Chapter 6 - Gene Expression at the Molecular Level

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Questions and Answers

What is the main functional product of protein-coding genes?

Ribosomal RNA (rRNA)

Messenger RNA (mRNA)

Transfer RNA (tRNA)

Polypeptide (correct)

Which type of RNA is synthesized from non-coding RNA genes?

Functional RNA (correct)

mRNA

DNA

Polypeptide

During elongation, RNA is synthesized in which direction?

Random direction

3’ to 5’ direction

5’ to 3’ direction (correct)

3’ to 2’ direction

What is the strand called that is used as a template for RNA synthesis during transcription?

Template strand Signup and view all the answers

Which feature is a difference between RNA polymerases and DNA polymerases?

RNA polymerases do not have exonuclease activity Signup and view all the answers

What does alternative splicing of mRNA allow for?

Creation of multiple proteins from a single gene Signup and view all the answers

How does the sequence of the coding strand compare to the sequence of the mRNA produced?

Identical, with U instead of T Signup and view all the answers

What primarily differentiates basic transcription processes in prokaryotes and eukaryotes?

The complexity of associated protein components Signup and view all the answers

What is the initial role of aminoacyl tRNA during translation?

It binds to the A site through codon/anticodon recognition. Signup and view all the answers

What is the result of the peptidyl transfer reaction?

A peptide bond is formed between the amino acid in the A site and the polypeptide chain. Signup and view all the answers

What occurs during the translocation process of the ribosome?

tRNA moves from the A site to the P site. Signup and view all the answers

What triggers the termination of translation?

Recognition of a stop codon by release factors. Signup and view all the answers

What happens to the tRNA in the P site once the polypeptide is released?

It exits the ribosome via the E site. Signup and view all the answers

What is the function of the 5' cap in mRNA processing?

It promotes the binding of ribosomes during translation. Signup and view all the answers

What type of sequences do exons represent in mRNA?

They are coding sequences that appear in the mature mRNA. Signup and view all the answers

Which polymerase is NOT involved in eukaryotic transcription?

RNA polymerase IV Signup and view all the answers

What is the role of polyadenylation in mRNA processing?

It adds adenines to the 3' end, aiding in stability and export. Signup and view all the answers

What component is primarily responsible for catalyzing the splicing of pre-mRNA?

snRNPs Signup and view all the answers

What is the primary purpose of alternative splicing?

To generate different protein products from the same gene Signup and view all the answers

How do eukaryotes differ from prokaryotes in terms of transcription initiation?

Eukaryotes require general transcription factors, while prokaryotes use sigma factors. Signup and view all the answers

Which statement about introns is true?

Introns are removed from pre-mRNA during the splicing process. Signup and view all the answers

What is gene expression?

The conversion of encoded information in a gene into a functional product. Signup and view all the answers

What was Archibald Garrod's contribution to genetics?

He linked mutant genes to metabolic diseases. Signup and view all the answers

What does the one gene – one enzyme hypothesis suggest?

Each gene controls the production of one specific enzyme. Signup and view all the answers

What type of protein is primarily associated with Beadle and Tatum's research?

Enzymes. Signup and view all the answers

How did Beadle and Tatum categorize the mutant strains of Neurospora crassa?

By enzyme defects involved in arginine synthesis. Signup and view all the answers

What does a mutation in a gene potentially affect?

Gene function due to alterations in the gene sequence. Signup and view all the answers

What is an inborn error of metabolism?

An inherited disease caused by a defective gene affecting metabolic processes. Signup and view all the answers

What was the main organism studied by Beadle and Tatum?

Neurospora crassa. Signup and view all the answers

Why do some proteins consist of two or more polypeptides?

To perform complex biological functions. Signup and view all the answers

What is one of the roles of enzymes in biochemical pathways?

To catalyze each step in the pathway. Signup and view all the answers

What does the term 'degenerate' refer to in the context of the genetic code?

The ability of multiple codons to specify the same amino acid. Signup and view all the answers

Which component of tRNA is specifically responsible for binding to the amino acid?

3' single-stranded region (Acceptor stem) Signup and view all the answers

What is the primary function of aminoacyl-tRNA synthetases?

