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MCP > Unit 2 > Flashcards

Unit 2 Flashcards

0
Q

imperfect base pairing with single stranded DNA probe occurs under what conditions

A

lower temperatures

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1
Q

a collection of methods used to isolate, manipulate, amplify, re organize, and analyze genes at the molecular level

A

Recombinant DNA technology or molecular genetics

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2
Q

perfect base pairing with a single stranded DNA probe occurs under what conditions

A

higher temperature

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3
Q

cut dsDNA in palindromic sequences

A

restriction enzymes

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4
Q

most useful function of restriction enzymes

A

leave staggered ends, with 5’ or 3’ overhangs

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5
Q

why are staggered ends created by restricted enzymes useful

A

they can be efficiently ligated to complementary ends with T4 DNA ligase

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6
Q

how do restriction enzymes serve as landmarks on DNA sequences

A

used for linkage analysis
RFLPs
cut at specific pattern points

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7
Q

why do you use gel electrophoresis

A

to separate nucleic acids based on size

voltage moves negatively charged molecule toward the positive anode

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8
Q

Vehicles used to move, manipulate, and amplify cloned genes/fragments of genes. Altered versions of naturally occurring DNA elements used to transfer genetic information

A

vectors

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9
Q

which vector/host carries the smallest insert size range in molecular cloning (go from smallest to largest, there are five)

A 
plasmids in bacteria/yeast
then bacteriophage lambda in bacteria
then cosmids in bacteria
then BACs in bacteria
and YACs in yeast are the biggest
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10
Q

YAC

A

yeast artificial chromosome, can be tricked into carrying the largest amount of recombinant DNA

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11
Q

how does bacteriophage lambda spread into the growth medium

A

lysis

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12
Q

a large collection of random inserts for a genome of interest in a cloning vector

A

library

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13
Q

cDNA library doesn’t contain ___

A

introns

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14
Q

where does DNA come from in a cDNA library

A

directly from a tissue via mRNA/reverse transcriptase, so you only get mRNA being expressed in that specific tissue

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15
Q

allows you to amplify known sequence of RNA or DNA from complex mixtures of nucleic acids even if the copies of that sequence are extremely inabundant

A

PCR

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16
Q

how does PCR work

A

reiterative rounds of primer directed DNA replication employing a thermophilic DNA polymerase
cycles of heating and cooling (heat to separate strands, cool to hybridize primers and synthesize DNA)

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17
Q

binomial expansion using PCR

A

amount of DNA made= # starting templates x 2^# cycles

product then analyzed by gel electrophoresis

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18
Q

method to determine size and quantity of purified DNA

A

DNA gel electrophoresis

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19
Q

method used to detect presence and size of a specific DNA sequence in a complex mixture/sample

A

Southern blot/assay

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20
Q

method used to amplify a specific DNA sequence from a complex mixture/sample

A

PCR

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21
Q

method used to amplify a specific RNA sequence from a complex mixture

A

rtPCR (reverse transcriptase)

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22
Q

method used to amplify multiple specific sequences from a complex mixture in a single PCR reaction

A

multi plex PCR

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23
Q

method used to detect the presence and size of a specific RNA sequence in a complex mixture/sample

A

Northern blot/assay

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24
Q

method used to separate proteins by size/molecular weight

A

denaturing gel electrophoresis of proteins

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25
Q

method used to separate proteins based on size/shape and charge at a particular pH

A

non-denaturing/native protein gel electrophoresis

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26
Q

method used to separate proteins based on pI (pH at which protein is not charged)

A

isoelectric focusing

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27
Q

method used to detect presence, size/shape, and abundance of specific protein in a complex mixture/sample

A

Western blot/assay

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28
Q

method used to detect the presence and localization of a protein in a fixed tissue/cell sample

A

Immuno Fluorescence Microscopy

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29
Q

method used to determine the location and dynamics of a protein of interest fused to GFP

A

GFP Fluorescence

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30
Q

method used to determine the presence and relative abundance of all mRNA species in different samples/cells/tissues etc

A

micro array based expression analysis

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31
Q

method used to down regulate the expression of a specific gene in a cell/tissue

A

RNAi/morpholinos

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32
Q

specific use for non-denaturing/native protein gel electrophoresis

A

can be used to compare proteins with mutations in charge amino acids such as certain mutations in hemoglobin that cause sickle cell disease

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33
Q

at high pH, a protein is (+/-) charged

A

negatively

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34
Q

at low pH, the protein is (+/-) charged

A

positively charged

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35
Q

two dimensional protein gel electrophoresis-protemics

is a combo of:

A

gel electrophoresis with mass spec

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36
Q

2D protein gel electrophoresis shows what specifically

A

all the proteins expressed in a cell or tissue and how they are post translationally modified

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37
Q

antibodies raised in animals by injecting them with the antigen of interest

A

primary antibody

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38
Q

antibodies raised against the constant regions of antibodies from a different animal species

A

secondary antibodies

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39
Q

labeled antibodies can be used as

A

molecular tags

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40
Q

immuno fluorescence microscopy analysis can give information about cells involved in which disease (example)

A

muscular dystrophy

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41
Q

what do micro array expression experiments tell us

A

relative expression levels of all genes in the genome under specific conditions
how this expression pattern changes when the system is perturbed
identifies groups of coordinately regulated genes that may be functionally related
provides a diagnostic tool to type a tissue/tumor/disease state

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42
Q

how we handle all the data from micro array expression experiments

A

cluster analysis
-compare all expression patterns to each other, join patterns that are most similar (the painting example), compare joined patterns to all other unjoined patterns and repeat repeat repeat

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43
Q

cluster analysis and display of genome wide expression patterns

A

hierarchical clustering

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44
Q

next thing in DNA methods after micro arrays phase out

A

next generation sequencing–whole genome sequencing

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45
Q

introduction of dsRNA corresponding to a cellular mRNA will induce degradation of the mRNA and downregulation

A

RNA interference aka RNAi, discovered in C elegans

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46
Q

what is the purpose of RNAi

A

can suppress dominant alleles or diseases due to inappropriate over expression

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47
Q

short single stranded oligos complementary to a transcript you want to knock down
inhibit expression by blocking progress of the ribosome/translation or by blocking a splice site

