Transcript JSCh4StudentPPT

Chapter 4:
Translation and Protein
Structure
Protein Macromolecule Review
4.1 Proteins are linear polymers of amino acids that
form 3-dimensional structures with specific
functions.
• Protein is 1 or more polypeptide chains;
composed of amino acid building blocks
– Up to 20 different a.a.
– Differ by side chain (R group)
– R groups give the amino acid its chemical
properties (Fig 4.2)
Amino Acid Structure
Base
20 different a.a.
Acid
Protein Macromolecule Review
•
Successive amino acids are
peptide-bonded together
into a long polymer called a
polypeptide chain (about
55 aa long)
•
Each peptide bond is the result of
a dehydration synthesis reaction
between the the carboxyl group
of one amino acid and the amino
group of the next amino acid:
–
Each polypeptide is the result of a
gene encoded in the DNA
–
Sometimes it takes multiple
polypeptides to make one
protein
Image credit: http://www.uic.edu/classes/bios/bios100/lectures/protein-peptidebond.gif
Where do our cells get their protein?
Genetic Flow of Information
DNA gene from the
cookbook of life
template DNA sequence
GATC
transcribed
into mRNA
translated into
cellular protein
mRNA sequence
amino acid sequence
GAUC
20 amino acids
Image credits: http://www.pureandhealthy.com/blog/wp-content/uploads/grilled-steak.jpg http://recipecurio.com/recipecopies/collection5/chefsgrilledsteak.jpg http://ecx.images-amazon.com/images/I/61uSy%2BvUzPL._SX258_BO1,204,203,200_.jpg
20 Amino Acids
• Symbolized by three letters
– First letter is capitalized
– E.g. Met for Methionine, Cys for Cysteine
• Or by a single capital letter
– True in all the online research databases
– E.g. M for Methionine, C for Cysteine
The primary amino acid SEQUENCE
determines protein SHAPE and FUNCTION
• Form fits function: if a protein does not have the right 3D
shape (conformatin), it cannot do its job
• 3D protein shape is determined by how the amino acid chain
(called a “polypeptide”) folds up
• Folding behavior is determined by the chemical properties of
adjacent amino acids
• So it matters which amino acids are next to which amino acids
(the amino acid sequence)
Functions of Proteins
•
•
•
•
•
•
•
Enzymes: speed up all chemical reactions; lactase
Defense: antibodies
Storage: casein (protein of milk)
Transport: hemoglobin
Hormonal proteins: insulin
Receptors: for signaling and cell communication
Contractile and movement: actin and myosin (muscle
proteins)
• Structure: collagen and elastin (animal connective tissue
fibrous framework)
How do we read an amino acid sequence?
(See Fig. 4.2 on Pg. 4-3)
Image credit: http://cnx.org/content/m39433/latest/CG12C2_022.png
3 to 4 Levels of Protein Folding Needed for Function
Image credit: http://cnx.org/content/m44402/latest/Figure_03_04_09.jpg
Protein Folding Animation
https://www.youtube.com/watch?v=swEc_sUVz5I
Citizen Science: Fold It Game
http://fold.it/portal/info/about
Triplet Code
• There is not a 1:1 relationship between nitrogenous bases and
the a.a. they specify
• Why? Only 4 nucleotides, but 20 a.a.
• 3:1 ratio….3 bases for each a.a. = 43 = 64 a.a.
• Codon: term for triplet code; nucleotide triplet sequence in
mRNA that “codes” for the appropriate a.a.
Codon Dictionary
4.2 Translation is the process in which the sequence of bases in mRNA specifies the
order of successive a.a. in a newly synthesized protein.
NOTE: UAA,
UGA, UAG only
code for stop
AUG codes for Met
and start
Image credit: http://www.nature.com/scitable/content/ne0000/ne0000/ne0000/ne0000/6903567/EssGen1-5_genetic_code_0.jpg
How do ribosomes read mRNA?
• mRNA codons consist of 3
consecutive nucleotides
• Three stop codons do not code
for any amino acid
• AUG codes for Met but also
functions as a start codon
• The code is unambiguous (it
always means what it says)
• The code is redundant (there
are multiple ways to code for
the same amino acid; since 61
of the 64 triplets code for 20
aa)
Image credit: http://www.nature.com/scitable/content/ne0000/ne0000/ne0000/ne0000/6903567/EssGen1-5_genetic_code_0.jpg
Quick Review
•
•
•
•
•
3 adjacent bases on mRNA = codon
mRNA usually has about 1,500 bases
Therefore, about 500 codons on mRNA
Since 1 codon translates to 1 aa…….
Then, a polypeptide chain is usually about 500
aa long
STOP codons STOP TRANSLATION
• UAG, UGA, or UAA
• Note they do NOT code for an additional
amino acid to be added to the growing
polypeptide chain
Translate THIS #1
5’-UUAUACCAUGCAUGGAUCAUGACCCAAG-3’
(Table 4.1, pg. 4-12)
Translate THIS Answer #1
5’-UUAUACCAUGCAUGGAUCAUGACCCAAG-3’
N-Met-His-Gly-Ser-C
Translate THIS #2
5’-CGAUGGAUUUACCAUGGCCGCAUAGUGGC-3’
(Table 4.1, pg. 4-12)
Translate THIS Answer #2
5’-CGAUGGAUUAACCAUGGCCGCAUAGUGGC-3’
N-Met-Asp-C
N-Met-Ala-Ala-C
(Table 4.1, pg. 4-12)
Remember transcription?
STRETCH your brain: what would the DNA template strand have looked like?
