Describe Dense Fibrillar Component

processing factory in the nucleolus where rRNA is cleaned up and prepared

Describe Granular Component

ribosome assembly area where ribosomal parts come together before leaving the nucleolus

Name three nuclear substructures and their functions

PML bodies (tumor suppression), Cajal bodies (snRNP maturation), Speckles (mRNA splicing).

What is the nuclear lamina?

A fibrous layer providing structural support; composed of lamin proteins.

What are consequences of lamin A mutations?

They cause nuclear fragility, blebbing, altered gene expression, diseases like Hutchinson-Gilford Progeria.

"Blebbing" refers to the formation of bubble-like protrusions (called blebs) on the surface of the cell, typically involving the plasma membrane or nuclear envelope. It’s a physical sign that something is going wrong with cell structure or function.

Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic disorder characterized by dramatically accelerated aging in children. It’s one of the most well-studied examples of how defects in nuclear structure can lead to disease.

What is the function of nuclear pores?

They regulate import and export of molecules between nucleus and cytoplasm.

Describe the structure of the nuclear pore complex.

It includes FG-repeat proteins that form a selective barrier.

FG-repeat proteins are key components of the nuclear pore complex (NPC) that regulate what enters and exits the nucleus.

How does nuclear import/export occur?

It involves Ran-GTP/Ran-GDP, importins, exportins, and NLS signals.

Getting Into the Nucleus (Import)

1. A protein with a special tag called an NLS (Nuclear Localization Signal) is like having the right passcode.
2. Importin is the helper that reads the tag and carries the protein into the nucleus.
3. Inside the nucleus, a helper called Ran-GTP makes importin let go of the protein.
4. Importin and Ran-GTP go back to the cytoplasm.
5. Ran-GTP gets turned into Ran-GDP, and the cycle starts again.

Getting Out of the Nucleus (Export)

1. A protein that needs to leave has a tag called NES (Nuclear Export Signal).
2. Exportin and Ran-GTP help carry it out.
3. Once outside, Ran-GTP turns into Ran-GDP, and the protein is released.
4. Exportin and Ran-GDP go back inside to start again.

List the levels of DNA packaging.

DNA → nucleosomes → beads on a string → 30-nm fiber → solenoid → metaphase chromosome.

Steps of DNA packing

• DNA wraps around histone proteins to form nucleosomes (like "beads on a string").
• These nucleosomes coil into a thicker fiber called the 30-nanometer fiber.
• This fiber then coils even further into a spiral structure called a solenoid.

What proteins form the nucleosome?

Histones: H2A, H2B, H3, and H4 (two of each).

The nucleosome is the basic unit of DNA packaging in eukaryotic cells. It looks like "beads on a string" under a microscope.

Each nucleosome core is made up of 8 histone proteins:

• 2 × H2A
• 2 × H2B
• 2 × H3
• 2 × H4

Together, these form a histone octamer

Name parts of a mitotic chromosome.

• Arms: The two long sections of the chromosome on either side of the centromere.
• Centromere: The constricted region where sister chromatids are held together.
• Kinetochore: Protein structure assembled on the centromere where spindle fibers attach during mitosis.
• Telomeres: Protective end caps of chromosomes that prevent degradation and fusion.

What is junk DNA?

Non-coding DNA including introns, transposons, and repetitive elements.

• Introns: Non-coding sections within genes that are removed during RNA splicing.
• Transposons: "Jumping genes" that can move around the genome.
• Repetitive elements: DNA sequences repeated many times (e.g., satellite DNA, microsatellites).
• Though called "junk," many of these elements have regulatory or structural functions!

What do cohesins and condensins do?

Cohesins hold sister chromatids together; condensins compact DNA.

What triggers nuclear envelope breakdown in mitosis?

Phosphorylation of lamins.

Define euchromatin and heterochromatin.

Euchromatin is loosely packed and active; heterochromatin is dense and silent.

What is epigenetics? Give an example.

Heritable changes in gene expression without DNA sequence change.

Example: X-inactivation (Barr body).

How do histone modifications regulate genes?

They affect chromatin structure and transcription factor access.

List the phases of the cell cycle.

