Biochemistry - Cellular

Question 1

Cell cycle phases

• Regulation
• Phases

Answer 1

• Regulation
  
  • Checkpoints control transitions between phases of cell cycle.
  • This process is regulated by cyclins, cyclin-dependent kinases (CDKs), and tumor suppressors.
• Phases
  
  • G1 and G0 are of variable duration.
    
    • G = Gap or Growth.
  • ​S = Synthesis.
  • Mitosis (shortest phase of cell cycle) includes prophase, metaphase, anaphase, and telophase.

Question 2

Regulation of Cell Cycle

• CDKs
• Cyclins
• Cyclin-CDK complexes
• Tumor suppressors

Answer 2

• CDKs
  
  • Constitutive and inactive.
• Cyclins
  
  • Regulatory proteins that control cell cycle events
  • Phase specific
  • Activate CDKs.
• Cyclin-CDK complexes
  
  • Must be both activated and inactivated for cell cycle to progress.
• Tumor suppressors
  
  • p53 and hypophosphorylated Rb normally inhibit G1-to-S progression
  • Mutations in these genes result in unrestrained cell division (e.g., Li-Fraumeni syndrome).

Question 3

Cell Types

• Permanent
• Stable (quiescent)
• Labile

Answer 3

• Permanent
  
  • Remain in G0, regenerate from stem cells.
  • Neurons, skeletal and cardiac muscle, RBCs.
• Stable (quiescent)
  
  • Enter G1 from G0 when stimulated.
  • Hepatocytes, lymphocytes.
• Labile
  
  • Never go to G0, divide rapidly with a short G1.
  • Most affected by chemotherapy.
  • Bone marrow, gut epithelium, skin, hair follicles, germ cells.

Question 4

Rough endoplasmic reticulum

• Definition
• Nissl bodies
• Free ribosomes

Answer 4

• Definition
  
  • Site of synthesis of secretory (exported) proteins and of N-linked oligosaccharide addition to many proteins.
  • Mucus-secreting goblet cells of the small intestine and antibody-secreting plasma cells are rich in RER.
• Nissl bodies
  
  • RER in neurons
  • Synthesize peptide neurotransmitters for secretion.
• Free ribosomes
  
  • Unattached to any membrane
  • Site of synthesis of cytosolic and organellar proteins.

Question 5

Smooth endoplasmic reticulum

Answer 5

• Site of steroid synthesis and detoxification of drugs and poisons.
• Lacks surface ribosomes.
• Liver hepatocytes and steroid hormone–producing cells of the adrenal cortex and gonads are rich in SER.

Question 6

Cell trafficking

• Golgi
• Endosomes

Answer 6

• Golgi
  
  • The distribution center for proteins and lipids from the ER to the vesicles and plasma membrane.
  • Modifies N-oligosaccharides on asparagine.
  • Adds O-oligosaccharides on serine and threonine.
  • Adds mannose-6-phosphate to proteins for trafficking to lysosomes.
• Endosomes
  
  • Sorting centers for material from outside the cell or from the Golgi, sending it to lysosomes for destruction or back to the membrane/Golgi for further use.

Question 7

Cell trafficking:
Inclusion cell (I-cell) disease

• Definition
• Findings

Answer 7

• Definition
  
  • Inherited lysosomal storage disorder
  • Defect in phosphotransferase
    
    • Ž–> failure of the Golgi to phosphorylate mannose residues (i.e., decreased mannose- 6-phosphate) on glycoproteins
    • Ž–> proteins are secreted extracellularly rather than delivered to lysosomes
• Findings
  
  • Results in coarse facial features, clouded corneas, restricted joint movement, and high plasma levels of lysosomal enzymes.
  • Often fatal in childhood.

Question 8

Cell trafficking:
Signal recognition particle (SRP)

Answer 8

• Abundant, cytosolic ribonucleoprotein that traffics proteins from the ribosome to the RER.
• Absent or dysfunctional SRP –>Ž proteins accumulate in the cytosol.

Question 9

Cell trafficking:
Vesicular trafficking proteins

• COPI
• COPII
• Clathrin

Answer 9

• COPI
  
  • Golgi –>Ž Golgi (retrograde)
  • Golgi –>Ž ER.
• COPII
  
  • Golgi –>Ž Golgi (anterograde)
  • ER –>Ž Golgi.
• Clathrin
  
  • Trans-Golgi Ž–> lysosomes
  • Plasma membrane Ž–> endosomes (receptor-mediated endocytosis [e.g., LDL receptor activity]).

