Transcript Sept10

How does the cell manufacture these magnificent machines?
Proteins, that is…
Single-letter code:
M
D
L
Y
Disulfide bridge formation stabilizes protein structure
Cys - S - H + H - S - Cys
Cys - S - S - Cys
Proteins are 3-dimensional
molecules
Primary structure =
Amino acid sequence
Secondary structure =
1. Alpha helix
2. Beta sheet
-sheet
Tertiary structure =
3-D shape
Quaternary structure =
??
-helix
The Genetic Code
How the genetic code was deduced is quite an interesting but
horribly complicated story of prokaryotic genetics. I’ll just give
you the Cliff notes version:
Francis Crick and Sidney Brenner figured out that:
The genetic code maps ‘codons’ of 3 bases into one
amino acid.
AUA
->
Ile
GAU
->
Asp
AGA
->
Arg
mRNA
->
Amino Acid
The Genetic Code
Crick and Brenner figured
out that:
The DNA code is read
sequentially from a fixed
position in the gene
The mechanism and machinery for translating a protein
Three components:
Translation Requires:
Ґ Message in the form of
mRNA Й
Ґ A RibosomeЙ ..
Ґ Another type of RNA Й called
Transfer RNA ( tRNA)
Ґ A pool of amino acids in
cytoplasm
AA1
AA2
AA3
Free Amino Acids
tRNA is the adapter.
Amino acid is matched to
the Anti-codon.
Complementary to the Codon
Translation occurs 5’ to 3’
The translation is performed with the help of the Ribosome.
RNA is the major component of
the Ribosome.
About 2/3 of the
Ribosome is RNA
by mass. These
RNA molecules
are called rRNA
and they play a
central role in the
translation of
mRNA into
polypeptides.
mRNA, rRNA, tRNA and protein synthesis
In translation, the language of nucleic acids is translated into a new
language, that of proteins
mRNA provides the code, in linear digital form, for making a protein
tRNA provides an adaptor that links the code in a polynucleotide chain
to amino acids that make up the polypeptide chain
rRNA and ribosomes provide the decoder. Ribosomes bring together
mRNA and tRNA, and catalyze the translation of an mRNA into a
polypeptide chain. Ribosomes are the site of protein synthesis.
Ribosomes create peptide bonds between amino acids to create proteins
Translation normally
occurs on polyribosomes,
or polysomes
This allows for amplification
of the signal from DNA and
RNA, i.e.,…
One gene copy
Hundreds of mRNAs
Thousands of proteins
rRNAs form complex
2o and 3o structures
that are essential for
their function
What does this rRNA
molecule look like in
three dimensions?
3-D model of 16s rRNA
molecule as it folds in the
ribosome…
…and overlaid with
its protein subunits
Behold, the ribosome!
Proteins are blue, RNAs are red
and white
Two views of the adaptor molecule,
transfer RNA (tRNA), which guides
amino acids to the mRNA-ribosome
complex
The anticodon of the tRNA aligns with the codon in mRNA through
complementary base pairing
Translation - Initiation
fMet
Large
subunit
E
P
A
UAC
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA
Small mRNA
subunit
3’
Translation - Elongation
Polypeptide
Arg
Met
Phe
Leu
Ser
Aminoacyl tRNA
Gly
Ribosome
E
P
A
CCA
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA
mRNA
3’
Translation - Elongation
Polypeptide
Met
Phe
Leu
Ser
Gly
Arg
Aminoacyl tRNA
Ribosome
E
P
A
CCA UCU
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA
mRNA
3’
Translation - Elongation
Polypeptide
Met
Phe
Leu
Ser
Gly
Arg
Ribosome
E
P
A
CCA UCU
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA
mRNA
3’
Translation - Elongation
Polypeptide
Met
Phe
Leu
Ala
Ser
Gly
Aminoacyl tRNA
Arg
Ribosome
E
P
A
CCA
UCU
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA
mRNA
3’
Translation - Elongation
Polypeptide
Met
Phe
Leu
Ser
Gly
Arg
Ribosome
E
Ala
P
A
UCU CGA
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA
mRNA
3’
Translation - Termination
Met
Phe
Leu
Ser
Gly
Polypeptide
Arg
Ala
Ribosome
Val
E
P
A
CGA
CGA
GCA...TAAAAAA
STOP
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT
mRNA
3’
Translation - Termination
Met
Phe
Leu
Ser
Gly
Polypeptide
Arg
Ala
Val
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA 3’
mRNA
STOP
How many bases are required to make a genetic code to
serve 20 different amino acids?
# of 2-base combos = 42 = 16
Not enough!
# of 3-base combos = 43 = 64
Too many!
What is the solution?
How?
Evolve a code that is redundant!
Degeneracy at the third codon position
Let’s look at the Genetic Code
Transfer RNA (tRNA) and
the genetic code
Many different
base modifications
occur in tRNA
Why are these
modifications
necessary?
Transfer RNA (tRNA) and
the genetic code
Legitimate
G-U bp
Wobble bp
Point mutations
Point mutations can affect protein structure and function
Type of point mutations:
- substitutions (missense and nonsense mutations)
- insertions and deletions (frameshift mutations)
Frame Shift Mutations
What happens when you get insertions or deletions of bases in
the DNA sequence?
Usually you end up with a mess.
THE BIG FAT CAT ATE THE RAT AND GOT ILL
Deletion of one base
THE IGF ATC ATA TET HER ATA NDG OTI LL
And its all pops and buzzes.
Usually frame shift mutations result in premature stop codons.
Where can you get more information about the basic concepts
embedded within the Central Dogma of Molecular Biology?
Here is a great site, full of simple, clear, and animated (!) tutorials:
http://www.dnaftb.org/dnaftb/
Chapters 15-28 in this series provides an excellent review of the first
six lectures in Bioinformatics:
http://www.dnaftb.org/dnaftb/15/concept/
Ribosomes are large
ribonucleoprotein (RNP)
complexes
They are complex affairs,
composed of an array of
RNA + proteins