Chromatin Structure and Function Exam 1

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Questions and Answers

What is the role of telomeres in chromosomes?

  • To initiate DNA replication
  • To mark histones for remodeling
  • To prevent degradation and ensure complete replication (correct)
  • To enable proper chromosome segregation

The leading strand during DNA replication is synthesized discontinuously as Okazaki fragments.

False (B)

What enzyme is responsible for sealing nicks in the DNA backbone during replication?

Ligase

Euchromatin is the form of chromatin that is ______ and is transcriptionally active.

<p>less condensed</p> Signup and view all the answers

Which of the following processes occurs during PCR?

<p>Separating DNA strands by heat (D)</p> Signup and view all the answers

Match the parts of chromosomes with their functions:

<p>Telomeres = Prevent degradation and ensure complete replication Centromeres = Enable proper chromosome segregation Origins of Replication = Where DNA replication begins Chromatin = Complex of DNA and proteins</p> Signup and view all the answers

Heterochromatin is the form of chromatin that is transcriptionally active.

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

What is the resting potential of a neuron?

<p>-70 mV (A)</p> Signup and view all the answers

Inhibitory neurons increase the likelihood of firing action potentials.

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

What triggers synaptic vesicles to dock at the membrane?

<p>Calcium ions (Ca²⁺)</p> Signup and view all the answers

ATP production in mitochondria is powered by the flow of H⁺ ions through __________.

<p>ATP synthase</p> Signup and view all the answers

Match the following components of cellular respiration and photosynthesis:

<p>Electron Transport Chain = Creates a H⁺ gradient ATP Synthase = Uses H⁺ gradient to synthesize ATP Light Reactions = Pumps H⁺ into thylakoid lumen Calvin Cycle = Produces sugar</p> Signup and view all the answers

What role do +TIPs play in microtubule dynamics?

<p>They stabilize the growing end of microtubules. (C)</p> Signup and view all the answers

Gamma-tubulin is essential for initiating microtubule growth.

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

What are the three main types of microtubules present in the mitotic spindle?

<p>Astral, Kinetochore, Interpolar</p> Signup and view all the answers

In anaphase, __________ microtubules shorten to pull sister chromatids apart.

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

Match the motor proteins with their direction of movement:

<p>Dynein = Moves toward the '+' end Kinesin = Moves toward the '-' end</p> Signup and view all the answers

What happens to microtubules when GTP-tubulin cap is lost?

<p>Microtubules depolymerize rapidly. (D)</p> Signup and view all the answers

Kinesin proteins typically transport cargoes inward toward the cell center.

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

Where is the actin cytoskeleton primarily located within the cell?

<p>Near the cell cortex, just beneath the plasma membrane</p> Signup and view all the answers

What is the primary function of SNAREs in cellular processes?

<p>Vesicle fusion (B)</p> Signup and view all the answers

The __________ microtubules overlap at the center of the cell and help maintain spindle structure.

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

Rabs are responsible for regulating vesicle fusion with target membranes.

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

Match the phases with their events during mitosis:

<p>Metaphase = Chromosomes align at the metaphase plate Anaphase = Sister chromatids are pulled apart</p> Signup and view all the answers

What are the proteins that mediate endocytosis?

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

Proteins that lack specific sorting signals are typically transported by default to the __________.

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

Which intermediate filaments provide structural support and flexibility in epithelial cells?

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

The process known as ER-associated degradation (ERAD) involves tagging misfolded proteins with ubiquitin.

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

Match the following components with their respective roles:

<p>Clathrin = Mediates endocytosis COPI = Trafficking from Golgi to ER COPII = Trafficking from ER to Golgi Lamin = Forms the nuclear lamina</p> Signup and view all the answers

Name one type of protein involved in vesicle formation during transport.

<p>Clathrin, COPI, or COPII</p> Signup and view all the answers

What is the first step in the assembly of intermediate filaments?

