Lecture 8: The Central Dogma - From DNA to RNA to protein Part 2 Flashcards
1
Q
Transcription
A
- DNA —> RNA
- One-to-one correspondence of subunits
- Essentially the same language, except for minor changes (Thymine to Uracil, deoxyribose to ribose)
2
Q
Translation
A
- RNA —> protein
- No one-to-one correspondence: 20 amino acids, but only 4 bases
- Totally different chemical language
3
Q
Codon
A
- A set of 3 nucleotides
- Since there are more codons than amino acids, most amino acids have multiple corresponding codons
4
Q
Degenerate code
A
- Refers to the code corresponding between RNA sequence and amino acids
- You can’t be certain what the RNA sequence was for a specific protein since there are multiple codons for one amino acid
5
Q
Double nucleotide code
A
- 4 x 4 = 16 different combinations
6
Q
Triple nucleotide code
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- 4 x 4 x 4 = 64 different combinations
7
Q
What does it mean for there to be multiple codons for one amino acid?
A
- It means that the amino acids with more codons are more common
8
Q
Transfer RNAs (tRNAs)
A
- Match amino acids with codons
- Short RNAs with distinctive 3D structure
- Contains a loop with an “anticodon” that is complementary to the appropriate amino acid’s codon
9
Q
Structure of tRNAs
A
- Resembles the shape of a clover leaf
- 3 stem loops
- In 3D structure, the D and T loops associate with each other to form a bent L-shaped structure
10
Q
Aminoacyl-tRNA synthetase
A
- Job is to attach an amino acid to its corresponding tRNA
- Has to recognize more than one tRNA because each amino acid could have multiple anticodons that correspond to it
- Distinct to each amino acid
11
Q
Attach amino acid to tRNA
A
- Amino acid is first “activated” by conjugation to AMP
- Energetically expensive, since both high-energy phosphates are used up in the process
- Amino acid is then transferred from AMP to tRNA
- Energy to make this bond comes from the “activation” of the amino acid in the previous step
- Resulting conjugate has high-energy bond between amino acid and tRNA
- Once complete, the synthetase proofreads for accuracy
12
Q
N-terminal —> C-terminal
A
- Direction in which protein synthesis occurs
- New amino acid is added to C-terminal end of growing chain
13
Q
Process of creating a polypeptide chain
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- Peptide chain is attached to the last tRNA that was added
- The entire chain is added to each new amino acid added
- New aminoacyl tRNA replaced old tRNA, extending the chain by one residue
14
Q
Ribosome
A
- RNA message is decoded by this
- rRNAs make up structural and catalytic core: ribozyme
- Two subunits: large and small
- Makes sense why ribosome is made up of RNA instead of proteins in evolutionary perspective
- Reads a mRNA from 5’ —> 3’, reading 3 bases at a time
- Each mRNA has 3 potential “reading frames”, so it must choose one and remain consistent, or garbled translation occurs
15
Q
How does translation begin?
A
- With the codon AUG (Met) - this uses a special “initiator” tRNA, which is different from the Met tRNA used for the rest of translation
16
Q
Elongation
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- Facilitated by elongation factors (EF-Tu/EF-G in prokaryotes, EF1/EF2 in eukaryotes), which use GTPase activity to allow proofreading and to speed up ribosome translocation
- There is also a 3rd proofreading step at the initiator complex to make sure that the correct initiator tRNA was brought in with Met
- 3 total proofreading steps in translation
17
Q
Termination
A
- When the ribosome encounters a “stop” codon (UAA,UAG,UGA)
- Instead of a tRNA, a release factor binds to the ribosome, causing the hydrolysis of the peptidyl tRNA, releasing the completed protein
- The ribosome then dissociates into separate small and large subunits, releasing the mRNA, release factor, and remaining tRNA
- Water is used to hydrolize the reaction of cleaving the polypeptide chain off of the last tRNA
18
Q
Polyribosomes
A
- A single mRNA may thus have several ribosomes translating simultaneously
- Each ribosome can only synthesize one peptide chain at a time, but a cell may read many copies of a protein for every copy of the relevant mRNA
- Cells don’t wait for one ribosome to finish before having the next one start - once the first ribosome has moved far enough along, another can bind to the cap
19
Q
Benefits of 5’ end of mRNA communicating with 3’ end
A
- One benefit of this is that the ribosome knows that the mRNA is intact if the 5’ and 3’ ends are in communication with each other
- Another benefit is that once the ribosome dissociates off of the 3’ end, it can quickly reattach to the 5’ end, which facilitates a continuous translation process
20
Q
Antibiotics and Protein Synthesis
A
- Many important antibodies are protein synthesis inhibitors
- Most affect only prokaryotes, due to differences between prokaryotic and eukaryotic ribosomes
- Sometimes also affect ribosomes in mitochondria and chloroplasts due to eukaryotic ribosomes within these organelles being similar to prokaryotic ribosomes
- A few exceptions can block eukaryotic ribosomes - useful in cell biology research
- Cycloheximide blocks translocation reaction (eukaryotic only)
- Puromycin mimics aminoacyl-tRNA and is incorporated into the growing polypeptide chain, causing premature termination (both eukaryotic and prokaryotic)
- Be aware that most common antibiotics are actually protein translation inhibitors
21
Q
RNA and protein synthesis are very energetically costly
A
- 10 ATPs per amino acid added at least
- Each elongation step requires multiple ATP/GTP molecules
- Adding each subunit requires the conversion of an NTP into an NMP, equivalent of 2 ATPs to ADPs
- mRNA splicing and protein proofreading use up even more ATP/GTP molecules
22
Q
Information of protein sequence
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- Information for 3D-structure, cellular location, and protein function
23
Q
Information of mRNA
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- Same information as protein plus information about initiating and terminating translation (and sometimes mRNA stability)
24
Q
Information of DNA
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- Same information as mRNA plus information about initiating and terminating transcription, splicing (and anything useful in the introns themselves)
