Genome And The Cell Flashcards
1
Q
Which is the short arm and which is the long arm of the chromosome?
A
P is short
Q is long
2
Q
What are the 5 non coding DNA groups?
A
Non-translated RNA (micro RNA, long non coding RNA)
Chromatin binding sites
Transposons
Promoter and enhancer regions (for binding of transcription factors etc)
Special structural regions (centromeres, telomeres etc)
3
Q
What is euchromatin?
A
Actively transcribed area of chromosome
4
Q
What is heterochromatin?
A
Transcriptionally inactive part of the chomasome
5
Q
What is a nucleosome?
A
DNA wrapped around a histone core. 147bp to be specific.
6
Q
What are the 2 most common types of DNA variation in human?
A
Single nucleotide polymorphism and
Copy number variations
7
Q
What does the P stand for with regard to arms of a chromasome?
A
Petite. This is how you know it is the smaller arm. The Q arm is just named because it is next in the alphabet.
8
Q
What are the histone “marks” that impact DNA accessibility for transcription (i.e. euchromatin)?
A
Methylation, acetylation, phosphorylation, specific amino acid absence/presence
9
Q
What amino acids within histone are subject to methylation? What affect does this have on accessibility for RNA polymerase to transcribe DNA?
A
Lysines and arginines in histone can be methylated. Methylation of lysine residues can lead to either increased or reduced DNA accessibility depending on which residue is methylated.
10
Q
What amino acid residues within histone are subject to acetylation? What affect does this have on accessibility for RNA polymerase to transcribe DNA?
A
Lysine residues are acetylated by histone acetyltransferases. These, typically, open the chromatin for increased transcription. Histone deacteylases HDACs lead to condensation of chromatin and reduced transcription. HDACs are being targeted by cancer treatments as their overactivation (and so gene silencing) appears to be critical to cancer development.
11
Q
What amino acide residues with histone are subject to phsophorylation? What affect does this have on accessibility for RNA polymerase to transcribe DNA?
A
Serine residues can be modified by phosphorylation. Depending on which serine residues is phosphorylated will dictate whether this contributes to euchromatin or heterochromatin formation.
12
Q
Other than histone modification, what else can epigenetically effect the accessibility of DNA to RNA polymerase?
A
DNA methylation
13
Q
What is the effect of DNA methylation?
A
Transcriptional silencing. This a tightly regulated process.
14
Q
What do chromatin organising factors do?
A
Bind to noncoding regions and DNA to coordinate long range looping to bring promotor and enhancer regions together to influence transcription.
15
Q
How many sub componenets of histone are there?
A
8 - it’s an octamer. 9 if you count the H1 linker moleculres.
16
Q
Is this more likley to be euchromatin or heterochromatin?
A
Euchromatin. Acetylation of histone lysine residues is associated with the open chromatin state able to be transcribed. Selectly positioned lysine methylation, and selctly positioned serine phosphorylation can also contribute to the euchromatin state.
17
Q
Is this more likely to be euchromatin or heterochromatin?
A
Heterochomatin. Extensive methylation of histone lysine and arginine residues is consistent with a closed chromatin formation unable to be easily transcribed. Select phosphorylation of serine residues can also contribute to heterochromatin formation.
18
Q
Are histones positvely or negatively charged?
A
Positivley. This allows negatively charged DNA to stick to it.
19
Q
What steps are involved in the production of fucntional miRNAs?
A
Transribed from DNA to 1) Priamry miRNA.
Cleaved in the nucleus into 2) Pre-miRNA.
3) Exported out of the nucleus via export protein.
4) In the cytoplasm, trimmed by the protein ‘Dicer’.
5) Now miRNA at final length, associates with a protein complex known as RISC (RNA-induced Silencing Complex). RISC + miRNA can now bind to imperfectly matched mRNA in the cytoplasm to impair its translation at the ribosome, or perfectly matached RNA to cleave it.
20
Q
What happens when the RNA-induced Silencining Complex (RISC) + miRNA imperfectly binds to mRNA in the cytoplasm?
A
It causes the mRNA to be unable to be translated via ribosomes, so its corresponding gene is silenced.
21
Q
What happens when RNA-induced Silencing Complexes (RISCs) +miRNA bind perfectly to mRNA?
A
The RISC cleaves the target mRNA at the binding position, silencing the gene for which the mRNA was a transcript.
22
Q
What are siRNAs?
A
Small interefering RNAs. They are sequences that can be injected into cell cytoplasm to by trimmed by Dicer, then interact with RISC, experimentally, thus forming miRNA RISC complexes and gene silencing artificially.