Question 10

Peroxisomes & proteasomes

• Perioxisome
• Proteasome

Answer 10

• Peroxisome
  
  • Membrane-enclosed organelle involved in catabolism of very-long-chain fatty acids, branched-chain fatty acids, and amino acids.
• Proteasome
  
  • Barrel-shaped protein complex that degrades damaged or ubiquitin-tagged proteins.
  • Defects in the ubiquitin-proteasome system have been implicated in some cases of Parkinson disease.

Question 11

Microtubule

• Structure
• Molecular motor proteins
• Drugs that act on microtubules

Answer 11

• Structure
  
  • Cylindrical structure composed of a helical array of polymerized heterodimers of α- and β-tubulin.
  • Each dimer has 2 GTP bound.
  • Incorporated into flagella, cilia, mitotic spindles.
  • Grows slowly, collapses quickly.
  • Also involved in slow axoplasmic transport in neurons.
• Molecular motor proteins
  
  • Transport cellular cargo toward opposite ends of microtubule tracks.
  • ƒƒDynein = retrograde to microtubule (+ Ž–> -).
  • Kinesin = anterograde to microtubule (- Ž–> +).
• Drugs that act on microtubules (Microtubules Get Constructed Very Poorly)
  
  • ƒƒMebendazole (anti-helminthic)
  • ƒƒGriseofulvin (anti-fungal)
  • ƒƒColchicine (anti-gout)
  • ƒƒVincristine/Vinblastine (anti-cancer)
  • ƒƒPaclitaxel (anti-cancer)

Question 12

Cilia

• Cilia structure
• Axonemal dynein
• Kartagener syndrome (1° ciliary dyskinesia)

Answer 12

• Cilia structure
  
  • 9 + 2 arrangement of microtubules [A].
• Axonemal dynein
  
  • ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets.
• Kartagener syndrome (1° ciliary dyskinesia)
  
  • Immotile cilia due to a dynein arm defect.
  • Results in male and female infertility due to immotile sperm and dysfunctional fallopian tube cilia, respectively
  • ↑ risk of ectopic pregnancy.
  • Can cause bronchiectasis, recurrent sinusitis, and situs inversus (e.g., dextrocardia on CXR).

Question 13

Cytoskeletal elements & plasma membrane composition

• Cytoskeletal elements
  
  • Actin and myosin
  • Microtubule
  • Intermediate filaments
• Plasma membrane composition

Answer 13

• Cytoskeletal elements
  
  • Actin and myosin
    
    • Muscle contraction, microvilli, cytokinesis, adherens junctions.
    • Actins are long, structural polymers.
    • Myosins are dimeric, ATP-driven motor proteins that move along actins.
  • Microtubule
    
    • Movement.
    • Cilia, flagella, mitotic spindle, axonal trafficking, centrioles.
  • Intermediate filaments
    
    • Structure.
    • Vimentin, desmin, cytokeratin, lamins, glial fibrillary acid proteins (GFAP),
      neurofilaments.
• Plasma membrane composition
  
  • Asymmetric lipid bilayer.
  • Contains cholesterol, phospholipids, sphingolipids, glycolipids, and proteins.
  • Fungal membranes contain ergosterol.

Question 14

Immunohistochemical stains for intermediate filaments: Cell types stained by…

• Vimentin
• Desmin
• Cytokeratin
• GFAP
• Neurofilaments

Answer 14

• Vimentin
  
  • Connective tissue
• Desmin
  
  • Muscle
  • DesMin: Muscle
• Cytokeratin
  
  • Epithelial cells
• GFAP
  
  • Neuroglia
  • GFAP: NeuroGlia
• Neurofilaments
  
  • Neurons

Question 15

Sodium-potassium pump

• Definition
• Regulation

Answer 15

• Definition
  
  • Na+-K+ ATPase is located in the plasma membrane with ATP site on cytosolic side.
  • For each ATP consumed, 3 Na+ go out and 2 K+ come in.
• Regulation
  
  • Ouabain inhibits by binding to K+ site.
  • Cardiac glycosides (digoxin and digitoxin) directly inhibit the Na+-K+ ATPase, which leads to indirect inhibition of Na+/Ca2+ exchange –> increased [Ca2+]i –> increased cardiac contractility.