A

morpholinos

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48
Q

can be fused to any gene of interest and used to study the expression and/or localization of the gene product in living cells

A

Green Fluorescent Protein GFP (from jellyfish)

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49
Q

method that provides the greatest sensitivity for detecting specific nucleic acid sequences

A

PCR

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50
Q

method that can be used to clone genes

A

PCR

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51
Q

recognition site for a restriction enzyme

A

palindromic sequence

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52
Q

method used to detect specific nucleotide sequences in both Northern and Southern blots

A

nucleic acid hybridization

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53
Q

method used to create a large set of plasmids that contain random inserts of the expressed genes from a tissue of interest

A

construction of cDNA library

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54
Q

method used to determine if a patient with muscular dystrophy is making normal dystrophin protein in their muscle cells

A

western blot

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55
Q

method used to amplify and clone a specific exon from the dystrophin gene of a patient with muscular dystrophy

A

PCR

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56
Q

method used to examine the gene expression profile in the skeletal muscle cells of a patient with muscular dystrophy

A

DNA micro arrays

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57
Q

why use a control probe when trying to detect a deletion in FISH

A

because you need to rule out technical error, such as the probe just didn’t bind, although the sequence was present. the control probe proves that it is working, but there is something missing

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58
Q

FISH is best used for:

A

detailed information about a specific locus (not the whole genome)

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59
Q

three types of FISH probes

A

repeat sequences, single copy DNA (subtelomere FISH), chromosome painting (multicolor)

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60
Q

type of probes isolated from centromere or telomere regions

A

repeat sequences

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61
Q

what do centromere probes detect

A

gain or loss of specific chromosomes

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62
Q

syndromes identified using repeat sequence FISH probe

A

Down Syndrome, Turner Syndrome

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63
Q

FISH probe isolated from cloned DNA of a disease-causing gene or a fragment of DNA of known location associated with a particular gene

A

unique sequence aka single copy

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64
Q

FISH probes that are DNA sequences from the distal ends of the chromosomes in the regions proximal to the actual telomere regions

A

subtelomere probes

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65
Q

why use subtelomere probes for FISH

A

these are very gene rich regions

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66
Q

probes that are actually a cocktail of many unique DNA fragments from along the entire length of a chromosome such that following hybridization, the entire chromosome fluoresces

A

chromosome painting probes aka whole chromosome paints WCP

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67
Q

when is chromosome painting in FISH most useful

A

when identifying complex rearrangements or marker chromosomes

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68
Q

accuracy limitations when using FISH to detect deletions

A

most deletions are very large and the probes are much smaller, a deletion may be present that cannot be detected by the FISH probe designated for the disease

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69
Q

how do you use FISH when you want more info about a developmental delay

A

check for a subtelomeric microdeletion

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70
Q

what are caused by deletion or duplication in regions of the genome with clusters of closely associated genes whose normal functions are generally unrelated

A

continguous gene syndromes

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71
Q

contiguous gene syndrome caused by deletion of elastin gene

A

Williams syndrome

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72
Q

characteristics of _____ contiguous gene syndrome: aortic stenosis, thickening of skin, renal anomalies, low IQ, excellent music skills but terrible with math, outgoing and friendly, blue sclera, stellate iris

A

Williams

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73
Q

contiguous gene syndrome with presentations of learning disabilities, cleft lip/palate, facial anomalies, cardiac anomalies, weak immune system, difficulty feeding at birth

A

Velocardiofacial syndrome VCFS

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74
Q

how can a parent carry the VCFS deletion?

A

15% of the time, parent carries the deletion but may not be clinically abnormal–huge phenotypic variability

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75
Q

how is VCFS deletion caused

A

unequal crossing over

compensation on homologous chromosome

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76
Q

gene arrays tell you:

A

specific DNA sequences of interest

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77
Q

expression arrays tell you:

A

gene products to understand which genes are being expressed in a particular cell type at a particular time

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78
Q

clinical application of expression arrays

A

can create tumor profiles to show genes that are upregulated for each type of tumor to aid with diagnosis

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79
Q

what method is used to view the copy number variants in association with the chromosomes

A

chromosome microarray

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80
Q

gold standard for test used to identify problems that are not suited to just one disorder (seemingly unrelated presentations)

A

chromosome microarray

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81
Q

problem with next generation sequencing

A

more data than we know how to interpret, sequencing is complicated and so is reading the results

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82
Q

goal of panels in clinical sequencing

A

to get manageable amounts of data back

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83
Q

things to keep in mind when ordering genome sequencing (4)

A
  • is the lab accredited/the test validated/
  • it takes a long time (about 2.5 weeks)
  • cost is 3K-5K
  • do the patients have insurance?
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84
Q

what type of abnormalities will karyotype analysis detect

A

numerical and structural (large) abnormalities

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85
Q

what are the pros and cons of molecular diagnostics

A

pros: well defined, specific, can detect very small mutations
cons: need to know what you’re looking for already-targeted testing

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86
Q

what size mutations does FISH recognize

A

medium sized

targeted testing

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87
Q

pros and cons of microarray

A

pro: genome wide screen for small to large mutations
con: will not detect balanced rearragements

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88
Q

pros and cons of DNA sequencing

A

pro: high resolution, detect mutations on a single base level
con: trying to interpret all the data

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89
Q

which technology would be best to diagnose autism?