• G0: Resting or quiescent phase (non-dividing).
• G1: Cell growth and preparation for DNA replication.
• S: DNA synthesis (replication) phase.
• G2: Preparation for mitosis; checks for DNA damage.
• M: Mitosis and cytokinesis (cell division).

What are the cell cycle checkpoints?

G1 (DNA damage), S (replication), G2 (DNA replication), M (spindle checkpoint).

How do cyclins and Cdks regulate the cell cycle?

By phosphorylation, synthesis, and degradation of target proteins.

What is the function of the APC/C complex?

It targets proteins like cyclin B for degradation via ubiquitination.

Ubiquitination: A process where a small protein called ubiquitin is attached to a target protein, marking it for degradation by the proteasome

Name three CKIs and their roles.

p21, p27, p16: inhibit cyclin-dependent kinases (Cdks) and help control cell cycle progression by slowing or stopping the cycle when needed

What is the G0 phase?

A resting state where cells are not dividing.

What is the G1 restriction point?

A checkpoint deciding cell fate based on nutrients, growth factors, and DNA integrity.

What role does p53 play in the cell cycle?

It halts the cycle in response to DNA damage.

What is the key event in S phase?

DNA replication.

Describe DNA replication enzymes.

Helicase: Unzips the DNA double helix by breaking hydrogen bonds between base pairs, creating the replication fork.

Primase: Synthesizes short RNA primers that provide a starting point for DNA polymerase.

DNA Polymerase: Adds new nucleotides to the 3’ end of the primer to synthesize the new DNA strand.

Ligase: Joins Okazaki fragments on the lagging strand by sealing nicks in the sugar-phosphate backbone.

Topoisomerase: Relieves tension and prevents supercoiling ahead of the replication fork by making temporary cuts in the DNA.

SSBPs (Single-Strand Binding Proteins): Bind to and stabilize single-stranded DNA after helicase unwinds it, preventing the strands from re-annealing.

What are telomeres and telomerase?

Telomeres protect chromosome ends; telomerase extends them

How is DNA damage repaired?

Through proofreading, base/nucleotide excision, and mismatch repair

What regulates the G2/M transition?

Cdc25C activates Cdk1-cyclin B by removing inhibitory phosphates; Wee1 inhibits it.

How does Cdk1 activation trigger mitosis?

It initiates positive feedback loops and phosphorylates proteins needed for mitosis

What are the stages of mitosis?

Prophase, Prometaphase, Metaphase, Anaphase, Telophase, Cytokinesis

What happens in Prophase?

Chromosomes condense, centrosomes move to poles, spindle forms.

What occurs in Prometaphase?

Nuclear envelope breaks down, microtubules attach to kinetochores

What is the key event of Metaphase?

Chromosomes align at the metaphase plate or in the middle; Cyclin B and securin are degraded

What happens during Anaphase?

Cohesin is cleaved, chromatids separate via dynein and microtubules

What happens in Telophase?

Nuclear envelope reforms, chromosomes decondense.

What occurs during Cytokinesis?

Actin and myosin filaments form a contractile ring to split the cell

What happens to the Golgi during mitosis?

It fragments and reassembles in daughter cells.

What is the structure of the mitochondrion?

Outer Membrane

• Outer layer of the mitochondrion.
• Lets small molecules pass through.

Intermembrane Space

• Space between the outer and inner membranes.
• Stores protons (H⁺) for making energy.

Inner Membrane

• Inner layer that folds inward.
• Where energy (ATP) is made using proteins.

Cristae

• Folds of the inner membrane.
• Give more space to make energy.

Matrix

• Inside space of the mitochondrion.
• Where the Krebs cycle happens.
• Holds enzymes, DNA, and ribosomes.

How is mitochondrial DNA inherited?

Maternally, through the egg cytoplasm

What is heteroplasmy?

Presence of more than one type of mitochondrial DNA in a cell

What macronutrients are metabolized for energy?

Glucose, fatty acids, amino acids

What are key steps in glucose metabolism?