Question 16

Collagen

• Definition
• Type I
• Type II
• Type III
• Type IV

Answer 16

• Collagen
  
  • Most abundant protein in the human body.
  • Extensively modified by posttranslational modification.
  • Organizes and strengthens extracellular matrix.
  • Be (So Totally) Cool, Read Books.
• Type I
  
  • Most common (90%)—Bone (made by osteoblasts), Skin, Tendon, dentin, fascia, cornea, late wound repair.
  • Decreases production in osteogenesis imperfecta type I.
  • Type I: bone.
• Type II
  
  • Cartilage (including hyaline), vitreous body, nucleus pulposus.
  • Type II: cartwolage.
• Type III
  
  • Reticulin—skin, blood vessels, uterus, fetal tissue, granulation tissue.
  • Type III: deficient in the uncommon, vascular type of Ehlers-Danlos syndrome (ThreE** D).**
• Type IV
  
  • Basement membrane, basal lamina, lens.
  • Defective in Alport syndrome
  • Targeted by autoantibodies in Goodpasture syndrome.
  • Type IV: under the floor (basement membrane).

Question 17

Collagen synthesis and structure:
Inside fibroblasts

• Inside fibroblasts
  
  1. Synthesis
  2. Hydroxylation
  3. Glycosylation
  4. Exocytosis
• Outside fibroblasts
  5. Proteolytic processing
  6. Cross-linking

Answer 17

1. Synthesis (RER)
   
   • Translation of collagen α chains (preprocollagen)
     
     • Usually Gly-X-Y (X and Y are proline or lysine).
   • Glycine content best reflects collagen synthesis (collagen is 1⁄3 glycine).
2. Hydroxylation (RER)
   
   • Hydroxylation of specific proline and lysine residues
   • Requires vitamin C
     
     • Deficiency Ž–> scurvy.
3. Glycosylation (RER)
   
   • Glycosylation of pro-α-chain hydroxylysine residues and formation of procollagen via hydrogen and disulfide bonds (triple helix of 3 collagen α chains).
   • Problems forming triple helix –>Ž osteogenesis imperfecta.
4. Exocytosis
   
   • Exocytosis of procollagen into extracellular space
5. Proteolytic processing
   
   • Cleavage of disulfide-rich terminal regions of procollagen, transforming it into insoluble tropocollagen.
6. Cross-linking
   
   • Reinforcement of many staggered tropocollagen molecules by covalent lysine-hydroxylysine cross-linkage (by Cu2+-containing lysyl oxidase) to make collagen fibrils.
   • Problems with cross-linking Ž–> Ehlers-Danlos.

Question 18

Osteogenesis imperfecta

• Definition
• Findings

Answer 18

• Definition
  
  • Genetic bone disorder (brittle bone disease [A]) caused by a variety of gene defects.
  • Most common form is autosomal dominant with decreased production of otherwise normal type I collagen.
  • May be confused with child abuse.
• Findings
  
  • ƒƒMultiple fractures with minimal trauma
    
    • May occur during the birth process
  • Blue sclerae [B] due to the translucency of the connective tissue over the choroidal veins
  • ƒƒHearing loss (abnormal ossicles)
  • ƒƒDental imperfections due to lack of dentin

Question 19

Ehlers-Danlos syndrome

• Definition
• Types
• Hypermobility type
• Classical type
• Vascular type

Answer 19

• Definition
  
  • Faulty collagen synthesis causing hyperextensible skin, tendency to bleed (easy bruising), and hypermobile joints.
• Types
  
  • 6+ types.
  • Inheritance and severity vary.
  • Can be autosomal dominant or recessive.
  • May be associated with joint dislocation, berry and aortic aneurysms, organ rupture.
• Hypermobility type
  
  • Joint instability
  • Most common type.
• Classical type
  
  • Joint and skin symptoms
  • Caused by a mutation in type V collagen.
• Vascular type
  
  • Vascular and organ rupture
  • Deficient type III collagen.

Question 20

Menkes disease

Answer 20

• Connective tissue disease caused by impaired copper absorption and transport.
• Leads to decreased activity of lysyl oxidase (copper is a necessary cofactor).
• Results in brittle, “kinky” hair, growth retardation and hypotonia.

Question 21

Elastin

Answer 21

• Stretchy protein within skin, lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava (connect vertebrae –> relaxed and stretched conformations).
• Rich in proline and glycine, nonhydroxylated forms.
• Tropoelastin with fibrillin scaffolding.
• Cross-linking takes place extracellularly and gives elastin its elastic properties.
• Broken down by elastase, which is normally inhibited by α1-antitrypsin.

Question 22

Elastin

• Marfan syndrome
• Emphysema
• Wrinkles of aging

Answer 22

• Marfan syndrome
  
  • Caused by a defect in fibrillin, a glycoprotein that forms a sheath around elastin.
• Emphysema
  
  • Can be caused by α1-antitrypsin deficiency, resulting in excess elastase activity.
• Wrinkles of aging
  
  • Due to decreased collagen and elastin production.