Molecular Biology of the Cell 2 Flashcards
(147 cards)
1
Q
Where does glycolysis, TCA cycle and Oxidative phase occur, are they aerobic or anaerobic
A
Glycolysis in the cytosol and is anaerobic, TCA cycle is in mitochondrial matrix and Oxidative phase in the mitochondrial inner membrane and are both aerobic.
TCA cycle doesn’t require oxygen fo reactions but only runs when its present
2
Q
What enzyme in glycolysis regulates the rate
A
Phosphofructokinase which turns fructose-6-phosphate into fructose-1,6-phosphate
Regulates the rate through allosteric inhibition, when ATP is low or ADP is high phosphofructokinase will be high. If ATP or citrate is high it inhibits this enzyme
3
Q
What enzyme is needed for the first step of glycolysis and why is it important
A
Hexokinase converts glucose to glucose-6-phosphate
it is an irreversible step and commits the glucose to glycolysis
4
Q
Without what enzyme would we lose half of the ATP made in glycolysis
A
Triose phosphate isomerase, TPI enzyma- needed to create the second triode phosphate/ glycerol aldehyde-3
5
Q
What is the NET gain or loss of glycolysis
A
2NADH and 2ATP
lose 2ATP at beginning but gain 4 later
6
Q
From glycolysis pyruvate is made, what are the 3 possible fates it can have
A
Alcoholic Fermentation- anaerobic, makes ethanol, makes NAD+ so glycolysis can continue
Lactate Generation- anaerobic, makes lactate which is produced by muscle in exercise, makes NAD+ so glycolysis can continue
Acetyl CoA formation- aerobic conditions needed, happens in mitochondria and will be committed to TCA cycle
7
Q
Since ATP in muscle is depleted quickly, what do muscles store to sustain contraction
A
Creatine phosphate is stored in muscles so it can become creatine and ATP, providing energy
8
Q
What enzyme catalyses Acetyl CoA generation from pyruvate and what disorder can affect this enzyme
A
Pyruvate dehydrogenase causes this reaction and makes an NADH as it does so.
BERI BERI is a deficiency of thiamine, this damages the PNS as the brain needs thiamine nd causes low cardiac output and weak muscles
9
Q
What is the NET production of one turn of the Krebs cycle
A
2CO2, 3NADH, GTP, FADH
10
Q
How can amino acids enter the Krebs cycle and what reaction creates amino acids that the cycle can utilise
A
can enter by removing the amino group and feeding the carbon skeleton in, all of Krebs cycle can be made from degradation of Amino Acids just not citrate.
glycogenic AAs enter in cycle or at pyruvate, ketogenic AAs enter at acetyl COA
transamination reaction is used to swap NH3+amine and =O ketone group so it can be used in the cycle.
11
Q
The mitochondrial membrane is impermeable to NADH, how does it move in?
A
Glycerol-Phosphate shuttle: Dihydroxyacetone becomes Glycerol-3-phosphate and donates NADH in the form of electrons to DHAP, DHAP can then transfer these electrons to FAD inside the mitochondria to make FADH2 which CO-Q (part of the electron transport chain can use)
Malate-Aspartate shuttle- Oxeloacetate cannot cross the membrane so binds to NADH to become malate, malate then enters the mitochondria and reduced NAD to NADH+ within. Oxeloacetate then binds with glutamate to become aspartate and alpha-ketoglutarate, these move out of the cell and do the reverse reaction
12
Q
How much ATP does one turn of the Krebs cycle make
A
12 ATP
NADH = 3 ATP, FADH2= 2ATP
13
Q
How can Fatty acids enter the TCA cycle, explain
A
Beta Oxidation to create acetyl CoA
Fatty acid + ATP with ACYL COA SYNTHASE to make an Acyl CoA and AMP, this occurs on the outer mitochondria membrane
Acyl CoA will bind to carnatine to make Acyl carnatine which is catalysed by carnatine acyltransferase1 and then translocated in.
Within the cell Acyl carnatinewill become acetyl CoA and carnatine again via carnatine acetyltransferease II, carnatine will be tranlocased back out.
The acyl species then undergoes oxidation (FADH2 will be made), hydration, oxidation (NADH made) and thiolysis to make and Acetyl CoA and Acyl CoA species that’s two carbons shorter
14
Q
How would a 16C fatty acid become Acetyl CoA and what would it produce
A
16C + 7FAD + 7NAD + 7H2O -> 8 Acetyl CoA + 7FADH2+ 7NADH
15
Q
what condition can affect the conversion of an Acyl CoA species into an Acetyl CoA
A
Medium chain acyl CoA dehydrogenase deficiency
To become an Acetyl species the Acyl CoA has to undergo oxidation which happens through different Acyl CoA dehydrogenases aka short chain, medium, long very long.
This medium chain acyl con dehydrogenase deficiency is autosomal recessive and means the person cannot get energy from fatty acids that are larger than C12 so need a high carb diet. I.V glucose if vomiting or lose appetite
16
Q
On what condition will the Acetyl CoA from Fatty acid metabolism enter the TCA cycle
A
if carbohydrate metabolism and beta oxidation are balanced as oxeloacetate is needed to bind with Acetyl CoA to begin TCA cycle.
