G&D- Cells Flashcards
1
Q
What % of genome is translated into proteins?
A
3%
2
Q
What % of genome is transcribed as part of protein-coding gene expression but not translated into proteins?
A
27%
3
Q
What % of genome is transcribed and not translated AND is not associated with protein-coding gene expression…?
A
25%
4
Q
How many non-functional pseudogenes in the genome?
A
20,000
5
Q
What is a pseudogene?
A
Section of chromosome that is an imperfect copy of a functional gene.
- Related to real genes
- Contain biological and evolutionary histories
6
Q
What are the 4 nucleobases in DNA?
A
- Adenine
- Thymine
- Guanine
- Cytosine
7
Q
RNA nucleobases?
A
- Adenine
- Uracil
Guanine
Cytosine
8
Q
What is transcription?
A
Process by which gene information from DNA strand is transferred to an RNA molecule… genetic information is now on the coding strand!
This mRNA molecule is complimentary to the DNA template strand!
9
Q
What is RNA polymerase?
A
Protein that binds onto the promoter sequence on an DNA template strand sequence to begin transcription.
- No primer required
Polymerase 2- used for mRNA precursors
10
Q
How might translocation mutations of enhancers and promoters lead to cancer?
A
Translocation may place genes that should be turned off in proximity of strong promoters and enhancers- these control transcription rates and gene expression (timing and in which specific cell types!)
11
Q
What is the 3’ strand?
A
Coding strand
12
Q
What is the 5’ strand?
A
Template strand
13
Q
What is pre-mRNA?
A
Type of primary transcript that becomes mRNA after processing (alternative splicing- removing non-coding introns with a splicesome)
14
Q
What is mRNA?
A
Wide range of sizes depending on polypeptide size.
Common to most cells- proteins needed by all cells.
15
Q
What is rRNA?
A
Builds ribosomes, machinery for synthesising proteins by translating mRNA…
4 kinds in eukaryotes: 18s, 28s, 5.8s, 5s
s= sedementation rate
16
Q
What is tRNA?
A
32 different kinds in eukaryote cells…
- Carries AAs (1/20) at the 3’ end
Most AAs have more than 1 tRNA
17
Q
What is ncRNA
A
non-coding RNA
2% of genome.
90% of genome is transcribed.
- Modify protein levels by mechanisms independent of transcription…
- ncRNA: plays a role in cellular physiology, development, metabolism
- Epigenetic modulator
18
Q
snRNA
A
Small nuclear RNA
Mediate processing steps of precursor molecules/primary transcripts before they can be exported into cytosol…
- Part of splicesome?
19
Q
snoRNA
A
small nucleolar RNA
Help make ribosomes by helping cut large precursors.
- Can add methly groups to ribose
- Involved in splicing of pre-mRNA
20
Q
What are microRNAs?
A
Tiny RNA molecules
- Regulate gene function post-transcriptionally
- Account for 1/3 of protein-coding genes
- Bind to mRNA, cause degradation/ inhibit protein syntehsis
18-25 nucleotides
- Time specific expression!
21
Q
Name 3 energy yielding nutrients
From diet
A
Fats
Carbohydrates
Proteins
22
Q
Name 3 energy-poor, end-products (made through catabolism of energy-high products)
A
H2O
CO2
NH3
23
Q
Name some precursor molecules for cell macromolecules… (4)
A
- AAs
- Sugars
- Fatty acids
- Nitrogenous bases
24
Q
Name 4 cell macromolecules made through anabolism of precursor molecules
A
- Nucleic acids
Proteins
Lipids
Polysaccharides
25
Name the 2 types of protein (turnover) regulation
Allosteric
| Transcriptional
26
What are the 3 types of AAs?
- Essential; from diet
(synthesised in body)
- Non-essential
- Conditionally essential AAs
27
What are essential AAs?
```
From diet only.
9
1- histidine
2- isoleucine
3- leucine
4- lysine
5- methionine
6- phenylalanine
7- threonine
8- typtophan
9- valine
```
28
What are non-essential AAs?
```
Synthesised in body
Can be made from:
- Glucose + Nitrogen source
or...
