Molecular Biology of the Human Genome
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Questions and Answers

What percentage of the human genome is made up of exons?

  • 1-2% (correct)
  • 90%
  • 45%
  • 10%
  • Which type of DNA makes up the largest portion of the human genome?

  • Alpha-satellite DNA
  • Introns
  • Dispersed repetitive DNA (correct)
  • Exons
  • How long can LINEs (Long Interspersed Elements) be?

  • Up to 7,000 bp (correct)
  • Up to 500 bp
  • Less than 100 bp
  • Between 90 and 500 bp
  • What is the role of introns in the DNA sequence?

    <p>Non-coding regions within genes (D)</p> Signup and view all the answers

    What proportion of the human genome is estimated to be made up of repetitive sequences?

    <p>90% (D)</p> Signup and view all the answers

    What are tandem repeats and alpha-satellite DNA primarily found at?

    <p>Centromeres of chromosomes (A)</p> Signup and view all the answers

    What role do histone tail modifications play in gene regulation?

    <p>They control how tightly or loosely DNA is packed, affecting gene activity. (C)</p> Signup and view all the answers

    What structure is formed when nucleosomes coil together?

    <p>Solenoid structure (B)</p> Signup and view all the answers

    Which enzyme is responsible for adding acetyl groups to histone tails?

    <p>Histone Acetyltransferases (HATs) (B)</p> Signup and view all the answers

    What is the primary reason for DNA compaction in cells?

    <p>To fit DNA inside the cell nucleus. (D)</p> Signup and view all the answers

    What happens to the DNA when methyl groups are added to histone tails?

    <p>DNA becomes tightly packed, silencing genes. (A)</p> Signup and view all the answers

    Which type of chromatin is associated with active genes that can be transcribed?

    <p>Euchromatin (A)</p> Signup and view all the answers

    How many base pairs of DNA are typically wrapped around a single nucleosome?

    <p>150 base pairs (C)</p> Signup and view all the answers

    What is the function of scaffold proteins in DNA organization?

    <p>They support chromatin loops and maintain structure. (D)</p> Signup and view all the answers

    What is the primary role of DNA polymerase during DNA replication?

    <p>To proofread and correct errors in DNA synthesis (A)</p> Signup and view all the answers

    How does Type I DNA Topoisomerase relieve strain in a DNA molecule?

    <p>By cleaving one strand of DNA at the phosphodiester bond (D)</p> Signup and view all the answers

    What process occurs after DNA ligase activates the phosphate group at the nick?

    <p>A new bond is formed between the 3′-OH and 5′-phosphate (A)</p> Signup and view all the answers

    What is the significance of SSBs (single-stranded DNA-binding proteins) during DNA replication?

    <p>They prevent single-stranded DNA from folding back on itself (B)</p> Signup and view all the answers

    What does exonuclease activity refer to in DNA enzymes?

    <p>The action of cutting nucleotides from the end of the DNA strand (B)</p> Signup and view all the answers

    How does the proofreading function of DNA polymerase enhance replication accuracy?

    <p>By allowing corrections that improve accuracy by 100 to 1,000 times (B)</p> Signup and view all the answers

    What is the primary function of DNA helicase during DNA replication?

    <p>To separate the double helix into two single strands (D)</p> Signup and view all the answers

    What role do single-stranded binding proteins (SSBs) serve during DNA replication?

    <p>They prevent the strands from re-annealing (D)</p> Signup and view all the answers

    Which enzyme is primarily responsible for joining Okazaki fragments on the lagging strand?

    <p>DNA ligase (B)</p> Signup and view all the answers

    How does DNA polymerase maintain a low error rate during DNA replication?

    <p>It employs a proofreading mechanism. (A)</p> Signup and view all the answers

    Which type of topoisomerase makes single-strand nicks to relieve tension during replication?

    <p>Type I (A)</p> Signup and view all the answers

    What occurs to the phosphates when a new nucleotide is added during DNA replication?

