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MCM Final - First Year > Final Week 2 > Flashcards

Final Week 2 Flashcards

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
Q

What are Lim proteins?

A

TFs-homeodomain
Some bind to DNA some to cytoplasm
Involved in formation of virtually all body segments

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26
Q

What happens if there is an absence of Lim Proteins?

A

Headless

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27
Q

What are Dlx genes?

A

TFs-homeodomain
Patterning of outgrowing appendages in early embryogenesis
Morphogenesis of jaw and inner ear

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28
Q

What are Msx genes

A

TFs - homeodomain
Prenatal- inhibit cell differentiation
Postnatal-maintain proliferative capacity of tissue
Face, limb epithelial-mesenchymal interaction in face and limbs

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29
Q

What are T-box genes

A

TFs

Mesodermal germ layer development and specifying whether limbs will be forelimb or hindlimb

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30
Q

What do basic helix-loop-helix genes regulate?

A

TFs that regulate myogenesis - muscle tissue

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31
Q

What are forkhead proteins?

A

TFs that regulate expression of genes involved in cell growth, proliferation, differentiation, and longevity. Pioneering transcription activity - bind condense chrromatin

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32
Q

What happens if there is a disorder in Foxhead gene?

A

Disorder in speech and language development

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33
Q

What is a zinc finger?

A

TFs with Cys and His linked to Zinc
Regulate myogenesis, insert into DNA
Bone, cartilage, and tooth development

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34
Q

What happens if there is a zinc deficiency (Zinc Finger)?

A

Skeletal growth retardation; osteoporosis

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35
Q

What happens if there is a mutation in the SOX?

A

Abnormal development of tissues, wide variety of signs and symptoms
SOXA = SRY
Reproductive developmental problems along with skeletal growth retardation

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36
Q

What is WTI?

A

Wilms’ tumor suppressor gene
Kidney and gonadal development
Defect-urogenital abnormal

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37
Q

What is TGF-beta? Give an example

A

Transforming growth factor
BMP - block the action of neural formation
Regulatory molecules: noggin, chordin, WNT, FGF

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38
Q

What are FGFs?

A

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

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39
Q

What are the three types of hedgehogs? What is the receptor?

A

Desert, Indian, and sonic

Patched (PTCH)

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40
Q

What is PTCH bound to?

A

Smoothened transmembrane protein (SMO)

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41
Q

What is the function of SHH?

A

Regulating vertebrate organogenesis, facial and limb patterning and organization of brain
Remains important in adult by controlling cell division of stem cells

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42
Q

What is the function of IHH?

A

Chondrocycte differentiation, proliferation, and maturation

43
Q

What is WNT?

A

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
Q

What happens if there is a PTCH mutation?

A

Tumor suppressor mutation - cant control SMO and then leads to basal cell carcinoma

45
Q

FISH

A

Fluorescence in situ hybridization

Can be used to analyze presence and location of genes (cytogenetics)

46
Q

What is a stem cell?

A

Primitive cell, either self-renew or give rise to more specialized cell types

47
Q

Describe founder stem cells

A

Multipotent
Defined compacity to divide/fixed # of FC populations
Define the size of large final structures

48
Q

What label is taken up by stem cells in S phase? Possible reasons as to why

A

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
Q

What happens with ESC are exposed to retinoic acid?

A

Become neurons

50
Q

What happens when ESC are exposed to retinoic acid, insulin, and thyroid hormone?

A

Become adipocytes

51
Q

What happens if ESC are exposed to Fibroblast growth factors and EGF and PGF?

A

Become astrocytes and oligodendrocytes

52
Q

What gene regulatory proteins are currently being used to create SCNT cells?

A

Oct, SOX, Myc, KIF

53
Q

What are iPS cells?

A

Adult stem cells induced to become pluripotent stem cells

54
Q

What is derived from the ectoderm?

A

Attracto-derm = looks, eyes, smarts

55
Q

What is derived from mesoderm?

A

Means-o-derm=place to place

Bone, muscle, mysenchemal, heart, blood

56
Q

What is derived from endoderm?

A

endernal- lung, digestive, thyroid

57
Q

What are the layers of the epidermis?

A 
Basal lamina
Basal cell layer
Prickle cell layer
Granular cell layer where nuclei are lost
Keratinized squames
58
Q

Olfactory neurons have cilia with what type of receptor for odors?

A

GPCRs

59
Q

Odorant neurons can be replaced, how are new ones formed?

A

Odorant receptor proteins help axonal guidance and allow growth cone to migrate and establish connection with correct glomerulus

60
Q

Describe the fetal hematopoiesis time line

A
  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
Q

What are the two compartments of the bone marrow?