- Made from the essential AAs
```
```
5
1- alanine
2- aspargine
3- glutamate
4- asparate
5- serine
```
29
What are Conditionally essential AAs?
Synthesised in body (6)
Can be synthesised bu may not be enough i.e....
Arginine is essential during period of rapid growth so must be supplement throughout this period as cannot be made fast enough.
```
1- Arginine
2- cysteine
3- glutamine
4- glycine
5- proline
6- tyrosine
```
30
How many standard and non-standard AAs are there?
S- 20
| Non-s : 2
31
What are the 2 non-standard AAs?
1) Selenocysteine: Found on prokaryotes, eukaryotes too but not loaded by DNA?
2) Pyrolysine: found only in some archaea and bacteriu
32
2 types of AAs (in relation to how they are degraded/ where the carbons go to...)
1- Glucogenic: carbons are converted to glucose
2- Ketogenic: Carbons are converted to acetyl CoA or Acetoacetate (ketone bodies)
Some are both!
33
Where does amino acid degradation occur?
Liver
34
Where does the carbon and where does the nitrogen go?
Carbon: Glucose, CO2 , acetyl CoA, acetoacetate
Nitrogen:
Alpha amino group is removed; ammonia is formed which enters the urea cycle.
35
What is transamination?
When an amino group from one amino acid is transferred to another.
e.g. α ketoglutarate and glutamate are usually one pair
36
What enzyme and co-factors are needed for transamination?
transaminases/amino transferases
Cofactor- pyridoxyl phosphate (derived from vit. B6 )
37
How is ammonia produced from AAs?
Enzyme involved?
Where?
Glutamate can collect nitrogen from AAs and convert it to Ammonia...
Glutamate dehydrogenase
Liver mitochondria
38
Protein degradation intracellular-
Lysosomes: vesicles filled with protease
Ubiquitin: small proteins that targets proteins for degradation
Proteasome: protease complex, protein is unfolded & degraded (ATP)
39
Nitrogen
N2 not usable in biological systems
NH3, usable & crosses membranes
NH4+ toxic
40
Forms of nitrogen that are excreted
Ammonia
Uric acid
Urea
41
Who may have a positive nitrogen balance (above normal)?
Children
| Pregnant
42
Who may have a -ive N balance?
Disease
| Starvation
43
Urea cycle
5 steps.
Nitrogen enters as NH4+ and aspartate
Ornithine initiates and is regenerated.
Enzyme mediated
44
Control of urea cycle?
1- ‘Feed forward’ regulation: the higher the rate of ammonia production the higher the rate of urea
2- Allosteric activation of enzymes
(arginine stimulates carbamoyl phosphate synthase)
3- High protein diet or fasting induces urea cycle enzymes
45
What happens in muscles during fasting?
Muscle protein broken down to amino acids...
Pyruvate-> Alanine
Alanine (AA) and glutamine (mops up nitrogen) enter blood...
These AAs are broken down to (-> Pyruvate -> ) glucose and ketone bodies in the liver and used for energy!
46
What are ketone bodies?
Acetoacetate, beta hydroxybutyrate
- acidic
3 water-soluble molecuels containing the ketone group.
47
When glucose low, what happens to ketone bodies?
Acetoacetate, beta hydroxybutyrate
48
ketoacidosis?
Ketoacidosis is a metabolic state associated with high concentrations of ketone bodies, formed by the breakdown of fatty acids and the deamination of amino acids
49
What are some Inborn errors of amino acid metabolism?
Deficient enzymes in amino acid metabolism lead to accumulation of harmful products
Phenylketonuria: mutation in phenylalanine hydroxylase, mental retardation
Urea cycle disorders: accumulation of ammonia, toxic to the nervous system
50
What is Phenylketonuria?
mental retardation
mutation in phenylalanine hydroxylase
51
How are Non essential amino acids made
synthesised from intermediates of glycolysis and the TCA cycle
52
Where do the carbons in AAs go when AAs are degraded?
the carbons from amino acids form glucose or acetyl CoA/acetoacetate
53
Where do the nitrogens in AAs go when AAs are degraded?
Nitrogen is removed by transamination, formation of ammonia and formation of urea in the urea cycle
54
Functions of Cell communication?
adaptation,
co-ordination
and regulation
55
3 mechanisms of cell communication ?