23
Q
What is long non-coding RNA?
A
Recently discovered long transcripts of non-coding DNA that alters chromatin function amongs many other things. Best known clinically significant example is XIST - a long non-coding RNA (lncRNA) that inactivates the X chromosome as part of normal X-inactivation in females (complete gene silencing of one X chromosome). XIST is, interestingly, derived from the inactived chromosome but doesn’t cloak its own expression.
24
Q
What functions does long non-coding RNA have?
A
Gene activation - by facilitating transciption facotr binding
Gene suppression - by intercepting transcription factors and preventing them from binding to DNA.
Chromatin modification to indirectly impact transcription (image depicts two way this has been shown to occur - through direct aciton on methylases an acetylases, or through stabilisation of complet protein structures that allow chromatin changes).
25
What are CRISPRs? What is does Cas refer to?
Clustered, regularly interspaced, short palindromic repeats. (CRISPRs)
CRISPR associated genes (Cas)
-- the best known is CAS9, which is a nuclease, which brakes DNA of viral or plasmid invaders in prokaryotes.
26
What is the prokaryote physiological role the CRISPR Cas-9 combination?
In bacteria, CRISPRs are interpaced with sequences derrived from small broken parts of phage or plasmid DNA are inserted into the prokaryotic genome by a Cas1-Cas2 complex. This then allows the bacterial production of small targetting RNA based on the phage/plasmid specific spacers that complex with other Cas (e.g. 3, 9, 10) enzymes and are used to home in on the specific phage/plasmic DNA. The complexed Cas enzyme then destroys the DNA by cleaving it (they are nucleases).
27
How can the CRISPR-Cas 9 system be used for gene editing?
Artifical guide RNAs can be devloped to target sections of DNA to be cleaved, then complexed with Cas9. Cas9 will cleave the target sequence out of the DNA, in the same way that would to cleave and destroy an invading plasmid or phage.
28
What can CRISPR-Cas9 be used for?
1) Removal of phathogenic genetic material
2) Addition of genetic material - benefical therapeutically, of for investigation purposes in the lab.
29
Where are proteins destined for membrane bound status or secretion synthesised?
Rough endoplasmic reticulum and the golgi apparatus
30
What does smooth endoplasmic reticulum do?
Specifically, it used for the synthesis of steroid hormones and lipoprotines, as well as modification of hydrophobic compounds into water soluble compounds.
31
Where are proteins bound for the cytosol synthesised?
Free cytosolic ribosomes
32
What is the role of proteasomes?
They are protein complexes that degrade denatured or other proteins that have been tagged for destruction. The resulting protein products are displayed on MHC, and often can influence intracellular signalling pathwasys.
33
What is the role of lysosomes?
Lysosomes are intracelular packets of degradtive enzymes that fuse with endocytotosed components (e.g. microbes) to destroy them, but are also the site of intracellular organelle breakdown as part of normal cellular component recycling (autophagy). They contain enzymes that are capable of degrading a very large range of macromolecules.
34
What is the role of peroxisomes?
Intracellular packets of oxidative enzymes (e.g. catalase, peroxidase) important for the breakdown of very long chain fatty acids. They produce hydrogen peroxide in the process.
35
What are the key structural proteins intracellularly?
Filamentous actin (microfilaments)
Keratins (intermediate filaments)
Microtubules
36
What is meant by cell polarity?
The orientation of the cell relative to other structures. Critical for coordinated cell function to complete tasks like form a cell layer. Apical refers to the outer most surface. Basal is the deepest surface. Lateral are the other surfaces. Each surface requires the deployment of different proteins, so maintaining orientaiton/polarity with cytoskeletal structures (microtubules, microfilaments and kertatins) is critical.
37
What functions are completed within mitochondria?
Oxidative phosphoylation and ATP production
Production of metabolic intermediates
Syntesis of some macromoleculres (e.g. heme)
Contain important sensors for cell damage - the mitochondria can then responsd by initiating apoptosis.
38
What is the lifespan of a mitochondria?
10 days
39
What phospholipid heads are typically on the cytosolic surface of the bilayer?
Phosphatidyl-ethanolamine
Phosphadidyl-serine - important for maintaining the intracellular negative charge of the membrane.
40
What phospholipid bilayer components are typically on the extracellular face?
Glycolipids
Sphingomyelin
Phosphatidyl-choline
41
What phospholipid bilayer components are seen in the inner and out most layers about equally?
Cholesterols
Phosphatidyl-inositol
---when intracellular and phosphorylated, this forms an important intracellular signalling molecule scaffold. They can also hydrolysed intracellularly by phospholipase C to generate second signals like diacylglycerol and inositol triphosphate.
