Central Dogma of Molecular Biology Chapter 24
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Questions and Answers

What is the function of pre-mRNA in eukaryotic cells?

Made in the nucleus via RNA pol II, pre-mRNA contains exons and introns to make mature mRNA.

Where does the process of splicing pre-mRNA to produce mature mRNA take place?

In the nucleus

Which of the following modifications occur in tRNA and rRNA post-transcription?

  • Pseudouridine
  • Thiouridine
  • Dihydrouridine
  • All of the above (correct)

    • Ribozymes are RNA molecules that cleave RNA. Is this statement true or false?

    <p>True</p> Signup and view all the answers

    Telomerase extends the ends of eukaryotic chromosomes using ________ as the primer.

    <p>RNA</p> Signup and view all the answers

    Explain the Central Dogma of Molecular Biology.

    <p>The Central Dogma of molecular biology describes the process of genetic information moving from DNA to RNA to protein, in a one-way flow where information cannot be reversed.</p> Signup and view all the answers

    DNA supercoiling is important for the stability and accessibility of genetic information.

    <p>True</p> Signup and view all the answers

    The ____________ is a region in chromosomes that holds two daughter chromosomes during mitosis.

    <p>centromere</p> Signup and view all the answers

    Which of the following best describes the composition of the Human Genome?

    <p>It contains a small amount of genes that encode proteins, along with non-coding DNA.</p> Signup and view all the answers

    What is the result of defects in the activity of phosphotransferase in I-cell disease?

    <p>Accumulation of undigested materials</p> Signup and view all the answers

    Match the DNA replication term with its description:

    <p>Primase = Initiates the synthesis of RNA primers on the DNA template DNA polymerase = Adds nucleotides to the growing DNA strand Ligase = Seals the nicks between Okazaki fragments Initiator proteins = Recognize the replication origin and initiate replication</p> Signup and view all the answers

    Operons rely on __________ to activate or deactivate gene expression.

    <p>repressors and inductors</p> Signup and view all the answers

    Match the following regulatory processes with their descriptions: Induction, Repression, Positive Control, Catabolic Repression, Attenuation

    <p>Induction = Process where gene expression increases Repression = Process where gene expression decreases Positive Control = Induces transcription through protein activators Catabolic Repression = Prevents expression of genes needed for sugar catabolism Attenuation = Dependent on tryptophan availability in the transcription process</p> Signup and view all the answers

    Which antibiotics selectively inhibit bacterial protein synthesis by binding to the 30s ribosomal subunit?

    <p>Both a and b</p> Signup and view all the answers

    What is the main difference in genomic construction between prokaryotes and eukaryotes?

    <p>Prokaryotes have circular chromosomes, lack introns, and contain operons while eukaryotes have linear chromosomes, introns/exons, and histones.</p> Signup and view all the answers

    Interferons work by activating protein kinases to promote viral protein synthesis.

    <p>False</p> Signup and view all the answers

    What are the three domains of DNA polymerase?

    <p>palm, fingers, thumb</p> Signup and view all the answers

    What does the insertion site of DNA polymerase bind to?

    <p>Entering nucleotides</p> Signup and view all the answers

    DNA replication occurs bidirectionally from 3' to 5'.

    <p>False</p> Signup and view all the answers

    DNA replication begins with a specific __________.

    <p>origin</p> Signup and view all the answers

    Match the DNA polymerases with their functions:

    <p>DNA polymerase I (Prokaryotes) = Cleanup, low processivity DNA polymerase III (Prokaryotes) = Main polymerase in replication DNA polymerase alpha α (Eukaryotes) = Makes RNA primers for Okazaki fragments DNA polymerase delta δ (Eukaryotes) = Makes the lagging strand</p> Signup and view all the answers

    What is the purpose of the Ames test?

    <p>identify mutagenic potential</p> Signup and view all the answers

    Which repair system involves recognizing normal bases not forming Watson-Crick base pairs?

    <p>Mismatch repair system</p> Signup and view all the answers

    DNA repair mechanisms are essential to prevent cancer and genetic diseases.

    <p>True</p> Signup and view all the answers

    What is the phenomenon that occurs when DNA is exposed to UV light?

    <p>pyrimidine dimers</p> Signup and view all the answers

    What is the function of enhancer elements in transcription?