DNA:
Non
template: ?’-……………………………………………………………………………-?’
template: ?’-……………………………………………………………………………-?’
mRNA:
5’-CGAUGGAUUAACCAUGGCCGCAUAGUGGC-3’
Proteins?
The DNA NON-template strand RESEMBLES the mRNA
The TEMPLATE strand is READ 3’ to 5’ to PRODUCE the mRNA (antiparallel binding)
DNA:
Non
template: 5’-CGATGGATTAACCATGGCCGCATAGTGGC-3’
template: 3’-GCTACCTAATTGGTACCGGCGTATCACCG-5’
mRNA:
5’-CGAUGGAUUAACCAUGGCCGCAUAGUGGC-3’
Proteins:
N-Met-Asp-C
N-Met-Ala-Ala-C
TRY IT YOURSELF
Transcribe and Translate THIS
5’-CCTCACTATGCGGAAACCTTGATTTAGGAGCCCTG-3’
3’-GGAGTGATACGCCTTTGGAACTAAATCCTCGGGAC-5’
•Note that only the top strand has a 5’-ATG-3’ ( the start
codon written in DNA language)
•That makes the top strand the NON template strand; this is
what the mRNA will look like with U’s instead of T’s
TRY IT YOURSELF
Transcribe and Translate THIS
5’-CCTCACTATGCGGAAACCTTGATTTAGGAGCCCTG-3’
3’-GGAGTGATACGCCTTTGGAACTAAATCCTCGGGAC-5’
•Also note the TGA Stop codon in the same reading frame as
the ATG start codon
•We have found our protein-coding region: ATG - TGA
TRY IT YOURSELF
DNA is transcribed into mRNA
Non-template: 5’-CCTCACTATGCGGAAACCTTGATTTAGGAGCCCTG-3’
Template: 3’-GGAGTGATACGCCTTTGGAACTAAATCCTCGGGAC-5’
mRNA: 5’-CCUCACUAUGCGGAAACCUUGAUUUAGGAGCCCUG-3’
•The mRNA sequence is just like the non-template DNA
sequence, except it has U instead of T
TRY IT YOURSELF
mRNA is translated into protein
Non-template: 5’-CCTCACTATGCGGAAACCTTGATTTAGGAGCCCTG-3’
Template: 3’-GGAGTGATACGCCTTTGGAACTAAATCCTCGGGAC-5’
mRNA: 5’-CCUCACUAUGCGGAAACCUUGAUUUAGGAGCCCUG-3’
Protein:
N-Met-Arg-Lys-Pro-C
•The protein coding region spans from the blue AUG start
codon to the red UGA stop codon
•The stop codon just stops translation; it does not code for a
last amino acid
Translation Requirements
1. mRNA
2. Initiation and elongation factors
3. Ribosomes….made in nucleolus in nucleus
– Consist of a small and a large subunit
– Made up of 60% rRNA and 40% protein
4. tRNAs
5. Amino acids: 20 available
6. tRNA Synthetase enzymes: 20 available (each
unique to each aa)
7. GTP energy
Roles in Translation
amino acids
•
•
Protein building blocks
Produced by our bodies, recycled from old proteins,
or from food
mRNA
•
Encodes the aa.acid sequence in RNA language as
codons (secret message simplified)
ribosomes
•
Coordinates pairing of mRNA codon with tRNA
anticodon (“interpreter”); ribosomes are like a
“matchmaker”; also form peptide bonds between
incoming amino acids and the growing polypeptide
chain
tRNAs
•
Small RNAs that carry the encoded amino acids to the
mRNA and the ribosomes
tRNA Synthetases
•
Enzymes that stick an amino acid on its tRNA
Initiation factor
Elongation factor
•
A protein that must bind mRNA to initiate translation
•
A protein that breaks high-energy GTP bonds to
provide energy for ribosome movement and
polypeptide chain elongation
Ribosome Structure: 3 Pockets (EPA)
exit
peptidyl
aminoacyl
Each subunit made in nucleolus; go to cytoplasm separately to become functional
Image credit: http://classconnection.s3.amazonaws.com/768/flashcards/1177768/png/epa1333778594277.png
tRNA Structure
The tRNA ANTICODON determines which amino acid is attached
Amino acyl synthetase
enzyme “loads” or
“activates” tRNA with
appropriate aa
3 base sequence on tRNA that base
pairs with complementary codon on
mRNA
tRNA Function
The tRNA ANTICODON binds the complementary mRNA CODON
(antiparallel binding) and brings encoded amino acid
Translation: INITIATION
Translation: INITIATION
Next new aa always goes into A site
Translation: ELONGATION
After the peptide bond is made, the ribosome and its pockets shift by 1 codon
Translation: ELONGATION
Growing polypeptide chain always in P site and E site is for exit
Translation: ELONGATION
Translation: ELONGATION
Translation: ELONGATION
Translation: TERMINATION
• Ribosomes encounter an mRNA stop codon
– UUA, UAG, UGA
• There are no tRNAs that can bind a stop codon
• Instead a protein release factor binds in the Asite of the ribosome
• The polypeptide is released
• The mRNA, small and large ribosomal subunits
go their own way (recycled)
Review: Transcription and Translation
Additional Resources
• Translation animations
– http://www.phschool.com/science/biology_place/biocoac
h/translation/init.html
– http://www.biostudio.com/d_%20Peptide%20Bond%20Fo
rmation.htm
(note the E-site has not been labeled in the above)
• Gene expression (transcription & translation)
animation: http://www.wellcome.ac.uk/Educationresources/Education-andlearning/Resources/Animation/WTX057748.htm