42
What happens to cells that have a lot of phosphatidylserine displayed extracellularly?
Phosphatidylserine is displayed almost entirely intracellularly in healthy cells. When displayed extracellularly, this is a signal of cell stress and attracts other sells to destroy them in a controlled way (e.g. phagocytosis).
43
What do glycosylphosphatidylinositols do?
GPIs link proteins to phospholipid bilayers extracellularly.
44
Which part of the phospholipid bilayer is negatively charged?
The inside.
45
What is caveolin?
It's a protein concentrated with lipid rafts that helps make calveolae along the outer surface along a phospholipid bilayer capable of endocytosing extracellular fluid, some membrane bound proteins, and some receptor bound moleculels. GPI-linked moleculres, cyclic adenosine monophosphate (cAMP) binding proteins, src-family kinases and the folate receptor are also required for calveolae formation. They can subsequently fuse with endosomes and/or recycle back to the membrane. This process referred to as caveolae (little caves) mediated endocytosis.
46
What is clatharin? What does it do?
It creates a coating of the internal surface of the phospholipid bilayed deep ot receptors on the external surface involved in receptor-mediated endocytosis. The clathorin allows for internalisation of the external components and endosome formation. Clatharin-coated pits require a protein called dynamin to release the new vesicle into the cytosol.
47
In receptor mediated endocytosis, how is the ligand released from the receptor in teh endosome to enable it to be used by the cell?
Endosomes become progressively more acidic which disturbs the attraction between the protein-based receptor and its ligand. Depending on the ligand, their are different passive and active ways of then moving the ligand out of the endosome. The receptors can then be recycled back to the membrane. Alternatively, the endosome can fuse with lysosomes which smash apart the receptor to get the ligand out.
48
What is the role of receptor-mediated endocytosis in down-regulation of receptors on cell surface?
For cell surface receptors that bind protein for endocytosis, the resultant endosome can be directed to fuse with lysosome which will destroy both the receptor and the ligand. The net outcome of this, unless there are counterregulatory pathways that coexist, is downregulation of the receptor pathway due to receptor destruction.
49
Do actin microfilamnets extend at their negative or positive end?
G-actin monomers noncovalently polymerase into F-actin (the polymer known as microfilament) that then intertwines to forma double stranded helices with a positive and negative end. New subunits are added to the positive end, and removed from the negative end. Sometimes called actin treadmilling.
50
How do actin filaments move in muscle tissue?
ATP driven hydrolysis of actin by myosin slides the actin filaments relative to one another leading to movement e.g. muscle contraction.
51
Do intermediate filaments move like microtubules and microfilaments?
No - they form a rigid structure to provide tensile resistence for other things to anchor to, and to provide strength to the cell so it doesn't break under force.
52
Do intermediate filaments interact in adjacent cells?
Yes, through structures called desmosomes. They stick together at these points forming a strong superstructure.
53
Why are intermediate filiments helpful for determining cell line of origin when looking at tumour tissue?
The have specific patterns depending on the cell of origin. These have different names.
E.g. Vimentin: in mesenchymal cells (like fibroblasts and endothelium)
Desmin: in muscle cells - forms the scaffold that actin and myosin sit on.
Neurofilaments: critical fo neuronal axon structure and confer boht stegnth and rigdity.
Glial fibrillary acid protein (GFAP) - is expressed in glial cells specifically.
Cytokeratins - expressed in epithelial cells - 30 subtypes specifically expressed in different tissues (lungs, GI epithelium etc).
Lamins - form the nuclear lamina, define nuclear shape and can regulate transcription.
54
What is vimentin, and where is it typically found?
It's a cytoskeletal structure belonging to the group known as a intermediate fibres. It is found in, and can be used to identify, mesenchymal cells, such as endotherlium and fibroblasts.
55
What is desmin and where is it found?
It's a cytoskeletal structure belonging to the group known as a intermediate fibres. It is found in, and can be used to identify, muscle tissue. It forms a scaffold for actin (a dynamic cytoskeletal rope) and myosin (an enzyme that manipulates and moves actin).
56
What are cytokeratins, and where are they found?
They are a cytoskeletal structures belonging to a group known as a intermediate fibres. There are over 30 subtypes of cytokeratins that are found in, and can be used to identify, a range of different tissues including lung and GI tract.
57
What is laminin and where are they found?
It's a cytoskeletal structure belonging to the group known as a intermediate fibres. It is responsible for the shape of cell nuclei, and can influence DNA transcription.
58
What is Glial fibrillary acidic protein?
