MCP Flashcards
1
Q
DNA gel electrophoresis
A
presence size and quantity of purified DNA
2
Q
Southern blot/assay
A
presence and size of specific DNA sequence in a complex mixture/sample
3
Q
PCR
A
amplify a specific DNA sequence from a complex mixture
4
Q
rtPCR
A
amplify a specific RNA sequence from a complex mixture
5
Q
multi-plex PCR
A
amplify multiple specific sequences from a complex mixture in a single PCR reaction
6
Q
northern blot/assay
A
presence and size of a specific RNA sequence in a complex mixture/sample
7
Q
denaturing gel electrophoresis of proteins
A
separate proteins by size/molecular weight
8
Q
non-denaturing/native protein gel electrophoresis
A
separate proteins based on size/shape and charge at a particular pH
9
Q
iso-electric focusing
A
separate proteins based on pI (pH at which protein is uncharged)
10
Q
pI
A
pH at which protein is uncharged
11
Q
western blot/assay
A
presence, size and abundance of a specific protein in a complex mixture/sample
12
Q
immune-fluorescence microscopy
A
the presence and localization of a protein in a fixed tissue/cell sample
13
Q
GTP fluorescence
A
determine the localization and dynamics of a protein of interested fused to GFP
14
Q
micro-array based expression analysis
A
determine the presence and relative abundance of all mRNA species in different samples/cells/tissues
15
Q
RNAi/morpholinos
A
down regulate the expression of a specific gene in a cell/tissue
16
Q
Fragile X syndrome (physical and mental features)
A
physical: elongated face, large/protruding ears and large testicles (obvious when older)
mental: retardation, anxiety and aggression
* *most common cause of mental retardation
17
Q
Fragile X syndrome (molecular cause)
A
expansion of CGG triplet repeat affecting FMR1 gene on X chromosome resulting in the failure to express FMRP (fragile X mental retardation protein)
**methylation of FMR1 gene- deficiency of protein
18
Q
Fragile X syndrome (MOI)
A
X linked dominant with reduced penetrance (80% in males and 30% in females) and dependent on X inactivation pattern
19
Q
Fragile X syndrome (expansion)
A
occurs during transmission from a female permutation carrier and is dependent on length of repeat and whether the CGG repeats are interrupted with an AGG
20
Q
Fragile X related Tremor/Ataxia syndrome (FXTAS)
A
FXTAS- increased risk in premutation males of Fragile X syndrome
*lack of voluntary coordination of muscle movements
21
Q
POF
A
ovarian failure is at a higher risk to premutation carrying females of Fragile X syndrome
22
Q
CGG>200
A
abnormal methylation and unstable mitosis
23
Q
Repeats>200
A
abnormally methylated and also mitotically unstable resulting in a smear of bands
24
Q
Hemoglobinopathies
A
mutations in the alpha or beta globin chain genes which complex together with heme to carry oxygen in the blood
25
Thalassemias
imbalance in the quantity of the two chains
26
Beta Thalassemia
mutations involving beta globin genes leading to a deficiency of beta globin thus an excess of alpha globin forming alpha4 homotetramers (Heinz bodies) destroying RBCs
* beta globin gene mutations = point mutations
* *single bp sub with allelic heterogenity
27
embryology
study of development between fertilization and birth that has helped with new diagnostics, treatments and preventative strategies
28
embryogenesis
first 8 weeks in which organs form followed by fetal period (differentiation and growth) from weeks 9-38
29
Carnegie stages
based on physical attributes
30
Postovulatory age
based on time that has passed
31
Ovulation to implantation (long answer)
sperm fertilizes egg in fallopian tube with help of uterine contractions--> zygote --> cleavage (increase of number of cells which are tightly packed by tight junctions but size of zygote remains constant) --> morula (16 cells) with zona pellucida (ECM) --> blastocyst (ICM, blastocoel and trophoblast cells)-->implantation in uterus wall after protease on trophoblast cell membrane makes hole in zona pellucida so blastocyst can hatch and attach to endometrium with help of L-selectins (carbohydrate binding proteins)
32
ICM
inner cell mass; pluripotent cells that give rise to the embryo (ES- embryonic stem cells) and differentiates into hypoblast and epiblast layers on day 9 forming a flat bilaminar disc
33
Trophoblast cells
contribute to extra-embryonic tissues and differentiates on day 8 into cyotrophoblast (inner layer) and syncyiotrophoblast (outer layer)
34
ectopic pregnancy
abnormal blastocyst implantation which is usually fatal for fetus and harmful for mother
35
Placenta components
mother's uterine endometrium and baby's chorion
36
Chorions in twins
separate if split happens before formation of trophoblast during day 5 and shared if split happens between its formation on day 5 and aminon formation on day 9
37
Implantation
after week 1 and the trophoblast cells attach to the uterine wall epithelium
38
3 germ layers
ectoderm (skin and CNS), mesoderm (bone and muscle), endoderm (respiratory and digestive) formed from the bilaminar disc which is made up od ICM's layers (hypoblast and epiblast)
39
Gastrulation
**when the endoderm and mesoderm move from outer surface to inside giving rise to internal organs during the 3rd week of development
formation of a primitive streak which turns into the primitive node (narrow groove that organizes gastrulation events) surrounding a primitive pit. this is followed by invagination of epiblast cells
40
body axes
formed before and during gastrulation
41
neurulation
process by which the neural plate forms the neural tube and divides the ectoderm into 3 domains (surface, neural crest and neural tube)
day 25- closure of cranial end
day 28- closure of posterior end
42
Spina bifida
failure of neural tube closure at posterior end
43
Ancephalopathy
failure of neural tube closure at anterior end
44
Craniorachischisis
complete failure of neural tube closure
45
Folate
can help prevent neural tube defects (essential coenzyme)
46
neural crest cells
follow specific migration pathways from neural tube to contribute to several tissues (cranial, cardiac, trunk and enteric) and undergo an epithelial-to-mesenchymal transition
47
PCR and Southern blots in relation to Fragile X
PCR cannot detect the full mutation or larger pre-mutations due to allelic drop-out
Southern can detect it
48
what carries oxygen in the blood?
