Molecular Biology Quiz on RNA and Translation

Chapter 17: Expression of Genes

• Gene expression is the process by which DNA directs protein synthesis.
• This process has two main stages: transcription and translation.
• The information content of genes is in the specific sequences of nucleotides.
• DNA inherited by an organism dictates the synthesis of proteins.
• Proteins link genotype to phenotype.

The Flow of Genetic Information

• The information encoded in genes is contained in the specific nucleotide sequences.
• Inherited DNA leads to specific traits by directing protein synthesis, creating the observable characteristics.
• Proteins form the connections between genotype and phenotype (the observable characteristics).
• Gene expression includes transcription followed by translation.

How can one change in DNA result in such a dramatic change in appearance?

• A change in DNA can lead to a change in proteins.
• Proteins link genotype and phenotype.
• Gene expression is the process by which DNA directs protein synthesis.

Concept 17.1: Genes specify proteins via transcription and translation

• Genes specify proteins by directing the synthesis of proteins through a chain of command: DNA → RNA → protein

Basic Principles of Transcription and Translation

• Genes direct protein synthesis but do not directly synthesize them.
• RNA acts as a bridge between genes and proteins they code for.
• Transcription is the synthesis of RNA using DNA as a template.
• Messenger RNA (mRNA) is the product of transcription.
• Translation is the synthesis of a polypeptide using information in mRNA.
• Proteins are synthesized by ribosomes.

Prokaryotes vs. Eukaryotes

• In prokaryotes, translation of mRNA begins before transcription ends due to the lack of a nucleus.
• In eukaryotes, the nuclear envelope separates transcription from translation, requiring RNA processing before transport to the cytoplasm.
• Eukaryotic RNA transcripts are modified via RNA processing to yield mature mRNA.

More than One Type of RNA

• mRNA = protein synthesis
• tRNA = transfer amino acids during protein synthesis
• rRNA = essential role within the ribosome
• Other types of RNA exist (e.g. siRNA, snRNA)

Codons: Triplets of Nucleotides

• The flow of information from gene to protein is based on a triplet code (a series of non-overlapping, three-nucleotide words).
• Gene word are transcribed into complementary mRNA non-overlapping three-nucleotide words.
• mRNA words are then translated into amino acid chains forming a polypeptide.

The Template Strand of DNA

• One DNA strand serves as the template for RNA synthesis.
• This template strand is always the same for a given gene.
• The specific template strand is determined by the enzyme's orientation that transcribes the gene, which in turn depends on the DNA sequences associated with the gene.

The Genetic Code

• 64 codons were deciphered in the early 1960s;
• 61 codons code for amino acids.
• 3 codons are 'stop' signals.
• Each codon specifies a particular amino acid (one of 20) to be placed at the correct position in the polypeptide chain.
• The genetic code is redundant; more than one codon may specify the same amino acid, but each codon specifies only one amino acid.
•  Codons must be read in the correct reading frame (correct groupings) to produce the correct polypeptide.

Concept 17.2: Transcription

• Transcription is the first stage in gene expression.
• RNA synthesis is catalyzed by RNA polymerase.
• It does not need helicase.
• RNA polymerase does not need a primer.
• RNA synthesis follows the same base-pairing rules as DNA, except uracil replaces thymine.
• RNA polymerase synthesizes RNA in the 5' → 3' direction.
• Stages: initiation, elongation, termination

Molecular Components of Transcription

• RNA polymerase unwinds the DNA double helix, 10-20 bases at a time.
• Transcription progresses at around 40 nucleotides per second in eukaryotes.
• A gene is often transcribed simultaneously by several RNA polymerases.

Differences Between DNA and RNA Polymerase

• DNA Replication is the function of DNA Polymerase
• Transcription is the function of RNA Polymerase
• DNA Polymerase needs the origin of replication
• RNA Polymerase needs a promoter sequence
•  DNA polymerase needs a primer.
• RNA polymerase does not need a primer.
• DNA polymerase uses both strands for replication
• RNA polymerase only uses one strand

Initiation of Transcription

• The start point is the sequence that RNA polymerase binds to start transcription.
• Promoter sequences are found upstream of the start point, and transcription factors help RNA polymerase bind and begin transcription.
• A transcription initiation complex is formed.

Elongation of the RNA Strand

• RNA polymerase unwinds the DNA double helix (separating the strands).
• Nucleotides are added to the 3' end of the RNA strand, following the template strand pairing rules.
• The strand lengthens in a 5' → 3' direction.

Termination of Transcription

• Mechanisms differ between bacteria and eukaryotes.
• Bacteria stop at the end of the terminator.
• Eukaryotes use a polyadenylation signal (AAUAAA) as a stop point, where the transcript is released after a certain number of nucleotides.

Concept 17.3: Eukaryotic cells modify RNA after transcription

• Eukaryotic RNA modification (RNA processing) occurs in the nucleus before mRNA leaves for the cytoplasm.
• Modification of mRNA involves altering the pre-mRNA's ends and removing intervening sequences.

Alteration of mRNA Ends

• The 5’ end (beginning) gets a modified guanine nucleotide 'cap'.
• The 3’ end (end) gets a polyadenylation tail containing multiple adenine nucleotides (50-250).
• These modifications protect mRNA and help ribosomes attach.