    <p>Increase transcription rate</p> Signup and view all the answers

    Study Notes

    Central Dogma of Molecular Biology

    • The central dogma describes how genetic information moves from DNA to proteins
    • Genetic information in DNA cannot be reversed once it is translated into proteins
    • Replication: DNA is replicated into an identical copy of DNA
    • Transcription: DNA is transcribed into RNA (via mRNA)
    • Translation: RNA is translated into proteins

    Genes and Genomes

    • Genes: segments of DNA that code for RNA or proteins
    • Genomes: complete set of genetic information in an organism
    • Genes can code for different products
    • Eukaryotic DNA is non-coding, leading to complexity not being related to the number of chromosomes or DNA length

    Eukaryotes and Prokaryotes

    • Compare:
      • Both undergo transcription and translation for replication
    • Contrast:
      • Eukaryotes: diploid, linear DNA, telomeres, introns, histones
      • Prokaryotes: single chromosome, circular DNA, no telomeres, no introns

    DNA Organization

    • Cytosol: observed in prokaryotes, contains nucleoid with DNA
    • Nucleus: observed in eukaryotes, contains DNA arranged into chromosomes
    • Nucleoids: observed in prokaryotes, contains circular bacterial DNA
    • Mitochondria: contains double-stranded circular DNA encoding mitochondrial tRNA, rRNA, and proteins
    • Chloroplast: contains double-stranded circular DNA encoding proteins

    DNA Structure

    • DNA: deoxyribonucleic acid containing genetic information
    • Chromosome: large molecule composed of DNA and proteins
    • Genes: sequences of DNA or RNA coding for particular functions
    • Centromeres: regions holding daughter chromosomes during mitosis
    • Telomeres: regions ending eukaryotic chromosomes

    Human Genome

    • Contains a small number of genes encoding proteins (exons)
    • Non-coding DNA: introns, promoters, terminators, and regulatory sequences
    • Half of the human genome is repetitive, with sequences like transposons

    DNA Supercoiling

    • Level of organization allowing DNA packing in cells
    • Influences transcription and replication
    • DNA is most stable in the B-form structure
    • Twist, writhe, and linking number are important for DNA structure and function

    Topoisomerases

    • Enzymes catalyzing changes in the linking number
    • Type I: removes negative supercoils, relaxes DNA
    • Type II: relaxes negative and positive supercoils, introduces negative supercoils in bacteria

    Clinical Correlation

    • Antibiotics: inhibit topoisomerase function in bacteria
    • Chemotherapy: targets topoisomerase in cancer cells

    Cell Cycle

    • Goes through Go, G1, S, G2, and M phases
    • Chromatin is undefined and dispersed in interphase
    • Chromosomes condense and become visible during mitosis

    DNA Packing

    • Process of tightly packing DNA strands into the nucleus
    • DNA is wrapped around histones, forming nucleosomes
    • Nucleosomes are coiled into chromatin fibers

    Chromosome Structure

    • Cohesins: connect sister chromatids after replication
    • Condensins: condense chromosomes during mitosis
    • Positive supercoils are formed during chromosome condensation

    DNA Replication

    • Semi-conservative, using each DNA strand as a template
    • Bidirectional, proceeding in both directions from the origin
    • Discontinuous synthesis occurs in the lagging strand
    • Okazaki fragments are short pieces of DNA synthesized in the lagging strand

    Meselson-Stahl Experiment

    • Demonstrated semi-conservative replication of DNA
    • Used heavy nitrogen to label DNA

    DNA Replication Terms

    • Leading strand: synthesized continuously in the 5’ to 3’ direction
    • Lagging strand: synthesized discontinuously in the 5’ to 3’ direction
    • Continuous 5’-3’ synthesis: occurs in the leading strand
    • Discontinuous 5’-3’ synthesis: occurs in the lagging strand
    • Okazaki fragments: short pieces of DNA synthesized in the lagging strand
    • DNA polymerase: adds nucleotides to the 3’ end of the DNA strand
    • Primase: synthesizes RNA primers
    • Ligase: seals the gaps between Okazaki fragments

    Replication Bubble

    • Direction of synthesis: 5’ to 3’
    • Action of DNA polymerase: adds nucleotides to the 3’ end
    • Requirements of single-strand binding proteins: stabilize single-stranded DNA
    • Action of helicase: unwinds the DNA double helix
    • Action of topoisomerase: relieves stress caused by DNA unwinding

