The Cell as a Unit of Health and Disease:

Question 1

Discuss The Genome

Answer 1

⚫ The genome is the complete set of genes or genetic material present in a cell or organism.
⚫ The human genome is a complete set of nucleic acid sequences, encoded as DNA within 23 chromosomal pairs in the cell’s nuclei and in a small DNA molecule found within individual mitochondria.
⚫ It comprises of a total of 3.2 billion DNA base pairs.

⚫ The human genome encodes approximately 20,000 protein,
⚫ Protein-coding sequences account for only 1.5% of the total genome.
⚫ Up to 80% of the remaining DNA comprises of non-coding functional sequences that can bind proteins or otherwise regulate gene expression.

Question 2

The non-coding functional sequences include:

Answer 2

❖ Promoter and enhancer regions (binding sites for transcription factors.
❖ Binding sites for factors that maintain higher-order chromatin structures
❖ - Non-coding regulatory RNAs (e.g., microRNAs, and long noncoding RNAs)
❖ - Mobile genetic elements (e.g., transposons)
❖ - Special structural regions of DNA (e.g., telomeres and centromeres)

Question 3

Variations in genome

Answer 3

Any Two individual share >99.5% of their DNA sequences
⚫ Person-to person variation is encoded in <0.5% of total cellular DNA, i.e ~15 million base pairs.
⚫ The two most common forms of DNA variation are: SNP & CNV

Question 4

What are SNPs?

Answer 4

Single nucleotide polymorphism (SNPs) – variants at single nucleotide positions.
❖ ~6 million
❖ Occur across the genome – the exons,
introns, and intergenic regions
❖ Only 1% occur in coding regions
❖ SNPs in noncoding regions may impact gene expression by influencing regulatory elements
❖ Neutral SNPs can be useful markers for coinherited disease-associated genes (linkage disequilibruim).

Question 5

What are CNVs

Answer 5

⚫ Copy number variation (CNVs) – represent different numbers of repeated sequences of DNA – up to millions of base pairs in length.
⚫ Half of CNVs involve gene-coding sequences

Question 6

Define Epigenetics and Epigenetic factors

Answer 6

Epigenetics
⚫ Epigenetics: These are inheritable changes in gene expression that are not caused by primary variation in DNA sequence. Important in generating genetic diversity.
⚫ Epigenetic factors: are factors that drive lineage-specific programs of gene expression , thereby determining the distinct structures and functions of terminally differentiated cells.

Question 7

Epigenetic factors include:

Answer 7

1. Histones and histone-modifying factors viz

a. Chromatin-remodeling complexes
b. Chromatin writer complexes
c. Chromatin erasers and readers
d. Histone acetylation, methylation and phosphorylation
2. DNA methylation
3. Chromatin organizing factors

Question 8

Discuss micro RNA and what are siRNAs

Answer 8

MicroRNA
⚫ The miRNA are short RNAs (21 to 30 nucleotides)
⚫ They do not encode proteins
⚫ They are involved in post transcriptional
silencing of gene expression
⚫ Synthetic small interfering RNAs (siRNAs) are short RNA sequencing analogous to
miRNA, that can be introduced into the cells.

Question 9

Discuss Long Noncoding RNA

Answer 9

⚫ Long noncoding RNA (lnc RNA) are about tenfold to twentyfold more than miRNAs.
⚫ They are involved in modulating gene expression
⚫ They can restrict RNA polymerase access to specific coding genes, e.g. XIST
⚫ They can promote gene activation by facilitating transcription factor binding sites
⚫ They can facilitate chromatin modification or provide the scaffolding to stabilize chromatin
structure.

Question 10

CELLULAR HOUSEKEEPING
The cell’s viability and function depend on fundamental housekeeping activities, e.g.:

Answer 10

⚫ Membrane integrity
⚫ Nutritional acquisition
⚫ Communication
⚫ Movement
⚫ Renewal of senescent molecules,
⚫ Molecular catabolism
⚫ Energy generation

Question 11

Why are specific cellular activities often compartmentalized within membrane-bound organelles?

Answer 11

⚫ There is usually a unique intracellular environments (e.g. low pH or high calcium) that facilitates specific biochemical pathways and also sequester (isolate) potentially injurious enzymes or reactive metabolites.

Question 12

Describe the Plasma membrane

Answer 12

Protection and Nutrient Acquisition
⚫ Plasma and organelle membranes are fluid bilayers of amphipathic phospholipids.
⚫ Membrane components are heterogenously and asymmetrically distributed.
⚫ Some of them include: phosphotidylinositol phosphotidylserine, glycolipids, and sphingomyelin
⚫ Some membrane components tend to self-associate to form discrete domains known as “lipid rafts”.

Question 13

Passage of molecules across the plasma and organellar membrane is via:

Answer 13

⚫ 1. Passive membrane diffusion – for small nonpolar molecules (O2 and CO2), hydrophobic molecules (e.g. estradiol/Vit. D), small polar molecules(e.g., water, ethanol, urea)
⚫ 2. Carriers and Channels proteins – for polar molecules >75 daltons (e.g., sugar and nucleotides) and all ions (require specialized protein transporter)
⚫ Note that the Na+/K+ ATPase (affected in cell injury) on the cellular membrane helps maintain intracellular osmolarity.
⚫ These transport system also help maintain intracellular pH.