It's a cytoskeletal structure belonging to the group known as a intermediate fibres. It is found in glial cells in the central nervous system and can be used to identify these cells.
59
List the three cytoskeletal protein components in order of size
Smallest
1) actin microfilaments 5-9nm across
2) intermediate filaments 10nm across
3) microtubules 25nm across
Largest
60
What are microtubules made of?
Proteins called alpha and beta-tubulin that are polymerised together.
61
Are microtubules active or passive structures?
Extremely active.
62
What are the characteristics of microtubules?
They are polarised (+/- ends)
The -ve end is embedded in the microtubule organiszing centre and is paired with centrioles.
The +ve end elongates or reced in response to stimuli be the addition or subtraction of tubulin dimers.
63
What is the role of microtubules in the movement of molecules and organelles inside a cell?
They are mooring lines for molecular motor proteins that use ATP to do work - translocate vescicles, organelles or other molecules around the cell. The most famous of these motor proteins are the kinesins (transport cargo anterograde - away from the nucleus - from the -ve to +ve ) and dyneins (tranpsort cargo retrograde, that is toward the nucleus, from the +ve to the negative end of the microtubule).
64
What are kinesins? What do they do?
Kinesins are motor protein complexes that associate with microtubules to transport other porteins, moleculres or organelles inside cells. They move typically in the 'anterograde direction' - that is from the negative to the positive end of the microtubule they are associated with. There counterpart dyneins moves in the other direction.
65
What is dynein? What does it do?
Dynein is a motor protein complex that associates with intracellular microtubules to tranport other proteins, organelles or moleculres around the cell. It does this by moving along microtubules in the retrograde (toward the nuclear) direction, from the positive end to the negative end of the microtubule. It's counterpart kinesinn moves in the other direction.
66
What is the microtubule organising centre?
The negative poles of all the microtubules in the cell are usually anchored in the MTOC. It's located near the nucleas and associated with paired centrioles.
67
What is the role of microtubules in mitosis?
They attach to the centromeres of chromatid pairs and rip them apart into chromatid sisters.
68
What role do microtubules have in cell motility?
They form a propellar in sperm, and the beating cilia in bronchial epithelium.
69
What is the primar cilia? What is it made of? What is it's role?
Critical to embryogenesis, the primary cilia is a single non-motile projection that helps the cell to orientate itself in space, and guide its proliferation and differentiation. The primary cilia is itself a microtubule.
70
What are the three basic types of cell junctions?
Occluding junctions (aka tight junctions)
Anchoring junctions
Communicating junctions (aka gap junctions)
71
What is the role of occluding junctions, and what proteins are involved?
Tight, or occluding, junctions create a continuous barrier that restricts the movement of ions or other molecules between cells. The formation of these tight meshlike structure is mediated by transmembrane protines including 1) claudin, 2) TAMPs (tight junction asscociated MARVEL proteins). These transmembrane proteins are attached intracellularly to scaffolding proteins from the 3) zonula occludens family (ZO-1/2/3) and another protein called 4) cingulin.
72
The transmembrane proteins claudin and TAMPs, as well as the intracellular family of proteins zonula occludens (ZO-1, ZO-2, ZO-3) and cingulin, are associated with what type of cell-cell interaction?
The formation of tight junctions, or occluding junctions.
73
What are the two types of anchoring junctions? What are their roles? What proteins are involved?
There are two types of anchoring junctions - adherens junctions, and desmosomes.
1) Adherins junctions are usually closley associated with and just beneath tight junctions. They are formed by the coming together or transmembrane adhesion moleculres called cadherins. The cadherins are attached intracellularly to actin microfilaments and can directly affect cell chape and motility. Notably cadherin expression is lost in many cells allowing them to metastasise.
2) desmosomes tend to form closer to cell basal poles. They also involve cadherin-actin transmembrane proteins to link together cell cytocskeletons allowing mechanical force to be spread across cells. Hemidesmosome is the term given to a desmosome that binds cell cytoskeleton to extracellular matrix (ECM) rather than another cellls cytoskeleton. The proteins that connects the hemidesomsome to ECM are called integrins.
74
What is the role of integrins?
Transmembrane proteins that allow the binding or actin microfilaments (intracellularly) to intermediate filaments making up the extracellular matrix.
75
What is the role of cadhesins?
Transmembrane proteins that allow the formations of adherens junctions and desmosomes between two cells - sites that allow anchoring of cells to one another and the conversion of mechanical force from each cell into chemical intracellular signalling.
76
What are communicating junctions? What is their role? What are the key proteins?
These allow the diffusion of chemical or electrical signals between adjacent cells via pores formed by arrays of transmembrane protein complexes called connexons (formed by the protein connexin).
