Biotech Exam 2
single-nucleotide polymorphism (SNP) maps
Pharmacogenomics is a study of inter-individual variations in whole-genome to candidate gene ______, haplotype markers and alterations in gene expression or inactivation that might be correlated with pharmacological function and therapeutic response
exonucleases
RNAs are chemically unstable and rapidly degraded by ______.
biopharmaceutical drugs
Recombinant DNA technology is the basis for producing ________.
proteins
Recombinant DNA technology is the basis for understanding biochemical, cellular and physiological function (or dysfunction) of _____.
pharmacogenomics
Recombinant DNA technology is the basis of tests for production, diagnosis, and treatment of disease, also known as _____.
endonucleases
Restriction enzymes are _____ so that they can cut/digest DNA at specific recognition sequences.
protective mechanism
Restriction enzymes exist as a ______, so that if foreign DNA goes into an organism, it can cleave the foreign DNA to restrict it.
exon 7
SMN2 has a mutation that causes inefficient inclusion of ______.
termination
Sanger sequencing results in chain ______.
telomere
Since yeast artificial chromosomes are linear, they must have a _____ on each end to protect the ends.
mutant genes
Single gene defects are caused by individual _______.
endonucleases, exonucleases
Some clinical trials of gene therapy have seen innate immune responses by _____ and ____ because they are ubiquitous, resilient and very effective.
SMN2, SMN1
Spinraza (Nusinersen) allows ____ protein to substitute for missing ____ protein.
2'-O-(2-methoxyethyl), phosphates, thioate
Spinraza (Nusinersen) is an antisense oligonucleotide (ASO) drug with two major modifications- the bases have ______ nucleosides and the _____ are replaced with a _____ linkage.
totipotent
Stem cells in the morula are ____.
genetic testing
The term ______ covers an array of techniques including analysis of human DNA, RNA or protein.
recognizing, removing, DNA polymerase, DNA ligase
The three common steps in DNA Excision repair systems consist of _____ the DNA damage or mismatch, _____ the offending base(s) and filling in the resulting gap with a _____ and re-seal the nick with a ______.
Excision
The three common steps in DNA ______ repair systems consist of recognizing the DNA damage or mismatch, removing the offending base(s) and filling in the resulting gap with a DNA polymerase and re-seal the nick with a DNA ligase.
Zoo blot
The use of Southern blotting to test the ability of a DNA probe from one species to hybridize with the DNA from the genomes of a variety of other species.
regenerative
The use of adult stem cells, human embryonic stem cells and the use of somatic cell nuclear transfer (SCNT) are being seriously explored to meet the needs of people with chronic illness. The goal of ____ medicine is to regenerate damaged tissues or organs to effectively treat or even cure chronic diseases such as Parkinson's disease, type 1 diabetes, heart failure, liver failure or kidney failure.
antibiotic resistance
The yeast artificial chromosome (YAC) vector does not require a _______ gene, unlike the vectors propagated in bacteria.
BRCA1
The_____ mutation was identified by performed DNA sequencing on chromosome 17.
7000
There are approximately _____ types of rare diseases and disorders.
karyotype anomalies
There are concerns about _______ in conception via intracytoplasmic sperm injection.
exonuclease
There is proofreading activity by _____ in DNA polymerase in case an incorrect base pair is inserted.
Electroporation
This technique, known as ______, introduces a DNA fragment into a plasmid by taking a test tube of bacteria and another test tube of DNA that was ligated overnight, mixing these together and placed in an apparatus's cuvette. This cuvette has electrodes on each side that touch each other and the apparatus delivers electrical impulses that punch holes into the cell wall/membrane of E. coli so that the plasmid can get into the bacterial DNA. The (hopefully) recombinant plasmid is plated onto a plate with antibiotic media and left overnight in an incubator The next day, there will be colonies on the plate with the recombinant plasmid because of antibiotic resistance.
lambda phage
Through the _____, the lambda DNA is injected into the E. coli cell.
