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MCM Final - First Year > Final Week 2 > Flashcards

Final Week 2 Flashcards

(104 cards)

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1
Q

What major restriction endonuclease is commonly used?

A

EcoRI

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2
Q

What is required for the ends of plasmids and DNA fragment to be “glued” together?

A

ATP and Ligase

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3
Q

What is agarose gel used for?

A

separates population of DNA or RNA molecules based on size

DNA is already charged

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4
Q

What is SDS-PAGE used for?

A

separate population of proteins based on size

Adds negative charge to every protein to open them up

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5
Q

What is used to pull out all mRNA from a cell to make cDNA?

A

Poly A tail with poly T-primer

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6
Q

What can PCR be used for?

A

amplifying genes

Used to detect altered genes or foreign DNA

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7
Q

What method is used in forensics?

A

Short tandem repeats PCR

CACCA or GTGTGT repeats

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8
Q

What change can be used to find mutations?

A

RFLPs

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9
Q

What can be used to determine variations in gene expression?

A

DNA microarray

More intense signal->higher degree of binding of probe->higher level of expression

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10
Q

What is the advantage of using QPCR?

A

analyzing PCR in real time. Analyze different genes in same sample.
Faster the fluorescence shows up the higher amounts of target DNA of cell sample being created.
Show how many copies are being made in a person vs only a pos/neg result

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11
Q

What is an epitope?

A

Specific site on antigenic molecule recognized by Fab

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12
Q

What does indirect Elisa detect?

A

Presence of Ab to specific antigen

HIV

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13
Q

What does sandwich elisa detect?

A

Detection and quantitation of an antigen
Troponin-1
Pregnancy - Hormone immunoassays

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14
Q

What does western blotting used for?

A

compare protein levels in samples

Monoclonal or polyclonal - level and size of products

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15
Q

what two enzymes are most commonly used with antibodies? What do the enzymes catalyze?

A

HRP and AP
HRP catalyzes the oxidation of substrates (DAB) by hydrogen peroxide and Brown precipitate is product
AP hydrolyzes phosphate group from substrate (BCIP/NBT) and gives off dark blue/purple product

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16
Q

What is proteomics used for? How?

A

Dont know what proteins are altered, look for unknown
Protein expression and/or alteration and post-translational modification

Isoelectric focusing used and then electrophoresis with 2D-DIGE. Scanned and then use Mass spectrometry to identify

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17
Q

How is mass spectrometry done?

A

Used to identify unknown proteins. Chops them up into pieces with tryptic digestion. Then ionization, detection method and computer data base with known protein sizes

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18
Q

What is competence?

A

capacity to respond to inductive signal

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19
Q

What is the structure of homeodomain proteins? What is the general function?

A

Helix-turn-helix and the homeobox is involved in the regulation of patterns of morphogenesis

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20
Q

What are paralogs?

A

Genes related by duplication within a genome, each with a different function

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21
Q

Describe Hox genes

A

Transcription factors
Role in craniocaudal segmentation of body
3’ to 5’ expression order
Lay out big pattern
Retinoic acid: acts through Hox genes and serves as intercellular signaling molecule that guides development of posterior portion of embryo
Mutations: loss- posterior->anterior
Gain - Anterior->posterior

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22
Q

What happens if there is too much retinoic acid?

A

Too much vitamin A causes posterior part of body to have issues - not form or major deformities

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23
Q

What are Pax genes?

A

TFs-homeodomain
Role in formation of tissues and organs; nervous system/sense organs, epithelial-mesenchyme transition
maintain normal function after birth

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24
Q

What is Aniridia?

