Gene Expression: From DNA to Protein Synthesis

What is the information content of genes based on?

Specific sequences of nucleotides in DNA.

How do genes influence traits in organisms?

By dictating the synthesis of proteins.

What is the relationship between genotype and phenotype?

Proteins link genotype to phenotype.

What are the two stages of gene expression?

Transcription (DNA to RNA) and translation (nucleic acid to protein).

What is the revised hypothesis regarding genes and proteins?

One gene can code for one protein, not one enzyme.

What is the role of RNA in protein synthesis?

RNA acts as a bridge between DNA and protein synthesis.

What are the differences between RNA and DNA?

RNA has ribose sugar and uracil (U) instead of thymine (T), and is usually single-stranded.

What is the primary transcript?

The initial RNA transcript from any gene before processing.

What is the central dogma of molecular biology?

The flow of genetic information is DNA → RNA → protein.

What is the template strand in transcription?

The DNA strand that provides a template for complementary RNA nucleotide sequencing.

What are codons?

mRNA base triplets that specify amino acids during translation.

How many codons code for amino acids, and how many are stop signals?

61 codons code for amino acids, and 3 are stop signals.

What does it mean that the genetic code is redundant but not ambiguous?

More than one codon can specify an amino acid, but no codon specifies more than one amino acid.

What is the role of RNA polymerase in transcription?

It catalyzes RNA synthesis by unwinding DNA and joining RNA nucleotides.

What is a promoter?

The DNA sequence where RNA polymerase attaches to initiate transcription.

What are the three stages of transcription?

Initiation, elongation, and termination.

What modifications occur to eukaryotic mRNA?

5' end receives a modified G nucleotide 5' cap, poly-A tail addition to the 3' end, and splicing of introns.

What are introns and exons?

Introns are noncoding regions, while exons are coding regions that are translated into amino acids.

What is alternative RNA splicing?

A process that allows a single gene to produce multiple polypeptides by including different exons.

What is the function of tRNA in translation?

tRNA transfers amino acids to the growing polypeptide chain in the ribosome.

What is the structure of tRNA?

tRNA is L-shaped (cloverleaf) with an anticodon on one end and an amino acid on the other and has a nucleotide triplet that can pair with complementary codon on mRNA

What are the three binding sites of a ribosome?

A site (aminoacyl), P site (polypeptide), and E site (exit).

What are the three stages of translation?

Initiation, elongation, and termination.

What is the role of the start codon (AUG)?

It establishes the reading frame for the mRNA during translation.

What happens during termination of translation?

A stop codon in the mRNA reaches the A site, causing the release of the polypeptide.

What are free and bound ribosomes?

Free ribosomes synthesize proteins in the cytosol, while bound ribosomes are attached to the ER.

What are point mutations?

Chemical changes in one or a few nucleotide pairs of a gene.

What are the two categories of point mutations?

Nucleotide pair substitutions (missense) and insertions/deletions (nonsense).

What is a frameshift mutation?

A mutation caused by insertions or deletions that alters the reading frame of the genetic message.

What is the operon model in gene expression?

A mechanism that controls gene expression in bacteria, involving operators and promoters.

What is a repressor in the context of operons?

A protein that binds to the operator and blocks RNA polymerase, preventing transcription.

What is the difference between repressible and inducible operons?

Repressible operons are usually on and can be turned off, while inducible operons are usually off and can be turned on.

What is the function of a signal peptide?

It marks polypeptides destined for the ER or secretion.

What are mutagens?

Physical or chemical agents that can cause mutations.

What does E. coli preferentially use when present in the environment?

Glucose

What role does CAP (catabolite activator protein) play when glucose is scarce?

CAP acts as an activator of transcription.

How is CAP activated?

CAP is activated by binding with cyclic AMP (cAMP).

What effect does activated CAP have on the lac operon?

It increases the affinity of RNA polymerase, thus accelerating transcription.

What happens to CAP when glucose levels increase?

CAP detaches from the lac operon, leading to very low transcription rates even if lactose is present.

What is the significance of gene regulation in multicellular organisms?

It is essential for cell specialization.

What is differential gene expression?

The expression of different genes by cells with the same genome.

At what common control point is gene expression regulated in all organisms?