UV light
Thymine dimers can be caused by ______.
replication
Thymine dimers cause complications during ____ because their intrastrand crosslink puts a kink in the DNA
oligo(dT) primer, reverse transcriptase, digested, DNA polymerase
To produce cDNA from mRNA, a ______ anneals to the mRNA polyA tail. ______ copies the mRNA into DNA. The mRNA template is _____. Then ______ copies DNA to produce double-stranded cDNA.
plaques, nitrocellulose membrane, lyse, radioactive DNA probe
To screen a genomic library, you must grow _____ or bacterial colonies if screening a plasmid library. Then overlay and remove a piece of _______ onto the plate creating a replica of the plate. _____ the viruses causing the DNA from each to permanently bind to the nitrocellulose membrane at that location. Add a _______ to the gene of interest on the membrane. Then line the film with the plate and "pick up" the corresponding plaque or colony.
B-galactosidase, permease, transacetylase
Transcription of the polycistronic mRNA of the lac operon results in expression of _____, _____ and _____.
microinjection
Transgenic animals can be created through ____ of DNA.
self-complementary adeno-associated viral serotype 9 (ssAAV9)
Treatment of spinal muscular atrophy uses ________ virus.
translated, degradation, alteration
Targeting RNA (pre or post splicing) can inhibit the message from being _____, cause _____ of the message, or cause _____ of the message that could improve its translation.
approximately 1%
The 180,000 exon coding regions of the human genome make up how much of the entire genome?
integrate, blood brain barrier
The AAV9 virus is used in gene therapy treatment of spinal muscular atrophy because it does not _____ in the genome and it is good at getting past the _____.
frameshift
The BRCA1 mutation is a deletion of 4 base pairs in chromosome 17 which results in a _____ mutation.
FoundationFocus CDxBRCA
The FDA approved the _______ as a companion diagnostic for use with Rubraca, which is the first next-generation-sequencing (NGS)-based companion diagnostic approved. The NGS test detects the presence of deleterious BRCA General mutations that would be able to predict the response of the drugs.
genome
The Mus musculus (mouse) _____ is a rough replica of that of humans.
radiation sensitive mutant
The RAD from RAD51 protein means _____.
Sry
The ____ gene on the Y chromosome is the gene that regulates sex determination.
nu/nu
The ____ mouse is homozygous and nude, and lacks a thymus.
C57BL/6
The ____ mouse is the most common mouse strain used in research. Black colored and supposedly docile
c/c
The ____ mouse results from inbred lines and has a mutation in the albino locus that results in a lack of pigmentation.
C57BL/6
The _____ mouse is also referred to as B6.
exon
The _____ pattern of the same gene are similar between human and mouse
multiple cloning site (MCS)
The _____ provides more options to clone a DNA fragment.
yeast artificial chromosome (YAC)
The advantage of using the ____ vector is that it can incorporate/clone very large pieces of DNA
plaques
The clear areas on the bacterial lawn or petri dish, are referred to as ______.
holoclones
The ex vivo treatment of epidemolysis bullosa was able to work because of the patient's own ______ that had the ability to regenerate and differentiate after they were modified with the correct genetic information.
3', 5' (goes backwards up the DNA strand)
The exonuclease in DNA polymerase goes in a ___ to ____ direction when proofreading a newly synthesized DNA strand
Exome DNA sequencing
The first demonstrated use of _____ was in November 2009 when it identified the gene responsible for Miller syndrome
Miller Syndrome
The first demonstrated use of exome DNA sequencing was in November 2009 when it identified the gene responsible for _____.
dilute brown non-agouti (DBA)
The first inbred mouse strain, known as ______.
polymerase chain reaction (PCR)
The first notorious use of the ________ technology was during the O.J. Simpson trial.
gene
The genetic marker may be a part of a _____ or may have no known function.
polymerase chain reaction
The identification of MSI-H tumor status for patients interested in using nivolumab was determined using local laboratory-developed _____ tests.
pluripotent
The inner mass cells are stem cells that are _____.
tumors
Two technologies, affymetrix and agilent technologies, can be used to analyze gene expression patterns to determine differences between _____.