    <p>Two phosphates are removed as pyrophosphate. (C)</p> Signup and view all the answers

    What specific function does the exonuclease activity of DNA polymerase serve?

    <p>It corrects incorrectly paired nucleotides. (C)</p> Signup and view all the answers

    Which statement best describes the synthesis of the leading and lagging strands during DNA replication?

    <p>The leading strand is synthesized continuously while the lagging strand is in fragments. (B)</p> Signup and view all the answers

    Which of the following is not a challenge addressed during DNA replication?

    <p>Poor fidelity of DNA synthesis (D)</p> Signup and view all the answers

    What effect do histone tail modifications have on gene activity?

    <p>They regulate gene activity by altering DNA packaging. (B)</p> Signup and view all the answers

    Flashcards

    Repetitive DNA

    DNA sequences repeated multiple times in the genome, scattered throughout and making up nearly half (45%) of the human genome.

    SINEs (Short Interspersed Elements)

    Short DNA sequences (90-500 base pairs) repeated throughout the genome, with Alu elements being a common example.

    LINEs (Long Interspersed Elements)

    Longer DNA sequences (up to 7,000 base pairs) scattered throughout the genome.

    Exons

    Coding segments of DNA within a gene that are used to produce proteins.

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    Introns

    Non-coding regions within genes that are not translated into proteins.

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    DNA Function

    Most DNA (90%) in the human genome is repetitive or non-coding, while only a small portion (1-2%) codes for proteins.

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    Chromatin

    The complex of DNA and proteins that makes up chromosomes, allowing DNA to be tightly packed into the nucleus.

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    Nucleosome

    A basic unit of chromatin consisting of a segment of DNA wrapped around eight histone proteins.

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    Histone Tails

    The protruding ends of histone proteins that can be modified to influence the tightness of DNA packaging.

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    Acetylation

    The addition of an acetyl group to histone tails, loosening DNA and making genes accessible for transcription.

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    Methylation

    The addition of a methyl group to histone tails, tightening DNA and silencing genes.

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    HATs (Histone Acetyltransferases)

    Enzymes that add acetyl groups to histone tails, activating genes.

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    HDACs (Histone Deacetylases)

    Enzymes that remove acetyl groups from histone tails, silencing genes.

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    Euchromatin vs. Heterochromatin

    Euchromatin is loose, active DNA where genes are transcribed, while heterochromatin is tightly packed, inactive DNA where genes are silenced.

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    DNA Replication

    The process of copying DNA to ensure that each new cell gets an exact genetic copy during cell division.

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    Semi-Conservative Replication

    Each new DNA molecule consists of one original (old) strand and one newly synthesized strand.

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    Replication Fork

    The Y-shaped structure formed during DNA replication where the double helix is unwound and separated into two single strands.

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    DNA Helicase

    An enzyme that unwinds the DNA double helix, breaking the hydrogen bonds between the base pairs.

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    Single-Stranded Binding Proteins (SSBs)

    Proteins that bind to and stabilize the separated single strands of DNA, preventing them from re-annealing.

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    DNA Primase

    An enzyme that synthesizes short RNA primers, providing a starting point for DNA polymerase to build new DNA strands.

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    DNA Polymerase

    An enzyme that adds new nucleotides to the 3' end of an existing DNA strand, synthesizing a new strand.

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    Leading Strand

    The DNA strand that is synthesized continuously in the 5' to 3' direction during replication.

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    Lagging Strand

    The DNA strand that is synthesized discontinuously in short fragments (Okazaki fragments) in the 5' to 3' direction.

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    Okazaki Fragments

    Short DNA fragments synthesized on the lagging strand during replication.

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    Exonuclease Activity

    DNA polymerase can remove incorrect nucleotides from the end of a DNA strand during replication.

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    Endonuclease Activity

    DNA polymerase can also remove incorrect nucleotides from the middle of a DNA strand.