    DNA Replication Rules

    • Semi-conservative replication
    • Replication begins at a specific origin
    • Replication proceeds bidirectionally
    • Replication is semi-discontinuous

    Prokaryotic and Eukaryotic DNA Replication

    • Similarities:
      • Both use DNA polymerase with 3’ to 5’ exonuclease activity
      • Both use primers that are removed by RNase
    • Differences:
      • Prokaryotes: occurs in the cytoplasm, less complex, uses DNA gyrase, and has a single origin
      • Eukaryotes: occurs in the nucleus, more complex, regulated by cyclins and cyclin-dependent kinases, and has multiple origins### RNA Synthesis (Transcription)
    • Template Strand: Used as a template for RNA polymerase to act on, moves in a 3' to 5' direction
    • Coding Strand: Non-template strand with the same base sequence as the RNA transcribed, moves in a 5' to 3' direction, T is replaced with U
    • Promoter Sequence: DNA sequence that RNA polymerases bind to, directs the direction of transcription
    • Primary Transcript (hnRNA): Newly synthesized RNA molecules
    • Upstream/Downstream: Upstream located at the beginning of transcription, containing regulatory proteins; downstream located after the start of transcription

    Transcription Signals

    • Proximal Elements: Transcription signals found at the start of transcription
    • Distal Elements: Transcription signals found downstream
    • Cis-acting Elements: Binding sites for promoters, enhancers, and silencers, located in the same DNA molecule they regulate
    • Trans-acting Elements: Bind to cis-acting elements to regulate gene expression, regulate genes in different DNA molecules
    • Enhancer and Silencer Elements: Enhancers increase the rate of transcription, silencers decrease the rate of transcription

    Eukaryotic RNA Polymerases

    • RNA Pol I, II, and III: Each has a regulation mechanism
    • RNA Pol I: Responsible for synthesizing pre-ribosomal RNA
    • RNA Pol II: Responsible for synthesizing mRNA, fast and can recognize many promoters, inhibited by α-amanitin
    • RNA Pol III: Responsible for synthesizing tRNAs and small RNA products
    • RNA Pol IV: Used in plants to synthesize small interfering RNAs (siRNAs)
    • Mitochondrial RNA Polymerase: Used in mitochondria

    Maturation of mRNA

    • Synthesis of hnRNA: Also called pre-mRNA, transcribed in the nucleus by RNA pol II
    • 5'-Capping: 7-methylguanosine added to the 5' end of RNA to protect from ribonuclease
    • Poly-A Tail Addition: Poly-adenylation added to the 3' end to make mRNA stable
    • Intron Removal by Spliceosome: Introns removed from mRNA by spliceosome

    Intron Classes and Splicing

    • Group I and II Introns: Self-splicing, found in genomes of nuclear, mitochondrial, and chloroplast
    • Spliceosomal Introns: Most common introns, spliced by spliceosomes
    • tRNA Introns: Protein-catalyzed, spliced by ligase and splicing endonuclease

    Pre-mRNA Splicing Defects and Disease

    • Alternative Splicing: Defect can cause spinal muscle atrophy

    Eukaryotic RNA Species and Maturation

    • mRNA: Made in the nucleus via RNA pol II, matures through 5'-capping, poly-A tail addition, and splicing
    • rRNA: Made in the nucleus via RNA pol I, matures through processing and modification
    • tRNA: Made in the nucleus via RNA pol II, matures through processing and modification

    Base Modification in tRNA and rRNA

    • Pseudouridine, Thiouridine, and Dihydrouridine: Post-transcriptional modifications in tRNA and rRNA

    MicroRNAs and RNA Interference

    • MicroRNAs (miRNAs): Short, noncoding nucleotides that bind to specific regions of mRNA to affect translation
    • RNA Interference (RNAi): Mechanism for processing miRNAs to silence gene expression

    Ribozymes, Retroviruses, and Reverse Transcriptase

    • Ribozymes: RNA molecules that catalytically cleave themselves or other RNA
    • Retroviruses: RNA viruses that can convert RNA to DNA via reverse transcriptase
    • Reverse Transcriptase: Enzyme that converts RNA to DNA in retroviruses