complex of heme, alpha globin chain, and beta globin chain
49
sickle cell anemia vs. thalassemia
sickle cell anemia- change in structure of globin chain
| thalassemia- change in quantity of globin chain
50
sickle cell anemia
mutation that alters Mnl I and Dde I restriction site
selective advantage in heterozygotes (sickle cell trait)
disadvantage/disease in homozygotes (sickle cell disease)-- Hb S/ Hb S
51
beta gene
in a cluster with 5 other beta globin-like genes on chromosome 11
* 5/6 are active in different times during development
* 6th= pseudogene which is inactive
52
Heinz bodies
alpha4 homotetramers which precipitate and cause destruction of the RBC
53
Alpha Thalassemia
mutations (usually deletions) involving the alpha globin genes leading to a deficiency of alpha globin
* thalassemia 1= 2 alpha genes deleted from same chromosome
* thalassemia 2= 1 alpha gene is deleted from each chromosome
54
alpha gene
alpha 1 and alpha 2 are in a cluster on chromosome 16 with 3 alpha globin-like genes
*2 of the 3 alpha globin-like genes are pseudogenes
55
HbH
disease when 3/4 alpha genes are deleted forming beta4 homotetramers which form inclusion bodies that destroy the RBCs
56
Hydrops Fetalis
having no alpha genes--> lethal
57
locus control regions
coordinate the appropriate developmental expression of the genes within the alpha globin and beta globin gene clusters they also coordinate
58
Hereditary Persistence of Fetal Hemoglobin (HPFH)
results when the delta and beta globin genes are deleted and the gamma globin gene continues to be expressed later in development than usual
*this can compensate for the lack of beta globin chains in patients who also have beta thalassemia
59
cystic fibrosis
progressive chronic lung disease with pancreatic insufficiency caused by one of 1900 CF disease causing mutations such as delta F508
*no locus heterogeneity
60
probability of further CGG expansion in Fragile X
related to size of expansion in female carrier
61
Sherman paradox
effects of Fragile X occur more frequently with each passing generation
62
when does critical movement occur?
when hemoglobin shifts from oxygenated to deoxygenated state
63
what occurs at birth in terms of globin genes
gamma gene activity is replaced by beta gene activity
64
Hb Constant spring
mutation of UAA to CAA in normal termination codon 142 so that a longer and unstable alpha chain mRNA is produced (+31 AAs)
*results in tetramers of beta globin chains (Hb H) which do not release O2 in the peripheral tissues
65
cluster analysis
method to display DNA-microarray data
66
nucleic acid hybridization
annealing one strand to its complement
67
restriction enzymes
cut at specific DNA sequences
68
cloning
isolation and amplification
69
T4 DNA ligase
connects what was cut by restriction endonucleases
70
vectors
move, manipulate and amplify DNA
71
bacterial plasmids
transfer antibiotic resistance genes
72
bacteriophage lambda
reproduces genome by rolling circle replication
73
cosmids
gutted out bacteriophage lambdas that only contain a sequence to replicate DNA and package it into viral particles
74
BACs
way to fool bacteria to carry large pieces of DNA
75
YACs
way to carry human genomic fragments in yeast
76
library
recombinant DNA clones
77
genomic library
bacteria with plasmids containing human DNA fragments that were fragmented by restriction nuclease and put into plasmids by ligase
78
cDNA library
based on expression
79
Kalydeco
increases the time the CFTR channel remains open in G155Dmutated CF patients
80
dynamic mutation
disease becomes more severe with each generation and the greater the copy number, the more likely expansion will occur
* meiotic instability
* repeat expansion=genomic instability
81
two classes of pathologic mechanism
1. non-coding (loss of function)
- alter the stability or splicing of the mRNA
- disrupt regulatory elements or change gene dosage
2. coding (gain of function)
82
where is the oocyte fertilized
the ampullary region of the uterine tube
83
week 1 of embryogenesis
start- oocyte is fertilized
end- blastocyst implants into uterine wall
**cleavage of zygote to morula to blastocyst
84
what does the fertilization of oocyte create
diploid zygote
85
series of cleavage mitotic divisions
reduces the size of the cells and increases the number of cells
86
timing of cell clevages
(30 hrs)- 2 cells
(40 hrs)- 4 cells
(3 days)- 16 cells
(4 days)- late morula
87
compaction
after cleavage to 8 cells, there is maximum cell-cell adhesion which is stabilized by tight junctions
88
cavitation
trophoblast cells secrete fluid into the morula to create a blastocoel
89
totipotent
(morula); can differentiate into any cell type including extra-embryonic tissues
90
pluripotent
(ES cells); can differentiate into any cell type in the body
91
zona pellucida
extracellular matrix of the egg essential for sperm binding during fertilization and acts as a protective layer
*embryo hatches from here to adhere to uterine wall (implantation)
92
how does blastocyst attach to uterus
L selectins on trophoblast cells attach to carbohydrate receptors on uterine epithelium
* rolling and tethering
* proteases from trophoblasts degrade extracellular matrix of uterine tissues enabling blastocyst to bury itself within uterine wall
***abnormal= ectopic pregnancy (outside the uterus)
93
cytotrophoblast
inner that adheres to endometrium
94
syncytiotrophoblast
outer that furthers the progression of the embryo into the uterine wall by digesting uterine tissue
95
two components of placenta
uterine endometrium (maternal portion) and chorion (baby portion)
96
days of formation for chorion and amnion
chorion- day 5
| amnion- day 9
97
invagination
when epiblast cells migrate towards the primitive streak and slip beneath it during gastrulation giving rise to endoderm and mesoderm
98
ectoderm gives rise to:
CNS, neural crest and outer surface
99
mesenchyme
loosely organized connective tissue of any origin
100
FISH
fluorescence in situ hybridization that combines cytogenetics and molecular diagnostics
*used to determine if a gene, a specific mutation or a particular chromosomal rearrangement is present or absent using a well characterized and specific probe (that just covers the critical region and not the entire deletion)
101
control probe in FISH
used to make sure that a missing signal is due to a disease related issue and not a technical error (failure of probe to bind to target)
102
person with a deletion- what will be detected with FISH if there is a control
two signals on one chromosome and a single signal on the deleted chromosome (which would be the control probe)
103
the three types of FISH
1. repeat sequences
2. single copy DNA
3. chromosome painting
104
repeat sequences probes
isolated from telomere or centromere regions
| *recognizes base repeats present such as in a telomere
105
unique/single copy sequence probes
isolated from cloned DNA of a disease-causing gene or fragment of DNA known location associated with a particular gene
*identifies presence or absence of gene, gene region or chromosomal rearrangement of interest
106
sub-telomere probes
DNA sequences from the distal ends of the chromosomes in region sproximal to the actual telomere regions
*identifies very small deletions and rearrangements that cannot be seen by standard karyotype analysis
107
chromosome painting
cocktail of many unique DNA fragments from along the entire length of a chromosome such that following hybridization, the entire chromosome fluoresces
108
critical region of deletion
probe covers this region as opposed to the entire deletion
*could cause miss of other abnormalities that occur within the same gene that is outside of the region associated with the probe
109
contiguous gene syndromes
associated with a particular region in the genome where a group of adjacent genes are all related to a particular outcome even though individually, the normal functions of those genes are unrelated
110
Williams Syndrome
7q contiguous gene syndrome associated with the deletion of the elastin gene (ELN) and those adjacent to it leading to issues that occur without elastin and also low IQ, blue sclera, terribly math skills and stellate iris (which have to do with the unrelated genes that were also affected)
111
Velocardiofacial syndrome
VCFS- interstitial microdeletion on chromosome 22 including 40 genes and 8 pseudogenes in which there is an error during crossing over due to similarities in the sequences of the repeats
*cleft palate and conotruncal heart defects; learning disabilities
112
why parents may not be affected in those with VCFS
different set of alleles than the combination that the child has.