2-6
Typically ____-___ genes make up a polycistronic gene.
RNA-seq
Using _____, you can sequence the RNA that is expressed in a gene and also monitor levels of expression.
metal
Using genetic engineering, the rat growth hormone gene was cloned behind a mouse metallothionein promoter. Because of this, the gene is only expressed when there is _____ in the mouse's drinking water.
southern blotting
Using the technique known as ______, an investigator can detect a single DNA fragment amongst millions of DNA fragments.
primer
The key feature of site-directed/oligonucleotide directed mutagenesis is that the nucleotide change is incorporated into the _____.
promoters, repressor encoding gene, operator, polycistronic
The lac operon that encodes B-galactosidase has two ____, a _____, a _____ and a _____ mRNA made up of three genes.
Shotgun method
The method to sequence a genome in which random DNA with primer binding sites at the end of each segment and it is randomly sequenced, then the computer and bioinformatics software sequences it for you.
reproductive cloning
The nucleus is taken out of an oocyte, and is replaced by a somatic cell nucleus and then implanted into a surrogate female
placenta
The outer cells of the blastocyst give rise to the _____.
bacteria protein
The outside of the lambda phage is a coat of ________.
lacZ
The pUC18 vector has a ______ reporter gene, also known as B-galactosidase.
B-galactosidase
The pUC18 vector has a lacZ reporter gene, also known as _________.
polylinker
The pUC18 vector has a multiple cloning site. This site is also referred to as the _____.
inner mass cells
The part of the blastocyst that gives rise to all layers in the embryo (ex: endoderm, ectoderm, mesoderm)
infect, DNA/RNA
Viral-based gene therapy utilizes the ability of viruses to _____ cells, or deliver ______.
inactivating
Viruses would be used to infect cells in gene therapy only after _____ the ability of the viruses to replicate and propogate.
Southern Blotting
The procedure for screening a genomic library is similar to the technique for _______.
guide
The sequence of ___ RNA can be designed to target nearly any genomic sequence.
SMN2
The severity of spinal muscular atrophy depends on residual ______ expression.
5' cap, 3' poly (A) tail, coding region
What are the 3 key features of mRNA that can be modified?
equal division, sectional division, gradient division
What are the 3 types of division that an adult stem cell can accomplish?
DNA template, DNA primers, DNA polymerase, dNTPs
What are the four things required for polymerase chain reaction (PCR)?
1. origin of replication 2. at least one antibiotic resistance gene 3. cloning sites
What are the three features that all vectors propagated in bacteria have in common?
artificial insemination, in vitro fertilization (IVF), IntraCytoplasmic Sperm injection
What are the three methods of reproductive assistance?
1. Denaturing 2. Annealing 3. Extension
What are the three steps of the polymerase chain reaction (PCR)?
1. recombinant plasmids 2. reporter constructs (ex- green fluorescent protein) 3. large molecules (YACs, BACs)
What are the three types of transgenes?
agarose, acrylamide
What are the two gels that can be used in gel electrophoresis?
1. lytic pathway 2. lysogenic pathway
What are the two pathways that can occur once the viral lambda DNA is injected into the E. coli cell?
non-homologous end joining, homologous recombination
What are the two ways that a cell can repair damage occurring on both strands on DNA?
1. chemically competent cells 2. electroporation
What are the two ways that you can introduce a DNA plasmid into a bacteria, such as E. coli cells?
Types I, II, III, IV; Type I
What are the types of spinal muscular atrophy? Which type is most severe?
DNA plasmid vectors
What can propagate or deliver a cloned piece of DNA?
yeast artificial chromosomes
What cloning vector would you must likely use to clone human chromosome 4?
Clustered Regularly Interspace Short Palindromic Repeats
What does CRISPR stand for?
CRISPR associated protein 9
What does Cas9 stand for?
homeotic
What does Hox mean?
mRNA
What does cDNA complement?
complementary
What does the "c" represent for cDNA?
gene of interest
What gene would you add a radioactive DNA probe to?