1. Glycolysis

• Happens in the cytoplasm
• Glucose → 2 Pyruvate
• Makes 2 ATP and 2 NADH

2. Pyruvate → Acetyl-CoA

• Happens in the mitochondria
• Each pyruvate loses a carbon (as CO₂) → becomes Acetyl-CoA
• Makes 2 NADH total (1 per pyruvate)

3. The Citric Acid Cycle (Krebs Cycle)

• In the mitochondrial matrix
• Each Acetyl-CoA → makes CO₂, NADH, FADH₂, and a little ATP
• Total: 2 ATP, 6 NADH, 2 FADH₂

4. Electron Transport Chain (ETC)

• In the inner mitochondrial membrane
• NADH & FADH₂ drop off electrons
• Powers ATP production
• O₂ is the final electron acceptor → makes water

Total ATP (per glucose): About 32 ATP

What are the key steps in amino acid and lipid metabolism?

What is the proton motive force?

Electrochemical gradient that drives ATP synthesis.

What is the role of oxygen in respiration?

Final electron acceptor in the electron transport chain.

How is ATP synthesized in mitochondria?

H+ gradient drives ATP synthase in oxidative phosphorylation.

How do mitochondria balance ATP, heat, and ROS ( Reactive Oxygen Species?

Uncoupling proteins shift energy from ATP to heat, lowering ROS

What are the three main cytoskeletal proteins?

Intermediate Filaments

Job: Give the cell strength and hold things in place

Strong and rope-like

Found in: Skin, hair, and around the nucleus

Microtubules Job: Act like train tracks for moving things around the cell

Hollow tubes

Help with: Cell division, cilia/flagella movement

Built from: Tubulin

Grow from the centrosome

Actin Filaments (Microfilaments) Job: Help the cell move, change shape, and divide

Thin and flexible

Built from: Actin

Describe intermediate filaments.

Shape: Rope-like

•Function: Give the cell tensile strength (helps resist stretching and pulling) Made of:

Keratin (skin, hair, nails)

Vimentin (connective tissue)

Lamins (support the nuclear envelope)

Key Point:They hold the cell together and keep the nucleus stable.

Name diseases from intermediate filament mutations.

Epidermolysis Bullosa Simplex (EBS) skin disease where the skin is very fragile. Even a little rubbing or bump can cause blisters.

It's caused by problem with certain skin proteins.

Usually runs in families.

No cure, but you can take care of the skin to avoid problems.

Progeria: very rare disease where kids age much faster than normal.

Caused by a mistake in a gene that keeps the cell's "control center" strong. Kids look old early, with thin skin, hair loss, and heart problems.

Usually happens by chance, not inherited.

No cure, doctors help manage symptoms.

Describe microtubule structure.

Tiny hollow tubes inside cells made of two proteins called alpha and beta tubulin. They have a "fast" end (plus) that grows or shrinks quickly.

They have a "slow" end (minus) that changes slowly.

They help the cell keep its shape and move things inside.

What is dynamic instability?

Rapid switching between growth and shrinkage of microtubules.

What are microtubules used for?

Spindle formation, transport, cilia and flagella movement.

What do kinesin and dynein do?

They are like tiny trucks inside cells that carry stuff (cargo).

Kinesin moves cargo toward the plus (+) end of microtubules (usually outward from the center).

Dynein moves cargo toward the minus (-) end (usually inward toward the cell center).

These proteins "walk" along microtubules to deliver materials where needed.

Describe the ciliary axoneme structure.

The inside part of tiny cell hairs called cilia and flagella that helps them move. Made of 9 pairs of tubes around 2 single tubes in the middle (called the "9+2" pattern).

Has motor parts called dynein arms that pulI on the tubes to make them bend. Special links hold the tubes together so they don't slide too far.

Covered by the cell's outer membrane.

What is Kartagener’s syndrome?

disease where tiny hairs in the body called cilia don't move right.

This causes breathing problems and infections because mucus can't be cleared well.

Some people's organs are flipped the other way (like the heart on the right side). It can also cause trouble having babies. Happens because the cilia's motors (dynein) don't work properly.

Describe actin filaments.

The thinnest fibers inside cells. Made of a protein called actin that can join together (polymerize) when it has ATP attached.

Very flexible and help cells change shape, move, and carry stuff inside.

What is actin treadmilling?

Addition at plus end and removal at minus end

What are steps of cell crawling?

Protrusion The cell sticks out its front (called lamellipodia) using actin.