A

Pax6 mutation

Complete or partial absence of iris

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25
What are Lim proteins?
TFs-homeodomain Some bind to DNA some to cytoplasm Involved in formation of virtually all body segments
26
What happens if there is an absence of Lim Proteins?
Headless
27
What are Dlx genes?
TFs-homeodomain Patterning of outgrowing appendages in early embryogenesis Morphogenesis of jaw and inner ear
28
What are Msx genes
TFs - homeodomain Prenatal- inhibit cell differentiation Postnatal-maintain proliferative capacity of tissue Face, limb epithelial-mesenchymal interaction in face and limbs
29
What are T-box genes
TFs | Mesodermal germ layer development and specifying whether limbs will be forelimb or hindlimb
30
What do basic helix-loop-helix genes regulate?
TFs that regulate myogenesis - muscle tissue
31
What are forkhead proteins?
TFs that regulate expression of genes involved in cell growth, proliferation, differentiation, and longevity. Pioneering transcription activity - bind condense chrromatin
32
What happens if there is a disorder in Foxhead gene?
Disorder in speech and language development
33
What is a zinc finger?
TFs with Cys and His linked to Zinc Regulate myogenesis, insert into DNA Bone, cartilage, and tooth development
34
What happens if there is a zinc deficiency (Zinc Finger)?
Skeletal growth retardation; osteoporosis
35
What happens if there is a mutation in the SOX?
Abnormal development of tissues, wide variety of signs and symptoms SOXA = SRY Reproductive developmental problems along with skeletal growth retardation
36
What is WTI?
Wilms' tumor suppressor gene Kidney and gonadal development Defect-urogenital abnormal
37
What is TGF-beta? Give an example
Transforming growth factor BMP - block the action of neural formation Regulatory molecules: noggin, chordin, WNT, FGF
38
What are FGFs?
Fibroblast GFs-lots of variation Angiogenesis, wound healing, embryonic development (limbs/brain) and various endocrine signaling pathways Closely associated with ECM and bind to heparan sulfate to activate
39
What are the three types of hedgehogs? What is the receptor?
Desert, Indian, and sonic | Patched (PTCH)
40
What is PTCH bound to?
Smoothened transmembrane protein (SMO)
41
What is the function of SHH?
Regulating vertebrate organogenesis, facial and limb patterning and organization of brain Remains important in adult by controlling cell division of stem cells
42
What is the function of IHH?
Chondrocycte differentiation, proliferation, and maturation
43
What is WNT?
They have different roles in different vertebrates Mammals - gastrrulation and organogenesis Interact with ECM and regulate cell-to-cell interactions during embryogenesis WNT->beta-catenin->nucleus->transcription of target genes
44
What happens if there is a PTCH mutation?
Tumor suppressor mutation - cant control SMO and then leads to basal cell carcinoma
45
FISH
Fluorescence in situ hybridization | Can be used to analyze presence and location of genes (cytogenetics)
46
What is a stem cell?
Primitive cell, either self-renew or give rise to more specialized cell types
47
Describe founder stem cells
Multipotent Defined compacity to divide/fixed # of FC populations Define the size of large final structures
48
What label is taken up by stem cells in S phase? Possible reasons as to why
BrdU label Maybe b/c slow rate of division or asymmetric segregation Retain all original DNA strands to preserve stem cell and prevent genetic errors *Immortal strand hypothessis
49
What happens with ESC are exposed to retinoic acid?
Become neurons
50
What happens when ESC are exposed to retinoic acid, insulin, and thyroid hormone?
Become adipocytes
51
What happens if ESC are exposed to Fibroblast growth factors and EGF and PGF?
Become astrocytes and oligodendrocytes
52
What gene regulatory proteins are currently being used to create SCNT cells?
Oct, SOX, Myc, KIF
53
What are iPS cells?
Adult stem cells induced to become pluripotent stem cells
54
What is derived from the ectoderm?
Attracto-derm = looks, eyes, smarts
55
What is derived from mesoderm?
Means-o-derm=place to place | Bone, muscle, mysenchemal, heart, blood
56
What is derived from endoderm?
endernal- lung, digestive, thyroid
57
What are the layers of the epidermis?
``` Basal lamina Basal cell layer Prickle cell layer Granular cell layer where nuclei are lost Keratinized squames ```
58
Olfactory neurons have cilia with what type of receptor for odors?
GPCRs
59
Odorant neurons can be replaced, how are new ones formed?
Odorant receptor proteins help axonal guidance and allow growth cone to migrate and establish connection with correct glomerulus
60
Describe the fetal hematopoiesis time line
1. yolk sac - creates BC's and ECs 2. AGM - HSC and ECs 3. Placenta 4. Fetal liver - 4m. AGM shuts down, placenta switch roles 5. Bone marrow - CMP, CLP 7m.
61
What are the two compartments of the bone marrow?
Vascular niche and endosteal niche
62
Describe the vascular niche
