Molecular Biology: Genes and Expression

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Questions and Answers

What is the primary function of a gene?

To produce energy

To code for a specific protein (correct)

To regulate cell division

To synthesize carbohydrates

All genes in the human genome are expressed in every cell at all times.

False

What are the two main functional units of a eukaryotic gene?

Promoter region and coding region

The process by which DNA is converted into RNA is called __________.

Transcription Signup and view all the answers

Match the following types of genes with their characteristics:

Constitutive gene = Expressed at a constant rate Regulated gene = Expressed under specific conditions Housekeeping genes = Examples include enzymes of glycolysis Insulin gene = Expressed in pancreas Signup and view all the answers

Which of the following elements is NOT a conserved eukaryotic promoter element?

Poly-A tail Signup and view all the answers

Enhancers are always located close to the genes they enhance.

False Signup and view all the answers

What is the main function of messenger RNA (mRNA)?

To carry information from DNA to produce proteins. Signup and view all the answers

The process of synthesizing RNA from a DNA template is called ______.

transcription Signup and view all the answers

Match the following DNA sequences to their related function:

CAAT box = Promoter element TATA box = Promoter element Silencers = Depress transcription Enhancers = Enhance transcription Signup and view all the answers

What is the primary role of transcription factors?

To enhance or depress transcription Signup and view all the answers

What enzyme catalyzes the process of reverse transcription?

Reverse transcriptase Signup and view all the answers

What is the role of the TATA box in transcription?

It is a consensus promoter necessary for transcription initiation. Signup and view all the answers

The RNA transcript is a copy of the antisense strand of DNA.

False Signup and view all the answers

What is the purpose of the 5' capping in RNA processing?

To protect the 5' end of the primary RNA transcript from degradation by ribonuclease. Signup and view all the answers

The primary transcript RNA is converted into mature RNA through a process called _____ modifications.

post-transcriptional Signup and view all the answers

Match the following terms with their descriptions:

5' Capping = Addition of 7-methylguanosine to the RNA transcript 3' Polyadenylation = Addition of approximately 250 adenine residues RNA Splicing = Removal of introns from pre-mRNA Ribonuclease = Enzyme that degrades RNA into smaller components Signup and view all the answers

Which RNA polymerase is most sensitive to α-amanitin?

RNA Polymerase II Signup and view all the answers

HIV is an example of a retrovirus.

True Signup and view all the answers

What is the primary role of transcription factors in eukaryotic transcription?

They recognize and initiate transcription at specific promoter sequences. Signup and view all the answers

The final product formed during transcription is __________.

RNA Signup and view all the answers

Match the transcription factors with their primary roles:

TFIID = Recognizes TATA box TFIIB = Positions RNA polymerase at the start site TFIIF = Stabilizes RNA polymerase interaction TFIIH = Unwinds DNA and phosphorylates RNA polymerase CTD Signup and view all the answers

Which RNA polymerase is specifically responsible for synthesizing mRNA?

RNA Polymerase II Signup and view all the answers

RNA polymerases I and III transcribe mRNA.

False Signup and view all the answers

How many core peptides are there in RNA Polymerase II?

10 Signup and view all the answers

Transcription occurs in the __________ of eukaryotic cells.

nucleus Signup and view all the answers

What essential domain of RNA Polymerase II is required for transcription initiation?

C-terminal domain Signup and view all the answers

Which of the following is NOT a conserved eukaryotic promoter element?

Silencer region Signup and view all the answers

Enhancers are always located close to the genes they enhance.

False Signup and view all the answers

What is the primary function of transcription factors?

To regulate transcription by binding to enhancer or silencer regions. Signup and view all the answers

The region of DNA that initiates transcription of a particular gene is known as the __________.

promoter Signup and view all the answers

Match the following transcription elements to their functions:

Enhancers = Increase transcription likelihood Silencers = Decrease transcription rate Promoters = Initiate transcription Transcription factors = Regulate gene expression Signup and view all the answers

What type of RNA polymerase is responsible for synthesizing mRNA in eukaryotic cells?

RNA Polymerase II Signup and view all the answers

The __________ region is recognized by RNA polymerase II within the eukaryotic promoter.