<p>Two monomers wrap around each other to form a coiled-coil dimer (B)</p> Signup and view all the answers

Intermediate filaments have distinct polarity.

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

What happens to proteins without signals for vesicular trafficking?

<p>They remain in the cytoplasm (C)</p> Signup and view all the answers

What is the function of intermediate filaments in the nucleus?

<p>They support the nucleus, maintain its shape, and regulate DNA replication and transcription.</p> Signup and view all the answers

Intermediate filaments do not require ______ for their assembly.

<p>ATP or GTP</p> Signup and view all the answers

Match the following components with their description:

<p>Alpha-tubulin = A component of the microtubule that is slow-growing Beta-tubulin = A component of the microtubule that is fast-growing Centrosome = Microtubule-organizing center Dynamic instability = Cycle of growth and shrinkage at the '+' end of microtubule</p> Signup and view all the answers

What happens during phosphorylation of intermediate filaments?

<p>They lead to disassembly (C)</p> Signup and view all the answers

Microtubules are composed of heterodimers of alpha- and beta-tubulin.

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

What triggers the breakdown of the nuclear envelope during mitosis?

<p>Phosphorylation of nuclear lamins</p> Signup and view all the answers

During dynamic instability, _______ hydrolyzes to GDP, causing shrinkage.

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

What drives the fast-growing end of microtubules?

<p>Beta-tubulin exposure (D)</p> Signup and view all the answers

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Flashcards

Resting potential

The difference in electrical charge across a neuron's membrane when it's not transmitting a signal.

Excitatory neurons

Neurons that depolarize the membrane, increasing the likelihood of an action potential.

Inhibitory neurons

Neurons that hyperpolarize the membrane, decreasing the likelihood of an action potential.

Voltage-gated Ca²⁺ channels

Voltage-gated channels that open when an action potential reaches the axon terminal, allowing calcium ions (Ca²⁺) to enter.

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Chemiosmotic coupling

The process of using the energy stored in a proton (H⁺) gradient across a membrane to generate ATP.

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Ubiquitination

A process that marks histones for remodeling or degradation. It involves attaching a small protein called ubiquitin to histones, changing their structure and function.

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Chromatin Remodeling Complexes

Specialized protein complexes that use energy from ATP to reposition or remove nucleosomes from DNA. This allows access for transcription factors and other regulatory proteins.

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Telomeres

Repetitive DNA sequences found at the ends of chromosomes. They prevent degradation and ensure complete replication of the chromosome.

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Centromeres

The region on a chromosome where kinetochores attach, enabling proper chromosome segregation during cell division. It's made up of heterochromatin and satellite DNA.

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Origins of Replication

Specific DNA sequences where DNA replication begins. Eukaryotic chromosomes have multiple origins of replication to speed up the process.

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Euchromatin

The less condensed form of chromatin, allowing for active transcription. It's found in regions where genes are actively being expressed.

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Heterochromatin

The tightly packed form of chromatin, limiting transcription. It's often found in regions of the genome that are inactive.

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Apoptosis

Programmed cell death, a controlled process where a cell self-destructs to prevent damage to surrounding cells.

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Ubiquitin

A small protein tag that marks misfolded proteins for degradation.

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Proteasome

A protein complex responsible for breaking down misfolded proteins tagged with ubiquitin.

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ER-Associated Degradation (ERAD)

Degradation of misfolded proteins in the endoplasmic reticulum (ER).

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SNAREs

These proteins facilitate the fusion of vesicles with target membranes, ensuring correct delivery of cargo.

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v-SNAREs

These proteins are located on vesicles and help guide them to the correct target membranes.

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t-SNAREs

These proteins are located on target membranes and work with v-SNAREs for vesicle fusion.

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Rabs

These small GTPases regulate vesicle targeting and docking, ensuring vesicles go to the right location.