They are critical to allowing multiple cells to act as one large cell, such as occurs with the mycocardium.
77
What is the site of synthesis for all transmembrane protein and lipids? As well as the initial site of secreted protein synthesis?
The endoplasmic reticulum. Not the further processing in the golgi apparatus is required for secreted proteins.
78
What is the endoplasmic reticulum (ER) stress response?
Excess misfolded proteins left in the ER leads apoptosis.
79
How do some RNA molecules get directed to the ER for synthesis there?
They are initially translated by free ribosomes, but specific N-terminus sequences initially translated then direct the protein to the ER where it finishes translation. Free ribosomes and rough endoplasmic ribosomes complete the translation and deposit the protein into the ER.
80
What protein embeds into the intracellular vesicles that contain malfunctionoing or senescent proteins and organelles to indicate that they require destruction?
LC3 - may just epiphenominal but can be stained an observed to monitor or measure intracellular autophagy. Autophagosomes fuse with lysosomes to degrade their contents.
81
What is the role of ubiquitin?
Via ubiquitin ligases E1/2/3, cytosolic misfolded proteins are tagged with ubiquitin which directs them to the proteosome for destruction.
82
What is the role of the golgi apparatus?
It's like an assembly line of vesicles that modify proteins from the endoplasmic reticulum for eventual secretion from the cell or use inside cell organelles. Proteins move from one vesicle to another undergoing stepwise modifications until they are ready. Ths is referred to as cis (from close to the ER) to trans (close to the plamsa membrane) progression - or cisternal progression.
83
What cells is the golgi apparatus easiest to see in?
Cells that specialise in secretions - e.g. plasma cells, goblet cells, intestinal cells, bronchial epithelium.
84
What is the SER doing? It doesn't have ribosomes, so what does it do?
It 1) manfuactures vesicles for moving things around in the cell. It's particularly prominent in cells that secrete 2) steroid hormones - non-protein related. You'll see it clearly in the gonadal cells, the adrenals or hepatocytes. It's also responsible for 3) the catabolism of some drugs - e.g. phenobarbitol. It also 4) sequesters intracellular calcium (recall that the SER is full of calcium) to ensure the calcium gradient remains.
85
What does massose-6-phosphate (M6P) do? Hint: something to do with lysosomes.
Mannose-6-phosphate (M6P) is a tag that can be added to proteins. This occurs to all the nucleases, proteases, lipasies, glycosidases, phosphatases and suflatases destined for lysosomes. M6P tagging is done within the golgi apparatus, and allows binding to the M6P receptor in lysosome membranes, allowing them to be transported into the lysosome.
86
How many membranes do mitochondria have?
2
87
How does oxidataive phosphorylation work?
Protons are pumped out of the mitochondrial core matrix into the transmembrane space by the oxidation of various metabolites (e.g. glucose). This allows the flow of protons down their electrochemical gradient back into the core matrix via an H+/ATPase transporter producing ATP.
88
How many ATP molecules can be produced by 1 glucose molecule via oxydative phophorylation?
36-38
89
What does uncoupling protein 1 (UCP-1) do to oxidative phosphorylation in brown fat?
UCP-1 uncouples the electron tranport chain from the proton pump, leading to no production of ATP from the chain, with energy instead being released as heat.
90
How can mitochondria lead to cell death?
They can be involved in necrosis of apoptosis.
Necrosis: cellular injury from toxins, ischaemia or trauma can damage the mitochondrial membranes, leading to loss of the proton gradient required for ATP production, which leads to necrotic cell death.
Apoptosis: so called intrinsic apoptosis is mitochondria dependent. They synthesise signals for and against apoptosis and then trigger a all or nothing response ('go' or 'no go') to commence apoptosis. If proapoptotic signals are dominant, the 'go' is given by the mitochondria by rapidly increasing their membrane permeability by producing MOMP (mitochondrial outer membrane permeabilisation proteins). Cyt C is secreted amongst other things into the cytoplasm. Nuclear cell death protocols are activated via CASPASEs.
91
What is a MOMP?
Mitochondrial outer membrane permeabilisation protein. When the accumulation of pro-apoptotic signals reaches a threshold, and overcomes antiapoptotic signalling, the mitochondria produce lots of MOMP, which allows the escape of cytochrome C amongst other intramitochondrial proteins.
92
How do hormone bound intracellular hormone receptors exert effects on cells?
Directly penetrate the nucleus together and act as a transcription factor for select genes.
93
How do notch receptors influence change on cell function?
