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USMLE1 - Biochemistry > 2. Cellular Biochemistry and Lab Techniques > Flashcards

2. Cellular Biochemistry and Lab Techniques Flashcards

6
Q

how is entry into cell cycle phases regulated?

A

by cyclin CDK complexes

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7
Q

T/F the concentration of cyclins vary with each cell events

A

FALSE! The concentration of CDKs vary with cell cycle events

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8
Q

what is the order of cell cycle phases? what happens in each phase?

A

Mitosis then Interphase (G1, S, G2); in G1 is presynthesis phase, S is synthesis phase (DNA rep. etc), G2 is premitotic (making of MT spindle etc)

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9
Q

What goes on with G0 cell cycle phase?

A

cells that are stable go in and out of the G1 to G0 which is the stable/quiescent (can go into replication but dont) type of cells; cells that stay in G0 are permanent and can not enter G1

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10
Q

name two proapoptotic/tumor suppressor genes. how do they each act?

A

p53 and Rb; p53 activates BAX which inhibits BCL2 when there is DNA damage, Rb phosphorylation allows progression into S phase

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11
Q

what are permanent cells? which cells are permanent?

A

cells that stay in G0 and cannot replicate- instead they regenerate from stem cells; neurons, skeletal and cardiac muscles, and RBCs

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12
Q

what are stable/quiescent cells? which cells are stable?

A

they can enter G1 from G0 and replicate if they like; hepatocytes, lymphocytes, fibroblasts

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13
Q

what are labile cells? which cells are labile?

A

cells that never got into G0 and divide rapidly with a short G1; bone marrow, gut epithelium, hair follicles, skin

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14
Q

what dictates whether a cell will regenerate or repair after inflammation?

A

1) if it is stable/labile or permanent 2) intact BM and 3) intact ECM

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15
Q

where are secreted proteins synthesized? where are cellular/organellar proteins synthesized?

A

RER; free ribosomes

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16
Q

what is a nissl body?

A

RER in nucleus (synthesize NTs)

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17
Q

Which cell types have a high level of RER?

A

mucus secreting goblet cells, ab secreting plasma cells, nt secreting neurons

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18
Q

what functions are completed in the SER?

A

steroid synthesis and detoxification

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19
Q

which cells are rich in SER?

A

adrenal cells (steroid synthesis), hepatocytes (p450 detox)

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20
Q

T/F the golgi apparatus adds N linked oligosaccharides to proteins

A

False- the RER does; golgi apparatus modifies N linked oligosaccharides added on asparagines in the RER

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21
Q

T/F the RER adds O linked oligosaccharides to serine and threonine residues on proteins

A

False- the golgi apparatus does; RER adds N linked oligosaccharides to asparagines

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22
Q

how does an enzyme know to go to lysosome?

A

by addition of mannose 6 phosphate to proteins in the Golgi

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23
Q

which vesicular trafficking protein takes vesicles from the Golgi to the ER (retrograde)?

A

COP I

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24
Q

which vesicular trafficking protein takes vesicles from ER to the Golgi (anterograde)?

A

COP II

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25
Q

what vesicular trafficking protein takes proteins from the Golgi to lysosomes? in between the golgi? from the plasma membrane to endosomes (receptor mediated endocytosis)?

A

all clathrin

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26
Q

what type of disease is I cell disease? what is deficient?

A

a lysosomal storage disease; mannose 6 phosphate can not be added to lysosomal proteins

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27
Q

what causes the pathology in I-cell disease? what does I cell sidease

A

the lack of lysosomal proteins (are secreted- default from RER!) results in macromolecules accumulating in lysosomes- inclusions cause pathology

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28
Q

what are the clinical symptoms that result from I cell disease?

A

coarse facial features, psychomotor retardation, clouded corneas, restricted joint movement, high plasma levels of lysosomal enzymes

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29
Q

what are the functions of Microtubule proteins?

A

a cytoskeletal protein, apart of flagella, cilia, mitotic spindles and transport (in neurons for example)

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30
Q

What are cilia made of ?

A

MT!

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31
Q

what are flagella made of?

A

MT!

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32
Q

what is the structure of Microtubules?

A

cylindrical made up of a helical array of polymerized alpha and beta tubulin dimers, each dimer has 2 GTP bound

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33
Q

T/F there are 2 GTP per MT

A

false! there are 2 GTP per tubulin dimer!

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34
Q

what are the two molecular proteins that are used on MT for transporting in neurons? which direction do they go?

A

dynein- retrograde, kinesin- anterograde

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35
Q

which antihelminthic drugs act on microtubules?

A

mebendazole and thiabendazole

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36
Q

which antifungal acts on MT?

A

griseofulvin

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37
Q

Which anticancer drugs act on MT? how are they different?

A

vincristine, vinblastine, and paclitaxel; the vinca alkaloids block formation of the spindle and paclitaxel prevents breakdown of the mT spindle

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38
Q

which antigout drugs act on MT?

