Lecture 20: Central Dogma: Genetic Code, tRNA, tRNA Synthetases

In the 'Expanded Framework' of biology, what process involves the removal of introns and combinatorial assembly of exons?

Splicing

What is the defining characteristic of exons in mRNA processing?

They are the sequences that are kept in the final transcript.

What is the defining characteristic of introns in mRNA processing?

They are transcribed but physically cut out of the transcript.

In human genes, how does the length of introns typically compare to the exons they interrupt?

Introns are often massively longer than exons.

Which group of splicing is autocatalytic and requires a free guanosine molecule?

Group I

In Group I splicing, which specific chemical group on the free guanosine attacks the 5' splice site?

The 3' OH group.

What type of mechanism characterizes Group II autocatalytic splicing?

The lariat mechanism.

In Group II splicing, what internal nucleotide attacks the 5' splice site to form a cyclized loop?

A conserved internal Adenine.

Which hydroxyl group on the internal Adenine initiates the first step of Group II splicing?

The 2' OH group.

How many small nuclear RNAs (snRNAs) make up the spliceosome complex?

Five ($U1$, $U2$, $U4$, $U5$, and $U6$).

In the spliceosome, which snRNA is responsible for recognizing the 5' splice site?

U1

In the spliceosome, which snRNA is responsible for recognizing the branch site?

U2

What is the primary evolutionary advantage of the 'Cut & Paste' mechanism of splicing?

It allows a single gene to produce multiple unique proteins.

What process allows HIV to form viral DNA from its viral RNA genome?

Reverse transcription.

Which enzyme is responsible for inserting viral DNA into the host's genomic DNA?

Integrase

During HIV maturation, which enzyme cleaves new polyproteins to create an infectious virus?

Viral protease

What class of ART drugs targets the conversion of viral RNA into DNA by mimicking DNA building blocks?

Nucleoside reverse transcriptase inhibitors (NRTIs).

What class of ART drugs prevents the integration of the viral genome into the host's DNA?

Integrase inhibitors.

Which molecule acts as the 'adaptor' that allows the genetic message to be read during translation?

tRNA

Mathematically, why is a doublet code (4^2) insufficient for the 20 standard amino acids?

It only provides 16 unique combinations.

What is the minimum number of nucleotides per codon required to account for 20 amino acids?

Three (4^3 = 64 combinations).

If a genetic code is overlapping, how many amino acids are typically affected by a single-point mutation?

Three

According to the experiment by Tsugita and Fraenkel-Conrat, point mutations in the Tobacco Mosaic Virus (TMV) result in how many amino acid changes?

One

In Nirenberg's 1961 experiment, a synthetic poly(U) mRNA produced a polypeptide consisting of which amino acid?

Phenylalanine (Phe).

In cell-free protein synthesis experiments, what was used to precipitate the newly formed proteins for counting?

Acid

Rule: The genetic code is _____, meaning it contains no spare nucleotides or 'commas' between codons.

Back-to-back

What term describes a genetic code where multiple different codons can specify the same single amino acid?

Redundant (or degenerate).

What term describes a genetic code where a single specific codon never codes for more than one amino acid?

Unambiguous

What are 'nonsense' codons?

Stop codons that signal the end of translation.

What type of mutation results in no change to the amino acid sequence of a protein?

Silent mutation.

What type of mutation results in the replacement of one amino acid with a different one?

Missense mutation.

What type of mutation creates a premature stop codon, resulting in a truncated protein?

Nonsense mutation.

What type of mutation, caused by an insertion or deletion, shifts the entire reading frame of the mRNA?

Frameshift mutation.

Which end of the tRNA molecule is the site of amino acid attachment?

The 3' end.

What is the universal nucleotide sequence found at the 3' end of all tRNAs?

CCA

When are the unusual and modified bases in tRNA synthesized?

Post-transcriptionally.

What is the secondary structure model of tRNA called?

The cloverleaf model.

What is the actual tertiary shape of a tRNA molecule in three-dimensional space?

An L-shape.

How many sense codons exist in the standard genetic code?

61 (64 total minus 3 stop codons).

Roughly how many different tRNAs are present in a cell to read the 61 codons?

Approximately 40.

Which hypothesis explains how a single tRNA can recognize multiple different codons for the same amino acid?

The Wobble Hypothesis.

Which enzyme group is responsible for chemically joining amino acids to their specific tRNA adaptors?

tRNA Synthetases

In the context of translation, what is the role of the anticodon?

It base-pairs with the mRNA codon to ensure the correct amino acid is incorporated.