Split Genes and RNA Splicing

• Eukaryotic genes have coding regions (exons) and intervening sequences (introns).
• RNA splicing removes the introns and joins the exons together.
• This creates an mRNA strand that is a continuous coding sequence.

RNA Splicing and Spliceosomes

• RNA splicing is carried out by spliceosomes.
• These are protein and RNA complexes recognizing splice sites.
• The RNA molecules of spliceosomes catalyze the splicing reaction.

Ribozymes

• Ribozymes are catalytic RNA molecules that act as enzymes, like splicing RNA.
• The discovery of ribozymes demonstrated that not all biological catalysts are proteins. RNA can also act as enzymes.

Three Properties of RNA Enabling Enzyme Function

• RNA's single-stranded nature allows for base-pairing that forms secondary and tertiary structures.
• RNA bases have functional groups participating in catalytic reactions.
• RNA can hydrogen-bond with other nucleic acid molecules, facilitating reactions.

The Functional and Evolutionary Importance of Introns

• Introns may regulate gene expression.
• Introns in some genes can be involved in alternative RNA splicing, enabling one gene to code for multiple polypeptides.
• This increases the number of proteins that an organism can produce.

Proteins' Modular Architecture

• Proteins have a modular architecture (domains).
• Domains are discrete regions.
• Different exons often code for different domains within a protein.

Concept 17.4: Translation

• Translation is the RNA-directed protein synthesis process.
• Genetic information in mRNA is used to synthesize a polypeptide.

Molecular Components of Translation

• Transfer RNA (tRNA) translates the mRNA message into proteins.
• tRNA molecules transfer amino acids to ribosomes (the protein synthesis sites).
• Each tRNA is specific for a particular amino acid.
• There are different tRNA for each amino acid

The Structure and Function of Transfer RNA

• tRNA have two main functions.
• Each tRNA carries a specific amino acid at one end.
• Each tRNA has a specific anticodon at the other end.
• Anticodons bind to complementary mRNA codons, helping to place the correct amino acids in the polypeptide chain.

tRNA Synthesis and Structure

• tRNA is synthesized in the nucleus and later transferred to the cytoplasm.
• Individual tRNA molecules consist of a single RNA (~80 nucleotides).
• Flattened, base-paired tRNA forms a cloverleaf shape.

Hydrogen Bonds and tRNA Structure

• Hydrogen bonds cause tRNA to have a 3D roughly L-shaped structure.
• The protruding 3' end is the amino acid attachment site.
• The anticodon region (in the 3' ->5') is complementary
• to an mRNA codon (5'­3')

Accurate Translation and Wobble Pairing

• Accurate translation requires correct amino acid-tRNA pairings (done by aminoacyl-tRNA synthetases, an enzyme).
• Complementary mRNA & tRNA codon pairing.
• Wobble pairing allows some tRNAs to bind to more than one codon (helping efficiency).

Ribosome Structure and Function

• Ribosomes are made of rRNA and proteins (both subunits).
• Ribosomes facilitate the pairing of tRNA anticodons with mRNA codons.
• Bacteria and eukaryotic ribosomes are similar but have significant differences (this is why some antibiotics work on bacteria but not humans).
• Ribosomes have three tRNA binding sites (A, P, and E).

Three Stages of Translation

• Initiation, Elongation, Termination

Building a Polypeptide Initiation Stage

• The start codon (AUG) signals the start of translation.
• The small ribosomal subunit binds to the mRNA and a special initiator tRNA molecule carrying methionine.

Building a Polypeptide Elongation Stage

• Codon recognition: tRNAs carrying the corresponding amino acids bind to the A site.
• Peptide bond formation: The ribosome catalyzes peptide bond formation between the amino acids.
• Translocation: The ribosome moves one codon along the mRNA, moving the tRNA from the A site to the P site and the tRNA from the P site to the E site.

Building a Polypeptide Termination Stage

• Stop codons (UAA, UAG, or UGA) trigger termination of translation.
• A release factor binds to the stop codon on the mRNA.
• The release factor prompts the addition of a water molecule, releasing the polypeptide from the tRNA in the P site.
• Ribosomal subunits dissociate.

Making Multiple Polypeptides

• Multiple ribosomes can translate the same mRNA molecule simultaneously (forming polyribosomes).
• Polyribosomes allow for the rapid synthesis of multiple copies of the polypeptide.

Coupling Transcription & Translation in Bacteria

• Bacteria couple transcription and translation to streamline the process.
• Once mRNA is created, ribosomes begin translation before the entire mRNA is made.
• This allows the newly formed proteins to quickly diffuse to their locations of function.

In Eukaryotes

• The nuclear envelope separates transcription and translation in eukaryotes.
• RNA processing occurs in the nucleus before the mRNA leaves for the cytoplasm.

Test your knowledge on the roles of RNA polymerase and tRNA in the processes of transcription and translation. This quiz covers key concepts, including RNA processing, modifications of mRNA, and the function of aminoacyl-tRNA synthetase. Perfect for students studying molecular biology and genetics.