normal chromosome in parent may have alleles that could compensate for what is missing on the deleted chromosome
113
gene chip technology
*test DNA is compared to a reference DNA that has a known genetic component
gene arrays--> looking at specific DNA sequences
expression arrays--> looking at gene products to understand which genes are being expressed in a particular cell type at a particular time
114
gene arrays
identify: genetic polymorphisms, specific mutations or copy number variation (CNV)
* won't detect balanced rearrangements since chromosome number does not change in this case
115
expression arrays
detects high levels of expression (red) and low levels of expression (green) by labeling a cDNA, made from RNA extracted from a tissue of interest, with fluorochrome
116
chromosome microarray
```
peaks= duplications
valleys= loss
```
117
when should microarray analysis by the first study done?
in unexplained cases involving: developmental delay, intellectual disability, autism spectrum disorders and multiple congenital anomalies
118
next generation sequencing
provides a high resolution genome wide scan that will detect mutations associated with an individual's medical concerns
**usually targeted so there isn't an overwhelming amount of information
119
homologous gene
genes in different species that have similar structure, evolutionary origin and function
120
genome equivalence
genetic material is identical in every cell but different genes express different sets of genes
proven by cloning since somatic cell nuclei contain all of the genes necessary to generate an adult organism
121
differential gene expression and what it controls
genetic material is identical in every cell but different cell types express different sets of genes
controls fundamental cellular processes:
1. proliferation
2. movement
3. specialization
4. interaction
122
RNA in situ hybridization
technique use to detect mRNA expression in cells or tissues
123
induction
when one group of cells changes the behavior of an adjacent set of cells
* requires- inducer and responder with its ability to respond to the signal (competence)
* signals are often transmitted via paracrine or juxtacrine signaling
124
optic vesicle in frog Xenopus laevis
optic vesicle induces formation of lens in the anterior/head portion of ectoderm with help of Pax6 (TF) to provide competence
*no optic vesicle--> abnormal or absent lens
125
Pax6
transcription factor that provides competence to help lens respond to inducer (optic vesicle)
126
morphogens
paracrine signaling molecules that cause concentration-dependent effects that direct target cells into different developmental pathways
ex. zebra fish embryo
127
signaling cascases
extracellular signaling molecule binds to receptor thus changing its conformation and giving it enzymatic activity in the cytoplasm--> cascade of phosphorylation processing activating a TF in the nucleus that binds DNA and alters gene expression in the cell
ex. Transforming growth factor - beta (TGFBeta)
128
Sonic hedgehog homolog
turns on transcription of target genes
*example of signal transduction cascade
129
3 types of hedgehog homologs
1. desert
2. indian
3. sonic
130
situs solitus
normal symmetry
131
situs inversus totalis
complete mirror-reversal of organ LR asymmetry
132
heterotaxy
situs ambigus--> which can cause congenital disease
133
asplenia
right isomerism
134
polysplenia
left isomerism
135
cardiac looping
aligns chambers and vascular connections of the heart
136
Kartagener's syndrome
bronchiectasis
infertility
situs inversus (50%)
*suggests that ciliary beating somehow controls which way the left-right axis is oriented (asymmetric fluid flow--> signaling cascade which drives morphogenesis)
137
mitochondrial diseases
mutations of ox/phos
*mutation rates are high
most serious in CNS and muscle
commonly includes: neuropathies, encephalopathies and myopathies
usually progressive with late onset
138
mitochondria
has its own set of genes but depends on the nuclear genes since it is not a self sufficient organelle
139
homoplasmy for mitochondrial genes
same genetic composition
140
heteroplasmy for mitochondrial genes
2+ different populations of mitochondria present in a cell
141
differences in mitochondrial mutations
different levels of mutant mitochondrial lead to a range of phenotypes
*different tissues may receive different numbers of mitochondria resulting in differential expression of phenotype
142
diagnosis of mitochondrial mutations is complicated by:
1. heteroplasmy and variable expression
2. maternal inheritance
3. progressive nature of disease
143
DNA analysis
examine the regions of the DNA that have the highest degree of polymorphisms
144
sources of error in forensic DNA analysis
1. quality of specimen
| 2. statistical analysis and interpretation
145
mitochondrial analysis
siblings carry the same mitochondrial DNA due to same maternal inheritance
146
nuclear DNA analysis
able to identify individuals whereas mitochondrial analysis is only able to identify maternal lineage
147
congenital malformations
structural
metabolic
functional
behavioral
148
most common birth defect
congenital heart disease
149
Axenfeld-Rieger Syndrome
the result of a mutation in a two genes (FOXC1 and PITX2) and can alter the development of multiple systems
*primarily an eye disorder but can affect face, teeth, and belly button
150
PITX2 and FOXC1
mutated in Axenfeld-Rieger syndrome
| **produce transcription factor proteins that help the development of the eyes
151
complex traits
*multifactorial
| complex traits have many contributing genes and non-genetic influences
152
Holoprosencephaly
due to the failure of the forebrain/prosencephalon from dividing
* environmental factor= maternal diabetes
* genetic factors= chromosomal abnormality (deletion/duplication) or mutation in a single gene; multiple genes that use the hedgehog signaling pathway could be the cause
*autosomal dominant
153
SHH
human sonic hedgehog gene that could be mutated leading to a loss of function
154
Congenital rubella syndrome
if a mother is exposed to rubella viral infection, her embryo could have abnormalities including microcephaly, PDA and cataracts
*this could lead to congenital rubella syndrome in which the baby has heart defects and can be deaf
155
Hyperthermia
can interfere with neurulation and cause neural tube defects
| *example of how infectious agents could cause birth defects
156
which environmental factors could cause birth defects?
```
infectious agents
pharmaceutical agents
ionizing radiation
hyperthermia
metabolic conditions in the mother
```
157
Thalidomide
a pharmaceutical agent for morning sickness that caused a birth defect (limb defect) due to the induction of oxidative stress or disruption of angiogenesis
158
Teratology
the study of birth defects from environmental causes (such as drugs, infectious agents, hyperthermia, ionizing radiation and metabolic conditions of the mother)
159
teratogen
agents that cause birth defects
160
FASD- Fetal Alcohol Spectrum Disorders
all alcohol-related defects
* alcohol is the major cause of congenital mental retardation
* severity based on amount, timing and genetics
161
FAS- Fetal Alcohol Syndrome
most severe of the FASD; microcephaly, narrow upper lip, indistinct philtrum, flat midface, low nose bridge
*brain size and development are affected
162
how does alcohol affect an embryo?