Viruses are very good at infecting cells
What is the advantage of using viral-based gene therapy?
there is no 3' OH
What is the difference in a dideoxy analog and a typical DNA base?
VDJ recombination (non homologous end joining, antibody diversification)
What is the function of the ligase 4 protein?
90%
What is the lifetime risk of developing cancer if you have BRCA1 and BRCA2?
very high, family history
What is the lifetime risk of developing cancer with Hereditary non-polyposis colon cancer (HNPCC) (Lynch Syndrome)? ______ causes an even higher risk.
3 billion
What is the number of base pairs in the human genome?
100kb to 1000kb; 200bp to 15kb
What is the range of the size of DNA that can be inserted into a yeast artificial chromosome? Typically in bacteria, the size of the DNA fragment is _____ to ____.
SMN1
What is the survival motor neuron protein that is naturally expressed in most people?
linear
What is the unique shape of yeast artificial chromosome?
F1 hybrid
What mouse might be represented by this notation: CBA X C57BL/10?
mice with rat growth hormone behind mouse metallothionein promoter
What was the 1st example of a transgenic mouse?
Haemophilus influenzae
What was the first complete genome to ever be sequenced?
Homo sapiens
What was the first complete mammalian to be sequenced?
Saccharomyces cerevisiae (budding yeast)
What was the first eukaryote to be sequenced?
Caenorhabditis elegans (nematode)
What was the first multicellular organism to be sequenced?
Haemophilus influenzae
What was the first prokaryote to be sequenced?
exonuclease
When DNA polymerase detects an error, the mispaired base enters the ____ site, where it is chewed away/removed.
translation
When SMN2 has a mutation, exon 7 is spliced out during ______.
BRCA1
When _____ gene was disrupted in mice, they found that it affected mammary gland development as well as the formation of tumors.
glucose, lactose
When _____ is present, there are less than 10 molecules of B-galactosidase. When ____ is present, there are thousands of molecules of B-galactosidase.
sticky/overhang, blunt
When a restriction enzyme cleaves the DNA it can leave a _____ end or a ____ end.
white
When inserting a plasmid with the lacZ gene into bacteria, the colonies that you would want to harvest would be what color? This would indicate that the gene had been disrupted and the desired plasmid was inserted into the bacterial DNA.
first cell division of the embryo
When is the embryo implanted into the mom during in vitro fertilization?
about the size of the middle section that was taken out
When splicing together lambda DNA that has the middle section removed by restriction digestion, what size does the new foreign DNA that will be placed in the middle need to be?
smaller, year
When the BRCA1 gene was disrupted in mice, the development of mammary glands was abnormal since the ducts were _____, and the formation of tumors occurred in about a _____ because of extensive chromosome instability.
immunodeficiency
When the immune system recognizes foreign antigens, diversification occurs, then immunoglobulins have double strand breaks. If you cannot repair these breaks through VDJ recombination/NHEJ, you now have _____.
recombinant fragment, single-strand break, homologous recombination
When using CRISPR for gene editing, introduce the desired _____ to the CRISPR/Cas9 plasmid. Then a DNA ______ will occur. Then _____ allows for repair of the broken DNA which introduces the gene of interest to that DNA.
double-strand break, non homologous end joining
When using CRISPR to create a deletion in the gene of interest, a DNA _____ will occur, then ______ allows the ends of the DNA to come back together and causes a gene mutation.
electroporation
When using CRISPR, the CRISPR/Cas9 plasmid are introduced into the cell by using _______.
at specific recognition sequences (locations) within the DNA
Where do restriction enzymes cut DNA?
nu/nu
Which type of mouse would be used as an incubator for a patient's cancerous tumor into and used to see which treatments work?
Dr. Kary Mullis, Columbia, SC
Who is the inventor of polymerase chain reaction (PCR)? Where is he from?
locus heterogeneity (which gene/protein is affected)
Why do some xeroderma pigmentosum patients have cancer susceptibility and neurodegeneration?