CAAT box Signup and view all the answers

What is the primary role of transcription factors in eukaryotic transcription?

Recognize and bind to specific promoter sequences Signup and view all the answers

RNA polymerase II is responsible for transcribing tRNA genes.

False Signup and view all the answers

Name the RNA polymerase that is most sensitive to α-amanitin.

RNA Polymerase II Signup and view all the answers

Transcription factors interact with __________ at the promoter region to initiate transcription.

RNA polymerases Signup and view all the answers

Match the following RNA polymerases with their primary functions:

RNA Polymerase I = Transcribes rRNA genes RNA Polymerase II = Transcribes mRNA RNA Polymerase III = Transcribes tRNA and other small RNAs Signup and view all the answers

Which transcription factor is responsible for recognizing the TATA box?

TFIID Signup and view all the answers

Enhancer sequences are always located downstream of the genes they enhance.

False Signup and view all the answers

What role does TFIIH play in transcription initiation?

Unwinds DNA and phosphorylates the RNA polymerase CTD Signup and view all the answers

The __________ region is crucial for the accurate positioning of RNA polymerase at the start site of transcription.

BRE element Signup and view all the answers

Which of the following regions is found upstream of a eukaryotic gene and is critical for transcription initiation?

Promoter Signup and view all the answers

Enhancer sequences must be located immediately adjacent to the gene they regulate.

False Signup and view all the answers

What is the role of transcription factors in gene expression?

To facilitate the binding of RNA polymerase to the promoter region and regulate the transcription of genes. Signup and view all the answers

The enzyme responsible for synthesizing messenger RNA (mRNA) in eukaryotic cells is called __________.

RNA polymerase II Signup and view all the answers

Match the following RNA polymerases with their functions:

RNA polymerase I = Synthesis of rRNA RNA polymerase II = Synthesis of mRNA RNA polymerase III = Synthesis of tRNA RNA polymerase IV = Involved in RNA silencing Signup and view all the answers

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

To serve as a binding site for RNA polymerase Signup and view all the answers

Silencers are DNA sequences that enhance the transcription of adjacent genes.

False Signup and view all the answers

What sequences in the eukaryotic gene help regulate transcription aside from the promoter and enhancers?

Silencers and other regulatory elements. Signup and view all the answers

The __________ boxes, such as CAAT and GC boxes, are important promoter elements in eukaryotic genes.

consensus Signup and view all the answers

Study Notes

Gene

Is the fundamental unit of inheritance and determines all phenotypes.
Every gene contains instructions for a specific protein.
The human genome contains an estimated 30,000 to 120,000 genes.
Only a fraction of genes are expressed in a particular cell at any given time.

Gene Structure

Most eukaryotic genes consist of coding sequences (exons) interrupted by noncoding DNA (introns).
The average gene has 7-10 exons spread over 10-16kb of DNA.
Gene structure includes exons, start signals, stop signals, and regulatory control elements.
The two main functional units are the promoter region and the coding region.

Gene Expression

The process by which a gene's information is converted into a biologically functional molecule of either protein or RNA.
Gene expression is assumed to be controlled at various points in the sequence leading to protein synthesis.
The central dogma of molecular biology describes the flow of genetic information: DNA → RNA → protein.
- Transcription: DNA → RNA
- Translation: RNA → protein

Types of Genes

Constitutive genes (Housekeeping genes)
- Are expressed at a constant rate in everyday processes.
- Not subjected to regulation.
- Examples include enzymes of glycolysis.
Regulated genes
- Expressed only under certain conditions.
- Expressed in all cells or a subset of cells.
- Example: the expression of the insulin gene in the pancreas.

Flow of Genetic Information in Prokaryotes vs. Eukaryotes

Prokaryotes
- Transcription and translation occur simultaneously.
Eukaryotes
- Transcription occurs in the nucleus followed by RNA processing.
- Translation occurs in the cytoplasm.

