a time
o mRNA code is used to determine the actual order of amino acids

tRNA’s job is to bring the correct amino acid and place it in the proper position by matching
up the codon of mRNA to an anticodon on tRNA
tRNA

more than 20 kinds in each cell (1 or more for each kind of a.a. in cell)
o Wobble Hypothesis = only 40 (not 61) tRNAs are needed in cells because some can
pair with more than one codon

Helps to explain why the code is degenerate

Cloverleaf shape (see diagram below)

two attachment sites:
o Anticodon = binds to codon on mRNA
o 3’ end = attaches to a particular amino acid
tRNA Loading
Amino Acyl-tRNA Synthetase = enzyme that catalyzes the attachment of an amino acid to its tRNA

20 types of them

2 steps:
1) Activation of the amino acid with ATP: The enzyme’s active site binds the amino
acid and ATP

ATP is cleaved, releasing 2 phosphates (and energy) and attaches to the amino
acid as AMP
2) Attachment of the amino acid to 3’ End (of tRNA)


AMP releases

bond forms between the a.a. and 3’ end of tRNA

amino acid–tRNA complex is released
Later, when the tRNA anticodon matches to mRNA codon, the bond breaks between tRNA
and the a.a. and the tRNA is released, going back to pick up another a.a.
Translation also requires rRNA and tRNA

Made in the nucleolus

differ structurally and functionally from mRNA
Ribosomes

made of two subunits: one smaller, one larger

60% rRNA and 40% protein

Prokaryotic ribosomes are smaller and have different molecular composition
o This is how some antibiotics work  attack structure of prokaryotic ribosomes
without affecting eukaryotic ribosomes

Smaller subunit = binding site for mRNA
o 5’ end of mRNA attaches here

Larger subunit has binding sites for tRNA

Has 3 binding sites: A (amino acid) site, P (polypeptide) site, and E (exit) site
PROTEIN SYNTHESIS: Translation (how polypeptides are assembled: mRNA  a.a.)
3 stages:
1) Initiation

Smaller ribosomal subunit attaches to mRNA near 5’ end
o exposes initiator codon
o 1st tRNA pairs with initiator codon: usually (5’) – AUG – (3’)


Brings modified a.a. = fMet (which may later be removed)
Larger ribosomal subunit attaches to smaller subunit
o initiator tRNA locked into the P site

energy comes from GTP
2) Elongation

next complementary mRNA codon is exposed in the A site

the next tRNA anticodon and it a.a. are inserted

when both spots (A & P) are occupied peptidyl transferase helps form a peptide bond
between the two amino acids

ribosome slides over one codon and process repeats

when the ribosome moves, the tRNA in the P site is moved to the E site, and that tRNA
detaches and it exits the ribosome

when 5’ end portion of mRNA is free again, another ribosome can attach and build
another chain
o Polyribosome = a group of ribosomes reading the same mRNA molecule
3) Termination

“Stop” codon is near end of mRNA
o UAA, UGA, or UAG
o NO tRNA’s have the anticodon for these  release factor is inserted

translation stops and polypeptide chain is released

ribosomal subunits separate

all parts are reused or degraded
After Translation

The first few amino acids of a polypeptide act as a signal peptide that indicate whether a
protein is for export or not

Those polypeptides that are for secretion are then fed into the lumen of the ER, where they
are folded and modified by the addition of sugars, phosphates, or lipids
o Since prokaryotes do not have ER, this is a limitation on their use in genetic
engineering of eukaryotic proteins
EUKARYOTIC CHROMOSOMES

More than 60% protein

Humans have 2 m of DNA packed into a nucleus that is 5 µm in diameter

This requires extensive folding, which is accomplished by Histones
Chromatin Structure is based on Successive Levels of DNA Packing:
1) DNA strand
2) Nucleosomes or “beads on a string”

Histones = Small proteins that are rich in basic amino acids and that bind to DNA,
forming chromatin. (H1, H2A, H2B, H3, and H4 are used)

Partially unfolded chromatin (DNA and its associated proteins) resembles beads spaced
along the DNA string. Each beadlike structure is a nucleosome.

Nucleosome = The basic unit of DNA packing; it is formed from DNA wound around a
protein core that consists of 2 copies each of 4 types of histone.

may control gene expression
3) Chromatin Fiber

Nucleosomes are zig-zagged into a 3-D structure using H1 proteins
4) Looped Domains

Attached to another protein scaffold

Euchromatin = loosely attached, allowing access of RNA polymerase and, therefore,
transcription
5) Coil and fold further, compacting the chromatin into a mitotic chromosomes characteristic of
metaphase

Heterochromatin = chromatin that stays in this condensed state even in interphase and
is rarely (if ever) transcribed