1. Remote signalling by
Secreted molecules
2. Contact signalling by
membrane bound
molecules
3. Contact signalling via
Gap junctions
56
1. Remote signalling by
Secreted molecules
e.g. Chemical signalling (secreted)
4 mechanisms..
1- Endocrine
2- Paracrine
3- Autocrine
4- Synaptic
57
What is endocrine signalling?
Hormones
hormone produced, enters bloodstream and is carried to target cell.
58
What is paracrine signalling?
local chemical mediator released, acts on cells in immediate environment
(eg cytokine)
59
What is autocrine signalling?
Acts on itself
60
What is synaptic signalling?
neurotransmitters released at synapses, diffuse to post-synaptic target cell.
61
Examples of signals
```
Growth factors (hormones, endocrines)
Hormones
Extra-cellular matrix (can be insoluble)
Chemicals
Proteins
Sugars
Synaptic
```
62
Examples of cell responses to signals
```
Growth, cell division
Differentiation
Metabolism
Apoptosis
Gene transcription- start and stop
Secretion
Contract / relax- muscle cell
Membrane charge
Migration- chemokine/cytokine, move along conc gradient
```
63
Signal Transduction mechanisms (3)
Amplification,
phosphorylation cascades,
secondary messengers
64
Intracellular receptors- mechanism
Hydrophobic molecules– can pass through plasma membrane
Transported into nucleus
Response: influence gene transcription
65
Name some substances that may act on intracellular receptors
eg Steroids,
NO- nitrous oxide
66
What is Phosphorylation
Proteins can be modified… by phosphorylating
Any enzyme that is a kinase, sticks a phosphate on a protein
67
Name 4 membrane receptors
G-protein linked
Tyrosine kinases
Enzyme linked
Ion channels
68
What are G-protein coupled receptors
| ?
Integral trans-membrane proteins
Receptor occupation promotes interaction with G-protein
Promotes exchange of bound GDP -> GTP... activates G protein (α subunit) which leaves receptor
... initiates signalling through secondary messengers
69
What are Monomeric (small) G-proteins: Ras?
Function controlled by GDP/GTP cycle.
Stimulates cascade of kinases (effectors).
Involved in Proliferation, differentiation, cell death
70
Mutations in Ras proteins?
Mutations make Ras insensitive to GTPase activating proteins (active for longer).
Ras mutations in 30% of all tumours.
Cancerous!
71
Receptor tyrosine kinase mechanism- ...
Ligand binds.
Dimerise upon ligand binding.
Have intrinsic enzymatic activity.
Phosphate from ATP to tyrosine on itself (autophsophorylation).
Bind src homology-2 (SH-2) proteins.
Initiate series of phosphorylation reactions
72
What does MAP stand for?
Mitogen activated protein (MAP) kinase system
cascade trasnduction...
Phosphylation cascade...
73
What are enzyme-linked receptors?
Cytokine receptors – no intrinsic activity but associates with enzymes
e.g. JAKs
cytokine binds; dimerise reaction...
74
What are ion channels?
Ion channel= receptor.
Ligand (eg neurotransmitter) binds to& opens channel (some are voltage gated)
Response: influx of Na+, change in membrane potential, action potential
75
What are secondary messengers?
Small molecules
| Bind and activates other molecules
76
Examples of 2ndary messengers
Cyclic adensosine monophosphate (cAMP)
Inositol triphosphate (IP3)
Ca2+ - (muscle contraction)
Diacylglycerol
77
What are kinases/ phosphatases?
A kinase is an enzyme that attaches a phosphate group to a protein. A phosphatase is an enzyme that removes a phosphate group from a protein.
Together, these two families of enzymes act to modulate the activities of the proteins in a cell, often in response to external stimuli.
78
How is control of signalling?
Inhibition by protein phosphatases
79
Fibroblast growth factor receptor (FGFR) stimulation- what diff effects does it have on differing cell types...?
1) in fibroblasts - proliferation
| 2) in neuronal cells – differentiation
80
PD184352 (MEK) function?
Specific inhibitors - PD184352 (MEK) reduce tumour growth by up to 80%
81
What is PTEN?