Eukaryotic Promoter

Is a region of DNA that initiates transcription of a particular gene.
Located near the transcription start sites of genes, upstream on the DNA (towards the 5’ region of the sense strand).
Promoters can be about 100–1000 base pairs long.
Conserved eukaryotic promoter elements
- CAAT box
- TATA box
- GC box
- CAP site
Consensus sequence
- GGCCAATCT (CAAT box)
- TATAA (TATA box)
- GGGCGG (GC box)
- TAC (CAP site)

Enhancer Sequences

Are regulatory DNA sequences that enhance the transcription of an associated gene when bound by specific proteins called transcription factors.
Can be located upstream of a gene, within the coding region of the gene, downstream of a gene, or thousands of nucleotides away.

Silencers

Are regions of DNA that depress the rate of transcription when bound by specific transcription factors called repressors.

Transcription

Is the process by which certain areas of DNA are copied (transcribed) to mRNA, which carries the information needed for protein synthesis.
Processes include DNA replication, DNA repair, genetic recombination, and RNA synthesis (transcription).

Messenger RNA (mRNA)

mRNA is a type of RNA that is necessary for protein production.
It uses the information in genes to create a blueprint for making proteins.

Reverse Transcription

Is the synthesis of DNA from an RNA template catalyzed by reverse transcriptase enzyme.
Retroviruses contain RNA as their genetic material.
The retroviral RNA serves as a template for synthesis of DNA by reverse transcriptase.
Examples of retroviruses: HIV (AIDS), Hepatitis C.

Transcription in Eukaryotes

Pre-messenger RNA is formed, with the involvement of RNA polymerase enzymes.
- RNA Polymerase Reads DNA and makes an RNA copy of one strand/one gene.

RNA Polymerase

RNA polymerases I and III transcribe rRNA and tRNA genes, respectively.
Pol III transcribes a few other RNAs.
All three are big, multimeric proteins (500-700 kD).
All have two large subunits with sequences similar to those in E.coli RNA polymerase (Prokaryotes).
Pol II is the most sensitive to α-amanitin, an octapeptide from Amanita phalloides ("destroying angel mushroom").

Transcription Factors

The three polymerases (I, II and III) interact with their promoters via so-called transcription factors.
Transcription factors recognize and initiate transcription at specific promoter sequences.

Transcription in Eukaryotes: Post-Transcriptional Modifications or Gene Processing

The process by which primary transcript RNA is converted into mature RNA.
The pre-mRNA molecule undergoes three main modifications:
- 5' Capping
- 3' polyadenylation
- RNA splicing

Capping

Involves the addition of 7-methylguanosine (m7G) to the 5' end of the pre-mRNA.
Protects the 5' end of the primary RNA transcript from attack by ribonuclease.

Cleavage and Polyadenylation

Involves cleavage of the 3' end of the pre-mRNA molecule and the addition of about 250 adenine residues to form a poly(A) tail.
Protects the 3' end from ribonuclease digestion.

RNA Splicing

The pre-messenger RNA contains introns that are not required for protein synthesis.
The sequence AAUAAA in hnRNA serves as a signal for cleavage and addition of the poly(A) tail.
The pre-messenger RNA is chopped up to remove the introns and create messenger RNA (mRNA).

The Structure of a Eukaryotic Gene and its Products

5' flanking region
- Promoter
Transcribed region
- Intron
- Exon
Enhancer
CAAT box
GC boxes
TATA box
Protein
- Cap site
- Start signal
Left splice site
Right splice site
Protein stop signal
Poly (A) addition signal
Polyadenylation site

Synthesis of Messenger RNA (mRNA) in Eukaryotes: hnRNA, heterogeneous nuclear RNA.

Nucleus
- 5' cap
- Intron
- 3' poly (A)
DNA
Nuclear envelope
Nuclear pore

Clinical Correlates

The most common causes of β-thalassemia are defects in mRNA splicing of the ẞ-globin gene.
Mutations that affect splicing create aberrant transcripts that are degraded before they are translated.
Thalassemia minor is a mild anemia caused by inheriting a single mutated gene.
Thalassemia major is a severe transfusion-dependent anemia caused by inheriting two mutated genes.