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Coats (Clathrin, COPI, COPII)

These proteins coat vesicles during formation, shaping the membrane and selecting cargo for transport.

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Microtubule Dynamics at the Growing End

Proteins like +TIPs bind to the growing (+) end of microtubules, stabilizing them and influencing microtubule dynamics. GTP-tubulin caps the growing end, promoting stability. When this cap is lost, microtubules rapidly depolymerize.

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Microtubule Nucleation

Microtubules are nucleated from the microtubule organizing center (MTOC), primarily within the centrosome. Gamma-tubulin complexes form rings that serve as templates for the addition of alpha- and beta-tubulin dimers, initiating microtubule growth.

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Types of Microtubules in the Mitotic Spindle

Astral microtubules radiate outward from the centrosome, connecting the spindle to the cell membrane. Kinetochore microtubules attach to kinetochores on chromosomes, responsible for pulling chromatids apart. Interpolar microtubules overlap at the spindle's center, pushing the poles apart and stabilizing the spindle structure.

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Spindle and Chromosome Events: Metaphase and Anaphase

In metaphase, chromosomes align centrally at the metaphase plate with each sister chromatid's kinetochore attached to kinetochore microtubules from opposite spindle poles. Anaphase marks the separation of sister chromatids: kinetochore microtubules shorten (Anaphase A), pulling chromatids apart, while interpolar microtubules lengthen (Anaphase B), pushing poles further apart.

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Microtubule Motor Proteins: Dynein and Kinesin

Dynein moves towards the (-) end of microtubules, typically towards the cell center. It transports cargoes inwards, like vesicles and organelles. Kinesin moves towards the (+) end of microtubules, usually towards the cell periphery. It carries cargoes outwards, like vesicles and organelles.

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Actin Cytoskeleton: Location and Function

The actin cytoskeleton is present throughout the cell, but it's particularly concentrated near the cell cortex (just under the plasma membrane). It provides structural support, influencing cell shape, adhesion, and movement.

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Intermediate filaments

Intermediate filaments are strong, rope-like structures made of fibrous proteins. They provide support to the cell and help regulate DNA processes.

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How are intermediate filaments built?

Intermediate filaments assemble through a specific process involving monomers, dimers, tetramers, and protofilaments, creating a complex interwoven structure.

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What makes intermediate filaments unique?

Intermediate filaments differ from actin and microtubules by lacking polarity, meaning they don't have distinct ends like the others.

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How is intermediate filament assembly regulated?

Phosphorylation typically leads to the disassembly of intermediate filaments, while dephosphorylation promotes their reassembly, regulating their structure and function.

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What are microtubules made of?

Microtubules are hollow tubes formed by alpha- and beta-tubulin dimers arranged in a precise pattern, crucial for many cellular processes.

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What is the polarity of microtubules?

Microtubules have distinct ends: the plus end (beta-tubulin exposed) grows faster, while the minus end (alpha-tubulin exposed) grows slower.

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What is dynamic instability?

Dynamic instability refers to the continuous growth and shrinkage of microtubules at the plus end, driven by GTP hydrolysis, allowing them to explore space.

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Where do microtubules start from?

The minus end of a microtubule is often anchored at the microtubule-organizing center (MTOC), such as the centrosome.

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Where do microtubules extend to?

The plus end of microtubules extends towards the cell periphery, reaching out to the cell's outer edges.

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Why are microtubules important?

Microtubules play a crucial role in cell division, transporting cargo, and maintaining cell shape, showcasing their dynamic and essential nature.

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Study Notes

Exam 1

  • Chromatin: A complex of DNA and proteins, primarily histones, that compacts DNA in the nucleus.
  • Nucleosome: The fundamental unit of chromatin, which is 147 base pairs of DNA wrapped around a core of 8 histone proteins (an octamer of H2A, H2B, H3, and H4).
  • H1 histone: Links nucleosomes, forming higher-order structures.
  • Chromatin Organization Levels: Nucleosome → 10 nm fiber → 30 nm fiber → higher-order folding into chromosomes.