    Telomeres and Telomerases

    • Telomeres: Region at the end of eukaryotic chromosomes, maintained by telomerase
    • Telomerase: Enzyme that extends the ends of chromosomes, serves as a reverse transcriptase

    Genetic Information Flow

    • Universal Flow: Genetic information in DNA is replicated and transcribed into RNA, then translated into proteins
    • Exceptions: Reverse transcription, RNA viruses, Prions, and RNA editing

    Genetic Code

    • Degenerate: Multiple codons can code for the same amino acid

    • Unambiguous: A specific codon only codes for a specific amino acid

    • Nonoverlapping: Each nucleotide base is only part of one codon

    • Universal: Codons are the same across most species### Regulation of Gene Expression

    • Repression: a process where gene expression decreases in response to a change in a regulatory protein.

    • Positive Control: induces transcription through protein activators, allowing for signals to bind to DNA and induce transcription.

    Catabolite Repression

    • Prevents the expression of genes needed for the catabolism of sugars (e.g., lactose, arabinose) in the presence of glucose.
    • Mediated by cAMP and cAMP receptor protein (CRP).

    Attenuation

    • Depends on the availability of tryptophan.
    • High Trp: tRNATrp is high, leading to attenuation; transcription stops due to the formation of a hairpin structure.
    • Low Trp: tRNATrp is low, allowing for transcription to proceed; ribosome halts at Trp codons, enabling segment 2 and 3 to pair.

    Prokaryotes vs. Eukaryotes

    • Prokaryotes: circular chromosomes, less complex, one chromosome, lack introns, have exons, lack histones, and have operons.
    • Eukaryotes: linear chromosomes, more complex, 23 chromosomes, have introns/exons, have histones, and have positive/negative regulators.

    Regulatory Processes in Eukaryotes

    • Gene alteration: changes made in the gene sequence affecting gene expression.
    • Transcriptional control: regulates gene expression during transcription.
    • Posttranscriptional control: regulates gene expression after transcription, including RNA splicing, alternative splicing, and RNA editing.
    • Translational control: regulates gene expression during translation.
    • Posttranslational control: modifies newly translated proteins via enzymes to their active conformation.

    SOS Response and RNA-mediated Regulation

    • SOS response: when excessive DNA damage triggers an induction of genes involved in stopping DNA replication and repair.
    • SOS response involves RecA proteins and LexA repressor.
    • RNA-mediated regulation: regulates the expression of genes involved in producing ribosomes (r-proteins) via translational feedback.

    Eukaryotic Gene Regulation and Hormonal Regulation

    • Eukaryotic gene regulation requires chromatin remodeling, activators, coactivators, architectural regulators, and transcriptional factors.
    • Hormonal regulation: hormones bind to receptors, affecting transcription via Hormone Response Elements (HREs).
    • Type I hormone receptors: nuclear receptors (e.g., sex hormones, glucocorticoids) that bind to hormones and move to the nucleus to activate transcription.
    • Type II hormone receptors: thyroid hormone receptors found in the nucleus, which activate transcription when bound to hormones.

    Iron Responsive Element (IRE) and Iron Responsive Factor (IRF)

    • IRF binds to IREs in mRNAs, regulating the synthesis of transferrin receptors and ferritin.
    • IREs: hairpin structures found on the ends of mRNA (5' for ferritin and 3' for transferrin receptor).
    • Iron deficiency: IRP binds to IRE, increasing transferrin synthesis and decreasing ferritin synthesis.
    • Iron excess (hemochromatosis): IRP does not bind to IRE, decreasing transferrin synthesis and increasing ferritin synthesis.

    Stem Cells and Gene Regulation

    • Stem cells can differentiate into various tissues and replenish themselves, regulated by signals.
    • Embryonic stem cells are pluripotent, meaning they can differentiate into many tissues.

    Clinical Correlation: Drug Resistance and Interferon

    • Methotrexate: inhibits dihydrofolate reductase, preventing the production of tetrahydrofolate, essential for DNA/RNA synthesis, killing cancer cells.
    • Interferon: signaling proteins released in the presence of viruses, inhibiting gene expression through two mechanisms:
      • Activating protein kinases to prevent viral protein synthesis.
      • Activating ribonuclease to break down viral RNA, reducing the availability of ribosomes for protein synthesis.

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