A

colchine

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39
Q

which syndrome results from microtubule polymerization defect? what are the clinical features?

A

Chediak Higashi Syndrome; decreased phagocytosis results in recurrent pyogenic infections, partial albinism, and peripheral neuropathy

40
Q

what is the cilia structure? what provides fluidity and motility of the cilia structure?

A

9+2 9 pairs of microtubules connected by an axonemal dynein ATPase in a cylinder with 20 MTs in the center; the connecting ATPase allows bending and differential sliding

41
Q

in what syndrome are their immotile cilia? why?

A

Kartaganer’s aka ciliar dyskinesia; lack of dynein arm ATPase

42
Q

where are cilia found? what symptoms are associated with kartageners syndrome?

A

in the reproductive tract and in the resp tract; infertility, bronchiectasis and recurrent sinusitis, associated with situs inversus

43
Q

what are the three main cytoskeletal elements?

A

actin/myosin, MT, intermediate filaments

44
Q

what does actin/myosin participate in?

A

microvilli, muscle contraction, cytokinesis, adherens junctions

45
Q

Which intermediate filament is found connective tissue? muscle? epithelial cells? neuroglia? neurons? what can intermediate filaments be used for?

A

vimentin, desmin, cytokeratin, glial fibrillary acidic protein (GFAP), neurofilaments; to differentiate between different cells

46
Q

T/F the plasma membrane is asymmetric

A

TRUE

47
Q

T/F the plasma membrane is 50% cholesterol, 50% phoshpolipids

A

TRUE

48
Q

what are the types of lipids found in the plasma membrane?

A

phospholipids, sphingolipids, glycolipids

49
Q

T/F low cholesterol prevents fluidity of plasma membrane

A

false- high cholesterol

50
Q

T/F cis unsaturated fatty acids interact with each other and decrease fluidity and increase melting temperature

A

false- long saturated fatty acids do this

51
Q

name a few intermediate filament defects. hints: alcohol, 2 neuro dx

A

damaged “ubiquinated” cytokeratin intermediate filaments build up in hepatocytes, damaged neurofilaments in idiopathic parkinsons disease build up to form Lewy bodies, Neurofibrillary tangles are build up of neurofilaments in alzheimers

52
Q

on which side of the cytoplasm is the ATP site in the Na+K+ ATPase pump? is a phosphorylated pump active or inactive?

A

cytoplasmic side; active

53
Q

which drug blocks the Na+K+ pump by blocking the K+ site?

A

Ouabain

54
Q

How do digoxin and digitoxin work? what class of drugs are they?

A

inbit Na+K+ ATPase; Cardiac glycosides

55
Q

what is the effect of the Cardiac glycosides?

A

indirect inhibtion of the Na+/Ca+2 exchange resulting in increased intracellular calcium which increases cardiac contractility

56
Q

what is the most abundant protein in the body? from what cell type is it made? how many types are there? where is it found (generally)?

A

collagen; fibroblasts; 4; ECM

57
Q

where is type 1 collagen found?

A

Bone, Skin, Tendon, dentin, fascia, cornea, late wound repair

58
Q

what is type II collagen found?

A

cartilage (including hyaline), vitreous body, nucleus pulposus

59
Q

where is type III collagen found?

A

reticulin, skin, blood vessels, uterus, fetal tissue, early phase of granulation tissue

60
Q

where is type IV collagen found? to what protein is bound? what is special about this type? how do the different types of collagen differ?

A

BM; laminins; most flexible; different aa composition

61
Q

what is the order of collagen synthesis- just the terms of the intermediate forms?

A

preprocollagen, procollagen, tropocollagen, collagen

62
Q

what is the main aa composition of collagen? what other 2 aa are common?

A

glycine; proline and lysine

63
Q

what is the first step of collagen synthesis? 2nd step? 3rd step? 4th step? where do all these steps occur?

A

formation of the alpha chains out of glycine, lysine, proline in the RER to make preprocollagen; hydroxylation of the proline and lysine residues in the RER; glycosylation of the lysine residues to make procollagen which is triple helix of alpha chains created by disulfide bonds between glycosylations; exocytosis

64
Q

what happens outside the fibroblast to procollagen?

A

proteolytic processing (of water soluble parts to less soluble) to turn into troprocollagen and then crosslinking between hydroxylated lysine residues by lysyl oxidase to make collagen fibrils

65
Q

what does cross linking to collagen do? what does this have to do with age?

A

make it stiffer/more tensile; continues as we get older so gets less and less elastic

66
Q

what cofactor is required of preprocollagen hydroxylation?

A

vit C

67
Q

what cofactor is required for lysyl oxidase cross linking? what reaction is required beforehand for crosslinking to occur?

A

Cu; hydroxylation

68
Q

what syndrome is characterized by hyperextensible skin and joints, and bleeding? what is the most common reason? what are other clinical symptoms?