To catalyze the attachment of amino acids to tRNA. Signup and view all the answers

In what direction is the mRNA read during translation?

5' to 3' Signup and view all the answers

What is the role of the start codon in mRNA?

To determine the reading frame of the mRNA. Signup and view all the answers

How is accurate tRNA charging ensured?

By having one aminoacyl-tRNA synthetase per amino acid. Signup and view all the answers

What distinguishes eukaryotic mRNA initiation from bacterial mRNA initiation?

Eukaryotic mRNA requires cap-binding proteins for binding. Signup and view all the answers

Which site on the ribosome is the location where a new aminoacyl-tRNA enters during translation?

A site Signup and view all the answers

What is the consequence of inserting or deleting bases in groups other than three from an mRNA sequence?

It changes the reading frame and alters the entire amino acid sequence. Signup and view all the answers

What is the shape of eukaryotic ribosomes composed of?

Ribosomal RNAs and multiple proteins. Signup and view all the answers

Study Notes

Gene Expression at the Molecular Level I

Gene expression is the process of converting genetic information into a functional product
It is studied at both the molecular and trait levels
Mutations are heritable changes in genetic material affecting gene function by altering the gene sequence
Research on mutations has shown the relationship between normal genes and functional proteins, and abnormal genes and non-functional proteins.
Inborn Errors of Metabolism are inherited diseases where abnormal levels of homogentisic acid accumulate, demonstrating a link between mutant genes, defective enzymes, and metabolic diseases.

Archibald Garrod

Studied patients with metabolic defects, such as alkaptonuria
In 1908, proposed a link between a mutant gene, missing/defective enzyme and metabolic disease, calling it an "inborn error of metabolism"

Phenylalanine Metabolism

Mutations can cause phenylketonuria or tyrosinosis or alkaptonuria
Mutations in genes related to these pathways cause metabolic disorders

Beadle and Tatum

Discovered Garrod's work in the early 1940s
Studied Neurospora crassa (common bread mold)
Determined minimum growth requirements
Focused on amino acid synthesis
Hypothesized that genes encode enzymes, and mutations can cause defects in enzymes needed for amino acid synthesis.
Proposed that each step in a biochemical pathway is catalyzed by a different enzyme, controlled by a different gene.
Collected mutant strains needing arginine supplementation for growth
Explored precursor molecules' effects on mutant strain growth
Identified three genes and enzymes for arginine synthesis
Found mutant strains grouped according to defective enzymes. Demonstrated single gene controlling synthesis of single enzyme

The Central Dogma of Gene Expression

The fundamental principle of gene expression
Shows the flow of genetic information from DNA to RNA to protein
Includes processes like replication, transcription, and translation

Prokaryotes vs. Eukaryotes

Prokaryotes have simpler gene expression processes. Transcription in the cytoplasm, no modifications occur. Translation takes place immediately.
Eukaryotes are more complex, with transcription in the nucleus and subsequent RNA modifications (splicing etc), and separate translation in the cytoplasm.

Genes

Organized units of DNA sequences transcribed into RNA
Protein-coding genes produce mRNA specifying amino acid sequences, to eventually make proteins
Non-coding RNA genes (e.g., tRNA, rRNA) produce functional RNA molecules

Gene Organization

DNA segments organized into promoter, transcribed region, and terminator (signals for transcription start and end)
Regulatory sequences influence transcription rate
The transcribed region carries the amino acid sequence coding information

Three Stages of Transcription

Initiation - RNA polymerase binds to promoter using sigma factor, forming an open complex
Elongation - RNA polymerase moves along template strand, creating RNA in 5' to 3' direction, complementary to template
Termination - RNA polymerase reaches the terminator sequence, and the RNA transcript and RNA polymerase dissociate from DNA template

A Closer Look at Elongation

RNA synthesis is 5' to 3'
Uracil (U) in RNA replaces Thymine (T) of DNA.
Template strand of DNA is used as a template and read in the 3' to 5' direction
Coding strand has same sequence as mRNA, except T instead of U

Transcription along the Chromosome

DNA strand used as template can differ for adjacent genes.
Determined by promoter sequence location

Eukaryotic Transcription

Eukaryotes contain three RNA polymerases instead of one, and need several initiation factors
Basic features are identical, but each step involves greater complexity compared to prokaryotes.