17
Q
If fat breakdown predominates what does Acetyl CoA become
A
acetoacetate, D-3 hydroxybutyrate, acetone
ALL KETONE BODIES
18
Q
What deficiency/ problem can affect whether Acyl CoA can move into the mitochondria
A
primary carnatine deficiency
autosomal recessive, mutations result in reduced ability for cells to take up carnatine so it cannot move in, need to take. carnatine supplement
19
Q
Describe fatty acid synthesis and where it occurs
A
occurs in the liver, adipose tissue and lactating breast
Acetyl CoA undergoes elongation due to ACETYL COA CARBOXYLASE enzyme to become Malonyl CoA. MAlonyl CoA regulates carnatine acetyltransferase and blocks so no more aftty acid can be broken down.
then undergoes reduction (NADP+), dehydration, reduction (NADPH+, condensation then linked to an Acyl carrier protein
20
Q
To make a C16 fatty acid what would be needed and what would be the products
A
Acetyl CoA + 7 Malonyl CoA + 7H+ + 14NADPH -> C16 + 7Co2 + 6H2O + 14NADP++ 8 CoA-SH
21
Q
What is the difference between beta oxidation and synthesis
A
Beta oxidation : in mitochondrial matrix, acyl group undergoes oxidation, hydration, oxidation, thiolysis. CoA is the carrier, FAD/NAD+ is the reducing power
Fatty acid synthesis : in the cytoplasm, Acetyl CoA undergoes reduction, dehydration, reduction, condensation, ACP is the carrier, NADPH is the reducing power
22
Q
If a person is fasting and has low plasma glucose, what will happen to avoid hypoglycaemic coma
A
liver glycogen stores will release glucose, adipose tissue will release free fatty acids, Acetyl CoA will be made into ketone bodies.
eventually glucose store will be depleted so pyruvate provided by lactate or amino acids will start to become glyceralaldehyde 3 phosphate, glycerol released from adipose tissue releasing free fatty acids and glycerol will turn it into fructose 1,6 bisphosphate and glucose eventually made
23
Q
What molecule is an indicator of cell death/damage
A
Creatine Kinase
24
Q
What are the three dimetric isoenzymes of creatine kinase and where are these dimers found
A
MM - skeletal muscle, MM will move furthered towards negative cathode
BM - cardiac muscle/ myocardium
BB- brain
25
How would Creatine Kinase activity be measured
coupled assay to measure NADPH formation
26
What are other markers of myocardial damage
BM dimer of creatine kinase
Cardiac Troponin- enters bloodstream fast
Seum Glutamate Oxeloacetate Transaminase- 2 days after for 5 days total
Lactate Dehydrogenase- late marker 2-3 days, stays longer due to inflammation
27
describe what junctions pores keep cells together or allow them to communicate
tight junctions- occludin interacts and seals them together
adherens junctions and demosomes- have cadherin and keep cells together (cell-cell anchoring)
gap junction- pores between cells (channel forming)
hemidesmosomes- integrins that connect cell to basal membrane
28
What are the different functional types of epithelium and their features
TRANSPORTING EPITHELIA- lots of ion transporters and mitochondria
ABSORPTIVE EPITHELIUM- carriers on brush border membrane, villi and microvilli, nutrients build in cytoplasm then down conc gradient into basal interstitial space.
SECRETORY EPITHELIUM- tubules and glands arrangement. can be endocrine (secretory granules by basal membrane) or exocrine (secretory granules by apical membrane)
29
What are the different types of secretion
Constitutive secretion- secretory vesicles move to plasma membrane and release directly as formed
Stimulated secretion- secretory vesicles need a stimulant to fuse with membrane
30
Epithelial cells are replace how and what problems can occur if this process is inhibited or increased
Replaced by proliferation of stem cells
stem cells in crypts replace lost villi tips, so if proliferation is inhibited a flattened mucose=a will occur
stem cells replace cells out at the top of Strat squampous. if hyerproliferation occurs then will caused a thickened layer, papilloma virus induces this and creates a wart
31
What are the three sources that fats are derived from
The diet
De novo biosynthesis in the liver
storage deposits in adipose
32
A lack of bile salts results in what
fat passing through the gut and being unabsorbed leading to steatorrhea
33
Where are bile salts made and stored
made in the liver and stored in the gallbladder
34
What do bile salts do
Emulsify fats so dietary fats can be absorbed and fat soluble vitamins ADEK can be absorbed
35
What medication treats obesity and how does it work? what are the side effects?
Orlistat. treats obesity, reduces fat absorption by inhibiting pancreatic and gastric lipase.
abdominal pain, urgency to defecate, increased flatus, steatorrhea
36
As bile salts have what feature
amphipathic
37
How are chylomicrons formed and what is their overall structure
enterocytes on the brush border absorb lipids, they are re-synthesised into triglycerides and then put into chylomicrons which travel via lymphatics and blood stream. In the bloodstream they acquire apoproteins from High Density Lipoproteins.
Hydrophobic inside with triglycerides and cholesterol esters encased by acyl chains of phospholipid.
Hydrophilic outside with polar group of phospholipids and apoproteins, has cholesterol in too
38
How are chylomicrons used by tissues
Chylomicrons travel from lacteals of intestine to thoracic duct to subclavian vein
Lipoprotein lipase on capillary endothelial cell membranes recognises the apoprotein and breaks down chylomicrons, the fatty acids undergo beta oxidation and glycerol is retuned to liver
39
What is cholesterol
A steroid, increases or decreases stiffness of membrane
| Polar head group, rigid planar steroid ring structure, non polar hydrocarbon tail
40
How is cholesterol made
2 acetyl CoA make acetoacetyl CoA.
Acetoacetyl CoA joins with another Acetyl CoA tome 3-hydroxy-3-methylglutaryl CoA (HMG-CoA) this is done by HMG CoA synthase
HMG-CoA is reduced to make mevalonate by HMG CoA reductase
mevalonate makes isopentenyl pyrophosphate, 6 molecules of this condensed to make squalene. undergoes cyclisation and demethylation to make cholesterol
41
What enzyme in cholesterol biosynthesis is important, and what looks similar to it
HMG CoA reductase because cholesterol and mevalonate both feed back negatively to inhibit its actions
statins look similar to this and are competitive inhibitors.