Notch receptors have and intracellular and extracellular domain joined across the plasma membrane. They bind their counterpart notch ligand on another cell via the extracellular domain. When bound, the extracellular part is snapped off, and this releases the intracellular domain free into the cytosol. It traffics to the nucleus and acts directly as a transcription factor.
93
What happens upon binding of ligand to a g-protein coupled receptor?
The GPCR associates with intracellualr gunosine triphosphate binding protiein (G-protein) which contains GDP. This association leads to phosphorylation of GFP to GTP. This leads to the generation of cAMP and inositiol - 1,4,5-triphosphate (IP3). The latter triggers calcium release from ER.
93
What steps are involved in receptor tyrosine kinase influence on growth?
Tyrosine kinase receptors dimerise upon binding of ligand. This brings together the intracellular tyrosine kinase domains which causes them to phosphorylate each others tyrosine residues. This leads to intracellular binding to inactive GDP-bound RAS, allowing the GDP to become GTP and activating RAS. Activated RAS interacts with RAF. This then phosphorylates MAP kinase, which phosphorylates other porteins and nuclear transcriptoin factors that culminate in a suite of growth promoting gene activation.
93
What was Src that the kinase family was named after?
Rous sarcoma virus.
94
How does the Wnt/Frizzled receptor system work?
Receptor specific to wnt receptor extracellular domains becomes bound. Conformational change of wnt leads to association with frizzled, which recruits another intracellular protein called dishevelled, which releives intracellular beta-catenin from a protein complex that usually consituitively inactivates it using ubiquitin tagging. With dishevelled impairing this complex, beta-catenin is then free to traffic to the nucleus and exert transcriptional effects.
94
What are the two types of tyrosine kinase? What are their features?
Receptor tyrosine kinase RTK - bound to transmembrane receptor on the intracellular surface an dimerise on receptor-ligand binding.
Non-receptor bound tyrosine kinase - NRTK. These are tyrosine kinases that are summoned to intracellular receptor domains after they have become bound to their ligands. An important family of these is the Src -family kinases. They have Src homology domains (SH1-3) - SH2 binds uniquely to proteins that have already been phosphorylated by other kinases and allow the aggregation of multiple enzymes. SH3 binding mediates other protein-protein interraction involving proline rich sequences.
94
How many times to g-protein coupled recepotrs span the membrane?
7 times. Often referred to as serpentine receptors.
95
What proportion of the human population needs to have the same single nucleotide polymorphism for it to be formally named a "SNP"?
1%
95
What is a haplotype?
A collection of SNPs that convey a certain phenotype at a specific genetic loci
95
Draw the the key downstream actions when GPCRs after ligand binding?
G protein GDP->GTP
->cAMP protuction -> IP3 production -> calcium release from ER.
96
What is linkage disequalibrium?
The concept that some SNPs are coinherited with disease causing genetic material, but are not involved in the disease causing process. The SNP can therefore be used for detecting the inheritence of pathogenic genes in this case.
97
BRCA1 is what?
Protein producing gene that has an important role in DNA repair, transcription regulation, and apoptosis.
98
What is the prevalence of BRCA1?
About 1/500
99
What increased risk does BRCA1 convey for breast cancer?
5x the risk of the background population.
100
What are the enzymes responsible for DNA methylation?
DNA methyltransferases.
101
What is G0 in the cell cycle?
Resting. No t replicating.
102
What is G1 in the the cell cycle?
Reproduction of internal cellular contents prior to mitosis. Centromeres double here. Checkpoint here. No duplication of nuclear material yet.
103
What are the primary regulator proteins of the cell cycle?
Cyclins and cyclin dependent kinases (CDK)
104
Where does CDK1 act?
G2 to M phase
105
What are the water hydrated gels of the ECM?
Prteoglycans and hyaluronan - provide compressive resistance and lubrication
106
What are the adhesive glycoproteins of the ECM?
Laminins and fibronectin - connect elements to one another.
107
What are the fibrous structures of the ECM made of?
Collagens! Functional and important things.
108
What cytoskeletal structures can be studied to determine the likelihood of an epithelial cancers invasiveness/liklihood to metastisise?
Cadherin expression. But also tight junction protein expression. These are both down regulated prior to metastasis to release the cell from those around it and allowing it to metastasise.
109
What does RAS mutation lead to?
Constituative activation of the growth factor receptor -> RAS (or PI3K -> AKT -> mTOR) -> RAF-> MAPK. Practical application of this is that EGFR receptor blockade can't be used as a treatment in pancreatic ductal adenocarcinoma or colorectal cancer if RAS mutations are present.
110
Other than mesenchymal cells, what cells contribute to the production of the basement membrane?