interferes with cell migration, proliferation, adhesion, survival and signaling
*several genes are misregulated following exposure to alcohol
163
antidepressants and birth defects
SSRIs could cause: heart defects, persistent pulmonary hypertension, neural tube defects, cleft lip and palate and autism
*teratogen
164
embryonic period
weeks 3-8 in which the embryo is most susceptible to birth defects from teratogens
165
congenital heart defects (ASD and VSD)
10% of all fetuses and is associated with laterality defects
Atrial septal defect (hole in septum that separates atria)--> LA to RA (then back to lungs) instead of going to the LV which would have pumped the oxygen-rich blood to the body
Ventricular septal defect (hole in septum that separates ventricles)--> oxygen-rich blood from LV to RV instead of the aorta
* usually from multifactorial causes
* same malformation can result from disrupting different targets
166
Dextrocardia
heart is positioned on the right side of the thorax instead of the left
167
heterotaxy in congenital heart malformations
could lead to:
1. septal defects
2. double outlet RV (DORV)
3. transposition of great arteries (TGA)
168
signs and symptoms of congenital heart defects
cyanosis, rapid breathing, fatigue, poor circulation
*cyanosis= oxygen-poor blood from the right side of the heart enter the left side of the heart directly instead of traveling to the lungs for more oxygen
169
22q11.2 deletion syndrome
3 million bp deletion on chromosome 22
autosomal dominant
*malformations of the cardiac outflow tract that are likely caused by defects in cardiac neural crest development
* truncus arteriosus
* tetraology of fallot
170
Truncus arteriosus
one common blood vessel combining the aorta and pulmonary artery
*single common valve (truncal valve) which has a mix of oxygenated and de-oxygenated blood
171
tetralogy of fallot
4 defects of the heart and its blood vessels:
1. VSD (ventricular septal defect)
2. pulmonary stenosis- pulmonary valve and artery are narrowed
3. overriding aorta- increases flow
4. ventricular hypertrophy
172
outflow tract
remodels to form the aorta and pulmonary artery in heart development
*cardiac neural crest cells contribute by migrating from dorsal neural tube to arterial pole
173
familial abnormality
parent is a known carrier of a structural chromosome rearrangement of there is a previous child which a chromosome abnormality
174
consanguinity
increased risk of inheriting deleterious alleles
175
MSAFP
maternal serum alphafetoprotein which is associated with fetal abnormalities
* measured in blood and refers to the AFP produced by the fetal liver that crosses the placenta
* correlates to age of gestation
* test is sensitive to various variables
* risk assessment, not diagnosis
176
age and risk of abnormalities
the greater your age, the higher the chance of chromosomal abnormalities
177
invasive sampling
a needle or other device is inserted to collect fetal cells, tissues or fluids
178
ultrasound
18 weeks
nuchal translucency ~ possible abnormality
-detects defects that are associated with known syndromes (neural tube defects, clefting) and anomalies due to isolated organ defects
179
anencephaly and encephalocele
anencephaly- absence of brain (lethal)
| encephalocele- brain is extruded from skull
180
AFP
albumin-like protein produced by the fetal liver that crosses the placenta and can be detected in mother's blood (MSAFP)
*correlated to age of gestation
181
maternal serum quad test
four different pregnancy related proteins increases the level of significance
*15-21 weeks
182
integrated pre-natal testing
low PAPP-A= increased risk for DS
| *10-13 weeks
183
NIPS/NIPT
non-invasive prenatal screening
184
cfpDNA
10-22 weeks
10-15%= fetal in origin
*DNA sequencing can be done to identify each individual fragment of cfpDNA and determine the chromosome of origin
185
aneuploidy
any increase or decrease in the total value for a particular chromosome
*screening test that needs to be confirmed by a diagnostic test
186
2 non invasive tests and 2 invasive tests
noninvasive- US, MSAFP
| invasive- aminocentesis and chorionic villus sampling
187
aminocentesis
needle is inserted through abdomen into amniotic cavity to withdraw amniotic fluid for testing
*16-18 weeks
*removing too much fluid or performing this before 13 weeks can result in developmental defects
188
AFAFP (and the meaning of high AFP and low AFP)
fetal analog to MSAFP and is a test done on the amniotic fluid retrieved from the aminocentesis procedure
*screening test that confirms MSAFP findings
* low AFP = trisomies, mosaic turner syndrome, triploidy, unbalanced translocations (confirmed by karyotype analysis)
* high AFP= ONTD, teratoma, renal agenesis/obstruction, uropathy, upper GI obstruction, bladder/cloacal exstrophy (confirmed by AChE testing)
189
AChE
confirms high AFP levels
| *ACH is obtained from the neural tube
190
chorionic villus sampling
invasive test
10-12 weeks
transabdominally or transvaginally
*good test to give an early option for termination
* <10 weeks= risk of limb reduction
* samples the PLACENTA (since placenta and fetus are derived from the original zygote and thus are usually biologically the same)
* therefore, it requires the placenta and the fetal cells to be the same
191
64 cell embryo components
3- fetal
10-12- amnion/yolk sac
50- chorion/placenta
192
confined placental mosacism
only the placenta has the mutation so the CVS will incorrectly assume the fetus is affected
193
confined fetal mosacism
only the fetus has the mutation and this will not be detected with CVS since this test only takes a look at the placenta
194
genetic counseling
NON-DIRECTIVE- provide the patient with all the relevant information so that they can make their own decision
*risk assessments (from inheritance patterns and recurrence risk) are developed/presented
195
ART- Assisted Reproductive Technologies
1. IVF (in vitro fertilization)
2. ICSI (intracytoplasmic sperm insertion)
3. ZIFT (zygote intrafallopian transfer)
4. donor egg
196
ICSI
intracytoplasmic sperm insertion
* single sperm is injected into an egg
* following fertilization, embryo is implanted into female
* for males with low sperm count
197
ZIFT
zygote intrafallopian transfer
* donor egg or sperm
* in vitro fertilized eggs are transferred to fallopian tube
198
IVF
in vitro fertilization
* eggs and sperm from partners are mixed in vitro
* after fertilization, embryo is implanted
199
polar body analysis
allows for embryo selection when it is known that parents are carriers
* if polar body has mutation, then the egg doesn't
* if the polar body does not have a mutation, then the egg does
200
pre-implantation genetic diagnosis
screening technique for embryos at the 8 cell stage in which a single cell is separated out and a general assay looks for chromosomal aneuploidies (FISH or molecular assay)
*karyotype analysis is not used because you will not have a metaphase cell to evaluate
201
donor egg
used for those with Turner Syndrome or mitochondrial mutations
*donor egg is mixed with father's sperm and implanted in woman's uterus (she can experience being pregnant and the baby will be at least biologically from the father)
202
the importance of proteins
- the machinery of life
- when defective, they cause genetic disease
- catalyze and control chemical reactions
- transmit information
- their structure affects their function
- the target of drugs
203
proteome
all of the proteins within a cell
204
Tipranivir
anti-HIV drug that is similar in structure to the natural peptide substrate but is non-hydrolyzable
205
AD
characterized by a misfolded protein (amyloid fibers) that occurred from the improper cleaving of the precursor protein (APP) which is 42 residues and should have been cleaved to 40
*extra two AA's --> conversion to a toxic/sticky peptide that builds up in the brain
206
protein folding
a polypeptide will spontaneously loop back and forth on itself to form a roughly globular, highly compact, 3D structure
207
formation of a peptide bond
```
condensation reaction (loss of H2O)
charges of terminal amino and carboxyl groups is lost
```
*planar (which reduces bond rotations to 2) and trans
208
Ramachandran map
tells the small fraction of phi and psi values that are allowed due to the limited amount of space (more are allowed for Gly due to fewer repulsions because of -H side chain)
209
pKa's of Asp, Glu, His, Cys, Lys, Arg, and carboxy and amino terminus
4, 4, 6.5, 8, 10, 12 (DGHCKR)
| 4, 8
210
Aromatic hydrophobic
MWFY
211
Aliphatic hydrophobic
PILVA
212
hydrophobic
poorly soluble in water and these residues would rather associate with themselves than with water
213
pKa
the pH at which half the ionizing groups are protonated and half are deprotonated
*can be changed by environment
```
high= tight bind to H+ (will protonate)
low= weak bind to H+ (will deprotonate)
```
214
polar side chains
presence of electronegative atoms- S,O,N (strong electron withdrawing effect)
*do not accept of give up another H+ except at extremely low or high pH
215
disulfide bond formation
oxidation of two -SH groups
| *introduction of cross links
216
what allows proteins to adopt their shape?
