Molecular Biology Quiz on DNA and Proteins
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Questions and Answers

What is the primary function of linker DNA in chromatin structure?

  • To facilitate transcription
  • To provide stability to nucleosomes (correct)
  • To encode genetic information
  • To form peptide bonds

    • H1 histone interacts only with DNA and does not affect nucleosome stability.

    False

    What type of bond forms between the carboxyl group of one amino acid and the amino group of another in a polypeptide?

    Peptide bond

    The genetic code is composed of __________ codons, with each codon consisting of three nucleotides.

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

    Match the type of histone interaction with its description:

    <p>Hydrogen bonds = Between amino acids and phosphate groups Nonpolar interactions = Involving deoxyribose sugars on DNA Helix-dipoles = Cause a net positive charge at interaction points Minor groove insertions = H3 and H2B tails fit into grooves of DNA</p> Signup and view all the answers

    How many amino acids are used in the synthesis of proteins in living cells?

    <p>20</p> Signup and view all the answers

    Translation occurs in both prokaryotes and eukaryotes in the same manner.

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

    What is the term for the fibers formed after the coiling of DNA due to histone binding?

    <p>Chromatin fibers</p> Signup and view all the answers

    What role does allolactose play in the regulation of the lac operon?

    <p>It binds to the Lac repressor and changes its shape.</p> Signup and view all the answers

    The lac operon functions optimally when glucose is present.

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

    What is the function of the CAP–cAMP complex in the regulation of the lac operon?

    <p>It recruits RNA polymerase to the promoter to initiate transcription.</p> Signup and view all the answers

    The enzymes specified by the lac operon are produced due to the binding of __________ to the Lac repressor.

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

    Which of the following enzymes is NOT encoded by the lac operon?

    <p>Lactate dehydrogenase</p> Signup and view all the answers

    The lac operon can produce a single polycistronic mRNA molecule.

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

    Match the following components with their roles in the lac operon regulation:

    <p>Lac repressor = Binds to the operator to inhibit transcription CAP = Promotes transcription when bound with cAMP Allolactose = Induces the dissociation of the Lac repressor cAMP = Activates CAP to bind upstream of the promoter</p> Signup and view all the answers

    Name one condition in which the lac operon is expressed at high levels.

    <p>When lactose is the sole carbon source.</p> Signup and view all the answers

    In the absence of lactose, the Lac repressor __________ the binding of RNA polymerase to the promoter.

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

    What is the primary role of RNA polymerase in the transcription of the lac operon?

    <p>To initiate transcription at a single promoter</p> Signup and view all the answers

    The lac operon is under positive control, allowing continuous transcription of the genes.

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

    Name the three structural genes found in the lac operon.

    <p>lacZ, lacY, lacA</p> Signup and view all the answers

    The ______ gene encodes the Lac repressor which regulates the lac operon.

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

    Match the following components of the lac operon with their functions:

    <p>Promoter = Site where RNA polymerase binds to initiate transcription Operator = Region where the Lac repressor binds lacZ = Gene encoding β-galactosidase lacY = Gene encoding permease</p> Signup and view all the answers

    What initiates the translation of the polycistronic mRNA in the lac operon system?

    <p>Ribosome loading at the 5' end</p> Signup and view all the answers

    Constitutive mutations map to areas affecting the promoter and the operator regions of the lac operon.

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

    Describe what happens when the Lac repressor binds to the operator.

    <p>It prevents RNA polymerase from binding to the promoter, blocking transcription.</p> Signup and view all the answers

    Study Notes

    Molecular Biology I (BOI131)

    • This is a course in Molecular Biology I offered at Galala University during Fall 2023-2024.
    • The course is part of the Molecular Biotechnology Program.

