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Flashcards in MCM Final Deck (170):
1

This protein sorting pathway is used for proteins destined for cytosol, mitochondria, nucleus, and peroxisomes

Cytoplasmic

2

This protein sorting pathway synthesizes proteins destined for the ER, lysosomes, plasma membranes, and for secretion

Secretory pathway

3

What is the protein sorting signal that, when present, destines proteins for the cytoplasm

> Trick question. No sorting signal for this destination.

4

What is the protein sorting signal that, when present, destines proteins for the mitochondria

A hydrophobic alpha helix

5

What is the protein sorting signal that, when present, destines proteins for the nucleus

Terminal Lys/Arg repeats

6

What is the protein sorting signal that, when present, destines proteins for the lysosome

M6P

7

What is the protein sorting signal that, when present, destines proteins for a secretory vesicle

Trp rich domain (absent of retention motifs too)

8

What is the protein sorting signal that, when present, destines proteins to stay in the ER

KDEL

9

What disease is caused by a defect in the enzyme required to tag proteins with an M6P signal?

I cell disease. Proteins (hydrolases to be specific) that should be sent to the lysosome are instead packaged for export from the cell and this causes release of harmful enzymes into the blood. Yikes.

10

Proteins sent to the mitochondria are recognized by what mitochondrial membrane transporters?

TIM and TOM

11

How are unfolded proteins protected in the mitochondria?

Binding to chaperones does the trick (HSP70 specifically)

12

How do nuclear proteins enter that membrane bound organelle?

Via specific nuclear pores

13

Large proteins destined for the nucleus require a nuclear localization signal which includes four basic residues. Which amino acids are present here?

Lys, Arg

14

Name the segment of a protein synthesized for secreting that binds ER targeting signal and then the ribosome during translation

Signal recognition particle

15

What is used to tether the ribosome/mRNA/peptide complex together (also causes temporary halt in translation)

Signal recognition particle (SRP)

16

Where do proteins undergo post-translational modifications?

ER or Golgi

17

When a protein contains an ER localization signal, that signal binds the SRP which will then bind what on the RER membrane?

SRP receptor protein

18

What confirmation will small proteins spontaneously assume

Native conformation

19

What could happen when large proteins fold without the help of chaperones

Aggregation or proteolysis

20

What is the term for a protein containing a barrel shaped compartment that admits unfolded proteins and catalyzes their folding? Does this require ATP?

Chaperonins, yes it is ATP dependent

21

What is the post translational process that converts inactive forms to active enzymes

Proteolytic cleavage

22

What are the 3 possible post translational protein modifications

Glycosylation, phosphorylation, disulfide bond formation

23

What post translational modification Occurs on extracellular proteins only

Glycosylation

24

What post translational modification can be either O linked or N linked

Glycosylation

25

What amino acids serve as binding sites for an O linked glycosylation of a protein post translationally

hydroxyl group of Ser or thr

26

What amino acids serve as binding sites for an N linked glycosylation of a protein post translationally

Amino group of Asn

27

What type of bond is formed with the addition of a glycosidic post translational modification

Ester

28

Disulfide bonds form between what functional group of cysteine residues?

Thiol (-SH)

29

Formation and reorganization of disulfide bonds occurs where

ER lumen

30

Beta cells of the pancreas produce what 20 residue peptide?

Preproinsulin

31

Preproinsulin has its signal peptide cut off in the ___ to form proinsulin

ER

32

How many intramolecular disulfide bridges form within insulin's structure

2

33

Insulin moves past the golgi before accumulating in what for storing?

B granules

34

Proinsulin is cleaved twice to release a residue called what?

C peptide

35

Mature insulin is stored in granules as a hexamer bound to what cofactor

Zinc

36

Mature insulin is made of an A and B chained linked together by what?

2 disulfide bridges

37

Most abundant structural protein in vertebrates? (Hint it is heterotrimeric)

Collagen

38

What post translational modification activates procollagen

Hydroxylation of lysines at the 5' end and prolines (and later it can be glycosylated)

39

What coenzyme is necessary for lysyl and prolyl hydrolases required to activate collagen?