Synthesis of Ribosomal RNA (rRNA) and Assembly of Ribosomes

Nuclear organizer
- 5'
- 3'
Nuclear envelope
Nucleolus
Nuclear pore
Cytoplasm
45S rRNA precursor

Synthesis of Transfer RNA (tRNA)

Nucleus
- Intron
- tRNA precursor
- tRNA
- tRNA
DNA
Nuclear pore
Cytoplasm
tRNA modification
- D, T, W, and (representing other modified nucleotides) are unusual nucleotides produced by post-transcriptional modifications.

Synthesis of Transfer RNA (tRNA)

RNA polymerase III produces tRNA.
The promoter is located within the coding region of the gene.
Primary transcripts for tRNA are cleaved at the 5' and 3' ends.
Some precursors contain introns that are removed.
During processing of tRNA precursors, nucleotides are modified.
Post-transcriptional modification includes the conversion of uridine to pseudouridine (Ψ), ribothymidine (T), and dihydrouridine (D).
Other unusual nucleotides are also produced.
Addition of the sequence CCA to the 3' end is catalyzed by nucleotidyl transferase.

tRNA

Found in all tRNAs
Not found in all tRNAs.Other variable sites are shown in blue as well
The modified bases are:
- I = inosine
- ml = methylinosine
- T = ribothymidine
- UH₂ = dihydrouridine
- m₂G = dimethylguanosine
- ψ = pseudouridine

Eukaryotic Transcription

Transcription is the process of copying DNA into RNA.
DNA is transcribed by RNA polymerase into messenger RNA (mRNA), which carries the genetic information needed for protein synthesis.
Eukaryotes have three RNA polymerases (I, II, and III) that are involved in transcribing different types of RNA.
RNA polymerase II is responsible for synthesizing mRNA.

Eukaryotic Promoter

A promoter is a DNA sequence that initiates transcription of a gene.
Promoters are located upstream of the transcription start site of genes.
Common eukaryotic promoter elements include:
- CAAT box
- TATA box
- GC box
- CAP site

Enhancers and Silencers

Enhancers are regulatory DNA sequences that increase the likelihood of transcription.
They can be located thousands of nucleotides away from the gene they enhance.
Silencers are regulatory DNA sequences that decrease the likelihood of transcription.

Transcription Factors

Transcription factors are proteins that bind to promoters and other regulatory sequences.
They regulate the transcription of genes by interacting with RNA polymerase and other proteins.
General transcription factors are required for the initiation of transcription by RNA polymerase II.
These include: TFIID, TFIIB, TFIIF, TFIIE, and TFIIH.

Post-Transcriptional Modifications

Pre-messenger RNA (hnRNA) is processed into mature mRNA through three main modifications:
- 5' capping
- 3' polyadenylation
- RNA splicing

5' Capping

7-methylguanosine (m7G) is added to the 5' end of the pre-mRNA molecule.
Capping protects the mRNA from degradation and helps initiate translation.

3' Polyadenylation

A poly(A) tail is added to the 3' end of the pre-mRNA molecule.
The tail protects the mRNA from degradation and helps with translation.

RNA Splicing

Introns (non-coding sequences) are removed from the pre-mRNA.
Exons (coding sequences) are joined together to form mature mRNA.
Splicing is essential for producing functional mRNA.

Ribosomal RNA (rRNA) Synthesis

rRNA is synthesized in the nucleolus, a specialized region within the nucleus.
The 45S rRNA precursor is processed into different rRNA molecules that are assembled into ribosomes.

Transfer RNA (tRNA) Synthesis

tRNA is synthesized in the nucleus and is responsible for transporting amino acids to the ribosome for protein synthesis.
The primary tRNA transcript is processed into mature tRNA through cleavage, intron removal, and post-transcriptional modifications.
Post-transcriptional modification includes the conversion of uridine to pseudouridine, ribothymidine, and dihydrouridine.
Other modified nucleotides, like inosine and methylguanosine, are also produced.

Clinical Correlations

Beta-thalassemia is a genetic disorder that results from defects in the splicing of the beta-globin gene.

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Description

Explore the fundamental aspects of genes, including their structure and the process of gene expression. This quiz covers key topics such as the human genome, gene coding sequences, and the central dogma of molecular biology. Test your knowledge on how genetic information is processed and utilized in living organisms.