Epithelial cells superficially, mesenchymal cells deep.
111
What do epithelial growth factor and TGF-alpha have in common?
They bind to an overlapping set of receptors.
112
Where do epithelial growth factor and tumor growth factor alpha receptors normally reside?
Epithelial cells, but also
Hepatocytes and fibroblasts
113
What types of receptor are EGF family receptors?
Epithelial growth factor receptors are intrinsic tyrosine kinase receptors.
114
What cancers are EGFR1 (aka EGFR) receptors thought to play a key oncogenic role?
Lung, head, neck, breast and brain.
115
EGFR1 has been successfully targeted as an oncogene in lung and other cancers. What is EGFR2 better known as? What cancer is it treated in?
HER2 - human epidermal growth factor receptor. Breast cancer.
116
What is the role HGF? Hepatocyte growth factor.
Mitogen effect on many cell lines - hepatocytes, epithelium everywhere. It also a morphogen (accelerates cell type differentiation) and promotes cell migration.
117
What is the receptor for hepatocyte growth factor? HGF
MET receptor
118
What type of receptor is the MET receptor?
Intrinsic tyrosine kinase heptocyte growth factor receptor.
119
What cancers are MET receptors typically overexposed in?
Renal and thyroid papillary carcinoma. MET inhibitors have been developed.
120
Platelet derived growth factor are released by what?
Platelets in cytoplasm granules when they are activated, but also activated macrophages, endothelial cells, and smooth muscle cells.
121
Where do the 5 PDGF isoforms act?
On PDGF receptors alpha and beta.
122
What types of receptors are PDGF alpha and beta receptors?
Intrinsic tyrosine kinase receptors.
123
What cell types are PDGF receptor tyrosine kinases typically found physiologically?
Fibroblasts, smooth muscle cells and endothelium. PDGF is important to wound healing after injury.
124
What is vascular epithelial growth factor's (specifically VEGFA) physiological role?
It binds to VEGF receptors and promotes angiogenesis. It also, with the other VEGFs, plays an important role in maintaining unusual endothelium like the fenestrations at the GBM.
125
What is the role of VEGFB and PlGF (placental growth factor)?
Embryonic vessel development
126
What is the role of VEGF-C and VEGF-D? Compared with VEGF-A (typically referred to as VEGF).
Lymphogenesis AND angiogenesis.
127
What most strongly inducer of VEGF production?
Hypoxia
128
VEGF and its receptors are implicated in pathogenic angiogenesis. What treatments target this pathway?
Anti vegf abs are used as part of chemotherapy regimens and to treat wet AMD. Though no treatments are available for pre-eeclampsia, soluble VEGF1 receptor levels appear to be elevated in this condition.
129
Fibroblasts growth factors, of which there are at least 20, typically reside where?
In the extracellular matrix- they act when the tissue is damaged.
130
Where are the fibroblasts growth factor receptors? What type of receptor are they?
Endothelium, smooth muscles bone marrow. Tyrosine kinase receptors. Enable angiogenesis and haematopoeisis when tissue is injured.
131
TGF-beta via its action on TGF-beta receptors does what primarily?
It has counteracting effects in tissue, but! In general, it's role is to reduce inflammation and promote scar formation. It reduces lymphocyte proliferation and is considered a key regulatory molecule.
132
What are the two basic forms of extracellular matrix?
Interstitial matrix and basement membrane.
133
What synthesises interstitial matrix?
Mesenchymal cells
134
What's the difference between fibrillar and non-fibrillar collagen?
Non-fibrillar collagen makes shorter mesh like polymers. Most notably collagen IV, a non-fibrillar collagen makes, up the mesh like structure of basement membranes. Fibrillar collagen forms long fibres that form large 3d structures that support in between cells.
135
What are then non-aqueous components of interstitial matrix?
Fibrillar and nonfibrillar collagens. Fibronectin, elastic, proteoglycans, hyaluronate.
136
Apart from collagen IV, what other proteins are a critical component of basement membrane?
Laminins. These can interact with receptors of cells adjacent to the basement membrane and trigger intracellular signalling cascades. Proteolgycans are also there.
137
What are the three families of extracellular components?
Fibrous structural proteins - e.g. collagen and elastic - strengthen and protect.
Water hydrated gels - lubricate and cushion. Proteoglycans and hyaluronic acid.
Adhesive glycoporteins - connect ECM elements together and to cells.
138
What strengthening step that happens to fibrillar collagen is vitamin C critical for?
Cross linking for wound healing. The enzyne lysyl hydroxylase is Vit C dependent and is responsible for collagen cross linking.
