[SET 1] 15 Genes and Proteins

15.1 The Genetic Code 15.2 Prokaryotic Transcription 15.3 Eukaryotic Transcription

What is the central dogma of molecular biology?

The central dogma states that DNA is transcribed into mRNA, which is then translated into proteins.

What are genes composed of?

Genes are composed of DNA and are linearly arranged on chromosomes.

What role do proteins play in the cell?

Proteins orchestrate nearly every function of the cell.

What is the function of messenger RNA (mRNA)?

mRNA serves as a mobile molecular copy of one or more genes.

How many amino acids are commonly found in proteins?

There are 20 commonly occurring amino acids.

What is the significance of the amino acid sequence in proteins?

The variation in amino acid sequence is responsible for the enormous variation in protein structure and function.

What is a triplet codon?

A triplet codon is a three-nucleotide sequence that defines an amino acid.

Why is the genetic code described as degenerate?

The genetic code is degenerate because a given amino acid can be encoded by more than one nucleotide triplet.

What is the role of stop codons?

Stop codons terminate protein synthesis and release the polypeptide from the translation machinery.

What is the start codon and its function?

The start codon, AUG, specifies the amino acid methionine and initiates translation.

How does the reading frame for translation work?

The reading frame is set by the AUG start codon, and the mRNA is read in groups of three nucleotides.

What happens when one or two nucleotides are inserted into a gene?

Insertion of one or two nucleotides changes the triplet reading frame, altering the message for subsequent amino acids.

What is the significance of the genetic code being nearly universal?

The nearly universal genetic code indicates that virtually all species use the same code for protein synthesis.

What is the relationship between nucleotide sequences and amino acids?

Nucleotide sequences in mRNA specify the sequence of amino acids in proteins.

What are nonsense codons?

Nonsense codons are codons that do not code for any amino acid and signal the end of protein synthesis.

What is the structure of an amino acid?

An amino acid consists of an amino group, a carboxyl group, and a side chain.

How do similar codons relate to amino acids?

Amino acids with chemically similar side chains are often encoded by similar codons.

What is the purpose of the genetic code's degeneracy?

Degeneracy helps reduce the negative impact of random mutations by allowing similar amino acids to be specified by similar codons.

What is the process of transcription?

Transcription is the process of copying DNA into mRNA.

What is the process of translation?

Translation is the process of converting mRNA into a protein at the ribosome.

What is the role of ribosomes in protein synthesis?

Ribosomes read the genetic information on mRNA and assemble amino acids into proteins.

What is the significance of the AUG codon in translation?

AUG is the start codon that sets the reading frame for translation and specifies methionine.

What is the relationship between DNA and mRNA during transcription?

During transcription, DNA is used as a template to synthesize mRNA.

What happens to the protein structure when three nucleotides are inserted?

Inserting three nucleotides adds an extra amino acid but maintains the integrity of the rest of the protein.

What are the implications of mutations in the genetic code?

Mutations can lead to changes in amino acids, potentially affecting protein function, but degeneracy can mitigate some effects.

What does the conservation of codons imply about mRNA?

A purified mRNA encoding a protein from one species can be transferred to a different species, allowing that species to synthesize the protein.

What is the significance of having only one genetic code?

It suggests that all life on Earth shares a common origin despite the vast number of possible combinations of amino acids and codons.

What happens when two nucleotides are deleted from an mRNA?

It shifts the reading frame, potentially creating a nonfunctional protein or terminating protein synthesis.

How many copies of each chromosome do mammals have?

Mammals are diploid, meaning they have two copies of each chromosome.

What is the chromosome composition of common strawberries and cultivated kiwis?

Strawberries are octoploid (8n) and kiwis are hexaploid (6n).

What is the purpose of DNA extraction buffer in DNA isolation?

It helps to liberate and precipitate DNA from the fruit cells.

What is a transcription bubble?

The region where the DNA double helix unwinds during mRNA synthesis.

What is the template strand in transcription?

The DNA strand that is used to synthesize mRNA, which is complementary to it.

What is the difference between the template strand and the coding strand?

The coding strand has the same sequence as the mRNA (except for T being replaced by U), while the template strand is complementary to the mRNA.

What is the role of RNA polymerase in transcription?

It synthesizes RNA by adding nucleotides complementary to the template strand in the 5'-3' direction.

What is the +1 site in transcription?

The nucleotide pair in the DNA double helix from which the first mRNA nucleotide is transcribed.

How do prokaryotes differ from eukaryotes in terms of transcription?

Prokaryotes lack membrane-bound nuclei, allowing transcription, translation, and mRNA degradation to occur simultaneously.

What is a polycistronic mRNA?

An mRNA that encodes more than one protein, common in prokaryotes.

What is the composition of prokaryotic RNA polymerase?

It consists of five polypeptide subunits: two α, one β, one β', and one σ subunit.

What is the function of the σ subunit in prokaryotic RNA polymerase?

It helps the polymerase recognize the correct initiation site for transcription.

What is a promoter in the context of transcription?

A DNA sequence where the transcription machinery, including RNA polymerase, binds to initiate transcription.

What is the significance of plasmids in prokaryotes?

Plasmids are circular DNA molecules that can carry genes, such as those for antibiotic resistance, and can be transferred independently of the bacterial chromosome.

What is the polymerase composed of all five subunits called?

The holoenzyme.

Where do most prokaryotic promoters exist in relation to the genes they regulate?

Upstream of the genes.