Ascorbic acid (vitC)

40

Each gene occupies a specific place in the genome known as what

Locus (plural loci)

41

The function of what structure is to temporarily hold together 2 daughter DNA helices after replication and serves as attachment site for microtubules during division

Centromere

42

Repeated nucleotide sequences at the two ends of a chromosome essential for stability

Telomere

43

This word. Refers to an. Entire set of chromosomes from a. Single cell

Karyotpe

44

How many pairs of human chromosomes are autosomes

22 pairs (and we have 1 pair of sex chromosomes)

45

Term for 2 Identicle chromosomes join at a centromere

Chromatids

46

This substance is sometimes used to detect the amount of circulating insulin in assays (it can even distinguish between hypoglycemic disorders due to islet cell tumors and infusion of exogenous insulin)

C peptide

47

a mendelian term meaning that two genes are inherited separately from one another: the inheritance of one does not increase or decrease your chances of inheriting the other

law of independent assortment

48

what are the 3 genetic mechanisms of disease and examples of each

loss of function: dystrophin, duchenne MD
gain of function: oncogenes causing cancer
protein alteration: sickle cell anemia

49

what do you call the first person diagnosed in a pedigree? (usually denoted by an arrow)

proband

50

what term do you use to describe that males have only 1 X chromosome? (This is why X linked disorders show up far more frequently in men)

hemizygous

51

whats an example of an X linked dominant disease where phosphorus and calcium in blood is very low due to wacky reabsorption in kidneys

hypophosphatemia

52

the frequency at which a gene manifests itself

penetrance

53

range of phenotypes that vary between individuals with a specific genotype

variable expressivity

54

term describing a single disorder (or any trait) caused by mutation in genes at different chromosomal loci

locus heterogeneity

55

with mutations in collagen genes (could occur in chromosome 7 or 17) we obtain brittle bones and this condition is called what? what process is responsible for the fact that this disease can be caused by mutation at multiple different loci?

osteogenesis imperfecta, locus heterogeneity

56

When binding proteins and enzymes depart from a site of crossing over (during prophases I) the structure that is left where maternal and paternal chromosomes have exchanged parts is called what?

Chiasma

57

Homologs being to pair in prophase I of meiosis and form a 4 chromatid structure called what?

A bivalent

58

What event occurs at the chiasma?

Crossing over

59

Homologs are joined by what protein complex to hold them together during crossing over?

Synaptonemal complex

60

There is a small region of homology between the X and Y chromosome called what? This allows them to pair during meiosis

Pseudoautosomal region

61

What are events that increase genetic diversity in offspring

Random assortment, crossing over

62

A Y chromosome directs the genital ridge to develop into what adult structure

Testis

63

How/Why are all womens technically mosaics?

Half of the cells in a woman's body inactivate the paternal X chromosome and the other half of the cells inactivate the maternal X.

64

What does it mean when a gene is "imprinted"?

Methylated (down regulation)

65

How many possible gametes can be produced from two parents thanks to random distribution of homologues

2^n = 2^23 = 8.4x10^6

66

When homologues fail to properly separate (common during egg development and increase with maternal age)

Nondisjunction

67

What meiotic deficiency is the leading cause of spontaneous abortion and mental retardation in humans?

Nondisjunction

68

Cells with an abnormal chromosome number are referred to as what? Cell with a normal number of chromosomes are called what?

Aneuploid, euploid

69

When in cell division is nondisjunction most likely to occur for an oocyte?

Meiosis I

70

Because male gametes undergo more mitotic cell divisions, they are more susceptible to what?

mutations

71

If the paternal chromosome 15 is deleted the child will develop what anomaly?

Prader willi syndrome

72

If the maternal chromosome 15 is deleted the child will develop what anomaly?

Angelman syndrome

73

What two. Equations are necessary to determine a value using hardy weinberg principle?

p2 + 2pq + q2 = 1
p + q = 1

74

What does consanguinity mean? Why is this a bad thing?

"Blood relation"
We use this to describe mating with a relative (incest) and it is more likely to produce offspring affected by rare autosomal recessive disorders

75

What is the difference between the terms plolygenic. And multifactorial?