42
What do isoprene units do
isoprene units make molecules lipophilic and keep Co-Q (ubiquinone) to the inner mitochondrial membrane
43
From cholesterol what three things can be synthesises
Pregnenolone which makes all other steroid hormones
Vitamin D
Bile Salts- Glycocholate and taurocholate
44
What do lipoproteins carry to pack the contents closer together
Cholesterol esters
45
Cycle of lipoproteins
Liver produces VLDL and releases into circulation
VLDL give off glycerol, FFA and cholesterol to tissues that recognise apoprotein.
after giving its contents its called a lipid depleted remnant
Liver and small intestine synthesises HDL which have the lipids and cholesterol from tissues take the apoproteins from the lipid depleted remnant to go back to the liver. the removal of triglycerides leaves an Intermediate density lipoprotein
HDL then donates cholesterol esters to IDL to make LDL which has lots of cholesterol and macrophages take up. The rest of LDL is taken up by liver
46
what is the difference in HDL and LDL's jobs
HDL lowers serum cholesterol taking it from tissues to liver
LDL transport cholesterol that liver synthesises to tissues and high levels can lead to atherosclerosis
47
What disorder can affect serum cholesterol levels, symptoms and
Familial hypercholesterolaemia
serum cholesterol -2-3 times more if inherit one gene, if inherit both then 5 times
will see orange/yellow xanthomas and plaque in arteries.
```
They lack functional LDL receptors
Class I- no LDLR
Class II- Low surface expression of LDLR
Class III- LDL doesnt bind well to LDLR
Class IV- LDL-LDLR doesn't cluster in clathrin coated pits
Class V- LDLR doesn't release LDL
```
LDLR are supposed to bind to LDL, enter a clathrin pit and be endocytose as a clathrin covered vesicle, take off this coat of clathrin to fuse with endoscope which released the LDL to lysosome and make free cholesterol inside the cell
48
Two ways to control hypercholesterolaemia
Statins - HMG-CoA Reductase inhibitors stop mevalonate pathway so stops more cholesterol being made
Resins- make bile acid-cholesterol complexes to stop intestine reabsorbing them, lowers LDL and raises HDL
49
Explain the electron transport chain
NADH donates electrons to Complex I, this causes it to become supercharged and pump H+ inter the inter membrane space. With this energy it donates protons to CoQ.
FADH donates electrons to Complex II (succinate dehydrogenase), this Complex cannot become supercharged as is only on one side of the membrane so donates its electrons to CoQ
CoQ becomes CoQH2 after these donations
CoQH2 passes these electrons to Cytochome B in Complex III where the electron donated turns Fe3+ to Fe2+, this supercharge the complex and pumps H+ into the inter membrane space. It then donates it's protons to Cytochrome C which has the same Fe3+ to 2+ process. Cytochrome C donates to Complex IV which becomes supercharged and also pumps protons to the inter membrane space. Complex IV then passes its electrons to oxygen which splits to make two water molecules. Ultimate electron acceptor is oxygen.
ATP Synthase takes advantage of proton gradient and protons move through, this energy causes the F0 subunit to create rotation creating potential energy to put ADP and Pi together to make ATP
50
what is chemiosmosis
protons moving from high to low concentration through ATP Synthase
51
What is redox couple and redox potential
A redox couple is something that can exist in oxidised and reduced forms
a redox potential is the ability of a redox couple to accept or donate electrons: if it is -Eo then its a reducing agent and donates electrons, if it is +Eo then It accepts electrons and oxidising agent
52
What controls the uptake of oxygen by the mitochondria
The amount of ADP that is available
53
Which metabolic poisons affect the ATP Synthase
Oligomycin inhibits the F0 subunit to stop ATP formation
2,4, Dinitrophenol (DNP) creates a hydrophobic pore and uncouples oxidative phosphorylation from ATP concentration, H+ move through to pore and no ATP- will see rise in temperature due to higher metabolic rate
babies have brown adipose tissue that creates thermogenin which creates a pore and uncouples to make heat for them
54
Glucose, citrate, different metabolic poisons what effect do they have on oxygen consumption
glucose or adding ADP+Pi will not speed up as the mitochondria can't metabolise
citrate will increase oxygen consumption
Antimycin, Cyanide, CO, Oligomycin will stop O2 consumption
2,3 DNP (dinitrophenol) will increase oxygen consumption as it uncouples it from ATP production
55
How are collagen fibres formed
Prolines and lysine are hydroxylated to form procollagen which has an N and C terminal, if its becoming a fibrillar collagen these domains are removed before secretion (post translational modification). ITs then secreted becoming collagen (3 alpha chains) This condenses to a fibril by cross linking then aggregation to a fibre.