At transcription.

How does chromatin structure influence gene expression?

The structural organization of chromatin packs DNA and can regulate gene expression.

What is the effect of heterochromatin on gene expression?

Genes within highly condensed heterochromatin are usually not expressed.

What is histone acetylation and its effect on transcription?

It involves attaching acetyl groups to histone tails, loosening chromatin structure and promoting transcription initiation.

What is DNA methylation?

The addition of methyl groups to certain bases in DNA, usually cytosine.

How is the methylation pattern inherited after DNA replication?

Enzymes methylate the correct daughter strand.

What do chromatin modifying enzymes do?

They control gene expression by making DNA more or less able to bind the transcription machinery.

What are control elements in eukaryotic genes?

Segments of noncoding DNA that serve as binding sites for transcription factors.

What is required for eukaryotic RNA polymerase to initiate transcription?

The assistance of proteins called transcription factors.

What are enhancers?

Groupings of distal control elements that may be far away from a gene.

What is the role of activators in gene transcription?

Activators bind to enhancers and stimulate transcription of a gene. two domains, one that binds DNA and a second that activates transcription

How do mediators function in transcription?

They interact with proteins at the promoter through bound activators.

What is the function of repressors in gene regulation?

They inhibit expression of a particular gene.

How do prokaryotic and eukaryotic gene expression differ?

Eukaryotic genes have individual promoters and control elements, while prokaryotic operons share a promoter.

What is alternative RNA splicing?

The production of different mRNA molecules from the same primary transcript.

How do regulatory proteins affect mRNA translation?

They can block the initiation of translation by binding to mRNA sequences.

What marks a protein for destruction in a cell?

The attachment of ubiquitin molecules. The length of time each protein function in a cell is regulated by means of selective degradation

What is the role of noncoding RNAs (ncRNAs) in gene expression?

They regulate gene expression at several points.

What are microRNAs (miRNAs)?

Small single-stranded RNA molecules that can bind to complementary mRNA sequences to degrade them or block translation.

What is RNA interference (RNAi)?

The phenomenon of inhibition of gene expression by small interfering RNAs (siRNAs).

How are codons read during translation?

In the 5' to 3' direction, with each codon specifying an amino acid.

What is a signal peptide?

A short peptide that marks a polypeptide for transport to the endoplasmic reticulum or secretion.

What is chromatin modification and its effect on gene expression?

Chemical modifications to histones and DNA that can influence chromatin structure, affecting gene transcription.

How many nucleotides correspond to an amino acid?

Three nucleotides.

transcription factors

Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.

transcription initiation complex

The completed assembly of transcription factors and RNA polymerase 2 bound to a promoter.

TATA box

A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex.

transcription rate in eukaryotes

40 nucleotides per second

RNA polymerase II

transcribes the polyadenylation

During RNA processing

Both ends are altered, introns are spliced out, and exons are kept in

Why modify

facilitate export of mRNA to the cytoplasm, protect mRNA from hydrolytic enzymes, and help ribosomes attach to 5' end

20 amino acids to

4 nucleotides

Sequences are transcribed into a chain of amino acids forming

polypeptides

splicing can occur without

enzymes by using ribozymes and intron auto cleaving themselves

First

Correct matching between tRNA anticodon and an amino acid done by the enzyme aminoacyl-tRNA synthetase

Second

correct match between tRNA anticodon and mRNA codon

wobble

A violation of the base-pairing rules in that the third nucleotide (5' end) of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position (3' end) of a codon.

initiation of translation

brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits

translation initiation complex

Assembly of mRNA, tRNA, and ribosomal subunits.

elongation (translation)

amino acids added at C-terminus

3 steps of elongation in translation

codon recognition, peptide bond formation, translocation

Operon

entire stretch of DNA (operator, promoter, games that are controlled) Can be switched on and off by protein repressor

Lac operon

the operon that controls the metabolism of lactose

inducer

A specific small molecule that inactivates the repressor in an operon.

Inducer of milk

allolactose

inducible enzymes

catabolic pathways

-synthesis induced by chemical signal

Repressible enzymes

anabolic pathways, synthesis repressed by high levels of end product

Proximal control elements

located close to the promoter