Polygenic- trait determined by many genes

Multifactorial- environmental factors cause variation

76

In multifactorial diseases, what threshold must be crossed before the disease will be expressed?

Threshold of liability

77

Females have a higher risk threshold and therefore require more risk genes before developing what condition?

Pyloric stenosis (hypertrophy between stomach and duodenum)

...side note: because women need more genes before expressing the phenotype, affected women are more likely to pass the trait on to offspring than affected men!

78

Random evolutionary process that produces large changes in gene frequency especially in a small population

Genetic drift

79

When a population begins form a small group of individuals who mate within the population, we see a special case of genetic drift known as what?

Founder effect (albinism in Panama is an example)

80

The RNA sequence produced from transcription is identicle (except for C's and U's) to which strand of DNA

Coding strand

81

What is the purpose of a complementary hairpin near the 3' end of a gene just before the polyU tail

It releases the newly synthesized strand from RNApol

82

What are the start and. Stop sequences of the genetic code??

Start- AUG
stop- UAA, UAG, UGA

83

Drug that binds 30S subunit of bacterial Ribosome to disrupt translation initiation

Streptomycin

84

Drug that binds 60S subunit of Ribosome to disrupt translation elongation

Shiga toxin

85

Drugs that binds 50S subunit of bacterial Ribosome to disrupt translocation of the ribosome

Clindamycin, erythromycin

86

Drug that binds 30S subunit of bacterial Ribosome to disrupt translation elongation

Tetracycline

87

What provides energy for assembly of the initiation complex to begin translation

GTP hydrolysis

88

What lab tests are used to diagnose Zika in the first 7 days of infection for individuals with symptoms

PCR of urine, serum, or saliva

89

What lab test would you use to diagnose Zika 2-12 days after onset of symptoms

Sandwich ELISA with anti-Zika IgM

90

These signaling molecules bind a promoter with a specific DNA binding domain plus a transactivating domain (binds RNA pol II) activating or inhibiting a gene

transcription factor

91

transcription factors can independently regulate the same gene in different tissues by binding to separate ___ for that gene?

enhancers

92

the capacity to respond to an inductive signal (such as a transcription factor signal during development)

competence

93

growth and differentiating factors are part of what family of signaling molecules essential to development? They are proteins (ligands) secreted by a cell and diffuse a short distance to interact with other cells.

paracrine signalling

94

60 amino acid helix turn helix DNA binding domain that is used to classify transcription factor family

homeodomain

95

the DNA sequence used to encode a homeodomain is a "homeobox" and homeobox containing genes are known as what?

HOX genes

96

genes that are related by duplication within a genome are called what? they evolve in function over time.

paralogous

97

this gene family plays an important role in caudo-cranial segmentation of the developing body

HOX genes

98

HOX genes are activated and expressed from 3' to 5'. genes found at which end of the coding region are expressed earlier and more ANTERIORLY in the developing organism

3'

99

HOX genes are activated and expressed from 3' to 5'. genes found at which end of the coding region are expressed later and more POSTERIORLY in the developing organism

5'

100

Which set of genes is complexly regulated and primarily is concerned with setting up segmental structures along the main body axis

HOX

101

what is the major regulator of HOX genes?

retinoid acid (vitA)

102

1) when HOX genes are mutated and upregulated (gain of function), what kind of malformation ensues?
2) when HOX genes are mutated and down regulated (loss of function), what kind of malformation ensues?

1) anterior to posterior transformation
2) posterior to anterior transformation

103

each gene in this gene family contains a 128 AA paired domain which binds DNA and plays critical role in formation of tissues and organs during embryo development

Pax genes

104

this pax gene disorder is characterized by complete or partial absence of the iris (PAX6 mutation)

aniridia

105

this pax gene is involved in making proteins that develop the eyes, CNS, and pancreas. when mutated, aniridia ensues

Pax6

106

this large family of homeodomain proteins bind both in the nucleus and cytoplasm. They are involved in formation of body segments and without them headless mammalian embryos result

Lim proteins

107

this phylogenetically conserved family of genes plays a role in patterning outgrowth of appendages in early embryogenesis and formation of jaws and inner ear