Cas9, guide RNAs
CRISPR utilizes a ____ protein and specific _____ to either disrupt host genes or insert sequences of interest.
point mutations
Cancer cells with dMMR have many thousands of _______.
mutation-association neo-antigens (MANA)
Cancer cells with dMMR have many thousands of point mutations. These can cause resulting proteins to become _______.
chromosomal aberrations
Cancer risk of patients with xeroderma pigmentosum comes from the sensitivity to ______ caused by UV light.
5', 3' overhang
Cohesive end formation of the restriction enzyme generates a ____ or ______.
double strand break repair
Consequences of defects in _____ include clastogenesis, partial or whole chromosome loss, chromosome fusion/translocation
personalized medicine
Customized drug therapy, integrated healthcare, omics based medicine and systems medicine are all synonyms for _____.
restriction endonuclease
DNA is digested with a ______ enzyme.
lagging strand
DNA ligase is used to join the ends of DNA breaks that were originally caused by restriction enzymes, but DNA ligase is also the same enzyme used in _____ synthesis.
DNA cloning
DNA plasmid fragments can be inserted into specific ______ sites.
host bacteria, E. coli
DNA plasmid vectors are replicated by _______, usually _________.
antibiotic resistance
DNA plasmid vectors contain _____ genes.
bacteria
DNA plasmids are isolated/purified from _____.
DNA template, RNA primer
DNA polymerase requires a _______ and a _______ to complete DNA replication.
inherited together
DNA segments close to each other on a chromosome tend to be ________.
palindrome
DNA sequence that is a restriction enzyme recognition site
3'-OH, 5'-PO4 (phosphate)
DNA single strand breaks between _____ and ____ ends are directly repaired by a DNA ligase.
transcription
Defects in NER can also affect ____. Not being able to fix this damage causes the neurological symptoms of XP.
transcription coupled repair
Defects in _____ cause the many diseases that can occur from mutations in the same gene, XP-D.
history, semen
Diagnosis of male infertility relies almost exclusively on a good ____ and ____ analysis.
protein, biochemical
Different mutations in the same gene can cause different diseases depending on what the ____ does and what ____ activity is disrupted.
antibiotic resistance gene
Do not introduce a _______ into an organism that is not already resistant to that antibiotic
gene
Each gamete carries only one ___ pair.
gametes
Each gene segregates equally into ____.
palindrome
Each restriction enzyme site will have a ______.
allelic heterogeneity
How can different mutations in the same gene cause different diseases- XP, Cockayne's syndrome and trichothiodystrophy (TTD)?
23
How many exons does the BRCA1 gene have?
10
How many restriction enzyme sites does the pUC18 vector's multiple cloning site contain?
DNA polymerase
Human _____ has an error frequency of 1 in 22,000.
SMN1, SMN2
Humans have two genes related to survival motor neuron proteins, _____ and _____.
XP-A
If a patient with xeroderma pigmentosum has the ____ gene affected, then "classical" XP results with neurological symptoms.
XP-C
If a patient with xeroderma pigmentosum has the ____ gene affected, then "classical" XP results with no neurological symptoms.
blue
If bacterial colonies are ____, nothing has been cloned to disrupt the B-galactosidase gene.
white
If bacterial colonies are ____, something has been cloned and has disrupted the B-galactosidase gene.
B-galactosidase OR lacZ gene
If the ________ gene from the pUC18 vector is expressed in the bacteria, the bacterial colony will turn blue.
too small
If the two ends of the lambda DNA come back together after the removal of the middle section by restriction digestion, it is ______ to be packaged.
chromosomes
If we cannot repair double strand breaks, abnormal fusion events between ____ may occur.
1st- all heterozygous dominant 2nd- 3/4 dominant, 1/4 recessive
If you cross a homozygous dominant individual and a homozygous recessive individual, the 1st generation offspring will be ______. If you then cross 2 of those offspring, the 2nd generation is _____.