Not all collagens form fibrils- type IX and XII associate with fibrillar collagens and regulate organisation
56
What is extracellular matrix and what is its key functions
Network of proteins and carbohydrates filling space between cells
provides physical support, determines mechanical and psysicochemical properties if the tissue, influences growth adhesion and differentiation status of cells and tissues, essential for development tissue function and organisation
57
what are the components of connective tissues
Collagens: I,II,III are fibrillar, IV is basement membrane
Multi-adhesive glycoproteins: Fibronectin, fibrinogen. laminins in basement membrane
Proteoglycans: aggrecan, versican, decorin. perlecan in basement membrane
58
What is collagen, describe its arrangement, how many genes code for each type
Fibrous proteins, lots in bone, tendon and skin
skin collagen layers are at right angles to each other to resist tensive force
has three alpha chains making a triple helix: Type I is a heterotrimer having chains from two genes, Type II and III are homotrimers
In the triple helix every third position has a glycine
59
Which metabolic poison affects Complex I, II, III and IV
I: Rotenone- stops transfer to CoQ
II: Malonate- resembles succinate and stops electron flow
III: Antimycin
IV: CO, Azide, Cyanide- cyanide binds strongly to Fe3+ so stops electrons being passes to water
60
What is the point of cross linking and what is involved
Provides senile strength and stability : bone will have more crosslinks than tendons
lysine and hydroxy-lysine residues involved in crosslinking
61
What deficiency can impact collagen formation
Lack of Vitamin C as portly and Lysol hydroxylates are needed to hydroxylate proline and lysine. causes scurvy
62
What syndrome causes stretchy skin and loose joints
Ehlers Danlos syndromes
| mutations in collagen
63
What disorders are associated with problems with the basement membrane
Diabetic nephropathy- lots of ECM causes a thicker basement membrane and restricts renal filtration
Alport syndrome- mutation in collagen IV abnormally spilts basement membrane
64
What do elastic fibres contain, what are they rich in and what disorder is associated with mutations of elastin or its components
Elastic fibres contains
1) elastin which has hydrophobic regions and alpha helical regions rich in alanine and lysine
2) microfibrils, microfibrils are rich in fibrillin and are responsible for the integrity of elastin
Marfans syndrome - mutation in fibrillin-1 affects skeletal system making spider like fingers
65
What are laminins and what disorders are associated with mutations related to laminins
Multi-adhesive glycoproteins (modular)
alpha beta and gamma chain
Large proteins can self associate as part of basement membranes and interact with other components of BM
muscular dystrophy= no alpha 2 chain so hypotonia
66
What are fibronectins, what are they important for and how does it bind
Multi adhesive glycoprotein (modular)
can exist as insoluble fibrillar matrix or soluble plasma protein
role in regulating cell adhesion and migration in embryogenesis and tissue repair: important for wound healing and blood clotting
firbonectin binds to interns on cell membrane
67
What are proteoglycans
Proteins attached to one of more GAG (glycosaminoglycan) chains. high negative charge so attracts Na + and water into ECM
cartilage matrix has lots of GAGS
68
What are the two main types of GAG chains, where are they locates, are they sulphated
Hylauran- in ECM of soft tissues- carb chain no protein, unsulphated just repeated disaccharide units. can be polymerised to make larger molecules which are more viscous
Aggrecan- in ECM of cartilage, highly sulphated negative charge which attracts water, when compressed gives up water but regains
69
What property of elastin9 allows it to stretch and relax
Hydrophobic region that contains glycine allows it to slide over eachother
70
Degradation of extracellular matrix leads to what condition
Osteoarthritis, aggrecan cleaved so cartilage loses cushioning cartilage
71
What diseases result from excessive production of fibrous connective tissue
Fibrotic diseases
like alcohol liver fibrosis- cirrhosis
kidney fibrosis - diabetic nephropathy
lung fibrosis
72
Why Is cell signalling necessary (4 points)
to process information
for self preservation- reflexes
for voluntary movement
for homeostasis
73
What are the 4 main modes of communication and describe them
ENDOCRINE Communication- hormone travels within blood to act on distant target cell e.g. hypoglycaemia causes glucagon secretion from pancreas, travels to liver to signal gluconeogenesis
PANACRINE communication- hormone acts on adjacent cell e.g. hyperglycaemia- beta cells act on alpha cells in IL to inhibit glucagon secretion
BETWEEN MEMBRANE RECEPTORS-plasma membranes on adjacent cells interact e.g antigen presenting cell interacts with T lymphocyte
Autocrine Communication - signalling molecule acts n the same cell e.g. T cell receptors express IL2 receptors and secretes Il2.
74
What are the four types of receptors and explain their function
Ligand acted ion channel receptors(ionotropic) : ligand binds to protein , conformation change opens a pore, ions move in or out
G protein coupled receptors- Has a G protein complex (G-alpha subunit, G-betagamma subunit and GDP molecule) a ligand binds ad causes GDP to become GTP, the G-alpha unit dissociated from G-betagamma, either can be the second messenger. Once ligand leaves GTPase reverses this
Enzyme linked receptors- ligand binds and receptors cluster which activates enzyme activity inside phosphorylating the receptor so signalling proteins bind and the cell generates a signal.
Intracellular receptors- Type I inside cytoplasm with chaperone molecules (hsp), hormone binds hsp escapes. hormone-receptor complex associates with another making a homodimer which enters nucleus, binds to DNA and acts as transcription factor
Type II are inside nucleus and already bound to DNA sometimes, ligand binds to receptor so direct action as a transcription
75
Name the receptor, ligand and effect of four ligand gated io channels
Receptor ACh, Ligand ACH for muscle contraction
Receptor GABAa, Ligand GABA for inhibition of neuronal activity
Receptor NMDA, Ligand Glutamate for synaptic plasticity and memory formation
Receptor 5-HT3, Ligand 5-HT for anxiety and vomiting
76
What are the three types of G-alpha subunits and what do they do
G-alpha q/11- Activated PLC : converts PIP2 to IP3 and DAG:IP3 stimulates Ca2+ release and DAG activated PKC
G-alphas- Activates Adenyl Cyclase- ATP to cAMP, activates PKA
G-alpha i/o- Inhibits Adenyl Cyclase- Stops cAMP and PKA
77
Give some examples of G protein receptors and what they do
G-alpha q subunit:
AT-1, Angiotensin II- vasoconstriction, higher BP
M3 Muscarinic, ACh- bronchoconstriction
G-alphas s subunit
Beta1 adrenergic, nor adrenaline, adrenaline- increased heart rate
D1 dompaminergic, dopamine- neuronal growth
G-alpha i subunit
a2 adrenergic, noradrenalin, adrenaline- vasodilation, lower blood pressure
M2 muscarinic, ACh-decreased heart rate
78
what are some examples of enzyme linked receptors
Insulin receptor and ligand, Tyrosine kinase enzyme: glucose uptake
NPR1 receptor
TGF Beta R1- TGF beta binds for apoptosis
ErbB receptor: Epidermal or transforming growth factor as ligand: for cell growth or proliferation
79
Examples of intracellular receptors
TYPE I:
GC-R (glucocorticoid receptor) , cortisol binds causes stress and immunosuppression
ERalpha , Estradiol binds for female sexual development
TYPE II :
TRalpha, Thyroxine binds for physical development
80
What is the order of passes in cell replication and what happens in each of them
M phase (mitosis) checks if chromosomes are attached to the mitotic spindle
G0 phase (quiescent phase) needs stimulation to move to next phase
G1 phase- beginning of interphase checks if DNA is damaged and if the environment is favourable.