Dlx genes

108

this family of genes prenatally inhibits cell differentiation and postnatally helps to maintain proliferative capacity of tissues (involved in epithelial-mesenchymal interactions in the face and limbs)

Msx genes

109

this gene family causes short tails in heterozygous mice, is important ion mesodermal germ layer development, and differentiates forelimb from hindlimb

Tbx genes

110

this family of transcription factors have 2 alpha helices separated by a short amino acid loop with adjacent basic regions

helix loop helix TF's

111

this configuration is common in TF's that regulate myogenesis

helix loop helix & zinc finger proteins

112

helix loop helix and zinc finger transcription factors are common in regulating what part of development

myogenesis

113

TF family that regulates expression of genes involved in cell growth, proliferation, differentiation, longevity (and they contain a winged helix)

Fox gene family

114

the first gene associated with disorders of speech and language development (which are highly heritable)

FoxP2

115

this configuration of transcription factors include cys and his units bound by a cofactor which causes puckering in the polypeptide chain which can be inserted into specific regions of DNA helix

zinc finger proteins

116

this configuration of transcription factor is implicated in bone, cartilage, and tooth development

zinc finger

117

a deficiency in this metal ion can result in skeletal growth retardation (risk for osteoporosis)

zinc

118

this gene family binds the minor groove in DNA using zinc finger proteins. they are part of HMG-box superfamily and mutations lead to abnormal development of tissues such as sex determining genes

Sox (SoxA=SRY sex determining region of Y)

119

this disorder is caused by sox9 mutations effecting skeletal, reproductive, respiratory, and face development resulting in short legs, dislocated hips, ambiguous genet alit, softened respiratory cartilage, ect

campomelic dysplasia

120

campomelic dysplasia is caused by mutations in which gene

sox9

121

this zinc finger protein affects an isolated gene with important role in kidney and gonadal development

WT1 (wilms' tumor supressor gene)

122

what are the zinc finger TF's that we need to know?

WT1 (wilms tumor- kidney)
and sox (bone, repro, respiratory issues)

123

this superfamily of signaling molecules plays a variety of roles in embryogeneiss and postnatal life (formation, structure, modification)

TGF-beta (transforming growth factor)

124

noggin, chordin, WNT3a, and FGF all "inhibit the inhibitor" of neural development. what is this inhibitor which they block so that neural development can occur?

BMP4 (important in skeletal development)

125

if bmp4 is present, then ectoderm becomes ___ whereas if it is blocked, then ectoderm becomes ____

epidermis, neural plate

126

angiogenesis, wound healing, embryo development of limb and brain, and various endocrine signaling pathways are all influenced by this family of proteins

fibroblast growth factors

127

this protein family uses ligand signaling by binding to PTCH receptors which signal transmembrane SMO protein

hedgehog

128

what are the 3 hedgehog proteins?

sonic, desert, indian

129

vertebrate organogenesis, facial and limb patterning, brain organization is all influenced by what signaling factor

SHH

130

this growth factor is essential in stem cell division in adults and has been implicated in cancer development

SHH

131

this signaling factor is involved in chondrocyte differentiation, proliferation, maturation especially during endochondral ossification

IHH (indian hedgehog)

132

defects in this signaling factor causes partial gonadal dysgenesis (PGD) and polyneuropathy

DHH (desert hedgehog)

133

this signaling factor is important in gastrulation and organogenesis and binds frizzled and LRP receptors, uses a signal transducer to beta catenin which enters nucleus to activate target genes

wnt

134

these genes regulate cell growth and differentiation and can lead to cancer when activated (usually code for mitogenic signals)

proto-oncogenes

135

these genes normally function to limit frequency of cell division and when they lose function, cancer may develop

tumor supressor genes

136

which tumor suppressor gene, when it loses function, leads to basal cell carcinoma

PTCH

137

RAS, HER2, EFT receptor, MYC, and ABL are all examples of what kind of cancer causing gene

proto-oncogene

138

p53, RB, APC, DCC, BRCA, and NF-1 are all examples of what kind of cancer causing gene

tumor supressor

139

activation of p53 leads to p21 activation which is a protein that binds cyclin-CDK complexes for G1/S transition. This process keeps ___ hypophosphorylated and active, and consequently sequesters ___