A

since autism is related to a wide variety of genes and none of the mutations have been associated with numerical or structural abnormalities (so no FISH or karyotype), you need to use microarray analysis

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90
Q

the study of development between fertilization and birth

A

embryology

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91
Q

study of embryonic and other developmental processes

A

developmental biology

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92
Q

what percent of all embryos are spontaneously aborted

A

50%

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93
Q

weeks 1-8 of human pregnancy when organ primordia are established

A

embryogenesis

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94
Q

the embryonic period is followed by the ___ period of continued differentiation and growth

A

fetal

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95
Q

system used by embryologists to describe the apparent maturity of embryos based on external features

A

Carnegie stages

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96
Q

system used by clinicians to describe the maturity of an embryo, refers to the length of time since the last ovulation before pregnancy

A

postovulatory age

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97
Q

by the end of the first week of embryogenesis, the blastocyst begins:

A

implantation into the uterine wall

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98
Q

zygote > cleavage > _____ > blastocyst

A

morula

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99
Q

how is the first cleavage division initiated

A

fertilization

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100
Q

what is the result of cleavage divisions

A

increase in number of cells but no change in size of the zygote

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101
Q

process during cleavage that segregates inner cells from outer cells

A

compaction

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102
Q

how is the compact ball after the third cleavage division stabilized

A

tight junctions that form between the outside cells of the ball

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103
Q

inner cells of the morula

A

inner cell mass ICM

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104
Q

the inner cell mass gives rise to:

A

tissues in the embryo proper

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105
Q

outer cells of the morula give rise to the

A

trophoblast that later contributes to the placenta

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106
Q

during a process called ______, the trophoblast cells secrete fluid into the morula to create a blastocoel, an internal cavity

A

cavitation

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107
Q

what is the function of the zona pellucida around the morula

A

protection

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108
Q

cells that can give rise to all of the cell types that make up the body

A

pluripotent

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109
Q

from which cells are embryonic stem cells derived?

A

inner cell mass

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110
Q

trophoblast cells contribute to ____ tissues

A

extraembryonic

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111
Q

______ are pluripotent cells that give rise to the embryo

A

inner cell mass

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112
Q

cells that can differentiate into any cell type including extraembryonic tissues

A

totipotent

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113
Q

cells at the morula stage of development are considered (pluripotent/totipotent)

A

totipotent

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114
Q

why does the blastocyst hatch from the zona pellucida

A

in order to attach to the endometrium/uterine wall

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115
Q

what does the zona pellucida prevent before the embryo reaches the uterus

A

implantation in oviduct walls

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116
Q

what is the mechanism of hatching from the zona pellucida

A

a trypsin like protease lyses a hole in the fibrillar matrix of the zona and the embryo squeezes out through that hole

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117
Q

uterine epithelium

A

endometrium

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118
Q

what type of embryonic cells attach to the uterine wall epithelium

A

trophoblast

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119
Q

molecules called ____ (carbohydrate binding proteins) on trophoblast cells interact with carbohydrate receptors on the endometrium to mediate attachment of the blastocyst to the uterus

A

L-selectin

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120
Q

after initial binding of the embryo to the endometrium, trophoblast cells express _____ proteins that bind uterine collagen, fibroconectin, and laminin to keep the blastocyst bound to the uterine wall

A

integrin

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121
Q

once in contact with the endometrium, the trophoblast secretes _____ enzymes to digest the ECM of the uterine tissue, enabling the blastocyst to bury itself within the uterine wall

A

protease

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122
Q

tethering of the blastocyst to the uterine wall

A

implantation

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123
Q

abnormal blastocyst implantation is called:

A

ectopic pregnancy

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124
Q

the trophoblast differentiates into two layers: the ___ and ___

A

cytotrophoblast and the syncyiotrophoblast

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125
Q

an inner layer of mononucleated cells that differentiates from the trophoblast

A

cytotrophoblast

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126
Q

an outer mutlinucleated layer that lacks distinct cell boundaries that differentiates from the trophoblast

A

syncytiotrophoblast

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127
Q

how does the cytotrophoblast adhere to the endometrium

A

adhesion molecules

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128
Q

cytotrophoblast cells contain ___ enzymes that enable them to enter the uterine wall and remodel the uterine blood vessels so that the maternal blood bathes the fetal blood vessels

A

proteolytic

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129
Q

on day __, the cells of the ICM differentiate into two layers: the ____ and the ____, which form a flat bilaminar disc

A

day 9

hypoblast and epiblast

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130
Q

on day __, the cells of the trophoblast differentiate into the cytotrophoblast and the syncytiotrophoblast

A

8

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131
Q

the amniotic cavity forms within which layer that has differentiated from the ICM

A

epiblast

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132
Q

what type of role does the hypoblast play after it has differentiated from the ICM

A

supportive role

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133
Q

what is the purpose of amniotic fluid

A

surrounds the embryo to protect it from abrupt movement and keeps it from drying out

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134
Q

the maternal portion of the placenta

A

the uterine endometrium

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135
Q

the fetal portion of the placenta

A

the chorion

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136
Q

how do soluble substances diffuse from the mother to the fetus

A

through villi

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137
Q

fertilization results in the formation of a (diploid/haploid) zygote and activates:

A

diploid

cleavage division

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138
Q

the process of ____ forms a tight ball of cells that separate into inner and outer layers in the embryo

A

compaction

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139
Q

the process of ____ transforms the bilaminar disc into three germ layers

A

gastrulation

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140
Q

three goals of gastrulation

A

1- bring inside the embryo areas destined to form endodermal organs
2- surround the embryo with cells capable of forming ectoderm
3- place mesodermal cells in proper positions in between

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141
Q

gastrulation begins with the formation of the ________ (2 words) on the surface of the epiblast

A

primitive streak

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142
Q

the primitive streak becomes a narrow groove with a structure called the primitive ___ surrounding a primitive ___ at the cephalic end

A

node

pit

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143
Q

what is the role of the primitive node during gastrulation

A

it is an organizing center

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144
Q

____ cells (which layer of cells) migrate into the primitive streak

A

epiblast

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145
Q

inward movement of epiblast cells toward the primitive streak

A

invagination

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146
Q

invaginating epiblast cells give rise to which two germ layers

A

endoderm and mesoderm

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147
Q

what is Hansen’s node (primitive node)

A

organizer tissue-the node tissue expresses genes that induce formation of the embryo

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148
Q

the ____ layer gives rise to the epidermal surface of skin, the CNS, and the neural crest (ex pigment cells)

A

ectoderm

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149
Q

the ___ layer gives rise to the notocord, bone tissue, RBCs, facial muscle, and the tubule cells of the kidney

A

mesoderm

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150
Q

the ___ layer gives rise to the digestive tube, pharynx, respiratory tube

A

endoderm

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151
Q

the anterior-posterior axis is signaled by cells at the cranial margin of the embryonic disc, an area called the:

A

anterior visceral endoderm (AVE)