S phase checks for damage, incomplete replication
G2checks if DNA is damaged
81
What stimulation moves the cell out of the G0-quiescent phase w
can be though extracellular factors, signal amplification, signal integration/modulation, Ras/Raf/MEk/ERK, cMyc is an oncogene that induces expression of Cyclin D
82
What recognises damaged DNA in G1 phase
p53 recognises damaged DNA then its activated by protein kinases, p3 then binds to p21 gene and arrests the DNA
83
What are Cdks and how do they work
Cyclin dependent kinases (serine, threonine and tyrosine) are present in proliferating cells and are only active when bound to cyclin
phosphorylation activates Cdks and vice versa
allows signal amplification. diversification of multiple pathways and regulation.
84
How is cyclin produced and what is the cycle
cMyc produced Cyclin D, the cyclin can bind to make a Cyclin -Cdk complex. Protein kinases then phosphorylate Cdks but both the inhibitory sites through Wee1 and activating sites through CAK are phosphorylated.
Cdc25 phosphatase dephosphorylates the inhibitory site to activate the C-Cdk complex.
Active Cyclin-Cdk complex does two things (1) positively feedback to inactivate Wee1, (2) active Cdc25can phosphorylate the phosphatase to keep removing the inhibitory phosphate
85
How are cyclins degraded
Undergo ubiqitination where ubiquitin sticks onto cyclin part of Cyclin-Cdks complex and degrades it into amino acids
86
Cyclins are transient throughout the cell cycle explain its changes
Active Cyclin-Cdk complexes are active they stimulate the synthesis of genes needed for the next phase, the cyclins needed for next phase will rise before the triggering of the phase and usually finish before their phase ends (G2 is a little longer)
cMyc makes cyclin D which Cdk 4/6 binds (G1) , stimulates synthesis of Cyclin E - Cdk2 (G1 to S phase), CyclinA-Cdk2 ( S to start of G2), Cyclin B- Cdk1 ( end of G2 into M phase)
4/6,2,2,1
D,E,A,B
87
What protein causes the unusual white flash in children's eyes and how does it work
Rb- retinoblastoma- tumour suppressor abundant in all nucleated cells
if its missing or inactive then the cell cycle progresses when it shouldn't.
Active Rb makes TF in an inactive form (E2F-TF) so the cell cannot progress in the cycle as it inhibits DNA polymerase.
Activation of The G1-Cdk (cyclin D-Cdk4/6) and S-Cdk (cyclin E-Cdk2) complexes phosphorylates Rb so E2F-TF is released allowing cell cycle progression
E2F are needed because they regulate the expression of genes needed for G1 and S phases
88
What cell regulatory problems can cause cancer with examples
ONCOGENES
EGFR/HER2 and Ras can be mutationally activated leading to cancer
Cyclin D1 and C-Myc can be overexposed leading to tumours
TUMOUR SUPPRESSORS
Rb and p53 lead to loss of function mutations
89
What is the difference between lethal and sublethal injury
Lethal- cell death
| sublethal- produces injury, may be reversible or progress to cell death
90
What are the 8 causes of cell injury
```
Oxygen deprivation - myocardial infarction leading to ischaema
Chemical agents
Physical agents
Infectious agents
Immunological reactions
Genetic defects
Nutritional imbalances
Ageing
```
91
What does the cellular response to injury depend on and what do the consequences depend on
Cellular response to injury depends on type of injury, duration and severity
consequence of injurious stimuli depends on type of cell (might have a low metabolic requirement) and its status (if proliferating lots and injured might cause cancer)
92
What four intracellular mechanisms are vulnerable to cell injury
cell membrane integrity
ATP generation
Protein synthesis
Integrity of genetic apparatus
cellular function is lost before death so might look morphologically okay
93
What are the cellular adaptations, define and give an example of each
Hyperplasia- increase in number of cells in an organ e.g. physiological can be hormonal like replacing endometrium after menstruation, pathological can be excessive hormonal or grown factor stimulation like carcinomas
Hypertrophy - increase in cell size and organ size e.g. physiological- uterus gets bigger during pregnancy or inc muscle size in athletes, pathological- hypertension or inappropriate hormonal stimulation
Atrophy - shrinkage in cell size or organ as lose cell substance e.g. dementia or atrophy from denervation
Metaplasia - reversible change where adult cell type is replaced by another e.g. physiological change of the columnar epithelial cells to squamous due to acid pH of vagina, pathological Barretts oesophagus turns squamous cell in oesophagus to columnar
Dysplasia - precancerous cells which show the genetic and cytological features of malignancy, don't invade underlying tissue e.g. see big nuclei and raised nuclei to cytoplasm ratio, down cross basement membrane seen in barrettes oesophagus
94
What things are seen on the light microscope in response to reversible injury
Fatty change - alcohol fatty change - see holes of fat,
| Cellular swelling - ballooning regeneration - see large holes but strands of damaged cells cytoskeleton inside
95
What is necrosis and what four types are there
Necrosis: cell death associated with inflammation
1) Coagulative necrosis: Coagulative necrosis generally occurs due to an infarct (lack of blood flow from an obstruction causing ischaemia) and can occur in all the cells of the body except the brain.e.g. myocardial infarct, nuclei is between inflammation reaction: will see enucleated cells and lots of pink eosinophils
2) Liquefactive necrosis: Liquefactive necrosis can be associated from bacterial, viruses, parasites or fungal infections. Unlike coagulative necrosis, liquefactive necrosis forms a viscous liquid mass as the dead cells are being digested. tissue becomes liquified, cerebral infarcts see large white spaces: macrophages and neutrophils should be seen