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    DNA Ligase: What does it do?

    DNA ligase seals the gaps (nicks) between DNA fragments by forming a phosphodiester bond, joining the 3' hydroxyl group to the 5' phosphate group.

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    Single-Stranded DNA-Binding Proteins (SSBs)

    SSBs prevent the unwound single strands of DNA from tangling or forming hairpins by binding to them, keeping them straight and ready for replication.

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    Type I Topoisomerase: What's its role?

    Type I Topoisomerase relieves overwinding stress in DNA by temporarily breaking one strand of the helix, allowing rotation, and then rejoining it.

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    DNA Polymerase: Proofreading Function

    DNA polymerase has a proofreading function that significantly increases replication accuracy by detecting and correcting errors.

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    Study Notes

    Genetics, Immunology and Molecular Biology

    • The course is divided into two sections
    • The first part covers essential molecular biology and cytogenetics
    • The second part delves into the immune system
    • Both topics build upon knowledge gained in the Human Biology course

    What's on the menu this week...

    • Revision of relevant human biology, including DNA structure and function
    • Mendelian inheritance, including variations in dominant and recessive inheritance and mitochondrial disorders
    • Organisation of the human genome and DNA replication
    • Cell cycle and mitosis/meiosis
    • RNA structure & function, RNA synthesis, processing and modifications
    • Regulation of gene expression and epigenetics
    • Protein biosynthesis, modification and inhibitors
    • Chromosomes and karyotyping
    • Chromosome abnormalities (numerical and structural)
    • Population genetics
    • Complex diseases (Polygenic/Multifactorial inheritance and Congenital/adult onset complex diseases)
    • Prenatal diagnosis
    • Genetic services
    • Genetic basis of cancer
    • Genetics and precision medicine

    Cell biology revision

    • The diagram shows the parts of a typical cell
    • Some key cells parts include: Microfilaments, Cilia, Cytoplasm, Vault, Cell junction (desmosome), Free ribosome, Ribosome, Chromosomes, Nucleolus, Nucleus, Nuclear Membrane, Centrioles, Plasma membrane, Smooth endoplasmic reticulum, Rough endoplasmic reticulum, Peroxisome, Microtubule, Microvilli, Vesicle, Lysosome, and Mitochondrion

    Introduction to Cellular Biology

    • Cells are the fundamental units of life with specialized functions for organism survival
    • Understanding cell diversity helps comprehend biological complexity
    • Studying diverse cell types provides insights into physiological processes and disease mechanisms for targeted medical interventions.

    In-depth Exploration of Cell Types

    • Somatic cells form the majority of the body, carrying functions from structural support to metabolism.
      • Neurons are specialized for rapid signal transmission
      • Muscle cells are responsible for contraction and force generation for movements.
    • Germ cells are specialized for sexual reproduction, crucial for genetic diversity.
      • Oocytes are larger and nutrient-rich for supporting early embryonic development
      • Spermatozoa are highly motile for delivering genetic material

    Comprehensive Overview of Organelles

    • Nucleus: controls gene expression and DNA replication; aberrations can cause uncontrolled cell division (cancer)
    • Mitochondria: site of the Krebs cycle and oxidative phosphorylation (energy production); disorders affect energy-dependent organs, causing neuromuscular diseases

    Endoplasmic Reticulum (ER)

    • Rough ER is involved in protein synthesis and quality control; Smooth ER plays a role in lipid metabolism and detoxification.
    • ER dysfunction is implicated in metabolic syndrome and protein folding diseases, illustrated by cystic fibrosis.

    Golgi Aparatus

    • Modifies proteins from the ER and directs them to their destinations.
    • Errors in processing result in disorders like congenital glycosylation disorders.

    Lysosomes

    • Contains acid hydrolases to break down various biomolecules for cellular recycling
    • Defects in lysosomes cause lysosomal storage disorders, such as Gaucher's disease, impacting multiple organs.