A

Vascular niche and endosteal niche

62
Q

Describe the vascular niche

A

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
Q

Describe endosteal niche

A

Located enar bone surfaces where quiescent HSCs reside. Where bone is broken down and built

64
Q

What is the purpose of marrow macrophages?

A

Remove apoptotic cells and residual nuclei from orthochromatic erythroblasts

65
Q

What is osteopontin?

A

Glycoprotein produced by osteoblasts and has a negative effect on the number of HSCs

66
Q

What is produced in the kidneys in response to hypoxia?

A

erythropoietin

67
Q

What effects does erythropoietin have?

A

Increased proliferation of erythoid progenitor cells by decreasing levels of cell cycle inhibitors and increase cyclins and anti apoptotic proteins

68
Q

What is leukopoiesis?

A

Formation of granulocytes and agranulocytes

69
Q

Name the granulocytes

A

Neutrophil, eosinophil, basophil

70
Q

Name the agranulocytes

A

Lymphocytes and macrophages

71
Q

What is used to treat neutropenia?

A

G-CSF

72
Q

What diseases can occur when there is a deficiency and excess of thrombopoietin?

A

Def: thrombocytopenia
Excess: thrombocytosis

73
Q

What is the function of Stem cell factor or C-Kit ligand?

A

Makes HSCs responsive to IL

Potential useful treatment of inherited/acquired disorders of hematopoiesis and BM transplants

74
Q

What is the function of neutrophil?

A

Phagocytosis of bacteria and dead cells

75
Q

What is the function of eosinophils?

A

Peroxidase and cationic proteins attack parasites and allergies

76
Q

What is the function of basophils?

A

Peroxidase, histamine, kallikrein - hypersensitivity

77
Q

What His is bound to the heme and is part of the symmetrical complex?

A

F8

78
Q

Where does Oxygen dock on and off?

A

Between iron and E7 His

79
Q

What subunits create Fetal hemoglobin?

A

a2g2

80
Q

What subunits create adult hemoglobin?

A

HbA: a2b2
HbA2: a2d2

81
Q

What is Thalassemia?

A

underproduction of chain
Mainly Beta
Rare to have alpha because there are 4 alleles

82
Q

What is an important enzymes that creates NADPH and without it, RBCs would crash?

A

Glucose-6-dehydrogenase

83
Q

What mutation occurs that causes sickle cell anemia?

A 
#6 Valine is substituted for glutamic acid
A hydrophobic for a hydrophilic 
Makes the hemoglobin polymerize because of stickiness = pole vaults
84
Q

Where is iron absorbed?

A

duodenum

85
Q

Describe how iron is absorbed

A

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
Q

How is iron delivered to the place of heme synthesis?

A

Transferrin brings iron to BM and then to erythroid precursors mitochondria. Iron enters via DMT1 and is transformed to Fe2+ by Steap3

87
Q

What is hereditary hemochromatosis?

A

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
Q

Why is B12 necessary for RBC DNA synthesis?

A

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
Q

What is used to figure out if macrocytic anemia is caused by B12 diet or absorption?

A

Schilling test

90
Q

If the macrocytic anemia is not caused by malnutrition of folate or B12, what could be the genetic defect?

A

Intrinsic factor (Chr. 11) produced by parietal cells

Pernicious anemia - autoimmune disease where Intrinsic factor or the parietal cells are attacked by self

91
Q

Describe acute hepatic porphyrias

A

Neurological symptoms from inherited metabolic disorders

92
Q

Describe erythropoietic porphyrias

A

Manifest primarily in skin creating photosensitivity due to inherited metabolic disorders

93
Q

Where are hemoglobins broken down?

A

reticulo-endothelial system (spleen)

94
Q

What is hepatitis?

A

Inflammation of the liver
There is increased conjugated and Unconjucated BR in blood
Yellow discoloration
Urine-tea

95
Q

What is cyanosis?

A

bluish/dark coloring of lips and skin

96
Q

What pathway does erythropoietin use?

A

JAK/STAT

97
Q

Iron is low, what type of anemia?

A

microcytic

98
Q

How much oxygen do RBCs carry?

A

1.34 mL O2/g of Hb

99
Q

What is oxygen capacity?

A

total amount of oxygen that can be carried in our blood ssuming every heme had O2 bound

100
Q

What is the normal amount of RBCs?

A

15 g Hb/dl

101
Q

What is oxygen content?

A

The amount of O2 actually being carried in our blood

Oxygen capacity X % saturation (oxygen availability)

102
Q

What do RBC need ATP for?

A

Flexibility
Ion-transport (ATPase)
Maintain Fe2+
Prevent oxidation of Hb

103
Q

What is polycythemia?

A

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
Q

What is methemoglobinemia?

A

Iron is in Fe3+ state and cant bind O2

MCM Final - First Year (2 decks)

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