Adhesion The front of the cell grabs onto the surface.

Traction The back of the cell pulls forward using actin and myosin (like tiny muscles)

Actin pushes Cell grabs Myosin pulls. That's how the cell crawls forward!

What regulates actin dynamics?

1. Rho proteins (Rho, Rac, Cdc42) tell the cell what actin shapes to make

2. Arp2/3 makes branched actin

3. Formin makes long, straight filaments

4. Cofilin cuts old actin to recycle it

5. Capping proteins stop actin from growing

6. Bundling/crosslinking proteins organize actin into structures

How do actin and myosin interact in muscle?

Actin and myosin are proteins that slide past each other to make muscles contract.

1. Myosin grabs actin (using its "head" like a hook) 2. ATP gives energy

Myosin uses ATP to move its head 3. Myosin pulls actin

This shortens the muscle (contraction) 4. ATP binds again

- Myosin lets go and resets for the next pull

What is the ECM?

A network of proteins and polysaccharides providing structural and biochemical support.

What cells contribute to the ECM?

Fibroblasts Make collagen and other fibers; help build and repair connective tissue

Mesenchymal Stem Cells (MSCS) Can turn into bone, fat, muscle, or cartilage cells

Immune Cells Defend the body (like crophages, T cells, B cells)

Adipocytes Fat cells that store energy Osteoblasts Build bone by making the bone matrix

What are major ECM components?

Collagen Strong fiber that gives tissue strength

Elastin Stretchy fiber that lets tissue bounce back

Proteoglycans Protein sugar combos that hold water and cushion tissues Hyaluronan (Hyaluronic acid) A big sugar molecule that makes tissues slippery and hydrated

Adhesive glycoproteins Help cells stick to the ECM (e.g., fibronectin, laminin)

Describe collagen structure

Triple helix Collagen is made of 3 chains twisted together

Gly-X-Y The repeating building block (Glycine-any amino acid-usually Proline or Hydroxyproline)

Needs vitamin C and oxygen For hydroxylation, a step needed to stabilize the helix

How does collagen organization relate to tissue function?

Parallel fibers in tendons; mesh in skin for flexibility.

What is elastin?

has hydrophobic regions (for recoil/ stretch)

And hydrophilic regions (for stability and crosslinking)

This pattern lets elastin stretch and snap back, like a rubber band

Define proteoglycans and GAGs.

Proteoglycans proteins with long sugar chains called (glycosaminoglycan chains) GAGS attached GAGS are polysaccharides like heparan sulfate, chondroitin sulfate, and dermatan sulfate

GAGS are negatively charged and hold lots of water, giving tissues cushioning and support

What do adhesive glycoproteins do?

Connect ECM to cells and mediate signaling; e.g., fibronectin

What is the basal lamina?

Thin ECM layer supporting epithelial cells, rich in laminin.

What do MMPs do?

Degrade ECM during remodeling; regulated by TIMPs

Name diseases linked to ECM defects

Osteogenesis Imperfecta bones break easily (bad collagen)

Marfan Syndrome stretchy, loose tissues (bad elastin fibers)

Ehlers-Danlos very stretchy skin and joints (collagen problem)

Chondrodysplasia = bones and cartilage don't grow right (growth problem)

Name the three types of cell junctions.

Occluding: seal

Anchoring: hold

Communicating: talk

What are tight junctions?

Occluding Junction

Function: Create a tight barrier between cells to stop leaks

Made of:

Claudins (main sealing proteins)

proteins (connect claudins to the cell's cytoskeleton)

What are adherens junctions?

Anchoring junction

Use cadherins to stick cells together Cadherins connect to actin inside the cell Help cells hold on tight and keep shape

What are desmosomes?

Desmosomes = strong spot welds

They use cadherins to stick cells together and connect to intermediate filaments inside for strength

What are focal adhesions?

Focal adhesions: cell's hands

They use integrins to grab the ECM and connect to actin inside so the cell can hold on and move

What are hemidesmosomes?

Hemidesmosomes: cell's feet

They use integrins to grab laminin outside, and connect to intermediate filaments inside to hold the cell steady

What are gap junctions?

Channels formed by connexons for direct cell-cell communication