non-covalent forces that are individually weak
*folded proteins are instable allowing them to unfold and refold (dynamic structure)
217
electrostatics
a non-covalent force that helps fold proteins due to the interaction between charges (based on Coulomb's law)
218
Fo ring of ATP synthase
buried charge (rare)
219
dipole
partial positive and partial negative charges without a formal net charge
* energetically favorable when aligned antiparallel (like in beta sheets)
* aligned in a parallel fashion in alpha helices
220
hydrogen bonding
electrostatic attraction in which Hs bound to electronegative atoms (S,O,N) end up with a more positive charge since these atoms pull the electron density of the H towards them
221
the 4 non-covalent forces
1. electrostatics
2. H bonding
3. van der waals
4. hydrophobic effect
222
H bonding
directional component (strongest when atoms lie in a straight light)
* S,O, N are electronegative and pull the electron density from H atom causing partial positive and partial negative to occur
* acceptor and donor
223
van der waals
non-covalent force
* electric dipole that is induced when two atoms are brought close together
* transient dipole= when electron density is temporarily asymmetric
*maximized when proteins fold
224
core packing in ubiquitin
nonpolar on inside and polar on outside
*repacking will causes changes such as gaps or crowding
this causes destabilization--> will not fold
225
hydrophobic effect
tendency of hydrophobic/nonpolar molecules to interact with themselves instead of water when place in aqueous solutions which is due to the properties of water
**driving force for folding
*hydrophobic molecules lack charge, polar groups and H-bonding groups
226
secondary protein structures
when non-covalent interactions are turned on forming:
1. alpha helix
2. beta sheet
3. beta turn
they are short, simple repeating structures
227
tertiary structures
when secondary structures interact with one another and form 3D conformation that is held by short and long range interactions
228
alpha helix
proteins are 31% alpha helix
NH of i residue to CO of i + 4 residue
3. 6 residues a turn (favorable backbone dihedral angles)
5. 4 Angstroms a turn
229
stabilizing interactions of alpha helices
backbone-backbone (H-bonding)
side chain-backbone (permanent dipole)
side chain-side chain (periodicity=4)
230
helix formers and breakers
former- Ala
breaker- beta branched or bulky--> Pro, Gly
indifferent- long and straight (rotate fairly well)
231
beta sheet
28% of protein
straight, extended and H bonded at each peptide group
periodicity=2
* pleated
* strands could be parallel (H-bonds are bent) or anti-parallel (which is seen more often)
232
what portion of residues are involved in tight turns?
1/3 (Pro- kinks; Gly- relieve steric clashes)
233
loop
lack regular H-bond conformations and aren't secondary structures
*not periodic
234
domains
assembled secondary structures forming distinct patterns (folds)
*stable and semi-independent units of structure
235
motif
short stretches of secondary structures and are usually not stable by themselves
236
HTH
helix-turn-helix
motif in which proteins recognize specific sequences of DNA
*recognition alpha-helix and a support alpha-helix connected by a turn
237
recognition alpha helix
sits in the major groove and binds to specific sequences of nucleotides (part of HTH- helix-turn-helix motif)
238
zinc finger motif
DNA binding motif
* Zn2+ holds it together without the need for a hydrophobic core
* hydrophobic side chains stabilizes the helix which binds to the major groove of the DNA
239
coiled-coil
heptad repeat
- found in fibrous proteins and TF's
- protein-protein recognition, mechanical force transduction, viral penetration
ex: GCN4 TF
a,d- glue
e,g- electrostatics
240
influenza haemagglutinin
harpooning mechanism to gain entry into cell
triple-stranded coiled-coil
* virus is endocytosed into a vesicle that becomes acidic due to vacuolar ATPase proton pumps...conformational change and then extended loop folds into alpha helix and the coiled-coil lengthens which then thrusts outward and penetrate the vacuolar membrane
* fusion of two membranes--> release of viral RNA into the cell causing infection
241
Hsp70
chaperone protein that prevents aggregation by covering up sticky hydrophobic patches
242
Hsp60
chaperone protein that is shaped like a hollow donut and allows the misfolded protein to come in. GroES cap seals it and ATP hydrolysis will unfold the misfolded protein so that it could be properly folded
243
GroEL/GroES mechanisms
isolation (Anfinsen box), confinement, forced unfolding (iterative annealing)
244
3 enzymes of ubiquitination
E1- activating enzyme
E2- conjugating enzyme
E3- ligating enzyme
245
protein degradation/turnover
goes one of two ways--> lysosomes/proteases or ubiquitin/proteasome pathway
246
ubiquitination
ligation involves ATP is it is the binding of ubiquitin to epsilon-amino group of Lys of the protein
*polyubiquitination chain (Lys are attached)
then degradation by the proteasome*
247
degradation by the proteasome and its structure
26S that has a 20S core and 19S caps
protein threaded through 20S which is where ubiquitin is taken off so it could be reused
20S degrades it (ATP helps unfold the protein) and 19S influences the cleavage
either sent to ER or recycled which requires further degradation
248
diseases of ubiquitin-proteasome pathway
cancer (degradation of tumor suppressors)
neurodegenerative diseases (accumulation of ubiquitin proteins in plaques)
CF
autoimmune
249
molecular basis of protein disease and how balance of structure matters
loss of protein function
gain of function
alternate conformations/aggregates
direct knockout- mutation in a residue--> altered critical side chain
destabilization- unfolded
toxic conformation- incorrectly folded
250
p53 function and structure
function: tumor suppressor protein that functions to cause cell death in the presence of DNA damage
* prevents the accumulation of chromosomal mutations
structure: (modular) DNA binding domain, C-term, disordered N-term
251
DNA, contact and stability mutants
DNA- alters side chains
contact- reduces DNA binding