PTEN is a tumour suppressor and is a IP3 phosphatase
82
Overexpression of what cell signals in cancer?
MAPK, PI3K
Activating mutations of G subunits & receptors
????
83
Therapeutic caner targets...
News: Experimental Drug Inhibits Cell Signaling Pathway and Slows Ovarian Cancer Growth
Trying to affect cancer cell signalling pathways... to inhibit growth
targeted agents currently under development interfere with function and expression of several signalling molecules,
including the EGFR family;
the vascular endothelial growth factor and its receptors;
and cytoplasmic kinases such as Ras, PI3K and mTOR
84
What are VNTRs?
"Variable number tandem repeats"
Repeat nucleotide regions usually bounded by specific restriction enzyme sites,
> Number of repeats at each loci is inherited from parents
30% non-coding region
There is large variation between people...
85
PCR and DNA amplification use?
Measuring transcription of a gene...
86
What is reverse transcription?
Using RNA to make cDNA and then using polymerase chain reaction to make more copies of a specific piece of DNA
- Once you have lots of DNa copies, can identify defect
87
3 steps of PCR
1- Denaturation
2- Annealing
3- Extension
88
What are SNPs
Single Nucleotide polymorphism
DNA sequence variation: when a single nucleotide in genome sequence has been altered!
Most commonly: C-> T
89
What % of all genetic variaton occurs due to SNPs
90%
| Has to occur in at least 1% of population
90
What is the cell cycle?
Ordered set of events that leads to cell growth and division.
Involves mitosis.
91
What is mitosis?
Production of 2 identical daughter cells.
| - DNA is duplicated exactly and divided equally. (complete set in daughter cells)
92
What is miosis?
Division that leads to gamete formation.
93
What happens in gap1 (8-10hrs)
Cell grows: it is metabollically active
| - duplicates organelles (excluding chromosomes)
94
What happens in S phase?
6-8hrs
"interphase"
Replication of DNA... there is now 46 chromosomes
95
What happens in gap 2 phase?
4-6hrs
Cell growth continues... as it prepares to divide.
Enzymes and other proteins are synthesised.
Double checks for errors are done in this phase too.
96
What happens during mitosis?
Cell division occurs!
- Prophase
- Metaphase
- Anaphase
- Telophase
+ Cytokenesis
97
Gap 0 phase?
Exit from cell cycle- for non-dividing cells
98
What happens in interphase?
Chromosomes duplicate, thicken and coil
99
What happens in prophase?
Nuclear membrane breaks down
100
What happens in metaphase?
Centromeres attach to spindle fibres and line up at the equator
101
What happens in anaphase?
Centromeres split and are pulled to each half of the cell
102
What happens in telophase?
Cytokenesis occurs. cells are pulled apart.
| - Nuclear membranes form around the separated chromosomes.
103
Name 3 cell cycle regulation checks
G1 checkppoint- Growth and environment
G2 checkpoint- DNA replication
M checkpoint- Chromosome alignment on spindle
104
What are cyclins?
family of regulatory proteins that control the progression of cells through the cell cycle by activating cyclin-dependent kinase (CDK) enzymes.
Levels rise and fall within stages of the cell cycle
105
Cyclins present in G1 phase
D
106
Cyclins present in S phase
D?, E and A
107
Cyclins present in M phase
D?, B and A
108
What are Cyclin dependent kinases (Cdks)
Enzymes that Trigger major cell cycle transitions
via: Phosphorylate proteins that control cell cycle
-> Activity controlled by Cdk inhibitors
109
Cyclin dependent kinases (Cdks) bind to which cyclin...
in G1 phase!!
Cdk4 & 6 D Cyclin
110
Cyclin dependent kinases (Cdks) bind to which cyclin...
in G1 to S phase!!
Cdk 2 E Cyclin
111
Cyclin dependent kinases (Cdks) bind to which cyclin...
in s phase!!
Cdk2 A Cyclin
112
Cyclin dependent kinases (Cdks) bind to which cyclin...
in S to G2 phase!!
Cdk1 A Cyclin
113
Cyclin dependent kinases (Cdks) bind to which cyclin...
in M phase!!
Cdk1 B Cyclin
114
What is MPF?
