ch 9 (lectures 17-18) Flashcards
What are amino acids, and how many are there?
Amino Acids are the building blocks of proteins.
There are 20 standard amino acids used in protein synthesis.
How many bases are required to code for one amino acid, and what does this imply about the genetic code?
3 bases (a codon) are needed to encode one amino acid, giving 4 × 4 × 4 = 64 possible codons.
Since there are only 20 amino acids, the code is degenerate — meaning some amino acids are encoded by more than one codon.
How do suppressor mutations demonstrate polarity in the genetic code?
Insertion or deletion mutations affect amino acids downstream of the mutation, shifting the reading frame (frameshift mutation).
* This demonstrates that the genetic code is read in one direction and sequentially, without skipping bases.
* Single nucleotide changes alter only 1 AA, showing a non-overlapping code
If the code were overlapping, one mutation would change multiple amino acids.
* This confirms the genetic code is read in non-overlapping triplets.
What are the key characteristics of the genetic code?
Linear– Read from 5’ to 3’ along the mRNA.
Non-overlapping– Each nucleotide is part of only one codon.
Triplet-based– Three nucleotides (codon) encode one amino acid.
Degenerate– Some amino acids are encoded by multiple codons.
What is the structure and function of transfer RNA (tRNA)?
Adapter Molecules– Connect mRNA to protein during translation.
3D Structure– Essential for function, conserved across tRNAs.
Superimposed tRNAs– Fold into a specific shape for efficient binding.
What enzyme attaches an amino acid to its corresponding tRNA?
Aminoacyl-tRNA synthetase– Catalyzes the attachment of an amino acid to its specific tRNA.
* Key Role– Ensures correct amino acid incorporation during translation.
* Recognizes both the amino acid and tRNA with high specificity.
What is the wobble hypothesis in translation?
Wobble allows a single tRNA to recognize more than one codon by flexible base pairing at the third position of the codon.
* This explains why there are fewer tRNAs than codons (e.g., 61 codons but fewer than 61 tRNAs).
* Example: Inosine (I) in the tRNA anticodon can pair with U, C, or A in the mRNA codon.
How do prokaryotic and eukaryotic ribosomes differ in structure and subunits?
Prokaryotic Ribosome (70S)
* Large subunit (50S): Contains 23S rRNA, 5S rRNA, and proteins
* Small subunit (30S): Contains 16S rRNA and proteins
* Found in bacteria & archaea
* Function: Translation occurs co-transcriptionally
Eukaryotic Ribosome (80S)
* Large subunit (60S): Contains 28S rRNA, 5.8S rRNA, 5S rRNA, and proteins
* Small subunit (40S): Contains 18S rRNA and proteins
* Found in eukaryotic cells (cytoplasm & ER-bound)
What is the role of rRNA in ribosomes?
rRNA is not just a structural component of the ribosome—it plays a catalytic role in protein synthesis.
rRNA folds by intramolecular base pairing into 3D structures.
rRNA stabilizes ribosomal structure and helps position mRNA and tRNA.
The peptidyl transferase center in the ribosome catalyzes peptide bond formation, making the ribosome itself a ribozyme!
What are the three tRNA binding sites in the ribosome?
The three tRNA binding sites are:
* A site (Aminoacyl site): Where the tRNA carrying an amino acid binds.
* P site (Peptidyl site): Where the tRNA holding the growing polypeptide chain is located.
* E site (Exit site): Where the tRNA exits after its amino acid is added to the chain.
How does the ribosome determine where to start translation in prokaryotes and eukaryotes?
Prokaryotes:
* The Shine-Dalgarno sequence (8-10 nt upstream of AUG) helps position the ribosome.
* The first amino acid is N-formylmethionine (fMet), brought in by tRNA-fMet, and it is placed in the P site of the ribosome.
* Initiation Factors (IFs) ensure only tRNA-fMet is used.
Eukaryotes:
* The ribosome recognizes the 5’ cap and scans for the first AUG.
* eIFs (Eukaryotic Initiation Factors) assist in unwinding secondary RNA structures and guiding ribosome binding.
* The first amino acid is Methionine (Met), inserted by tRNA-iMet.
How does translation terminate in prokaryotes?
When a stop codon (UAA, UAG, or UGA) reaches the A site, Release Factors (RFs) bind:
* RF1 recognizes UAA, UAG
* RF2 recognizes UAA, UGA
* RF3 assists RF1 and RF2
No tRNA matches the stop codon — instead, a water molecule is used in the peptidyl transfer center, releasing the polypeptide.
The ribosome disassembles and is recycled for new rounds of translation.
What is the outcome of alternative splicing?
Alternative splicing allows a single pre-mRNA to produce related but distinct protein isoforms by including or excluding different exons.
This increases protein diversity—for example, humans produce over 70,000 proteins from ~21,000 genes.
What are the main types of enzymes involved in post-translational modifications of proteins?
Kinases– add phosphate groups (phosphorylation)
Phosphatases– remove phosphate groups (dephosphorylation)
Acetylases– add acetyl groups (acetylation)
Deacetylases– remove acetyl groups (deacetylation)
Methylases– add methyl groups (methylation)
Demethylases– remove methyl groups (demethylation)
Ubiquitylation enzymes– attach ubiquitin to proteins (ubiquitylation)
What are the effects of post-translational modifications on proteins?
Post-translational modifications can:
* Increase or decrease protein activity
* Create or disrupt binding sites
* Target proteins to specific cellular regions
* Mark proteins for degradation (e.g., ubiquitylation)
* Induce allosteric changes that alter protein structure and function
What protein sequences target proteins to specific locations in the cell?
Nuclear Localization Sequence (NLS): Recognized by cytoplasmic receptors that transport proteins into the nucleus via nuclear pores.
Signal Peptide (Signal Sequence): A 15–25 amino acid sequence at the N-terminus that directs the protein to the ER for further targeting or secretion.