3. Receptor-Mediated and Fluid-Phase Uptake:
   ⚫ Involves endocytosis which allows the import of
   macromolecules > 1000 daltons.

Question 14

Endocytosis can be via

Answer 14

⚫ A. Caveolae-mediated endocytosis (“little caves”)
⚫ B. Pinocytosis (“cellular drinking)
⚫ C. Receptor-Mediated endocytosis (mainly for macromolecules like transferrin and LDL)
⚫ Defect in receptor-mediated uptake or processing of LDL can be responsible for familial hypercholesterolemia.

Question 15

Describe Cytoskeleton and Cell-Cell Interaction

Answer 15

⚫ Cell shape, polarity, intracellular trafficking, and motility depend on intracellular cytoskeleton proteins.
⚫ These proteins include:
⚫ Actin microfilaments
⚫ Intermediate filaments: lamin A, B and C, Vimentin, Desmin, Neurofilaments, GFAP, Cytokeratins
⚫ Microtubules
⚫ Cell-cell interaction: cells interact and communicate via junctional complexes.

Question 16

Describe Cytoskeleton and Cell-Cell Interaction

Answer 16

⚫ Cell shape, polarity, intracellular trafficking, and motility depend on intracellular cytoskeleton proteins.
⚫ These proteins include:
⚫ Actin microfilaments
⚫ Intermediate filaments: lamin A, B and C, Vimentin, Desmin, Neurofilaments, GFAP, Cytokeratins
⚫ Microtubules
⚫ Cell-cell interaction: cells interact and communicate via junctional complexes.

Question 17

Junctional complexes in the cell include

Answer 17

A. Occulding junctions (tight junctions)
B. Anchoring junctions (desmosomes associated with cadherins):
- spot desmosomes/macula adherens,
-belt desmosomes,
- hemidesmosome,
- focal adhesion complexes

C. Communicating junctions (gap junctions): mediate the passage of chemical or electric signals between cells.
⚫ These juctions are formed by hexamers of transmembrane proteins called connexins.
⚫ The permeability of gap junction is reduced by acidic pH or increased intracellular calcium
⚫ Important in cell-cell communication in cardiac myocytes.

Question 18

Discuss the Biosynthetic Machinery: Endoplasmic Reticulum

Answer 18

⚫ Endoplasmic reticulum:
-membrane proteins, lipids, molecules destined for exported are synthesized within the ER.

⚫ Rough endoplasmic reticulum (RER)
⚫ Smooth endoplasmic reticulum (SER)
⚫ *ER Stress response/Unfolded protein response (UPR) apoptosis.

With a highly regulatory mechanism, called unfolded protein response (UPR), it protects cells from the accumulation of misfolded proteins. This is done by the ER

Question 19

Discuss the cell Waste disposal component: Lysosomes

Answer 19

⚫ They are involved in cellular constituent degradation
⚫ Lysosomes contain acid hydrolases, including proteases, nucleases, lipases, glycosidases, phosphatases, and sulfatases.

Question 20

Discuss the cell Waste disposal component: Proteosomes

Answer 20

⚫ Proteosomes (“cylinder of death”), a protease complexes that degrade:
- cytosolic proteins, including denatured or misfolded proteins
- other macromolecules whose lifespan must be regulated (e.g. transcription factors)
⚫ Many proteins destined for proteosome destruction are covalently bound to a small protein called ubiquitin

Question 21

Discuss the mitochondria

Answer 21

MITOCHONDRIA
⚫ “Power-house” of the cell
⚫ Contain its own DNA
⚫ Involved in oxidative phosporylation
⚫ Sensitive to antibacterial antibiotics
⚫ Half lives of 1 to 10 days
⚫ Has two separate membranes surrounding a core matrix containing most mitochondrial metabolic enzymes

⚫ The inner membrane is folded into cristae which contains the enzymes of the respiratory chain
⚫ The outer membrane contain porin proteins that form aqueous channels permeable to small (<5000 molecules).
⚫ Larger molecules will require a specific transporter
⚫ The intermembrane space is the site for ATP synthesis

Question 22

Roles of mitochondria

Answer 22

⚫ Energy generation (ATP from carbohydrate and
fatty acid substrates)
⚫ Intermediate metabolism (an “importer”, a source of molecules used to synthesis lipid and proteins – exploited by tumour cells in Warburg effect)
⚫ Cell death; involved in necrosis and apoptosis, regulating the balance between cell survival and death

Question 23

Molecules for lysosomal degradation are taken in via

Answer 23

❖ - M6P-modified protein targeted to the lysosome
❖ - Pinocytosis or receptor-mediated endocytosis
❖ - Autophagy, for senescent organelles and large, denatured protein complexes
❖ - Phagocytosis, e.g. for micro-organism

Question 24

What is Ubiquitin

Answer 24

Ubiquitin is a small protein that targets other proteins to be broken down (degraded) within cells. These enzymes attach a small molecule called ubiquitin to proteins that should be degraded