Mitosis promoting Factor (MPF)… initiates mitosis
- Activates anaphase promoting factor/ anaphase
115
What is the G0 phase?
Quiescent cells that have permanently or temporally left the cell cycle e.g. lymphocyte.
116
Why might a cell enter the G0 phase?
Terminal differentiation e.g. neuron, epithelial cell.
Active repression of genes needed for cell cycle.
117
What is the p53 gene?
cell cycle regulatory genes
also a tumour suppressor genes
p53 blocks cell cycle if DNA is damaged.
- Mutated in approx. 50% of cancers
118
p27 cyclin dependent kinase inhibitor... reduced levels can lead to...
poor breast cancer outcomes?
119
What is apoptosis?
Programmed cell death, essential for normal development.
120
3 functions for apoptosis
1) destroys cells that may be a threat:
- virus infected, immune, DNA damage
2) withdraw of positive signals
eg growth factors, hormones
3) receipt of negative signals
eg UV, death activators, hypoxia
121
Features of apoptosis...
```
> Controlled
> Energy dependent
> Cells shrink
> Membrane intact
> Non-inflammatory
> No scarring
> No individual or small cell groups
> Nuclear fragmentation
> Physiological (or pathalogical)
```
122
Features of Necrosis...
```
> Uncontrolled
> No ATP required
> Cells swell
> No membrane integrity
> Inflammatory
> Scarring
> Large cell groups
> Nuclear dissolution
> Pathological
```
123
2 main pathways that tell a cell to die...
1- intrinsic: integrity of mitochondrian membrane- cytochrome C release into cytoplasm... binds to Apaf-1 protein... there is a cascade of enzyme reactions
2- extrinsic: ligand binding to 'death receptors'... there is a cascade of 'caspase activation'... apoptosis...
124
What are caspases?
Key players: Bcl-2, Fas/L, Caspases
Proteolytic enzymes... cystein proteases
Effectors of apoptosis...
- Present as inactive proenzymes (zymogen)
125
Apoptosis examples in dental physiology?
```
Craniofacial growth & development
Homeostasis in mucosa, skin & pulp
Tooth development
Bone remodelling
Wound healing
```
126
Apoptosis in disease examples?
Avoidance in cancer = survival/proliferation
Human Papilloma virus inactivates p53
Epstein Barr Virus protein similar to Bcl-2
Melanoma inhibits expression of Apaf-1
Fas antagonists – block T cell cytotoxicity
Autoimmune eg SLE, Rheumatoid arthritis
Increase in apoptosis
eg Neurodegenerative, HIV
127
Apoptosis in oral disease
Oral cancer
Lymphomas- reduced apop
Odontogenic tumours/cysts
Sjogren's syndrome
128
Apoptosis in oral pathology
Common in Lichen planus?= chronic inflammatory dematosis... keratinocyte apoptosis
129
What are pluripotent cells?
Can diff into Any type of cell in the adult
| e.g. Embryonic
130
What are multipotent cells?
Limited diff, found in bone marrow and most organs
131
What is SHED?
Stem cells from human exfoliated deciduous teeth (SHED):
| multipotent, capable of differentiating into neural cells, odontoblasts.
132
Dental applications of SHED
- Growing teeth
- Repair/regeneration of dental tissues... e.g. pulp/ pdl
- Craniomaxillofacial bone repair
133
Problems with stem cells
- Rejection/ immune reaction
- Legal, ethical, political issues
- Adult stem cells difficult to isolate and purify
- May result in cancer
134
What is gene therapy?
Correcting defective genes responsible for disease development
Vector: commonly viruses; e.g. retro, adeno, adeno-associated
135
What is salivary gland gene therapy?
S.glands are encapsulated and accesible.
- Stable cell populaiton which export a large amount of proteins
- Can be removed if problem arises...
- Sjogren's syndrome... radiation damage...
- Systemic conditions
136
What is epigenetics?
Heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence (IVF)
- Identical DNA, but diff terminal phenotypes
137
how does epigenetics occur?
- DNA methylation
- Histone modification
- Nucleosome modification
- non coding DNA (micro DNA)
138
What are exosomes?
Durable cell specific lipid microvesicles...
- Reside in a number of biofluids
- Have immune functions