139
What are the two proteins most responsible for the elasticity of tissues that expand and contract? What is the significance of Marfan's syndrome here?
Elastic fibres are a core of elastin with a fibrillin mesh surrounding them. Fibrillin gene is mutated in Marfan's disease. This, plus the fibrillins affect onf TGF-beta's availability, is the reason for the Marfan phenotype.
140
What substances are primarily responsible for the spongey shock absorbing nature of joint tissue?
Proteoglycans bound to a hyaluronan (hyaluronic acid polymer) core. Proteoglycans form a negative charge which attract positive ions (mostly sodium) which pulls water into a mesh/gel like structure. Cartilage is the combination of collagen, proteoglycans and hyaluronan.
141
The adhesive glycoprotein fibronectin is typically located where?
Interstitial extracellular matrix
142
The adhesive glycoprotein laminin is located where?
The basement membrane (ECM).
143
What is the role of ecm fibronectin?
It can bind to cell integrins, as well as to other ECM components (collagen, fibrin, heparin, prtoeoglycans), to form a scaffold for wound healing and angiogenesis.
144
What is the role of laminin; the most abundant protein in basement membranes?
It connects cells to the extracellular matrix, but can also influence and modulate cell proliferation, differentiation and motility.
145
What does CAM stand for? What type of CAM is an integrin? What are some other types of CAMs?
Cell adhesion molecule. Integrins are CAMs between ECM and cells. Integrins also bind cell-cell adhesive functions (e.g. integrin-ICAM binding during neutrophil rolling). Other CAMs include cadherins and immunoglobulin like adhesion molecules.
146
What occurs during G1 of the cell cycle?
Increased production of cellular components in preparation for mitosis. Centrosome duplication.
147
What is the meaning of the g1 restriction point?
The cell is committed to progressing to G2 after this point.
148
Where are the 2 checkpoints in the cell cycle?
Between G1 and S phases, and between G2 and M (mitosis) phases.
149
What is CDK (cyclin dependent kinase) activity dependent on?
The quantity of corresponding cyclin in the cell. The phosphorylation activity of CDKs is proportionate to the availability of their cyclin correlate which complexes with the CDK to allow it to act.
150
Which cyclin/CDKs regulate the G1 to S transition? How do they do it?
Cyclin D and E both increase in concentration leading to the formation of more Cyclin D-CDK4/6 and E-CDK2 complexes which lead to increased phosphorylation of their target- Rb->pRb. This is the key step in transitioning from G1 to S phase.
151
Which cyclins and CDKs chaperone the cell cycle through the S phase of the cell cycle?
Increased concentrations of Cyclin A leads to increased cycling A-CDK2 and A-CDK1 complexes which increases phosphorylation of their targets.
152
Which cyclins/CDKSs regulate the G2/M checkpoint of the cell cycle?
Increased cyclin B concentration leads to increased Cyclin B-CDK1 complex formation and activity phosphyrlating targets relevant to commencing mitosis.
153
How is the cell cycle halted when issues are discovered during one of the phases?
CDK inhibitors (the 'p' proteins) are produced in large quantities. These prevent CDK activity from reaching the thresholds required to allow the cycle to pass through its checkpoints and usually causes p53 mediated apoptosis.
154
What is the role of the G1-S checkpoint?
Assessing existing DNA integrity before commiting to DNA replication
155
What is a totipotent stem cell?
A cell that can prolfierate into any cell type in a human. Only seen during embryology.
156
What is the role of the G2-M checkpoint?
Ensuring the duplicated DNA was accurate before commiting to cell devision
157
What is the Warburg effect? How is utilised by cancer cells?
The Warburg effect (also known as AEROBIC glycolysis) refers to glycolysis in the cytoplasm being preferentially used for the generation of ATP over oxidative phosphorylation in the mitochondria DESPITE the presence of O2. This takes place when there is an abundence of glucose (i.e. when glut transporters are maximally expressed in a glucose abundant microenvironment). The Warburg effect is observable for cells that are replicating in the G1 phase, as abundent glycolysisis is essential to allow for the mass production of glucose intermediates that are necessary for the duplication of cytosolic components and organelles prior to S, G2 and M phases of the cell cycle.
Cancer cells take advantage of the Warburg effect by using it continuously to sustain continuous growth. For cancer cells, it also provides a level of protection from impending hypoxia with the mass accumulation of aneorbic metabolism substrates should growth rate outstrip angiogenesis. Lastly, it leads to the production of excess lactate, lowering tumour microenvironment pH which preferentially impacts the function of immune cells and so aids in tumour protection from the immune system.