3) Caseous necrosis :occurs when the immune system and body cannot successfully remove the foreign noxious stimuli. The immune system seals off the foreign matter by using fibroblasts and white blood cells such as lymphocytes, neutrophils, NK cells, dendritic cells and macrophages. A granuloma may form with fibroblast cells (which creates an encasing layer), leukocytes and the formation of Langhans giant cells (fusion of epithelioid cells). The organism is not killed but rather contained. cheesy, pulmonary TB will see granuloma
4) Fat necrosis:Fat necrosis does not denote a type of necrosis pattern. Instead, it is used to describe the destruction of fat, for example, due to pancreatic lipases that have been released into the surrounding tissues where the pancreas itself is at risk along with the peritoneal cavity. In acute pancreatitis will see white chalky areas in tissue, on slide basophilic (bluish) calcium deposits are present. Anucleated adipocytes with a cytoplasm that is more pink and contains amorphous mass of necrotic material. Inflammation would be present.
96
Difference between apoptosis, necrosis and necroptosis
Necrosis is associated with inflammation as cell membrane parts break off and lose integrity. Always associated with a pathological process
Apoptosis- programmed cells death with controlled inflammation or none as the membrane remains intact and killed. apoptosis may be physiological or pathological, is an ACTIVE ENERGY DEPENDENT process
Necroptosis- programmed cell death with inflammation e.g. due to viral infections
97
What are the causes of apoptosis
embryogenesis- separate fingers
Deletion of auto reactive T cells in thymus
Hormone dependent physiological involution- endometrium in periods
cell deletion in proliferating populations
Irreparable DNA damage
98
What is an osmole, what is osmolarity and what is tonicity
An osmole is on mole of fully dissociated substance dissolved in water
osmolarity is the concentration of osmoles in a mass of solvent - doesn't rely on cell permeability
tonicity is the strength of a solution and depends on cell membrane, permeability and composition of a solution
99
What are the three tonalities and explain
Hypertonic solution: osmolarity of the impermeant solutes on outside is greater than inside so water moves out and cell will shrink (higher osmolarity outside so water moves)
Hypotonic solution: osmolarity of impermeant solutes on inside is higher so water moves inside and the cell swells
Isotonic solution: osmolarity of impairment solutes are identical in and out of the cell so cell volume doesn't change
100
What are the main anions and cations in the body
Cations are Na+ and K+
| Anions are organic phosphates and Cl- as well as proteins
101
How are cell membranes maintained if there are different osmolarities
Na+/K+ ATPase maintains concentrations, low Na+ inside the cell as its pumped out this balances the osmolarity of impermeable solutes (proteins inside the cell with low Na+) with the extracellular osmolarity of impermeable solutes (high Na+)
102
How does the management of fluid composition help to preserve tissues
When a tissue loses its blood supply it becomes ischaemic. These changes can be slowed by cooling however, cooling can stop the Na+/K+ ATPase especially since no oxygen and ATP so a solution called Wisconsin solution is used
Wisconisn solution lacks Na+ or Cl- so there's no influx, There are extracellular impermeant solutes again stopping Na+from moving into the cell, presence of the macromolecule starch
103
Discuss the solute change across blood vessels
There are higher concentration of plasma proteins inside the capillary which generates osmotic pressure and moves solute and liquid inside
The flow of blood through the capillary generated hydrostatic pressure greater than the tissues and pushes molecules through capillary pores
In a normal capillary the hydrostatic pressure is slightly higher which results in net leakage
104
Difference between a normal capillary and a leaky capillary
In a normal capillary the hydrostatic pressure due to blood pressure will be slightly higher than the osmotic pressure which is caused by plasma protein. This results in a slight net loss
Leaky capillaries occur when the hydrostatic pressure is much higher than the osmotic pressure which means fluid will accumulate in the interstitial spaces. Could be due to an increased pore size in the capillary
105
How do lymphatic capillaries help with lost plasma fluids and hat happens if leakage of plasma exceeds the lymphatic capacity
Lymph fluid is picked ups by lymph capillaries, through lymph veins, then lymph ducts or lymph nodes which will then drain into a duct
If plasma leakage exceeds the lymphatic capacity then it will lead to oedema
106
What are the different causes of oedema
INFLAMMATORY OEDEMA Infections/ Inflammatory stimuli like bug bites making local blood vessels leaky and leading to wheal and flare reactions
HYDROSTATIC OEDEMA: individual has high blood pressure so increased hydrostatic pressure in vessels, pushes more fluid out of vessels which accumulated in interstitial fluid
COMPROMISED FUNCTION OF LYMPHATICS: breast cancer survivor may have had axillary nodes removed which may lead to oedema of that arm. In elephantiasis parasitic worms can block lymphatic vessels and stop drainage of the lymph
107
What is inflammation, why does it occur and what cells are raised during it
Protective process, removes damaged cells and clears threats which may be toxins or infections, occurs at any vascularised tissue
Occurs when cellular damage leads to DAMPS (damage associated molecular patterns) or the body recognises PAMPS (pathogen associated molecular patterns) This causes cells in damaged tissues to secrete signals and inside inflammation. change structure of blood vessels and use chemokine to recruit immune cells
Inflammation is associated with higher fluid and leukocyte numbers