Rb, E2F

140

during early development, this signal molecule is generated in a region of the embryo to determine anterior/ posterior axis development by acting through box genes. what is the signaling molecule?

retinoid acid (vitA)

141

cultured embryonic stem cells can be coaxed into becoming neurons if you add what signaling molecule?

retinoic acid

142

the heavy and light chains of an antibody together form what portion of the structure

Fab portion

143

the Fc portion of an antibody contains components of which chains?

heavy chains only

144

the portion of an antigen to which an antibody attaches

epitope

145

in a method known as indirect detection, two ___ are used (the second one is fluorescently labeled) to amplify a detectable signal

antibodies

146

enzyme amplification assay frequently used in medicine the amount of antibody present in solution as it binds an antigen coated well (test for HIV Ab's)

indirect ELISA

147

enzyme amplification assay where production of color indicates the quantity of antigen between one bound and one unbound monoclonal antibody which emit color when substrate is added (test for hCG: pregnancy)

sandwich ELISA

148

what lab method is used to detect cardiac troponin T before and after an MI

ELISA

149

what lab method uses DNA transcription as a diagnostic tool to find short tandem repeats (STRs) or viral particles

PCR

150

what are examples of conditions diagnosed using PCR?

chlamydia, CMV, Hep C, tuberculosis, gonorrhea
MSUD, ornithine transcarbamoylase deficiency, PKU, CF, Duchenne MD, Rb, familial hypercholesterolemia, sickle cell anemia, G6P dehydrogenase deficiency, tay sachs, hemophelia, lesh nyhan syndrome

...so when in doubt, its probably diagnosed using PCR :)

151

what are examples of conditions diagnosed using qPCR?

strep, HIV

152

name the technique where reverse transcriptase is used to make DNA from RNA sample and we add fluoresent marker linked to a probe to find a complementary sequence. a scanner measures expression. What are examples for use of this method?

microarray
chemo-resistant tumors

153

which viruses are known to be oncogenic

EBV, Hep B, HPV, HTLV-1, KSHV (kaposi sarcoma herpes virus)

154

Zika has an advantage in humans because of what disguise?

It acquires an envelope from our cells

155

What is the most devastating time to acquire zika in a pregnant woman? Why?

First trimester
Organogenesis (infects neural cells)

156

What property of signalling molecule allows it to diffuse across the cytoplasmic membrane and bind intracellular receptors?

Small hydrophobic (steroid hormones for example)

157

Most signalling molecules require cell surface receptors because they have what property?

Hydrophillic (such as growth factors)

158

Retinoic acid is a vitamin A derivative that acts through which set of developmental genes? These genes control positioning along which body axis?

Hox genes, these control anterior/posterior patterning

159

what method of cell signaling elicits a fast response

change in function of enzymes

160

what method of cell signaling elicits a slow response

change in expression of genes

161

Long distance signaling in the bloodstream of freely diffusible signals

Endocrine

162

Signaling acting locally on cells nearby using short lived signals such as neurotransmitters

Paracrine

163

Cells respond to signals released by themselves such as growth factor

Autocrine

164

Signalling involving direct contact with receptor such as with antigen presentation in immune cells

Juxtacrine

165

the same ligand can elicit different responses when introduced to different tissues for example: acetylcholine causes heart muscle cells to do what? skeletal muscle? salivary gland?

relax, contract, salivate

166

where would you find a receptor for a small hydrophobic ligand? what about a receptor for hydrophilic molecules?

intracellular, cell surface

167

what are the hydrophobic ligands?

cortisol, estradiol, thyroxine, testosterone, vitD3, retinoic acid

168

what kind of receptor is most commonly the target of drugs

GPCR

169

g proteins are regulated in part by two enzymes that help facilitate the production and hydrolysis of GTP. Which enzyme activates a GPCR and which inhibits?

activates- GEF- exchanges GTP for GDP and keeps GPCR in active state (GTP bound)
inhibit- GAP- hydrolyzes the GTP bound to GPCR so that it "turns off" (GDP bound)

170

which subunit of a gpcr is catalytically acitve

alpha