stability- decreases thermodynamic stability
252
how is p53 normally degraded
p53 activates transcription of its own E3 ubiquitin ligase MDM2
253
PhiKan083
small molecule that stabilizes the folded state of a mutated form of p53 (Y220C tumorigenic mutations)
254
treatment options for delta F508 CFTR mutation
CF patients
-small organic molecules (helps stabilize folded protein)
-chaperones (prevents misfolding)
inhibiting degradation by ubiquitin/proteasome pathway
255
alpha 1- AT deficiency
```
Z type (Glu 342--> Lys) and S type (Glu264--> Val)
*causes liver disease or emphysema
```
*usually is an inhibitor of polypeptide cleavage (serine protease inhibitor)
256
serpins
3 beta sheets and 9 alpha helices
target protease cleaves an internal site in reactive center
binding to target protease prevents it from binding substrate
257
alpha 1 AT
uses stored energy to trap its target
target protease binds and cleave reactive center loop (RCL)
RCL goes into beta sheet and drags the protease with it
*the central beta sheet must be flexible enough to accept the RCL as part of the normal inhibitory process
258
polymerization of alpha 1 AT
central beta sheet opens and allows part of the reactive loop of a second protein to inset into the lower portion of the sheet and stable (beads-on-a-string) aggregates form
*can be blocked and reversed by peptides
259
what is used to stain CJD
thioflavin T and congo red to detect amyloid plaques
| *vCJD forms vacuoles
260
TSE
transmissible spongiform encephalopathies
261
what reduces infectivity of prions
protein denaturants (NaOH, SDS)
262
PrP^sc
insoluble and protease resistant
* come together and form stable beta sheet
* forms seed since it is the building block for amyloid fibril
263
structural models of PrP^sc
a) trimer stacks
b) beta sheet backbone- PrP attach and spiral
c) extended sheet- stack of parallel beta strands
264
definition of amyloidosis and prevention mechanism
the formation of amyloid fibers from misfolded PrP^c
prevention-
1. reduce the amount of PrP^c by silencing siRNA
2. stabilize PrP^c by binding compounds to prevent it from changing to PrP^sc
3. immunotherapy to clear the toxic substance from the species
265
AD
incorrectly cleavage of APP leading to the formation of ABeta42 (beta amyloid) that has two extra residues
*small, soluble aggregates of the misfolded peptide that form before the mature amyloid fibril cause neuronal cell death
266
ABeta42
parallel in-register beta sheet stabilized by side chain interactions
267
problems with AD treatment ideas
inhibiting secretase could affect other cellular pathways besides ABeta
blocking fibril formation may cause pre-fibrillar aggregates to accumulate (pre-fibrillar species disrupt cell membranes)
268
insulin and IAPP
higher insulin causes higher IAPP which binds to lipid bilayers which accelerates the rate of formation of amyloid fibrils
269
peptide inhibitors of ABeta and IAPP fibril formation
stabilized by side chain side chain interactions and peptide peptide H bonds so blocking peptide nitrogens on the growing face of the beta strand prevents the formation of H bonds to neighboring peptides
*beta sheets and thus capped and prevented from growing
270
mature fibril
helps protect the cell membrane from being disrupted
| *process of amyloid fiber formation is what is harmful
271
tumor
benign or malignant
| overgrowth of abnormal cells
272
malignancy
significant changes in karyotype of the cells
273
metastasis
cells become invasive or migrate to another site but retain the original cell morphology
274
sarcoma
type of cancer of the mesenchymal tissue
275
carcinoma
type of cancer of the epitheloid tissue
276
how are cancers classified
location
tissue type
degree of malignancy
277
exposure to environmental mutagens
could lead to changes in normal cell regulation and/or development
278
CIN
chromosome instability: gain, loss or rearrangement of chromosomes
279
oncogene
associated with unregulated cell proliferation that can change host cells
normal: proto-oncogenes which can be mutated (increase in activity) to become oncogenes= gain of function
*only one mutation required
280
CML
chronic myelogenous leukemia
-translocation of chromosomes 9 and 22 resulting in chimeric protein (combination of proto-oncogene and 2nd gene) which causes the loss of control and increase in tyrosine kinase
281
Gleevec
drug targeted at inhibiting the overproduction of tyrosine kinase from the translocation of chromosomes 9 and 22 in CML (chronic myelogenous leukemia)
282
APL
acute promyelocytic leukemia
- translocation of chromosomes 15 and 17 which breaks the PML gene on chromosome 15 and the RARA gene on chromosome 17
* chimeric protein product--dual fusion probe
283
tumor suppressor
gatekeepers (prevent tumors by regulating cell cycles) and caretakers (repair DNA damage); tissue specific
mutation-recessive since it requires 2 mutations (loss of function)
loss or inactivation will lead to a change in phenotype and ultimately neoplasmic growth
284
examples of tumor suppressors
P53 Rb1
285
Rb1
tumor suppressor gene located on chromosome 13 that controls the progression from G1 to S
286
Retinoblastoma
mutation of Rb1 and affects the eye
- sporatic-unilateral
- inherited-bilateral; all of the cells of the body will have the mutation and symptoms occur earlier
secondary cancer= osteosarcoma (cancer of the mesenchymal cells of the bones)
287
Li Fraumeni
familial cancer syndrome associated with multiple neoplasia and an inherited mutation of p53
288
Breast cancer
familial or sporatic
- mutations from errors in homologous recombination and DNA repair defects
- two genes associated- BRCA1 (near 17-p53) and BRCA2 (near 13-Rb1)
* *survivor guilt, affected males
* increased risk in Ashkenazi Jews
289
caretaker mutations
defect in DNA repair ability
| *breakage syndromes- leads to deletion and genomic defects
290
triradicals
Y shaped chromosomes from being instable
291
HNPCC
hereditary nonpolyposis colon cancer
* error in mismatch repair genes
* **malfunction in a normal cellular process
- 90% risk in males who inherit one mutation
292
what does microsatellite analysis detect?