    Molecular biology revision

    • DNA has five prime and three prime ends.
    • DNA has a sugar-phosphate backbone, with bases (Adenine, Thymine, Cytosine, Guanine) with hydrogen bonding.
    • Chargaffs rules state the ratio of Purines and Pyrimidines

    DNA double helix structure

    • DNA has a double helix-based structure
    • DNA has a double-helix structure with specific dimensions: 34Å is the distance between base pairs in the helix.
    • Major and Minor grooves are present

    Types of DNA

    • Repetitive DNA makes up 45% of the genome
    • Short interspersed elements (SINES): 90-500bp
      • Alu repeat element is a prominent example, comprising approximately 10% Alu is a restriction site used to classify this DNA.
    • Long interspersed elements (LINES): up to 7kb
    • Exons (coding sequence): makes up only 1-2% of the genome

    DNA replication

    • Human DNA polymerase: slow (40-50 nucleotides/second)
    • Human chromosomes contain millions of nucleotides
    • Multiple replication origins to speed up the replication process

    DNA Replication steps

    • DNA polymerase: required for replication
    • DNA unwinds to form a replication fork
    • Replication proceeds in the 5' to 3' direction.
    • Multiple origins of replication (to speed up) are required

    DNA replication is very accurate

    • Enzyme mechanisms correct errors; about 1 in 10,000-100,000 nucleotides
    • Proofreading (rechecks) and error correction (deletions) processes are significant

    Histone tail modification

    • N-terminal histone tails key to transcriptional regulation.
    • Histone Acetyltransferases (HATs) and Histones Deacetylases (HDACs) and Histone Methyltransferases (HMTs)
    • Acetylation of tails causes a relaxation and permits transcription factors to bind to DNA
    • Methylation causes a tightening, silencing genes which inhibit transcription.

    DNA polymerase

    • The enzyme is important in DNA replication because it has two functional domains
      • Polymerizing domain which adds nucleotide to the three prime end of a strand.
      • Editing domain which can remove a nucleotide from the three prime end if it is not the correct pair.

    Tautomers

    • Hydrogen atoms can change position, which results in different bonding
    • These can lead to non-standard base pairs and contribute to errors in replication

    Replication errors

    • Mismatches may occur during replication, which need correction.
    • DNA repair mechanisms correct the mistake once the mistake is found

    Supercoiling is relieved by Topoisomerases

    • Type I topoisomerases breaks the DNA to allow some conformational changes in the single strand DNA
    • Type II topoisomerases break the DNA in both strands, allowing conformational changes in the double-stranded DNA, and restoring

    DNA Replication Fork

    • Both the leading strand, and the lagging strand undergo replication.
    • The leading strand replicates continuously; the lagging strand in short fragments (Okazaki fragments)
    • DNA primase produces small RNA primers in the lagging strand

    DNA ligase

    • Seals the gaps between Okazaki fragments to make DNA continuous

    ssDNA-binding proteins

    • Maintain stability of unwound DNA, preventing hairpin formation and providing straight DNA for DNA Polymerase

    The "winding problem"

    • Ahead of the replication fork (unwrapping of the DNA), DNA becomes supercoiled
    • Topoisomerases relieve DNA supersoiling

    Conclusion

    • DNA has much more than its classical function of encoding proteins.
    • DNA's precise packaging within chromosomes is essential for cell function.
    • Replication is a complex process involving many steps and safeguards ensuring accuracy
    • Various mechanisms of correction and maintenance of DNA integrity.
    • DNA replication is critical to many fundamental cellular processes.

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    Description

    Test your knowledge of the human genome with this quiz that covers key topics such as exons, introns, repetitive sequences, and the role of histone modifications. Explore essential concepts in molecular biology and DNA organization, including structural elements like nucleosomes and chromatin. Perfect for students studying genetics and molecular genetics.

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