The cell in health and disease

Question 1

The genome

Answer 1

20,000 protein encoding genes.
non coding DNA
80% of the genome is transcribed - 80% associated with the regulation of gene expression.

Question 2

Non protein coding DNA sequence

Answer 2

Promoter and enhancer regions that bind protein transcription factors
Non coding regulatory RNAs - of the 80% of the genome dedicated to regulatory function vast majority transcribed into RNAs (micro RNA and long coding)
mobile genetic elements

special structural regions

Question 3

SNP and CNV

Answer 3

single nucleotide polymorphisms = variants at single nucleotide positions and almost always bi-allelic
1% in coding regions (what you’d expect by changes)
often occur in regulatory non coding areas
can be useful markers especially if coniherited “linkage disequilibrium”

CNVs: 50% of CNVs involve gene-coding sequences. (therefore may underlie a large portion of human phenotypic diversity)

Question 4

HISTONES:

Answer 4

all cells in human body have the same genetic composition HOWEVER lineage specific programs of gene expression

1) chromatin organisation
- nucleosome 147 base pair wrapped around histone

2) DNA methylation - high level of methylation in gene regulatory elements generally results in chromatin condensation and transcriptional silencing (tightly regulates -

3) histone modifiying factors
- histone methylation: can either increase or suppress depending on which histone residue is markers
- histone acetylation: of lysine residues (histone acetyl transferase) tends to open up chromatin condensation

Question 5

Micro RNA and Long coding RNA - another important mechanism of gene regulation.

Answer 5

MICRO-RNAS

primarily function to modulation the translation of target mRNAs into their corresponding proteins

conserved in all eukaryotes

less miRNAs than the protein coding genes- individual miRNAs may regulate multiple protein coding genes.

Dicer enzyme - snips into single standed miRNAS 20-30 nucleotides - miRNA associated with a multi protein aggregate called RISC - subsequent base bearing between the miRNA strange and it’s target mRNA directs the RISC to induce mRNA cleavage or repress it’s translation

Question 6

siRNAs - synthetic version of of miRNAs

Answer 6

small interfering RNAs = short RNA sequences that can be introduced into cells.
interact with DICER and RISC

important in laboratories “knockout” technology

Question 7

Long non coding RNA

Answer 7

lncRNAs modulate gene expression in lots of ways
can bind to chromatin restricting RNA polymerase access to coding genes within the region

1) gene activation
2) gene suppression
3) promote chromatin modification
4) may act as scaffolding to stabilise secondary or tertiary structrures and or multi=subunits complexes that influence gene activity.

Question 8

CRISPR

Answer 8

clustered regulatory short palindromic repairs

CAs = CRISPR associated gene

usually CRISPRs are transcribed and processed into a RNA sequence that binds and directs the nuclease cas9 to a sequence (i.e a phage) leading to its binding and destruction

gene editing - artificial guide RNAs that bind cas9 and are complementary to a DNA sequence of interest
once directed to the target sequence - it induces double stranded DNA breaks

repairs of these highly specific cleavage sites can lead to random disruption mutations in the targeted sequences or the process introduction of new sequences of interaction

Question 9

Golgi

Answer 9

assembly of new proteins

Question 10

RER

Answer 10

new proteins are synthesised in the RER

proteins intended for the cytosol are synthesised on free ribosomes

smooth endoplasmic reticulum - (SER) may be abundant in certain cells types - site of steroid hormone and lipoprotein synthesis as well as the modification of hydrophobic compounds

Question 11

Protoeomses

Answer 11

degrade denatured or otherwise tagged cytosolic proteins and release short peptides 
in some cases the peptides are then processed to be presents on MHC class one as part of the adaptive immune response. 
proteosomal degradation of regulatory proteins or transcription factors can trigger or shut down cellular signalling pathways

Question 12

Lysosomes

Answer 12

intracellular organelles enzymes that digest enzymes

(vs. PEROXOMES - specialised organelles - containing catalase, peroxides and other oxidative enzymes. - role in breakdown of very long chain fatty acids genera hydrogen peroxidase in the process)

Question 13

Mitochondrial

Answer 13

oxidative phosphorylation - makes most of the ATP which powers the cells

also important source of metabolic intermediates for anabolic metabolism

other things:

• synthesise certain macromolecules - haem
• contain important sensors of cell damage (in the process of apoptotic cell death)

Question 14

Growth

Question 15

The cell cycle and proliferation

Answer 15

the sequence of events resulting in cell division = the cell cycle.

G1 = pre syntheticgrowht
S = DNA synthesis
G2 (pre-mitotic)
M mitotic

G0 –> cellular quiescence

can progress to G1 from G0 are progress through there after mitosis

Question 16

Cell cycle regulations

Answer 16

progression driven be proteins called cyclins
cyclin dependant kinases (are the enzymes associated cyclins)

checkpoints are another regulatory point in the cycle cycle.

Question 17

Checkpoints in the cell cycle: sense DNA or chromosomal damage.

Answer 17

G1-S checkpoint = monitors the integrity of DNA before irreversibly committing cellular resources towards DNA replication.
G2 - M checkpoint ensures that there has been accurate DNA replication before the cell actually divides

when damage is sensed –> checkpoint activation –> leads to DNA repair mechanisms being activated
If the DNA damage is too severe the cell will actually undergo apoptosis or enter non replicative phase call senescence. (primarily through P53 dependant mechanism)

enforcing the cell cycle checkpoints is the CDK inhibitors - modulate the CDK-cycline complex activity

when growth occurs also stimulations changes cellular metabolism so that all of the cellular components to make two daughter cells are ready. chief among this is the WARBURG effect

Question 18

Warburg effect

Answer 18

important concept particularly in cancer cell growth
concept that increased cellular uptake of glucose and glutamine and increased glucolysis and decreased oxidative phospphylaration …….

Question 19

STEM CELLS:

Answer 19

totipotent stem cells can give rise to all types of differentiated tissues
in the mature organism adult stem cells in tissues can only replace damaged cells and maintain cell populatio
ns within the tissues they reside.

under homeostasis stem cells have two features
1) self renewal which permits them to maintain their numbers
2) Asymmetric division - cell replication which is cell replication where one daughter cell enters a differentiation pathway and gives rise to mature cells whereas the other remains undifferentiated and retains its self renewal capacity
in symmetric division both retain self renewal capacity. (such is seen in embryogenesis or under conditions of stress - such as in the bone marrow following chemotherapy)

embryonic stem cells - the least differentiates and limitless renewal capacity. “totipotent”
tissue stem cells are found in intimate associated with differentiate cells of a given tissue - have a limited repertoire of differentiate cells they can generate.

mesenchymal stem cells - multipoint cells that can differentiate in to a variety of stromal cells INCLUDING chondrocytes (cartilage) and osteocytes (bone), adipocytes (fat) and myocytes (muscle)

tissue stem cells are normallyprotected within specialised tissue environments called stem cell niches

such niches have been demonstrated in lots of regions……

Question 20

Different stem cell NICHES

Answer 20

haematopoeitic stem cells - perivascular niche
hair follicles - bulge region 
limbus of the cornea 
crypts of the gut
canals of hering in the liver 
sub ventricular region of the brain