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152
Q

AVE expresses genes that direct formation of what body part

A

head

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153
Q

when are body axes established

A

before or during gastrulation

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154
Q

what gene establishes left/right body axes

A

BMP4

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155
Q

____ is the process by which the neural plate forms the neural tube

A

neurulation

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156
Q

neurulation divides the ectoderm into three distinct domains:

A

surface ectoderm (epidermis), neural crest (nervous system), and neural tube (brain and spinal cord)

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157
Q

how many sites of neural tube closure are there

A

three

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158
Q

what does neural tube closure depend on

A

genes and dietary factors such as cholesterol and folate

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159
Q

neural tube closure defect results in

A

spina bifida

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160
Q

specific location of neural tube closure defect that causes spina bifida

A

posterior neurospore

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161
Q

condition in which the forebrain remains in contact with amniotic fluid and degenerates, always fatal

A

anacephaly

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162
Q

complete failure of closure along the entire neural tube results in

A

craniorachischisis

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163
Q

which dietary supplement can prevent neural tube defects

A

folic acid

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164
Q

free cells that can migrate away from their epithelial layer linkage

A

mesenchymal

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165
Q

what type of cells undergo an epithelial-to-mesenchymal transition

A

neural crest cells

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166
Q

___ neural crest cells produce craniofacial cartilage, bone, neurons, glia, and connective tissue

A

cranial (cephalic)

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167
Q

____ neural crest is a subregion of cranial neural crest that develops into melanocytes, neurons, cartilage, and connective tissue. Also gives rise to large arteries

A

cardiac

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168
Q

____ neural crest migrates to form dorsal root ganglia containing sensory neurons or sympathetic ganglia and the adrenal medulla

A

trunk

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169
Q

____ neural crest form the parasympathetic ganglia of the gut

A

enteric (vagal and sacral)

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170
Q

how do neural crest cells migrate

A

on specific paths

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171
Q

why is the second week of embryogenesis regarded as the week of 2’s

A

the trophoblast differentiates into cytotrophoblast and synctiotrophoblast
the inner cell mass forms the hypoblast and the epiblast

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172
Q

_____: when the epiblast cells give rise to endoderm, ectoderm, mesoderm

A

gastrulation

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173
Q

origin of embryonic stem cells

A

inner cell mass

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174
Q

when does implantation of the blastocyst occur

A

one week post fert

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175
Q

cardiac neural crest cell migrate into the heart to contribute to which structures

A

septum of the outflow tract that separate the aorta and pulmonary artery

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176
Q

there is a (high/low) level of genetic similarity among different animals

A

high. 40% of human genes are present in flies and worms!

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177
Q

what percentage of human genes are present in mice

A

92%

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178
Q

genes that can function interchangeably during development of different species

A

homologous–functions the same no matter the organism

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179
Q

how do genes drive development?

A

the genetic material is identical in every cell, but different cells express different sets of genes

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180
Q

_____ _____: all cells contain the same set of genes

A

genetic equivalence

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181
Q

_______ provides evidence that all cells contain the same genes (experiment)

A

somatic nuclear transfer (cloning)

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182
Q

____: only a small percentage of the genome is expressed in each cell type (turn off wrong genes and turn on right genes)

A

differential gene expression

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183
Q

four level of gene expression level regulation

A

differential gene transcription
selective nuclear RNA processing
selective mRNA translation
differential protein modification

184
Q

what does RNA FISH show you?

A

detects mRNA expression in cells or tissues (only cells expressing heart genes, for example, will be colored)

185
Q

producing many cells from one

A

cell proliferation

186
Q

creating cells with different characteristics at different positions

A

cell specialization

187
Q

coordinating the behavior of one cell with that of its neighbors

A

cell interactions

188
Q

rearranging the cells to form structured tissues and organs

A

cell movement

189
Q

when one group of cells changes the behavior of an adjacent set of cells

A

induction

190
Q

the two components to every inductive interaction

A

inducer and responder (responder must have the ability to respond to the signal=competence)

191
Q

responder’s ability to respond to signal from inducer

A

competence

192
Q

transcription factor in the ectoderm that makes ectoderm competent to respond to inductive signals from the optic vesicle (allows it to form eye lens)

A

Pax6

193
Q

autosomal dominant mutations in Pax6 cause:

A

aniridia (affects iris, intraocular pressure, lens, cornea, optic nerve)

194
Q

homozygous loss of Pax6 results in:

A

fatal condition, complete failure of entire eye formation

195
Q

cell-cell signaling using proteins that are secreted into the EC space to deliver signals to neighboring cells

A

paracrine signaling

196
Q

cell-cell signaling achieved by direct contact between inducing and responding cells

A

juxtracrine

197
Q

paracrine signaling molecules that cause concentration-dependent effects

A

morphogens

198
Q

a morphogen can specify more than one cell type by forming:

A

a concentration gradient

199
Q

what organism is used to test whether a molecule can function as a morphogen

A

zebrafish

200
Q

when a cell has competence to respond to an inducer, how are signals then received and interpreted in the cell?

A

signaling cascades/transduction pathways

201
Q

___ signaling pathway is an example of a signal transduction cascade: secreted molecules bind receptors at cell surface of responding cells, proteins are then phosphorylated and enter the nucleus where they modulate gene transcription

A

transforming growth factor B (TGFB)

202
Q

the two gradients that tell neural tube cells what to do

A

Bmp/wnt

Shh

203
Q

high concentration of Bmp/Wnt along the neural tube indicates which side (dorsal/ventral)

A

dorsal

204
Q

high concentration of Shh along the neural tube signals which side (dorsal/ventral)

A

ventral

205
Q

normal left/right organ symmetry

A

situs solitus

206
Q

completely reversed left/right organ symmetry

A

situs inversus

207
Q

type of abnormal left/right organ symmetry in which the organs are abnormally abnormal (not a complete reversal)

A

heterotaxy

208
Q

asymmetric gene expression of the ____ gene is greater on the left side

A

Nodal

209
Q

in normal embryos, Nodal is expressed on the left _______

A

lateral plate mesoderm

210
Q

what is the role of cilia in establishing right/left axes

A

cells in the node on its internal face have cilia beat in a helical fashion to drive fluid toward the left side

211
Q

syndrome with bronchitis, infertility, and situs inversus

A

Kartagener’s syndrome (cilia defect)