mismatch repair defects alter total number of repeats so presence of extra bands is indicative of a disease diagnosis (ex. HNPCC)
293
proto-oncogenes vs tumor suppressors mutations
proto- GOF, chromosome translocation, amplification
| tumor- LOF, deletions, chromosome loss
294
clonality
a normal cell may have a single mutation which proliferates and generates an abnormal clone
acquired change in a limited number of cells in which further chromosomal changes may modify the karyotype and produce additional clones
295
loss of heterozygosity
loss of the entire gene and surrounding chromosomal region
296
remission and relapse
suppression of a disease by a treatment but if the symptoms recur and tests indicate that the genetic abnormality has returned, the patient is considered to be in relapse
297
Somatic stem cells
can only differentiate into the cell types present in the tissue of origin
298
autologous vs allogeneic
from self vs from matched donor
299
mRNA processing
making RNA usable for protein synthesis
300
central dogma
genetic information flows from DNA to RNA to protein
(some viruses use RNA as a source of genetic information and template for replication- Polio; whereas HIV converts RNA into DNA to integrate it into the host genome)
301
mRNA
carry information coding for proteins
302
special feature of RNA
is single stranded and can fold up or base pair with other nucleic acids (DNA or RNA)
303
RNA-RNA hybrids
ribozymes (catalytic)
| miRNA (regulatory)
304
terminators and promoters
promoter- start sequences located at 5' (not transcribed)
*orientation dictates which strand will be transcribed
terminator- stop sequence located at 3' (transcribed even though is non-coding)
305
steps of transcription
1. initiation
* **cells regulate which proteins are produced and at what rate
2. elongation
3. termination
306
5' and 3' UTR
sequences prior to the first AUG initiation codon and after the termination codon present in RNA transcripts that are not translated (untranslated sequences)
307
differences between RNA and DNA polymerases
RNA-
rNTPs instead of dNTPs
Uracil instead of thymine
de novo without primers instead of using primers
no exonuclease activity instead of exonuclease activity
308
RNA polymerase II
transcribes protein-coding genes
* eukaryotes have two more types (I, III)
* bacteria- only have one type commonly targeted by antibiotics
309
Amanita phalloides
poisonous mushrooms that contain a toxin, alpha-amanitin that inhibits eukaryotic RNA polymerase II
310
RNA Pol II transcription steps
TBP (TATA binding protein) binds to TATA box
TFs are recruited
RNA polymerase is recruited
**formation of pre-initiation complex
phosphorylation of RNA pol II
recruitment of enzymes
pol II leaves promoter and transcribed mRNA
***co-transcriptional covalent modification
(bacteria- modification does not occur and mRNA is translated immediately)
311
prokaryotic vs eukaryotic translation
prokaryotes- mRNA is translated co-transcriptionally without modification
eukaryotes- mRNA is processed then transported out of the nucleus into the cytoplasm where mRNA can be translated into protein
312
modification of eukaryotic mRNA
covalent modification that occurs co-transcriptionally
*5' capping (5'-5' linkage of 7-methyl G to RNA) and 3' polyadenylation (non-templated)
- stabilizes the mRNA by protecting it from degradation
- modifications are necessary for nuclear export and translation initiation
313
creation of mature mRNA
introns are removed (and then degraded) by mRNA splicing from the pre-mRNA (primary transcript) to become the mature mRNA
314
snRNPs
recognize specific sequences at introns and cleave them while covalently linking exons together (RNA splicing)
*lariat intermediate*
315
lariat formation
intermediate in RNA splicing which contains an unbranched intron sequence that has a unique 2' to 5' phosphodiester linkage and is released and degraded
cut at 5' end of intron and attaches to adenine forming a loop
* free 3' end of EXON reacts with beginning of second exon sequence that is attached to the intron thus cutting the intron at its 3' end
* lariat (loop of intron)
316
alternate splicing
genes can be spliced in various ways to produce different mRNAs (protein isoforms from same gene)
*normally programmed event as opposed to splicing mutations which lead to Progeria
317
Progeria
splicing mutation
* normal= splicing of LMNA= lamin A
* 1824C-->T mutation leads to abnormal splicing deleting 150 bases from the mRNA removing 50 AAs
* abnormal progerin remains bound to membrane
318
OMIM
online mendelian inheritance in man
| *genetic information online database
319
similarity percentage between two individuals
99.5% similar
320
evidence of personalized medicine
drug therapy
idiopathic disease (spontaneous origin)
cancer diagnosis, prognosis, treatment (oncology)
prenatal testing and newborn screening
321
pharmacogenetics
relation of heritable variation with inter-individual variation in drug response
322
pharmacogenomics
field of new drug development based on out increasing knowledge of all genes in the human genome
323
pharmacokinetics
mechanisms of absorption and distribution of an administered drug
324
different outcomes of drug ingestion
drug- toxic or not toxic
| outcome- beneficial or non-beneficial
325
CYP2C19
mutation in a gene that leads to the inability to interact with the drug
326
cytochrome p450
gene family in which a variety of different enzymes are involved in drug metabolism (mutations will change enzyme's ability to perform function)
327
CYP2D6 and its classes of function
affects the ability of an individual to metabolize certain drugs
*classes of function
1. poor- no functional allele (cannot convert drug to useable form--accumulation of chemicals= toxic)
2. intermediate- one functional, one mutant (utilize drug at slower rate so require lower dose to prevent toxic build-up)
3. extensive- two functional alleles (work in expected fashion)
4. ultra- duplicate copies of functional alleles (degrades drugs rapidly so more of drug is needed to prevent degradation before therapeutic levels are reached)
328
Warfarin
synthetic anti-coagulant that inhibits the enzyme epoxide reductase which inhibits Vitamin K metabolism
(Vitamin K- clotting factors)
(Coumadin= natural anti-coagulant)
* garlic and ginger help it
* green veggies (vit K) decrease its effectiveness
329
thrombosis
blood clotting
330
genes that affect Warfarin metabolism
VKORC1 allele of the VKOR gene
| CYP2C9 of cytochrome p450 (involved in drug metabolism)
331
microarray technology in terms of personalized medicine
can be used to do a genome wide scan of an individual's genetic complement and utilized to manage the patient's health throughout life
*increased personal approach to individual disease
332
ROH
regions of homozygosity- kinship is same
| *identity by descent
333
GINA
genetic information nondiscrimination act
| *prohibits discrimination in health coverage and employment based on genetic information
334
3 types of screening
1. prenatal (MSAFP, AFAFP, maternal quad)
2. newborn (disorders- endocrine, hemoglobinopathies, infectious disease, inborn errors of metabolism)*required
3. carrier
335
similarities and differences between PWS and AS
both Prader-Willi Syndrome and Angelman syndrome have microdeletions of proximal long arm of chromosome 15 and FISH will detect their presence but clinical diagnosis will distinguish between the two
* PWS- gain weight quickly, temper, small hands and feet, hypogonadism, developmentally delayed
* AS- severely mentally retarded and laugh at inappropriate times, hyperactivity, short stature, microcephaly, seizures and ataxia
336
maternal vs. paternal origin difference
PWS- deletion on chromosome from father or maternal uniparental disomy (two copies of mother's chromosome)
AS- deletion on chromosome from mother or paternal uniparental disomy (two copies of father's chromosome)
337
how to detect UPD
molecular probe technology and microarray since in karyotype, homologs will look alike
338
heterodisomy
from different sources
*from nondisjunction error leading to trisomy and then a loss of one- 1/3 of time will lead to uniparental heterodisomy where as 2/3 times it will lead to biparental heterodisomy
339
isodisomy
```
duplicate copies (thus from same source)
*nondisjunction error followed by duplication
```
340
expected inheritance
biparental heterodisomy (can result from nondisjunction error causing trisomy in which one is lost (2/3 times it results in biparental heterodisomy whereas 1/3 of the time it results in uniparental heterodisomy)
341
imprinting
differential modification leads to differential expression of parental alleles during development and in the adult
not sufficient to have a pair- they need to be the correct configuration
* chromosomes look alike at the molecular level but there are important differences between male and female chromosomes
* associated with methylation of DNA (epigenetic modification)
342
methylation
epigenetic effect in which a methyl group is attached to a cytosine residue in DNA
* pattern lasts one generation (applied at meiosis)
* reimprinting (stripping down and replacement)
343
causes of PWS
1. deletion of paternal chromosome 15 resulting in only maternal alleles
2. UPD with only maternally imprinted alleles
3. imprinting error where complement is comprised of one chromosome from father and one from mother but paternal chromosome has a maternal imprint resulting in functionally only maternal alleles