Adipose cells, fibroblast, stromal cells, vascular endothelial cells, macrophages, Blood vessels Provides maintenance, self-renewal and expansion of SCs Produce HGF and cytokines Barrier to prevent immature HC from leaving
63
Describe endosteal niche
Located enar bone surfaces where quiescent HSCs reside. Where bone is broken down and built
64
What is the purpose of marrow macrophages?
Remove apoptotic cells and residual nuclei from orthochromatic erythroblasts
65
What is osteopontin?
Glycoprotein produced by osteoblasts and has a negative effect on the number of HSCs
66
What is produced in the kidneys in response to hypoxia?
erythropoietin
67
What effects does erythropoietin have?
Increased proliferation of erythoid progenitor cells by decreasing levels of cell cycle inhibitors and increase cyclins and anti apoptotic proteins
68
What is leukopoiesis?
Formation of granulocytes and agranulocytes
69
Name the granulocytes
Neutrophil, eosinophil, basophil
70
Name the agranulocytes
Lymphocytes and macrophages
71
What is used to treat neutropenia?
G-CSF
72
What diseases can occur when there is a deficiency and excess of thrombopoietin?
Def: thrombocytopenia Excess: thrombocytosis
73
What is the function of Stem cell factor or C-Kit ligand?
Makes HSCs responsive to IL | Potential useful treatment of inherited/acquired disorders of hematopoiesis and BM transplants
74
What is the function of neutrophil?
Phagocytosis of bacteria and dead cells
75
What is the function of eosinophils?
Peroxidase and cationic proteins attack parasites and allergies
76
What is the function of basophils?
Peroxidase, histamine, kallikrein - hypersensitivity
77
What His is bound to the heme and is part of the symmetrical complex?
F8
78
Where does Oxygen dock on and off?
Between iron and E7 His
79
What subunits create Fetal hemoglobin?
a2g2
80
What subunits create adult hemoglobin?
HbA: a2b2 HbA2: a2d2
81
What is Thalassemia?
underproduction of chain Mainly Beta Rare to have alpha because there are 4 alleles
82
What is an important enzymes that creates NADPH and without it, RBCs would crash?
Glucose-6-dehydrogenase
83
What mutation occurs that causes sickle cell anemia?
``` #6 Valine is substituted for glutamic acid A hydrophobic for a hydrophilic Makes the hemoglobin polymerize because of stickiness = pole vaults ```
84
Where is iron absorbed?
duodenum
85
Describe how iron is absorbed
Fe3+ in intestinal lumen is converted to Fe2+ by Dcytb Then it enters enterocyte through DMT1 Iron exits enterocyte into blood via ferroportin and is changed back to Fe3+ by hephaestin. Transferrin transfers iron in blood
86
How is iron delivered to the place of heme synthesis?
Transferrin brings iron to BM and then to erythroid precursors mitochondria. Iron enters via DMT1 and is transformed to Fe2+ by Steap3
87
What is hereditary hemochromatosis?
Disease with iron overloading because Hfe gene is mutated. Hfe can not upregulate Hepcidin via SMAD pathway. Hepcidin cant then bind to ferroportin and internalize the protein
88
Why is B12 necessary for RBC DNA synthesis?
DHF is absorbed in the jejunum and is altered to form N5-Methyl FH4 This unusable form of folate will be stuck at this point (folate trap) if B12 is not around to accept the methyl group and then pass to homocysteine to create methionine. Final product with B12 is THF( the active form of folate) THF + serine -> N5,10, methylene-THF + dUMP ->dTMP which is used for DNA synthesis
89
What is used to figure out if macrocytic anemia is caused by B12 diet or absorption?
Schilling test
90
If the macrocytic anemia is not caused by malnutrition of folate or B12, what could be the genetic defect?
Intrinsic factor (Chr. 11) produced by parietal cells Pernicious anemia - autoimmune disease where Intrinsic factor or the parietal cells are attacked by self
91
Describe acute hepatic porphyrias
Neurological symptoms from inherited metabolic disorders
92
Describe erythropoietic porphyrias
Manifest primarily in skin creating photosensitivity due to inherited metabolic disorders
93
Where are hemoglobins broken down?
reticulo-endothelial system (spleen)
94
What is hepatitis?
Inflammation of the liver There is increased conjugated and Unconjucated BR in blood Yellow discoloration Urine-tea
95
What is cyanosis?
bluish/dark coloring of lips and skin
96
What pathway does erythropoietin use?
JAK/STAT
97
Iron is low, what type of anemia?
microcytic
98
How much oxygen do RBCs carry?
1.34 mL O2/g of Hb
99
What is oxygen capacity?
total amount of oxygen that can be carried in our blood ssuming every heme had O2 bound
100
What is the normal amount of RBCs?
15 g Hb/dl
101
What is oxygen content?
The amount of O2 actually being carried in our blood | Oxygen capacity X % saturation (oxygen availability)
102
What do RBC need ATP for?
Flexibility Ion-transport (ATPase) Maintain Fe2+ Prevent oxidation of Hb
103
What is polycythemia?
Excess RBC caused by either mutation receptor for thrombopoietin and BM is abnormal or Low O2 due to altitude (physiological) or lung/heart disease
104
What is methemoglobinemia?
Iron is in Fe3+ state and cant bind O2

MCM Final - First Year (2 decks)

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