108
What is inflammation
Protective process, removes damaged cells and clears threats which may be toxins or infections, occurs at any vascularised tissue
Occurs when cellular damage leads to DAMPS (damage associated molecular patterns) or the body recognises PAMPS (pathogen associated molecular patterns) This causes cells in damaged tissues to secrete signals and inside inflammation. change structure of blood vessels and use chemokine to recruit immune cells
Inflammation is associated with higher fluid and leukocyte numbers
109
What are the four signs of acute inflammation
redness
heat
swelling
pain
110
What is acute inflammation and what are the steps after damage to the cell
rapid, non-specific response to cellular injury
Damage to skin causes :
- inflammatory signals
- vasodilators released like histamine and NO
- vascular changes: higher permeability, dilation, reduced flow, plasma leakage : this can allow more cells to migrate, build a barrier between the site and the circulation called exudate
Immune cells are then recruited: chemokine produced and fiddles out to form a gradient, leukocytes which have complement chemokine receptors migrate to chemokine source
111
How does neutrophil extravasation work
1) chemo attraction : cytokines up regulate adhesion molecules called selectins
2) rolling adhesion: Carbohydrate ligands in a low affinity state on neutrophils bind to P and E selectin
3) tight adhesion: chemokine promote low to high affinity switch in the integrins LFA-1 and Mac-1 which enhance the binding to ligands like ICAM-1
4) Transmigration: Cytoskeletal rearrangement and extension of membrane mediated by PECAM
112
What is a neutrophils function at the site of inflammation
1) uses TLR4 and CD14 to identify lipopolysaccharides that are in gram positive bacteria
2) clear pathogens through phagocytosis (particles engulfed into phagosome which fuses with lysosome which has elastase and lysozyme to become a phagolysosome which reactive oxygen species and NADPH oxidase) or ketosis
3) cytokine secretion to recruit and activate other immune cells
113
What is the resolution of acute inflammation
1) pathogen are recognised by immune cells and antimicrobials
2) neutrophils have a short half life so inflammatory mediators are turned over
3) macrophages: clear apoptotic cells, produce anti-inflammatory mediators
4) repair wound/healing
114
What is an antigen and what are some types of antigens
A molecule or molecular structure that an antibody can recognise, any substance that your immune system can put an antibody on
Foreign antigen
Self antigen
Immunogen: antigen independently capable of driving an immune response
Hapten: small molecule that doesn't act as a antigen ut when bound to a larger molecule can create and antigen
115
What is chronic inflammation
There is a persistent inflammatory stimuli (e.g in Hep B or unclearable allergens or self antigens)
A distinct immune cell infiltrated of inflammatory macrophages, T cells and plasma (in acute its just neutrophils)
A vicious cycle as can't clear the inflammatory agent so release more inflammatory mediators. Bystander tissue destruction and concurrent repair processes
116
Why are macrophages and lymphocytes recruited and what are some properties of thrm
Macrophages can be recruited as monocytes to the site but are also tissue resident. Activated by IL-4 and IFN gamma. are cytotoxic, phagocytic, anti inflammatory, and assist in wound repair. However the cytotoxicity causes damage in surrounding tissues and can cause more recruitment of neutrophils, they are inflammatory and pro-fibrotic - they promote collagen to wound site but f can't then collagen builds up.
lymphocytes : T cells are pro inflammatory - stimulated by IL-17, TNF and FIN gamma) are cytotoxic as they have granzymes and perforin and are regulatory
B cells generate plasma cells that secrete antibody, are protective and clear infection: local to inflammatory site or operate remotely
117
What is the distinct inflammation pattern of chronic inflammation
Granulomatous inflammation
granuloma formation
aggregation of activated macrophages, triggered by strong T cell response
118
Differences between acute and chronic inflammation
Acute: immediate onset, vasodilation, vascular leakyness, neutrophils predominate, prominent necrosis, complete resolution or progresses
Chronic: delayed onset, persistent inflammation, ongoing injury with attempts of healing, monocytes and macroppahegs dominate, ongoing cytokine release, prominent scarring, can lose function
119
What are the outcomes of inflammation
Clear the inflammatory agent and remove damaged ells to restore tissue function
but there's excess tissue damage, scarring and loss of oxygen
wound heeling leads to deposition of collagen in extracellular matrix
120
What are the consequences of inflammation and in what tissues /conditions can this be a problem
Inflammation causing scarring
thin walls are replaced with cell filled areas so no gas exchange can take place. broncho-pneumonia
wound healing in sensitive tissues like the heart can cause organ failure
121
What is the difference between a histopathologist and cytopathologist
Histopathologis= tissues, examine architecture. works with biopsies, resection specimens, frozen sections, post-mortems
cytopathologist= cells -
122
What is a biopsy, how is it used, what stains are used and how long does it take
small sections of tissue that are preserved (cross linking of proteins) and put in wax, then cut in very thin sections
biopsies are used to make diagnosis, they can see if tissue is normal, if its inflamed, if its cancerous, see if there is a need for surgery.
Haemotoxylin and Eosin can be used to stain nuclei and cytoplasmic granules
Ziehl Neelsen stain will stain acid fast bacteria red (TB)
2-3 days
123
What is a resection
Taken from tissue that is removed from surgery, processed for biopsy.