**dads info is missing!
344
causes of AS
1. deletion of maternal chromosome 15 resulting in only paternal alleles
2. UPD with only paternal imprinted alleles
3. imprinting error where the complement is comprised of one chromosome from father and one from mother but the maternal chromosome has a parental imprint resulting in functionally only paternal alleles
**mom's info is missing
345
Paternal imprint genes
SNRPN
| necdin
346
Maternal imprint genes
UBE3A
347
epigenetics
the study of heritable changes in gene function that are NOT caused by change in the DNA sequence
*modification of transcription that alters gene expression
1. methylation (important in X inactivation and imprinting)
2. histone modification
3. chromatin remodeling
348
methylation in cancer
hypomethylation- development of oncogenes
| hypermethylation- inactivation of tumor suppressors
349
TF as epigenetic modifiers
bind to DNA to alter expression
350
miRNA as epigenetic modifiers
bind to mRNA and can alter expression
351
Rett syndrome
mutation in the MECP2 TF leading to lack of proper neural development causing a variety of negative phenotypic expressions
*disease severity is also linked to X inactivation since MECP2 is on distal long arm and is subject to X inactivation
****regions of methylated CpG that are normally repressed by recruitment of HDACs (deacetylation) are now activated
352
main site of gene control
initiation of transcription this affecting gene expression
353
examples of transcription diseases
cancer
R-T and Rett syndromes
thalassemia
354
eukaryotic DNA binding domains
contain a recognition alpha helix that inserts in the major groove of DNA and makes multiple contacts
355
operon
cluster of genes in bacteria that is transcribed from a single promoter
356
polycistronic mRNA
bacterial characteristic signifying that a single mRNA can create multiple proteins
357
operator
binding sites in bacteria for repressor proteins
358
activator
helps recruit and/or stimulate RNA polymerase to begin transcription
359
modularity
fusion of different factors could result in a novel activity (could be bad)
360
overexpression of HOX11
overexpression of protein in hemapoietic cells causing uncontrolled growth
361
what do transcription regulators recruit
```
RNA polymerase II
chromatin modifiers (loosened so pol II can bind)
```
*they increase the rate of transcription initiation
362
types of chromatin modifiers
covalent histone modifications
| ATP-dependent nucleosome remodeling (use ATP)
363
histone modifications
occurs on the Lys N terminal tails of H3 and H4
HATs- acetyltransferase--> activation
HDACs- deacetylases--> deactivation
* methylation (activation or deactivation)
* phosphorylation (coupled to acetylation)
364
chromatin remodeling enzymes
displace nucleosomes from promoters or reposition them thus clearing the way for the assembly of the transcription initiation complex
365
mechanisms that regulate TF synthesis and activity
covalent modification
intracellular trafficking
selective degradation
366
what causes drug side effects?
the fact that each regulator targets multiple genes
367
hematopoiesis is a good example of:
cell differentiation pathways being controlled by transcription regulators
368
how can you measure relative mRNA levels?
```
DNA microarray (large chunks)
RNA seq (whole genome)
```
369
Beta globin gene regulatory proteins
has two enhancers (upstream and downstream) that recruit chromatin remodeling complexes, histone modifying enzymes, the general TF and RNA polymerase
370
LCR mutation
locus of control region- when not expressed the (beta) gene is tightly packed into a heterochromatin-like structure
*if LCR is mutated, the gene is silenced and prevents (beta) globin production--> beta thalassemia
371
autoregulation transcriptional mechanism
transcription factor activates other genes but also its own gene
372
what does the HWE (Hardy-Weinberg Equation) allow us to do?
estimate how many people in a population are asymptomatic AR carriers and compare this to the likelihood of a new mutation
373
assortative mating
choosing mating like yourself
* reduces proportion of heterozygotes
* increases inbreeding and frequency of AR diseases
374
assumptions of HWE
1. random mating (in regard to disease gene)
2. large population (decreases chance for inbreeding and stabilizes allele frequencies)
3. no natural selection/constant selection
375
consanguinity
inbreeding (recent ancestor in common)--> increases homozygosity and AR diseases
376
drift
random change in allele frequency
377
outcome of no mutation
no variation or ability to adapt to environmental change thus no capacity to evolve
378
two types of breast cancer
lobular, ductus (lobes and ducts)
379
how does a breast tumor cell proliferate
it has estrogen receptors and when estrogen binds it proliferates
380
how to stop breast tumor cell proliferation
drugs- Tamoxifen and Raloxifene
(estrogen receptor antagonists)
or endocrine therapy
381
Gail Model
way to assess risk of developing breast cancer
382
endocrine therapy
prevents estrogen production or blocks estrogen receptors
383
ERBB2
protein encoded by oncogene
384
trastuzumab
binds ERBB2 and upregulates p27 which prevents cell proliferation
385
what is used for bone pain in stage 4 breast cancer
bisphosphonates
386
4 main molecular classes of breast cancer
A--> ERBB2 -
B--> ERBB2 +
ERBB2--> ER - PR -
Basal--> EGFR +
387
oncotype DX
for A and B (since ER +)
tests for presence of 16 cancer-related genes and 5 reference genes
RT-PCR
388
mammaprint
risk of metastasis
molecular assay using 70 gene signature for breast cancer
> 0.4 = good prognosis
389
percentages of familial vs sporatic breast cancer causes
familial- 10-15% (60% from having BRCA 1 and BRCA2)
| sporatic- 80%
390
BRCA1 and BRCA2 chances of getting breast cancer
BRCA1- 40-85%
BRCA2- 15-20%
*these are tumor suppressors
391
BRCA1 and BRCA 2 normal functions
1- generation of ssDNA at ds breaks, stabilization of genome, checkpoint control (G2-M), mitotic spindle formation and regulation of topoisomerase IIa
2-recruits RAD51
392
HER2
proto-oncogene, member of tyrosine kinase family
expression is increased in breast cancer
can't bind ligand but can form heterodimers
393
tests to detect presence of HER2
FISH
CISH (light microscope)
SISH (deposits metals onto probe target and requires fewer reagents)
IHC (antibodies)
394
Lapatinib
inhibitor of HER2 kinase activity