    DNA Replication

    • Gene: A specific DNA sequence that encodes a protein. The DNA sequence is first transcribed into mRNA, which is then translated into a protein.
    • DNA: The genetic material, existing as a double helix of paired, complementary base pairs (adenine-thymine, cytosine-guanine). It has a sugar-phosphate backbone and a nucleotide center.
    • Chromatin: A complex of DNA and proteins necessary for chromosomal organization.
    • Nucleosome: The fundamental unit of chromatin packaging. Double-stranded DNA is wrapped around a histone core.
    • Chromosomes: Packaged and organized thread-like structures of tightly coiled DNA around histone proteins (nucleosomes) found in the nucleus of a living cell.
    • Chromatid (Homologous chromosomes): A question mark indicating possible supplementary or related information, not discussed further.
    • Organization of Eukaryotic Chromosomes: Diagrams showing increasing levels of DNA packaging, starting with the DNA double helix and progressing through nucleosomes, chromatin fibers, and duplicated chromosomes.
    • Chromatin vs. Chromosomes: Chromatin is a less organized form of DNA, while chromosomes are more compact structures for cell division.
    • Watson and Crick Model of DNA: The currently accepted model explaining DNA's double helix structure.
      • Complementary and antiparallel strands.
      • Deoxyribose sugar and phosphates form the backbone.
      • Nitrogenous bases are stacked inside.
      • The diameter of the double helix is uniform (2 nm).
      • Purines (A,G) always pair with pyrimidines (T,C).
      • One turn of the helix contains ten base pairs.
    • Polynucleotide Chain: Diagram illustrating the chemical structure of a polynucleotide chain with 5' and 3' ends.
    • DNA and RNA Differences: Diagrams highlighting the differences in sugar (deoxyribose vs. ribose) and base composition (thymine vs. uracil) between DNA and RNA.
    • Components of a Nucleotide: Each nucleotide is comprised of a nitrogen-containing nucleobase (cytosine, guanine, adenine, or thymine), a deoxyribose sugar, and a phosphate group.
    • Nucleotide Joining: Nucleotides are joined in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next.
    • Base Pairing Rules: (A with T, and C with G) are the instructions for how hydrogen bonds bind the nitrogenous bases to make double-stranded DNA.
    • Antiparallel Strands: The two DNA strands run in opposite directions (antiparallel).
    • Genetic Code and Transcription: The sequence of DNA bases in a gene determine the sequence of the messenger RNA (mRNA) bases, which specifies the sequence of amino acids in a polypeptide. mRNA is made based on the DNA template as part of transcription.
    • DNA Replication is semi-conservative and bidirectional: The process of DNA replication follows the semi-conservative model, where each new DNA molecule consists of one original strand and one new strand. It proceeds in two directions (bidirectional), from a starting point called the origin of replication (OriC).
    • Components of DNA Replication: -dNTPs (deoxyribonucleoside triphosphates): Building blocks for DNA. -DNA template: The original DNA strand that serves as a pattern for the new strand. -DNA polymerase (Kornberg enzyme): The enzyme that catalyzes the addition of new nucleotides. -Mg2+: A cofactor that optimizes DNA polymerase activity.
    • Mechanism of DNA Elongation: DNA polymerase utilizes the energy from dNTPs to add nucleotides to the 3' end of the growing strand in a 5' to 3' direction.
    • DNA Replication Main Features: -Three stages: Initiation, Elongation, Termination. -DNA must be accessible to proteins/enzymes. -Replication starts at specific sites (origins of replication). -Semi-conservative and bidirectional. -5' to 3' direction of synthesis.
    • Step 1: DNA Replication Initiation: -Gyrase (topoisomerase): Relaxes supercoiled DNA. -Initiator proteins: Identify and bind to OriC. -DNA helicase: Unwinds DNA, forming replication forks. -SSB proteins: Stabilize single-stranded DNA. -Primase: Creates RNA primer for DNA synthesis.
    • Step 2: DNA Replication Elongation: -Leading strand synthesis (continuous): DNA polymerase III adds nucleotides in 5' to 3' direction. -Lagging strand synthesis (discontinuous): DNA is copied in fragments (Okazaki fragments). Multiple RNA primers are needed. -DNA polymerase I: Removes RNA primers and fills in gaps. -DNA ligase: Joins Okazaki fragments.
    • Step 3: DNA Replication Termination: -Replication forks meet. -Terminator sites arrest fork movement. -Topoisomerase II unlinks the two circular DNA molecules.

