An antibiotic blocks peptidyl transferase activity by binding to the 50S ribosomal subunit. Which organisms would be directly harmed by this antibiotic?
AEukaryotes only, since they have a 60S large subunit
BProkaryotes only, since they have a 50S large subunit — the 60S eukaryotic large subunit would be unaffected
CBoth prokaryotes and eukaryotes equally, since peptidyl transferase is identical in both
DNeither — peptidyl transferase is a protein enzyme and not part of the ribosomal subunits
Prokaryotic ribosomes are 70S complexes with a 50S large subunit and 30S small subunit. Eukaryotic ribosomes are 80S complexes with a 60S large subunit and 40S small subunit. An antibiotic targeting the 50S subunit selectively attacks prokaryotes — their ribosomes are structurally different enough that the drug does not bind the 60S subunit. This difference in ribosome structure is the basis for many clinically important antibiotics (chloramphenicol, erythromycin, clindamycin). Option D reflects a common misconception: the peptidyl transferase center is made of rRNA, not protein — the ribosome is a ribozyme.
Question 2 Multiple Choice
A ribosome begins translating an mRNA in the cytoplasm. Moments later, the growing polypeptide chain is being threaded directly into the ER lumen. What caused the ribosome to relocate to the ER?
AThe ribosome detected that the mRNA was tagged for ER-localized translation before synthesis began
BThe emerging signal sequence on the nascent polypeptide was recognized by the signal recognition particle (SRP), which docked the ribosome onto the ER
CER-bound ribosomes are structurally different from cytoplasmic ones and are recruited by ER membrane proteins
DThe mRNA was transported to the ER and the ribosome followed, since ribosomes always stay with their mRNA
Ribosomes do not know their destination in advance. A ribosome begins translation in the cytoplasm regardless of the mRNA it is reading. If the growing protein contains a signal sequence (a hydrophobic stretch near the N-terminus), that sequence emerges from the ribosome and is recognized by the SRP — a ribonucleoprotein complex in the cytoplasm. SRP binds the signal sequence and the ribosome, halts translation, and escorts the entire complex to an SRP receptor on the ER membrane. Translation resumes with the polypeptide being fed directly into the ER lumen. Crucially, option C is false: the ribosome on the ER is the same machine as a free cytoplasmic ribosome — the protein being synthesized, not the ribosome itself, determines the destination.
Question 3 True / False
The peptidyl transferase center of the ribosome — the site where peptide bonds are formed — is composed of ribosomal RNA rather than protein.
TTrue
FFalse
Answer: True
This was confirmed by X-ray crystallography in the early 2000s (work that contributed to the 2009 Nobel Prize). The active site where amino acids are joined is entirely made of 23S rRNA (in prokaryotes) / 28S rRNA (in eukaryotes). The ribosomal proteins help fold and stabilize the rRNA but do not perform catalysis. This makes the ribosome a ribozyme — an RNA enzyme. This discovery strengthened the 'RNA world' hypothesis: in the early evolution of life, RNA molecules both stored genetic information and catalyzed chemical reactions, before proteins took over most catalytic roles. The ribosome preserves a relic of this earlier chemistry.
Question 4 True / False
Ribosomes attached to the rough endoplasmic reticulum are a specialized subtype of ribosome that is structurally adapted for membrane insertion of proteins.
TTrue
FFalse
Answer: False
This is a common misconception. ER-bound ribosomes are structurally identical to free cytoplasmic ribosomes — they are not a different type. The same ribosome that starts translation in the cytoplasm can end up tethered to the ER if the growing polypeptide contains a signal sequence. Once the protein is fully synthesized and released, the ribosome detaches from the ER and can be reused for cytoplasmic translation. There are no specialized 'ER ribosomes' with different structures. The cell does not need two kinds of ribosomes; the mRNA's own sequence determines where the protein ends up.
Question 5 Short Answer
Why is the ribosome described as a ribozyme, and what does this classification imply about the evolutionary origins of protein synthesis?
Think about your answer, then reveal below.
Model answer: A ribozyme is an RNA molecule that performs catalysis. The ribosome qualifies because its peptidyl transferase center — the active site that forms peptide bonds — is made of rRNA, not protein. The ribosomal proteins serve structural scaffolding roles. This means that at the origin of life, before proteins existed, RNA molecules could have catalyzed peptide bond formation to build the first proteins. The ribosome is thus a molecular fossil: it preserves the chemistry of an 'RNA world' in which RNA served both informational and catalytic functions, before the division of labor in which DNA stores information and proteins catalyze reactions.
The ribozyme nature of the ribosome has deep evolutionary implications: it suggests that peptide synthesis originally arose in an RNA-dominated world, and the modern ribosome retains the original RNA-based catalysis even after billions of years of evolution. Proteins now dominate catalysis elsewhere in the cell, but the ribosome — the very machine that makes proteins — still uses RNA to do the most critical bond-forming step.