BIOC2000 Lecture Notes - Lecture 11: Nucleic Acid Tertiary Structure, Wobble Base Pair, Transfer Rna
Lecture 11: Translation
Translation is the solution to the problem of “how do we get
information from one form into another form?”
- nucleic acid to protein language – very different chemically thus the
name ‘Translation’
- DNA has riboses, P groups; amino acids have NCCNCC backbones –
really different to phosphodiester backbone
- DNA and mRNA are very similar molecules - talk each other’s language,
proteins do not. Cell has developed a way of making something of a new
language of a template that does not look like it – with ribosome and tRNA
Transfer RNAs are specifically folded single stranded RNA
molecules.
-ss RNA
-the way it folds defines the way if functions
- clover-leaf structure, allowing tRNAs base-pair to themselves
- T sized C arm, D arm, anti-codon arm, aminoacid arm where aa is added
- Synthesized from 5’ to 3’
In the diagram, A of aa is the last base to be added on
There is an OH there on end of 3’OH – what is used to add amino acid –
only time protein and RNA speak the same language – aa is covalently
bonded on 3’ O
The structure of tRNA can be
decomposed into its primary
structure, its secondary
structure (usually visualized as
the cloverleaf structure), and
its tertiary structure (all tRNAs
have a similar L-shaped 3D
structure that allows them to fit
into the P and A sites of the
ribosome). The cloverleaf
structure becomes the 3D L-
shaped structure through
coaxial stacking of the helices,
which is a common RNA
tertiary structure motif.
Different arms fold into different parts of the structure
• White/silver – body parts, ds regions, non-functional
• Arms – where action occurs
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Bases in PINK are invariant bases, bases that are always the same
Bases in BLACK can change, as long as they base-pair – they just
make the backbone
-T sized C arm (blue)
-D arm (yellow)
-anti-codon arm (pink)
-aminoacid arm
• Once tRNA is folded up, anticodon (where it recognizes the mRNA)
and amino acid are a long way apart
• When ribosome is working, it is recognizing codons but it has no
idea whether the aa it is adding has anything to do with that codon –
it does not proofread, it just adds – other machinery to ensure ‘x’ aa
is right for this anticodon
NEXT FEW SLIDES
ARE ASSUMED
KNOWLEDGE,
SKIPPED IN
LECTURE
In molecular
biology, a reading
frame is a way of
dividing the
sequence of
nucleotides in a
nucleic acid (DNA or
RNA) molecule into a
set of consecutive, non-overlapping triplets. Where these triplets equate to
amino acids or stop signals during translation, they are called codons.
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Do not need to
memorize ‘dictionary of
aa code’ – however, be
able to use!
tRNA (reading 3' to 5')
has anticodons
complementary to the
codons in mRNA and
can be "charged"
covalently with amino
acids at their 3' terminal.
Looking at Table 27-3, it can be seen that many different codons can
equate to 1 amino acid (e.g. Arg, Leu and Ser – 6 codons) – Does this mean
1 tRNA is required for every single possible option? – Very expensive!
Crick thought maybe you didn’t – he realized if you looked at the
sequence, and you looked at the aa makeup of what was made from the
sequence – codons are only different in the 3rd position.
Crick said what is there is an adaptor that can read all four of these or at
least more than one of these and bring in a Ser – called Wobble
hypothesis.
UCU
UCC
UCG
UCA
- all encode Ser
There are 61 codons (there would be 64 but 3 of them are stop codons) =
there would be 61 potential anticodons = 61 different types of tRNA found
in the cell = but most cells only contain about 40 different types of tRNA.
How can we have 61 codons but only 40 tRNA to translate them? Wobble
hypothesis!
Wobble Hypothesis: There is some unconventional base pairing in the 3rd
base of the codon/anticodon
e.g. if codon is UUC (Phe) ; anticodon would be AAG
However let’s say the only tRNA for Phe is one with an anticodon of AAA
UUC is the codon, anticodon is no longer a perfect match; Base 1 and 2 are
fine, H bonds will form between U and As, normally there is a G binding to
a C not an A however a match between A and C will occur because of
‘Wobble’ - ‘Not perfect fit but will still work’; the 3rd base of anticodon can
actually have an imperfect match to what base is on codon – we thus do not
need tRNA for every single codon, some tRNA are flexible and will be able
to bind to more than one codon
AAA - anticodon
UUC – codon
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find more resources at oneclass.com
Document Summary
Translation is the solution to the problem of how do we get information from one form into another form? . Nucleic acid to protein language very different chemically thus the name translation". Dna has riboses, p groups; amino acids have nccncc backbones really different to phosphodiester backbone. Dna and mrna are very similar molecules - talk each other"s language, proteins do not. Cell has developed a way of making something of a new language of a template that does not look like it with ribosome and trna. Transfer rnas are specifically folded single stranded rna molecules. The way it folds defines the way if functions. Clover-leaf structure, allowing trnas base-pair to themselves. T sized c arm, d arm, anti-codon arm, aminoacid arm where aa is added. In the diagram, a of aa is the last base to be added on.