212
Q

asymmetric fluid flow caused by cilia creates:

A

a morphogen gradient that orients the left/right sides of the body

213
Q

how is Lefty activated

A

activated by Nodal signaling cascade

214
Q

what does Lefty do

A

restricts/inhibits asymmetric domain of Nodal signaling

215
Q

the transcription factor ___ is expressed on the left side of the developing heart, gut, and brain, and is thought to regulate expression of genes that mediate asymmetric morphogenesis of these organs

A

Pitx2

216
Q

method used when looking for specific mutations within genes (but don’t use for something like CF, which has 1000’s of possible mutations)

A

gene array

217
Q

many mutations, gain or loss of DNA at base level, related to a disease, and may be able to use it to identify disease causing mutations when compared to normal

A

copy number variation

218
Q

mitchondrial diseases occur mainly in organs like (three), where there is a high level of _____

A

nerve, brain, muscle

ox/phos

219
Q

MOI of mitochondrial diseases

A

may show autosomal or X linked or matrilineal inheritance

220
Q

male affected with mitochondrial disease (will/will not) transmit to children

A

will not

221
Q

refers to a population of mitochondria that all have the same genetic composition–all mitochondria are the same within a given cell

A

homoplasmy

222
Q

when there are two or more different populations of mitochondria present in a cell

A

heteroplasmy

223
Q

how can there be different levels of expression of the same mitochondrial disease within a family

A

heteroplasmy–mother has a low frequency of mutant cells but passes higher frequencies on to her children

224
Q

what is a mechanism that explains why mitochondrial disorders are often progressive with late onset

A

replicative segregation

225
Q

why is there a high mutation rate in mit DNA

A

oxidative environment creates damage to DNA and causes a high frequency of mutations

226
Q

acquired mutations in mit DNA (are/are not) passed on to children

A

are not–occur in somatic cells

227
Q

what should you look for if there are unexplained neurological defects

A

mitochondrial disease

228
Q

three reasons why diagnosis of mit disease is complicated

A

heteroplasmy/variable expression
maternal inheritence
progressive/late onset

229
Q

use of DNA tech (PCR, RFLP, sequencing, etc) to obtain info on the genetic identity of an individual and how that relates to a criminal, medical, or scientific investigation

A

forensic DNA analysis

230
Q

what does mitochondrial DNA analysis tell you in forensics

A

maternal inheritance-family identity

NOT individual identity

231
Q

cons of using nuclear DNA for forensics

A

linear, degrades quickly

232
Q

what do you need when doing a DNA paternity test

A

minimum of two probes
mother’s DNA
child’s DNA

233
Q

STR

A

short tandem repeat DNA

234
Q

benefit of nuclear (genomic) DNA forensics

A

identify an individual

235
Q

how many individuals are necessary to show mitochondrial DNA relationships

A

at least two additional (mom and sibling preferably)

236
Q

most common parasitic diseases in the US

A

trichomoniasis, giardiasis, cryptosporidiosis, toxoplasmosis

237
Q

immature stages of certain parasites must partially develop inside of another species, such as an insect, snail, mammal. these are called:

A

intermediate hosts

238
Q

host in which sexual reproduction occurs for the parasites

A

definitive

239
Q

host in which asexual phase of lifecycle occurs for the parasite

A

intermediate host

240
Q

why are parasites so difficult to get rid of

A

complicated life cycles

241
Q

another name for definitive host for a parasite

A

principal

242
Q

two major categories of parasites

A

parasitic protozoa-unicellular

parasitic helminths-multicellular

243
Q

five ways in which host mammals can be infected by parasites

A

1-direct ingestion of infective larvae, eggs, cyst
2-eating the intermediate host (problem with raw fish)
3-parasite actively penetrates the principal host (hookworms)
4-parasite may be maternally transmitted (toxoplasma-kitty litter)
5-vector borne transmission (insect bite)

244
Q

IgE

A

humoral response element as a result of parasite, allergy, autoimmune

245
Q

helminth therapy

A

for autoimmune disease and allergies

246
Q

what immune response do parasites elicit

A

cell mediated

247
Q

what immune response can achieve complete immunity from a parasite

A

adaptive

248
Q

which immune response results in the destruction and removal of the parasite, thus preventing the establishment of an infection

A

innate/nonspecific (cytokines, phagocytosis, activate complement system)

249
Q

most important survival strategy that parasites have

A

complicated lifecycle–each stage has a different antigen

250
Q

parasite strategies to evade adaptive immune responses

A

antigenic concealment
antigenic variation
antigenic shedding
antigenic mimicry (mimic host molecules)

251
Q

in the intermediate host, you can observe the parasite in which forms

A

development from asexual stage to sexual stage before being transmitted to definitive host

252
Q

most frequent of human prion diseases

A

Creutzfeldt-Jacob Disease

253
Q

causes of CJD

A

sporadic (85-95% of cases)
familial (7-10%)
iatrogenic (1%)

254
Q

symptoms of sCJD

A

spongiform encephalopathy
RAPID onset of Alzheimer’s type loss of brain function
death within a year of onset

255
Q

irregular involuntary contraction of a muscle seen in sCJD

A

myoclonus

256
Q

what causes prion diseases

A

infectious proteins

257
Q

difference between PrPc and PrPsc

A

alpha helix => protein misfolding => beta sheet

sc=scrapie form, leads to prion disease

258
Q

what does PrPc normally do

A

involved in maintaining the brain’s white matter, regulating innate immune cells, responses to oxidative stress, neuron formation

259
Q

how does PrPsc form arise

A

from mutation or exogenous source (meat, blood)

260
Q

PrP

A

prion protein

261
Q

what type of protein is the PrP

A

membrane protein

262
Q

what results from PrPc misfolding (clinical presentation)

A

encephalopathy

263
Q

__ (#) different types of prions

A

four

264
Q

how do you distinguish the different types of prions

A

Western blot ratio of banding patterns

265
Q

what is the purpose of prion fragmentation

A

liberates new ends to allow for amplification

allows the dissemination of infectious material

266
Q

gold standard for sCJD diagnosis

A

brain biopsy–look for spongiform vacuoles

267
Q

what population is most at risk for sCJD

A

elderly

268
Q

vast majority of sCJD cases occur in which race

A

white

269
Q

characteristics of Variant CJD (vCJD)