Types of Chromatin

  • Euchromatin: Loosely packed, transcriptionally active regions.
  • Heterochromatin: Densely packed, transcriptionally inactive regions.
    • Constitutive Heterochromatin: Always inactive, found in centromeres and telomeres.
    • Facultative Heterochromatin: Can switch between active and inactive states, for example, X-chromosome inactivation.

Gene and Sequence Complexity in Eukaryotic Genomes

  • Unique Sequences: Single-copy genes coding for proteins.
  • Repetitive Sequences:
    • Moderately Repetitive: Includes rDNA, tRNA, and histone genes.
    • Highly Repetitive: Found in centromeres and telomeres (e.g., satellite DNA).
  • Complexity arises from both coding and non-coding regions.

Nature of the Nucleolus

  • Definition: A subnuclear structure where rRNA is synthesized and ribosome assembly begins.
  • Location: Found in tandem arrays on acrocentric chromosomes.
  • Function: Involved in rRNA transcription, catalyzed by RNA polymerase I, and ribosomal subunit assembly.

Consequences of Genetic Rearrangements

  • Heterochromatin Rearrangements: Often silent because of the inactive state.
  • Euchromatin Rearrangements: Can disrupt genes or regulatory elements, causing diseases like cancer.

Posttranslational Modifications and Complexes

  • Histone Modifications:
  • Acetylation (HATs): Activates transcription by loosening chromatin.
  • Methylation (HMTs): Can activate or repress transcription depending on the site.
  • Phosphorylation: Associated with chromatin condensation; and DNA repair.
  • Ubiquitination: Marks histones for remodeling or degradation.
  • Chromatin Remodeling Complexes: ATP-dependent complexes such as SWI/SNF, reposition or eject nucleosomes to allow access to DNA.

Functional Parts of Chromosomes

  • Telomeres: Repetitive sequences (e.g., TTAGGG in humans) at chromosome ends, prevent degradation and ensure complete replication. Maintained by telomerase.
  • Centromeres: Region where kinetochores attach, enabling proper chromosome segregation during mitosis. Composed of heterochromatin and satellite DNA.

DNA Replication and Repair

  • Replication Process: Semi-conservative, bi-directional, involves enzymes such as helicase, primase, DNA polymerase, and ligase. Leading strand is synthesized continuously, while lagging strand is synthesized discontinuously as Okazaki fragments, later joined by ligase.
  • PCR: Mimics DNA replication in a test tube; involves denaturation, annealing, and extension.

Exam 2

  • Types of Chromatin in Eukaryotic Chromosomes: Euchromatin and Heterochromatin (facultative and constitutive).

Exam 4

  • Ion and Solute Transport: Ions and solutes move across membranes via channels or transporters, depending on their properties and membrane permeability. Passive transport moves down concentration gradients, while active transport moves against gradients, requiring energy. Different types include channels, transporters (passive and active), symport, and antiport.
  • Electrochemical Gradient: The combined effect of concentration and electrical gradients, influencing ion movement.
  • Na+/K+ ATPase: A carrier protein, not a channel, that maintains the resting membrane potential by actively transporting 3 Na+ ions out and 2 K+ ions in.
  • Action Potentials: Initiated by depolarization and propagated along the membrane by the sequential opening and closing of voltage-gated Na+ channels.

Additional Topics (Page 31 ff)

  • Inhibitory vs. Excitatory Neurons: Neurons can affect post-synaptic potentials (PSP) by altering membrane potentials. Excitatory neurons depolarize to increase the likelihood of action potentials; inhibitory neurons hyperpolarize.
  • Voltage-Gated Ca2+ Channels and Synaptic Vesicle Docking: Ca2+ influx through these channels into the presynaptic terminal triggers synaptic vesicle fusion to release neurotransmitters via exocytosis.

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