    PCR (Polymerase Chain Reaction)

    • Introduction: A laboratory technique used to amplify segments of DNA or RNA sequences, using DNA polymerase.
    • Components: -Target DNA: DNA segments to be amplified. -Primers: Short DNA sequences to initiate replication. They bind to the 3'OH end of target DNA strands. -dNTPs: deoxynucleotide triphosphates (dTTP, dCTP, dGTP, and dATP). -Heat-stable DNA polymerase: Taq Polymerase, Pfu Polymerase, or Vent Polymerase. -Mg++ and Mn++ ions: Cofactors for DNA polymerase. -Buffer solutions: Maintain pH and ionic strength.
    • Difference between polymerases: Pfu and vent polymerases have superior thermostability and proofreading properties compared with Taq DNA polymerase
    • Primers: Typically 18–28 bases long, balanced G/C and A/T composition, not complementary at the 3' ends to avoid primer dimers.
    • Steps of PCR: -Denaturation (90-98°C): Separation of DNA strands for primers to bind. -Annealing(40-60°C): Primers bind to the target DNA. -Elongation(70-75°C): DNA polymerase III extends primers by building new DNA.

    RNA and Transcription

    • RNA in the cell: Plays a central role in the life of a cell. It stores information like DNA and catalyzes chemical reactions. Involved in protein synthesis (ribosome) and splicing of mRNA.

    • major players in transcription: mRNA, a type of RNA that encodes information for proteins and carries it to a ribosome from the nucleus.

    • Reading the DNA code: Every group of three DNA bases pairs with three mRNA bases (codon), which encodes a single amino acid.

    • tRNA: Small RNA molecules acting as adapters between mRNA codons and the amino acids they code for.

    • rRNA: Four different RNA molecules forming the ribosome structure, performing the catalysis of adding an amino acid to a growing peptide chain.

    • Transcription: A process where the cell's machinery copies a gene sequence into mRNA, a molecule similar to DNA. The base uracil (U) replaces thymine (T) in mRNA.

    • Transcription in prokaryotes: Initiation, Elongation, and Termination. A gene is a sequence of DNA that is transcribed into RNA. -Promoter: Specifies the starting point of transcription, and defines the direction for it, -RNA coding sequence : The part of the transcribed DNA sequence that codes for a protein. -Terminator: Specifies the stopping point of transcription.

    • Prokaryotic RNA polymerase: -Core enzyme: 2α + β + β' subunits. -Sigma factor(s): One subunit providing specificity.

    • Initiation of transcription:

    1. RNA polymerase holoenzyme loosely binds to DNA.
    2. Scans DNA until finding a promoter region.
    3. Sigma factor recognizes and interacts strongly with the -35 and -10 regions.
    4. Closed complex forms
    5. Open complex when RNA polymerase unwinds the DNA
    6. Sigma factor releases. 7.Short RNA copy of template strand within the denatured region is made.

    • Eukaryotic initiation of transcription: Uses an initiation complex (PIC) consisting of RNA polymerase and multiple transcription factors. The TATA box (TATAAA) is a common eukaryotic core promoter element. Transcription factors bind to this sequence and help start transcription.

    • Transcription in eukaryotes: RNA polymerase proceeds down the DNA, synthesizing the RNA copy of the gene. -Initiation -Elongation -Termination

    • RNA splicing: A process where introns (non-coding regions) are removed from pre-mRNA to create a mature mRNA molecule.