A

type 4 prion

bovine-to-human transmission of BSE (muscle and milk DO NOT contain infectious BSE)

270
Q

difference between vCJD and sCJD symptoms

A

vCJD progresses slower

vCJD peripheral pathogenesis (involvement of lymphoreticular tissues)

271
Q

staining difference between vCJD and sCJD

A

vCJD: plaques
sCJD: diffuse

272
Q

mean age at onset for vCJD

A

29

273
Q

vCJD has a (long/short) incubation period

A

long 10-20 years

274
Q

only way to sterilize against prions

A

auto claving

275
Q

do prions contain genetic material

A

no

276
Q

how were viruses discovered to be distinct from bacteria (experiment)

A

bacteria could be filtered but viruses passed through into the filtrate

277
Q

why can viruses not be cultured

A

they are obligate intracellular parasites–can only replicate in cells

278
Q

definition of a virus

A

capsid encoding organism

279
Q

protein shell that encapsulates the nucleic acid genome

A

capsid

280
Q

the particle encoded by a virus genome

A

virion

281
Q

three gene modules of virus genome

A

1-capsid protein
2-replicon
3-host cell interacting factors

282
Q

structural proteins encoded by the virus genome

A

capsid, some replication proteins

283
Q

non structural proteins encoded by the virus genome

A

host interacting factors (they are not packaged into the virion)

284
Q

virion structure

A

genome + capsid +/- envelope

285
Q

what type of virions lack an envelope

A

naked virions

286
Q

what is a virion envelope made of

A

lipid bilayer from the host cell

287
Q

three ways of classifying viruses

A 
host cell (eukaryotic or prokaryotic, plant/insect/animal)
genome type (RNA or DNA, single or double stranded)
virion structure (enveloped or naked, helical or icosahedral or complex)
288
Q

virion component found in the center

A

nucleocapsid

289
Q

virion component: gel in between the capsid and the envelope

A

tegument

290
Q

virion component right under the envelope

A

matrix

291
Q

virion component name for spikes embedded in the membrane

A

glycoprotein

292
Q

virion component not embedded in the membrane but sticking out from it

A

spike or fiber

293
Q

adenovirus appearance

A

icosahedral, contains fibers, DNA

294
Q

poxvirus appearance

A

helical, DNA genome

295
Q

flu virus structures

A

helical, glycoproteins, lipid bilayer, segmented RNA genome

296
Q

HIV structure

A

icosahedral, glycoproteins, mRNA, morphs into a trapezoid capsid

297
Q

limiting factor of virus lifestyle

A

Ro infectivity of virus

298
Q

virus strategy for survival (three things)

A

1-capsid
2-genome
3-transmission to a new host

299
Q

____ consist of a few genes encased in a protein shell that may be enveloped by a membrane

A

virions

300
Q

what do viruses need in order to grow? (six things)

A 
1-right host (tropism)
2-cells with the right receptors (susceptible)
3-appropriate environment (permissive)
4-biosynthesis machinery
5-abundant building blocks
6-time to finish replication
301
Q

step of virus replication with interactions between virions and tissues

A

recognition (1)

302
Q

step in virus replication with binding of a virion surface molecule to its specific cellular receptor

A

attachment (2)

303
Q

step of virus replication with internalization of the virion into the cell

A

entry (3)

304
Q

what happens to the virus when replication is incomplete

A

abortive infection

305
Q

cells that a virus can enter

A

susceptible

306
Q

cells that support virus replication and virion synthesis

A

permissive

307
Q

preferred cell type for virus infection

A

tissue tropism

308
Q

preferred species for virus infection

A

host range

309
Q

virus entry method: engulfment of entire virion into cell via receptor-mediated endocytosis/pinocytosis/phagocytosis

A

penetration

310
Q

viral entry into a cell when the virion envelope fuses with plasma membrane, leaving parts of the virion behind

A

fusion

311
Q

step of viral replication when there is a release of the genome into the cell

A

uncoating

312
Q

uncoating marks the beginning of the _____ phase, past which you cannot culture the virus anymore

A

eclipse

313
Q

what factors regulate mRNA synthesis in the virus

A

viral and host transcription factors

314
Q

viral mRNA’s are translated into what three types of proteins by the host machinery

A

ribosomes, tRNAs, amino acids

315
Q

what do RNA viruses use to make mRNA and genomes

A

RNA dependent RNA Polymerase

316
Q

what stage of viral replication marks the end of the eclipse phase

A

assembly of the virion

317
Q

how the virion is assembled

A

first the capsid forms an empty shell

then viral DNA is inserted into the capsid

318
Q

how to enveloped viruses acquire their membranes

A

from a cellular source–ER, Golgi, plasma membrane

319
Q

how does a virus kill a cell

A

enters cell, duplicates itself

cell explodes to release the viruses

320
Q

the number of infectious viral progeny from a single round of replication

A

burst size

321
Q

name for virus growth curve

A

single step

322
Q

phase of virus growth curve when virus particles are made and can infect other cells

A

maturation and release

323
Q

cell lysis produces viral _____

A

plaques

324
Q

how are infections virions measured

A

PFUs-plaque forming units

325
Q

the entry of enveloped viruses into cells involves expression of ______ on the cell surface

A

specific receptors

326
Q

how do enveloped viruses obtain their membranes

A

from a cellular compartment

327
Q

virion envelopes are contructed from (viral/cell) glycoproteins and (viral/cell) membranes

A

viral glycoproteins

cell membranes

328
Q

how do virus membrane proteins reach the site of envelopment

A

secretory pathways

329
Q

MOI fragile X

A

X linked dominant with reduced penetrance (80% in males and 30% in females)

330
Q

cause of FRAXA

A

expansion of a CGG triplet repeat

331
Q

disease that affects pre mutation male in family with FRAXA

A

Fragile X related Tremor/ataxia

332
Q

disease that affects pre mutation female in family with FRAXA

A

premature ovarian failure

333
Q

when a larger PCR product which does not amplify as well as a shorter product is not detected in 35 cycles

A

allelic drop out

334
Q

diseases that involve mutations in the alpha or beta globin chain genes which complex together to carry oxygen in the blood