A

Ehler Danlos; type III collagen def; joint dislocation, berry aneurysm, ecchymoses, organ rupture

69
Q

What is the most common cause of Osteogenesis Imperfecta? what is the inheritance pattern?

A

type I collagen; AD

70
Q

what are five clinical features seen in Osteogenesis Imperfecta?

A

multiple bone fractures, blue sclerae, hearing loss (abdnormal middle ear bones!), dental imperfections, retarded wound healing

71
Q

what is the reason for blue sclerae in Osteogenesis Imperfecta?

A

thinned cornea from lack of connective tissue so see underlying choroidal lens

72
Q

what is the defect that causes Alport’s Syndrome? what is the most common inheritance pattern? what are the three mc clinical presentations?

A

type IV collagen defect; X linked recessive; hereditary glomerulonephritis, deafness, ocular disturbances

73
Q

what is elastin? how is it different from collagen? where is it found? how is it broken down?

A

a fibrous protein (ie produced by fibroblasts); it has lysine and proline but nonglycosylated; arteries, lungs, elastic ligaments, vocal cords, ligamenta flava (connect vertebrae); broken down by elastase which is inhibited by alpha 1 antitrypsin

74
Q

name two diseases that have to do with elastin; discuss their pathogenesis.

A

marfans and emphysema; marfans is a fibrillin protein defect, fibrillin is a supporting protein in tropoelastin scaffolding and results in aorta, skeletal and eye defects; emphysema is due to a deficiency in the function of alpha 1 antitrypsin

75
Q

what is the pathogenesis of Goodpasteurs syndrome? what are the main targets?

A

Abs against type IV collagen; pulmonary and glomerular capillaries

76
Q

what is the pathogenesis of skurvy? name some clinical symptoms.

A

prolonged deficiency of Vitamin C results in decreased tensile strength of collagen because lack of hydroxylated lysines to crosslink (hydroxylation required vit C); bleeding gums, bone pain, poor wound healing, hemarthroses, glossitis, hemorrhages

77
Q

polymerase chain reaction (PCR)- name an application for it

A

genotyping for mutant alleles (different sizes)

78
Q

describe the three steps of PCR

A
  1. denature by heating 2. during cooling anneal with DNA primers 3. elongation- add heat stable DNA polymerase 4. repeat
79
Q

what is the purpose of the PCR?

A

to amplify a specific desired fragment of DNA

80
Q

how would one use a PCR to id an RNA virus?

A

do an RT PCR (reverse transcriptase)- RT the RNA first, then PCR the DNA

81
Q

after the PCR reaction, how do you actually visualize the DNA?

A

do agarose gel eletrophoresis to separate the different sizes of the PCR products (sizes id the the fragment)

82
Q

what are the three types of blotting procedures ? what are blotting procedures used for? what are steps in a blotting procedure?

A

Southern- DNA, Northern- RNA, Western- Protein; blotting procedures are used to detect a specific nucleic acid or aa sequence; the sample is electrophoresed and then transferred to a filter which is then soaked in a denaturant and then a radiolabeled probe complementary to what you are trying to detect recognizes and anneals, double stranded piece is then visualized when filter is exposed to film

83
Q

what is a microarray and what is it used for?

A

a piece of glass or silicon chip with thousands of grids with different nucleic acid sequences and DNA or RNA probes are hybridized to the chip and a scanner detects the complementary binding; used to study a persons genome and to detect snps (single nucleotide polymorphisms)

84
Q

what is an ELISA? what are the two ways to perform it? what is the sensitive and specificity? give a relative clinical example.

A

testing for antigen-antibody reactivity; can either add an antibody to a persons blood sample to see if there is binding or add an antigen to a persons blood sample to see if there immune system recognizes it; close to 100% for both; HIV eliza- an HIV antigen is added to a persons blood and tested to see if they have anti HIV Abs

85
Q

What does FISH stand for? What is it used for? Give an example.

A

Flourescent DNA/RNA IN SITU hybridization; for visualization of anomalies (like microdeletions) that are too small to be seen on karyotype; Prader-Willi syndrome

86
Q

What are the two different ways you can insert genes into transgenic mice for experiments?

A

constitutive- random insertion of gene into mouse genome; conditional- targeted through homologous recombination

87
Q

What does the Cre-lox system allow in Gene expression modifications?

A

can inducibly manipulate genes at specific developmental points

88
Q

what is RNAi? and how is it used in gene expression modification?

A

double stranded RNA is created that is complementary to the mRNA of interest and when inserted into cells the strands separate and attach to the mRNA preventing it from being translated

89
Q

in what stage of the cell cycle must cells be in order to be analyzed for karyotyping? and from what fluids can you draw the cells? and for what is karyotyping is used for?

A

metaphase (all lined up); blood, bone marrow, amniotic fluid, placental tissue; used to diagnose chromosomal abnormalities (deletions, trisomies, sex chromosomal disorders)

USMLE1 - Biochemistry (6 decks)

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