    • RNA processing steps: -Capping the 5’ end (7-methyl guanine) -Splicing out introns -Adding a poly- A tail to the 3' end (AAAAAAA)

    • Regulation of Gene Expression -The regulation of gene expression is a fundamental property of living cells allowing them to adapt to changes in their environment. Cells control gene expression in response to extracellular signals to produce specific proteins at the right time and amount needed (regulated genes) or at all times (constitutive genes).

    • Operons – Significantly, genes which encode proteins that work together are typically organized into operons; genes are adjacent and transcribed onto a single polycistronic mRNA.

    • Lac operon of E. coli: A system where genes are involved in lactose metabolism. -Genes under this operon- are induced, so they are only activated when lactose is present, –In wild-type bacteria, the amount of the associated enzymes (β-galactosidase, permease, and transacetylase) increases thousands-fold. This is due to coordinate induction of the genes, by the inducer molecule allolactose. –The laco region is the regulatory region to regulate transcription. lacl is the repressor gene that produces Lac repressor to bind to laco regions. -The regulatory substance for induction is called an inducer. When lactose is in the medium, a small molecule of allolactose is formed to bind to Lac repressor and change its shape/loss of affinity for the lac operator. The repressor dissociates from the site, and the operon can now be transcribed.

    • Positive control of the Lac operon: The lac repressor only exerts a negative control function; a positive control system exists to ensure the lac operon is expressed at high levels only if lactose is the sole carbon source. Catabolite activator protein (CAP) and cyclic adenosine 3',5'-monophosphate (cAMP) bind to form a complex that facilitates RNA polymerase binding to the lac promoter.

    • Chromatin remodeling • Chromatin remodeling processes enable access to condensed genomic DNA for the regulatory transcription machinery proteins.

    •Covalent histone modifications and ATP-dependent chromatin remodeling complexes. These complexes act on nucleosome architecture, either moving, ejecting or restructuring them,

    • Epigenetic modification: The study of chemical modifications to genes or gene-associated protein that affect gene expression without changing the DNA sequence.

    • DNA methylation: Adds a methyl group onto the 5th carbon of cytosine; this can regulate gene expression by preventing or allowing transcription factor binding.

    • Histone acetylation and deacetylation: Addition or removal of acetyl groups to lysine residues on histone tails; this affects gene expression by changing chromatin structure.

    Translation in Eukaryotes

    • Translation involves: Converting mRNA sequence (genetic code) into amino acid sequence of a polypeptide.

    • Amino acids: Twenty used in all living cells; joined by peptide bonds. Polypeptides have a free amino group (N terminus) and a free carboxyl group (C terminus).

    • The genetic code: -Triplet code: Each codon consists of three mRNA nucleotides.

    • Continuous code: Read continuously without interruption.

    • Universal: Shared by almost all organisms (with some minor variations).

    • Degenerate: More than one codon can code for a single amino acid.

    • Initiation: The ribosome, initiation complex (contains small ribosomal subunit + initiation factors + initiator tRNA), bind to the mRNA. The complex is scanning to find the AUG (methionine). The large ribosomal subunit adds to the complex. Translation begins.

    • Elongation: Aminoacyl-tRNAs bring amino acids to the A site on the ribosome. A peptide bond is formed between amino acids. The small ribosome moves three nucleotides along mRNA, ejecting the spent tRNA. The next aminoacyl-tRNA binds to the A site. Repeat steps until a stop codon is reached.

    • Termination: Ribosome encounters a stop codon (UAA, UAG, or UGA). A protein release factor binds; the polypeptide is released; ribosome subunits dissociate.

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    Related Documents

    DNA Replication - Molecular Biology I (BOI131) - Fall 2023-2024 - PDF

    Description

    Test your knowledge on key concepts in molecular biology including DNA structure, histones, the genetic code, and the regulation of the lac operon. This quiz explores various aspects of protein synthesis and the interactions involved in chromatin configuration. Challenge yourself with questions designed for advanced biology students!

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