A

hemoglobinopathies

335
Q

_____ result when mutations at alpha or beta globin chain genes cause an imbalance in the quantity (rather than quality) of the two chains

A

Thalassemias

336
Q

heterozygous sickle cell advantage

A

sickle cell trait, confers resistance to malaria

337
Q

results from genes involving the beta globin genes that lead to a deficiency of beta globin

A

beta thalassemia

338
Q

how are the alpha and beta globin gene clusters coordinated

A

locus control regions

339
Q

what results in individuals with one normal alpha gene and one copy of Hb Constant Spring and two deleted alpha globin genes

A

deficiency leads to beta globin tetramer formation

340
Q

number of CF disease causing mutations

A

1900

341
Q

delta F508

A

most common CF mutation

342
Q

HD is due to a (gain/loss) in function

A

gain

343
Q

FRAXA is due to a (gain/loss) in function

A

loss due to expansion of CGG repeat

344
Q

triplet repeats in FRAXA account for phenomenon of

A

anticipation

345
Q

a normal person usually has _ beta globin genes

A

2-one each on chromosome 11

346
Q

a Fragile X Normal Transmitting male has a risk of

A 
developing FXTAS (greater than 1/3 risk)
his daughters will be carriers who are at risk of having affected children
347
Q

molecular mechanism of the triplet repeat expansion responsible for FRAXA

A

mutation leading to a deficiency via methylation and gene silencing

348
Q

a slight difference on a southern blot for a male child with possible FRAXA shows

A

normal transmitting male–modest increase in copy number but no methylation

349
Q

most common cause of inherited mental retardation

A

Fragile X

350
Q

Fragile X arises from what type of mutations

A

dynamic

351
Q

CF has (allelic/locus) heterogeneity

A

allelic

352
Q

Fragile X presentations

A

MR, large ears and head, long face, large testicles in males

353
Q

how do you detect the triplet expansion involved in Fragile X

A

PCR and/or southern blot

354
Q

three classes of Fragile X mutations

A

normal, pre mutation, full mutation

355
Q

FXTAS and POF occur through (gain/loss) of function

A

gain

356
Q

how many bands does a Fragile X pre mutation carrying female have on a southern blot

A

four (as opposed to normal two)

357
Q

what characterizes Fragile X full mutation on a southern blot

A

smear

358
Q

on what chromosome are the alpha globin genes clustered

A

11

359
Q

site of erythropoiesis in a fetus

A

spleen and liver

360
Q

types of Hb in fetus

A

alpha and gamma

361
Q

types of Hb in adult

A

alpha and beta

362
Q

presentation of sickle cell disease

A

anemia, failure to thrive, splenomegaly, repeated infections, painful swelling of hands and feet

363
Q

compensation used in beta thalassemia

A

fetal hemoglobin remains turned on (gamma)

364
Q

most people have _ functional alpha globin genes

A

four

365
Q

homozygous deletion of alpha globin gene leads to:

A

hydrops fetalis

366
Q

mutation in a normal termination codon so that longer unstable alpha globin chain is produced

A

Hb Constant spring–instead of folding into globin, remains a chain and results in tetramers of beta

367
Q

problem with beta tetramers (Hb)

A

do not let go of oxygen

368
Q

a baby that tastes salty when kissed is a sign of

A

CF

369
Q

4 ways for things to go wrong in CF

A

protein is absent, not processed properly, not regulated properly, not delivered

370
Q

the variation in copy number is in some way related to stability such that the higher copy number the more likely to expand, thus the mutability of a product of mutation is different from that of its precursor

A

dynamic mutation

372
Q

disease becomes more severe with every generation

A

dynamic mutation

373
Q

single gene mutation birth defect with ocular defects, facial abnormalities

A

Axenfeld-Rieger Syndrome

374
Q

2 specific gene mutations in Axenfeld-Rieger Syndrome that code for proteins that affect eye developent

A

PITX2, FOXC1

375
Q

holoprosencephaly is caused by (a single gene mutation/multiple causes)

A

multiple factors (chromosomal abnormalities, environmental conditions such as maternal diabetes and alcohol intake, gene mutations)

376
Q

genes that have been implicated in holoprosencephaly are part of the ___ pathway

A

SHH–important for development of forebrain (SHH, GLI2, PTCH)

377
Q

where is the SHH expressed in the developing embryo

A

at Hensen node, the floor plate of the neural tube, the early gut endoderm, limb buds, throughout notocord

378
Q

what is the first example of when we understood that an infectious agent in the mother would cause birth defects

A

congenital rubella (German measles) syndrome-cataracts in baby

379
Q

how does hyperthermia (fever) during pregnancy affect baby

A

can interfere with neurulation and cause neural tube defects

380
Q

first known case of a pharmacological agent that caused birth defects

A

thalidomide (a sedative used to treat nausea in pregnant women)

381
Q

what did thalidomide cause in babies

A

limb malformation

382
Q

the study of birth defects

A

teratology

383
Q

agents that cause birth defects

A

teratogens

384
Q

susceptibility depends on three factors:

A

1-development stage at time of exposure
2-dose and duration of exposure
3-genotype of embryo; gene-environment interactions

385
Q

most sensitive period for inducing birth defects

A

weeks 3-8 during embryogenesis

386
Q

leading cause of mental retardation

A

alcohol

387
Q

most serious type of Fetal Alcohol Spectrum Disorders

A

Fetal Alcohol Syndrome FAS

388
Q

presentation of FAS

A

structural defects, growth deficiency, intellectual disability
small head, narrow upper lip, low nose bridge, flat midface

389
Q

most debilitating feature of FAS

A

defective brain development

390
Q

what happens when pregnant moms take SSRIs

A

slight increase in congenital heart defects (but what would be the alternative)

391
Q

most common birth defect (1% of all live births)

A

congenital heart defect

392
Q

____ defect: a hole in the heart

A

septal

393
Q

an opening in the wall (septum) that separate the left and right atria

A

atrial septal defect

394
Q

a hole in the part of the septum that separates the ventricles

A

ventrictular septal defect

395
Q

a condition where the heart is positioned on the right side of the thorax instead of the left