Looks at stage of cancer, how its spread and if all has been removed
5-7 days
124
What are frozen sections
Taken during surgical procedures and examined by pathologists in real time during operation
frozen by cryostat machine, mounted on glass slides and stained for biopsies
can see if cancerous, if all cancer removed or if there's another pathological process going on.
30 minutes
125
Why are fine needle aspirates useful
Fine needle can get into a lesion and aspirate which can be analysed. Needle can access inaccessible tissues without surgery
can't comment on architecture but
126
What are antibody conjugates
Are manufactured antibodies that can be used to specifically bind molecules
can be attached to :
Enzymes
Fluorescent probes : can measure levels of the target molecule in a sample
Magnetic beads:
Drugs:
127
How antibodies can be used for diagnosis
Primary antibodies can directly detect antigen and have a label on themselves
Secondary antibodies are antibodies that are labelled and fins to primary antibody
Can be used in blood group serology, immunoassays and immunodiagposis
128
What is ELISA
In an ELISA assay, the antigen is immobilized to a solid surface. It is then probed with a specific antibody raised against the molecule of interest, The antibody is conjugated with a molecule that allows for detection such as an enzyme or a fluorophore.
129
What is Flow cytometry
Cells labelled with differently conjugated antibodies, cells run through a laser beam, the forward or side scatter denoted the identity of the cell as well as the size and granularity
130
What is KM and what does a low or high Km mean
The concentration of a substrate when it works at half its maximal velocity (VMAX)
useful as it can compare the strength of enzyme substrate complexes
low KM= tight strong binding of substrate to enzyme
high KM= weak binding - higher concentration needed to saturate
131
What is the Y and X intercept of an enzyme kinetics graph and the slope
X intercept= KM - KM is in substrate unitslike mM
Y intercept = 1/VMAX aka -VMAX : is conc per ml per min
Slope= Km/VMAX
132
What is the absorbance equation and what is V0 equation
conc= absorbance (slope)/ molecular absorbability of substance
conc is same as V0 even tho V0 is initial velocity of substance
133
How do competitive inhibitors and non competitive inhibitors of enzymes affect KM and VMAX
COMPETITIVE: KM increased as more are competing for the same site so will take longer to reach half VMAX, VMAX will be unchanged though as just add more substrate, will be a steeper graph that will cross the normal graph since x intercept closer to zero but y intercept is same
NON COMPETITIVE: KM unchanged as its not competing for the active site so binding of substrate is unaltered but inhibits enzyme function which leads to a lower VMAX, just a. steeper graph won't cross
134
What is the turnover number of an enzyme and what is the equation for this
Kcat: number of molecules that an enzyme can process in a given time
Vmax/ enzyme conc= turnover numbers
135
How do cancer cells spread to other tissues
Invasive cancer cells secrete proteases that enable them to degrade the extracellular matrix , proteases allow them to create new passageways in tissues by breaking down junctions and entering new cells
metastasis is when cancerous cells enter the blood stream or lymphatic system and travel to a new place to divide and make secondary tumours : to do this must be able to penetrate normal barriers of body to enter and exit lymph
136
What is a tumour
Mass forming lesion can be neoplastic or non neoplastic
137
What are neoplasms
autonomous growth of tissue which has escaped normal constraints on cell proliferation
can be benign or malignant.
If it is malignant then its cancer if it benign then it is not
138
What is a harmartomas
benign overgrowths of mature cell types
| architectural not cytological abnormalities
139
What is a heterotopia
normal tissue but in the wrong place
140
What is the benign and malignant version of tumours in squamous, glandular and transitional epithelium
and what is the benign and malignant version of lymphocytes and bone marrow
Oma means benign and sarcoma means malignant
Squamous- squamous papilloma and squamous cell carcinoma
Glandular- Adenoma and Adenocarcinoma
Transitional- transitional papilloma and transitional cell carcinoma
soft tissue - sarcoma
lymphocytes- lymphoma is malignant and benign are rare
Bone marrow- leukaemia is malignant and benign are rare
141
What is a teratoma
tumours from germ cells and contain tissue from all three germ layers
142
What are the differences between benign and malignant tumours
invasion: extension into adjacent connective tissue or structures
metastasis: spread via blood vessels to other parts
differentiation and growth pattern:how much the architecture resembles the structure of tissue from , tumours less well defined architecture than tissues
143
How do tumours spread
Direct extension: stromal response to tumour and causes fibroblastic or vascular proliferation
Haematogenous: via blood vessels usually venues and capillaries first and often leads to sarcomas
Lymphatic: via lymphatics to lymph nodes and beyond, spread according to their drainage- epithelial cancers
Transcoelomic: via seeding of body cavities - pleural and peritoneal cavities
Perineural: via nerves
144
How are tumour grade and stage described
T(tumour) : size or extent of local invasion
N(nodes): number of lymph nodes invaded
M(metastases):presence of distant metastases
TNM is the stage how far its spread
Grade is how differentiated the tumour is
Stage is more important than grade
145
What is the overall Main concepts of glycolysis and the TCA cycle
Glycolysis : the making of a high energy compound by using ATP and the the breaking of this compound to produce energy
TCA- transfer of the 2C acetyl CoA to an oxeloacetate to make citrate, decarboxylations and stepwise redox reactions to make cofactors and ATP, these cofactors are what's used to generate ATP later
146
How is the malate aspartate shuttle possible- main concept about enzymes
There is a mitochondrial and cytoplasmic version of the enzymes on both sides
malate dehydrogenase and aspartate transaminase
147
What make molecules lipophilic and keep Co-Q (ubiquinone) to the inner mitochondrial membrane
Isoprene units