What are the two conserved consensus sequences found in prokaryotic promoters?

The -10 region (TATAAT) and the -35 region (TTGACA).

What role does the σ subunit play in prokaryotic transcription?

It recognizes and binds to the consensus sequences in the promoter region.

What happens during the transcription initiation phase in prokaryotes?

The core enzyme binds to the promoter, and abortive transcripts of about 10 nucleotides are produced and released.

What occurs during the elongation phase of prokaryotic transcription?

The core enzyme synthesizes mRNA in the 5' to 3' direction at a rate of approximately 40 nucleotides per second.

What are the two types of termination signals in prokaryotic transcription?

Rho-dependent termination and Rho-independent termination.

How does Rho-dependent termination occur?

The rho protein collides with the polymerase after it stalls at a run of G nucleotides, releasing the mRNA.

What characterizes Rho-independent termination?

It involves specific sequences in the DNA that cause the mRNA to fold back and form a stable hairpin structure.

What is the primary difference between prokaryotic and eukaryotic transcription?

Eukaryotic transcription occurs in a membrane-bound nucleus and involves more complex processes.

What are the three types of RNA polymerases found in eukaryotes?

RNA polymerase I, RNA polymerase II, and RNA polymerase III.

What does RNA polymerase I transcribe?

All rRNAs except 5S rRNA.

What is the function of RNA polymerase II?

It synthesizes all protein-coding nuclear pre-mRNAs.

What types of RNA does RNA polymerase III transcribe?

5S rRNA, tRNAs, and small nuclear RNAs.

What is the significance of transcription factors in eukaryotic transcription?

They are required to bind to the promoter region and recruit the appropriate RNA polymerase.

What is the term for eukaryotic mRNAs that specify a single protein?

Monogenic.

What happens to eukaryotic pre-mRNAs after transcription?

They undergo extensive processing before translation.

Why can prokaryotic transcription and translation occur simultaneously?

Both processes occur in the same 5' to 3' direction without membranous compartmentalization.

What is the role of tRNAs in translation?

They serve as adaptor molecules between the mRNA template and the growing polypeptide chain.

What function do small nuclear RNAs serve?

They are involved in splicing pre-mRNAs and regulating transcription factors.

What toxin is used to determine which polymerase transcribes a gene?

α-amanitin, an oligopeptide toxin produced by the fly agaric toadstool mushroom.

How does α-amanitin affect RNA polymerases I, II, and III?

RNA polymerase I is insensitive, RNA polymerase II is extremely sensitive, and RNA polymerase III is moderately sensitive.

What is the consensus sequence of the TATA box in eukaryotic promoters?

TATAAA, located at -25 to -35 bases relative to the initiation site.

What role do basal transcription factors play in eukaryotic transcription?

They bind to the promoter and help recruit RNA polymerase II to a protein-coding gene.

What is the core complex of transcription factors for RNA polymerase II?

TFIID, which includes the TATA-binding protein (TBP).

What additional elements may be found in eukaryotic promoters to enhance transcription?

CAAT box, GC-rich boxes, and octamer boxes.

What is the function of enhancers and silencers in transcription?

They regulate the frequency of transcription but are not necessary for transcription to occur.

What are the promoter sequences for genes transcribed by RNA polymerase I?

Two GC-rich promoter sequences in the -45 to +20 region.

How does transcription initiation differ between RNA polymerase II and RNA polymerases I and III?

RNA polymerase II requires a complex of transcription factors, while I and III have less complex requirements.

What is the role of the FACT complex during transcription elongation?

It pulls histones away from the DNA template to allow polymerase movement.

How does the termination of transcription differ among RNA polymerases I, II, and III?

RNA polymerase II continues elongation 1,000 to 2,000 nucleotides beyond the gene; I and III require specific termination signals.

What type of sequence is recognized by termination proteins for RNA polymerase I?

A specific 18-nucleotide sequence.

What mechanism does RNA polymerase III use for termination?

It involves an mRNA hairpin structure similar to rho-independent termination in prokaryotes.

What is the significance of the TATA box in eukaryotic transcription?

It helps in the unwinding of DNA for transcription initiation due to its A-T rich content.

What happens to pre-mRNA after it is synthesized by RNA polymerase II?

A pre-mRNA tail is removed by cleavage during mRNA processing.

Why do eukaryotic promoters evolve faster than protein-coding genes?

Promoters may adapt to increase efficiency in recruiting transcription factors for higher gene expression.

What is the primary direction of elongation during transcription?

5' to 3' direction.

What is the structure of chromatin in non-dividing eukaryotic cells?

A diffuse mass of DNA and proteins, tightly packaged around histone proteins.

What is the role of transcription factors in eukaryotic transcription?

They stabilize the pre-initiation complex and contribute to the recruitment of RNA polymerase II.

How do eukaryotic promoters differ from prokaryotic promoters?

Eukaryotic promoters are larger and more complex, often containing multiple regulatory elements.

What is the function of the TATA-binding protein (TBP)?

It is part of the TFIID complex that binds to the TATA box in eukaryotic promoters.

What is the significance of the A-T rich element in the TATA box?

It facilitates the unwinding of DNA, making it easier for transcription to initiate.

What is the general theme of transcription factor assembly in eukaryotes?

A complex assembly of factors is required to recruit RNA polymerase II to the promoter.

What is the role of upstream elements in eukaryotic promoters?

They bind cellular factors that increase the efficiency of transcription initiation.