A

dextrocardia

396
Q

how does dextrocardia occur

A

problem with left/right patterning (cilia> L/R signal > nodal > cascade > gene expression)

397
Q

result of reversed nodal signaling cascade

A

situs inversus

398
Q

result of correct nodal signaling cascade

A

situs solitus

399
Q

result of bilateral nodal signaling cascade

A

heterotaxy

400
Q

septal defects, double outlet right ventricle, and transposition of the great arteries all can result from:

A

heterotaxy

401
Q

when the aorta rises from the right ventricle instead of the left

A

double outlet right ventricle

402
Q

when the two main arteries carrying blood out of the heart (pulm and aorta) are switched

A

transposition of great arteries

403
Q

detection of congenital heart defects

A

sometimes ultrasound

cyanosis, rapid breathing, fatigue, poor blood circulation

404
Q

the ____ tract of the embryonic heart gives rise to the great arteries

A

outflow

405
Q

a defect in which a single common blood vessel comes out of the heart instead of pulm and aorta

A

truncus arteriosus (in 22q11.2 deletion syndrome)

406
Q

four heart defects of tetralogy of Fallot in 22q11.2 deletion syndrome

A

1-ventricular septal defect
2-pulmonary stenosis
3-overriding aorta (enlarged)
4-ventricular hypertrophy (heart trying to compensate)

407
Q

___ cells migrating from the dorsal neural tube into the arterial pole participate in separation of the outflow tract

A

cardiac neural crest cells

408
Q

how does the 22q11.2 deletion affect cardiac neural crest cell development

A

genes located in that deletion region code for proteins that regulate cardiac neural crest cell development

409
Q

when does the neural tube close (by which week of pregnancy)

A

by the 6th week (so not at risk of not closing if you get a fever after the 6th week)

410
Q

functions of proteins are dependent on what two factors

A

polymer length and aa composition, which specify 3D structure

411
Q

the content of proteins within the cell at any given time

A

proteome

412
Q

critical residues responsible for nucleophilic attack on the substrate in HIV protease

A

Asp26

413
Q

similar in structure to a natural peptide substrate of the HIV protease, but non hydrolyzable

A

tipranivir anti HIV drug

414
Q

disease characterized by extensive deposits of misfolded protein (amyloid fibers) in the brain

A

AD

415
Q

beta sheet phi and psi values

A

close to 180 degrees

416
Q

alpha helix phi and psi values

A

close to 0 degrees

417
Q

dark areas on a Ramachandran map mean

A

that these phi and psi values are allowed, all structures must satisfy this plot

418
Q

lots of black area on a Ramachandran map means that this protein is

A

flexible

419
Q

most flexible aa residue

A

glycine

420
Q

pKa of Asp

A

4.0

421
Q

pKa of Glu

A

4.0

422
Q

pKa of His

A

6.5

423
Q

pKa of Cys

A

8.5

424
Q

pKa of Lys

A

10.0

425
Q

pKa of Arg

A

12.0

426
Q

pKa of carboxy terminus

A

4.0

427
Q

pKa of amino terminus

A

8.0

428
Q

(high/low) pKa binds H+ tightly

A

high

429
Q

(high/low) pKa binds H+ weakly

A

low

430
Q

pH at which half the ionizing groups are protonated, half are deprotonated

A

pKa

431
Q

when the pHs want to (retain/give up) protons

A

retain, lots of H+ in solution forces H+ onto ionizing group

432
Q

when the pH>pKa, aa’s want to (retain/give up) protons

A

give up, low bulk of H+ in solution draws off the H+

433
Q

why is His used as a catalytic residue by enzymes engaging in acid-base catalysis

A

pKa is 6.5 so it can accept or donate protons at physiological pH

434
Q

how does Cys introduce crosslinks

A

remove a hydride from SH group, make disulfide links

435
Q

what type of bonding forces determine primary protein structure

A

covalent

436
Q

what type of bonding forces determine secondary, tertiary, and quaternary structure

A

non covalent

437
Q

function of Glu in ATP synthase Fo ring

A

proton binds the Glu and rides it like a merry go round

438
Q

function of Pro in ATP synthase Fo ring

A

kink

439
Q

what limits phi and psi angles

A

steric clashes

440
Q

how do proteins fold so as to maximize vdw’s forces?

A

almost no empty space between atoms

441
Q

what force contributes to protein structure more than any other force

A

hydrophobic effect

442
Q

origin of hydrophobic effect

A

formation of clathrates by water is energetically unfavorable

443
Q

what secondary structure of proteins expresses a peptide group H bonding pattern with the CO of residue i bonded to NH of residue i+4

A

alpha helix

444
Q

three ways that the alpha helix is stabilized

A

backbone-backbone interactions
backbone- side chain interactions
side chain-side chain interactions (i, i+4)

445
Q

aa that prefers to form an alpha helix

A

Ala

446
Q

aa’s that prefer to break alpha helices

A

Pro (lacks NH to hydrogen bond), Gly (flexible)

447
Q

characteristics and examples of aa’s that are medium level helix breakers

A

bulky or Beta branched
Val, Thr, Trp, Phe
lose much rotational freedom when in a helix

448
Q

helix indifferent aa’s

A

long, straight chains

Arg, Lys, Glu

449
Q

amphipathic alpha helix side chain arrangement

A

every fourth is hydrophilic, on the outside

every fourth is hydrophobic, on the inside

450
Q

aa used to relieve steric clashes at beta turns

A

gly

451
Q

aa used to make a kink at beta turns

A

pro

452
Q

what is random about loops and random coils

A

not periodic

453
Q

where are random coils found

A

usually at protein surface, hydrophilic residues

454
Q

short stretches of secondary structure that usually require additional structures for stability

A

motifs

455
Q

continuous stretches of polypeptide that are linked together by flexible loops, stable in isolation after the rest of the protein has been removed

A

domain

456
Q

what holds coiled-coil domains together

A

hydrophobic effect, knobs into holes packing, electrostatic interactions

457
Q

what forms the leucine zipper

A

C terminal half of GCN4 transcription factor is a classical heptad Leu/Val repeat every 4th position

458
Q

a protein domain that only folds when it binds its target ligand

A

intrinsically disordered protein domain

MCP (4 decks)

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