Eukaryotic RNA Processing

Pre-mRNA undergoes capping, splicing, and polyadenylation
Capping involves adding a 5' cap (7-methylguanosine)
Splicing removes non-coding introns, joining exons
Polyadenylation involves adding a poly-A tail at the 3' end

RNA Processing: Capping

Covalent attachment of 7-methylguanosine to the 5' end of the mRNA transcript (5' cap)
Occurs while RNA polymerase synthesizes the pre-mRNA
Recognized by cap-binding proteins
Needed for mRNA nucleus exit
Protects mRNA and binds to ribosome for translation

RNA Processing: Tailing

Adds poly-A tail (100-200 adenines) to the 3' end of the mRNA
Helps with export from the nucleus and enhances mRNA stability
Allows mRNA to persist longer in the cytoplasm

RNA Processing: Splicing

Removes non-coding introns and joins exons
Catalyzed by the spliceosome (snRNPs)
snRNPs are made of snRNA & protein
Alternative splicing allows different gene products through variation on how exons are joined

The Genetic Code

Specifies the relationship between mRNA nucleotide sequence and corresponding polypeptide amino acid sequence
Codons are three-nucleotide sequences specifying amino acids or signaling start/stop
Examples: CCC = proline, GGC = glycine
tRNAs bind to mRNA codons using anticodons

The Genetic Code: Degeneracy

Multiple codons may specify the same amino acid
Using 3 bases, 64 different codons are possible (4^3). But there are only 20 different amino acids

Bacterial mRNA Organization

Contains ribosomal-binding site, start codon, coding sequence, and stop codon
Specified to code for specific amino acid sequence

Reading Frame

Start codon defines the reading frame
Adjacent codons are read as triplets in a 5' -> 3' direction
Insertions/deletions (not multiple of 3) lead to altered amino acid sequences

The Translation Machinery

mRNA carries the genetic code for amino acid sequence
Ribosomes are the sites of protein synthesis, composed of proteins and rRNA molecules, and have A, P, and E sites
tRNAs carry amino acids, with anticodons that match mRNA codons

tRNAs

Diverse tRNAs encoded by different genes, sharing common features, and a cloverleaf structure
Have an anticodon to recognize their mRNA codon
Acceptor stem binds amino acid

Aminoacyl-tRNA Synthetases

Enzymes attach amino acids to tRNA molecules.
There is one amino acid-specific synthetase for each of the 20 amino acids
Two-step reaction to create charged (aminoacyl-tRNA)

Ribosomes

Macromolecular structures where translation takes place.
Composed of proteins and rRNAs forming large/small subunits
Eukaryotic ribosomes combine 40S and 60S to form 80s ribosomes, prokaryotic are 30S and 50S forming 70S

Ribosome Structure

rRNA determines overall ribosome shape
tRNAs bind to A, P, and E sites for polypeptide elongation

Three Stages of Translation

Initiation - mRNA, tRNA, and ribosomal subunits combine
Elongation - Ribosome moves along mRNA, forming polypeptide chain
Termination - Stop codon signals the end of translation and release of the polypeptide chain

Translation Initiation in Bacteria

mRNA binds to the small ribosomal subunit
Initiator tRNA binds to the start codon (AUG)
Large ribosomal subunit binds to form the complete initiation complex

Eukaryotic Initiation

mRNAs lack ribosomal binding sites
Cap-binding proteins and initiation factors required
Start codon is more variable and often the first AUG codon

Elongation -1

Aminoacyl-tRNA binds to A site on ribosome
Recognized by codon/anticodon matching
Peptidyl tRNA is in P site

Elongation -2

Peptide bond forms between amino acids at A and P sites
Catalyzed by rRNA (ribozyme activity)
Polypeptide chain moves from P site to A site

Elongation -3

Ribosome shifts along the mRNA by one codon
Uncharged tRNA moves from P to E site exiting
New aminoacyl-tRNA enters A site

Termination

Translation stops when a stop codon is reached in the A site
Release factors bind and complete polypeptide release, leading to ribosome sub-unit dissociation

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