Luxturna
In 2017 the FDA approved ______, a gene therapy to treat patients with a rare form of inherited vision loss.
3.5
In 430 normal fertilizations there were 0% karyotype anomalies, but in 430 intracytoplasmic sperm injection cycles, there were ___% karyotype anomalies.
DNA glycosides, apurinic/apyrimidic endonuclease, DNA polymerase, DNA ligase
In Base excision repair, _____ recognizes and removes damaged base(s). ____ produces a strand break. _____ re-inserts a new base. ____ seals the nick.
double-strand break, homologous
In CRISPR, a DNA _____ is generated at the targeted site. The DNA repair machinery of the cell will use a _____ donor template DNA fragment to incorporate the desired modifications into the targeted gene.
microsatellite instability
In Hereditary non-polyposis colon cancer (HNPCC) (Lynch Syndrome) genomes, ______ makes these cancers different. These cancers have mutations in mono, di and tri nucleotide repeats.
autosomal dominant
In Hereditary non-polyposis colon cancer (HNPCC) (Lynch Syndrome), a mutation in only one copy of the gene can cause this syndrome, so it is inherited in a ______ manner.
mRNA, cDNA, sequencing adaptors, reference genome, base resolution expression profile
In RNA-seq, ____ are converted into a library of ____ fragments. _____ are ligated onto the ends of cDNA, then a short sequence is obtained using high-throughput sequencing. Sequence reads are aligned with the _____, then a _____ is produced which has the RNA expression level on the y axis and the nucleotide position on the x axis
RNA expression level, nucleotide position
In RNA-seq, a base resolution expression profile is produced that has ______ on the y axis and _____ on the x-axis
dicer, antisense strand, RISC
In RNAi (RNa interference), double stranded RNA (can be added exogenously) is cut by _____ into 22-base pair fragments. The ____ of the 22-base pair fragment, the mRNA and RISC bind together. ____ cleaves the mRNA (with the complementary sequence) preventing translation.
antisense strand, mRNA, RISC
In RNAi, after the ds RNA is cut by dicer into 22-base pair fragments, the ____ of the 22-base pair fragment, the ____ and ____ bind together.
RISC, mRNA
In RNAi, after the ds RNA is cut by dicer into 22-base pair fragments, the antisense strand of the 22-base pair fragment, the mRNA and RISC bind together. ____ then cleaves the ____ (with the complementary sequence) which prevents translation.
22
In RNAi, double stranded RNA is cut by dicer into ____-base pair fragments.
DNA, gel electrophoresis, nitrocellulose, radioactive probe, radioactive probe, autoradiography
In Southern blotting, one would digest _____ and separate the fragments by _____. Then you would transfer the fragments to a ______ membrane. After that, you would add a ________ that binds (hybridizes) to a specific fragment on the membrane. Then you would detect the ______ (same as blank above) bound to DNA fragment by ______.
CRISPR
In ____, a DNA double-strand break is generated at the targeted site. The DNA repair machinery of the cell will use a homologous donor template DNA fragment to incorporate the desired modifications into the targeted gene.
microinjection
In _____ of DNA, you take a recently fertilized mouse egg, inject DNA into the male pronucleus (because it is larger than the female pronucleus) using a micropipette. Then hopefully, the DNA integrates into the male genome. The male and female nuclei will now fuse together to form a zygote. Then you implant the zygote into a pseudopregnant female.
in vivo, SMN cDNA, vector genomes
In _____ treatment of spinal muscular atrophy, the AAV9 virus is modified with ______. Then patients are injected with 6.7x10^13 or 2.0x10^14 _____ per kg of body weight.
bacterial NER
In _____, damage is recognized by the uvrABC proteins. uvrABC puts nicks on either side of the damage to remove the fragment. DNA polymerase resynthesizes the patch removed. DNA ligase seals the nick.
microchip hybridization
In _____, you use a slide or chip with thousands of spots that correspond to single genes. mRNA or cDNA from two different samples are labeled with two different dyes. If a gene is expressed at similar levels, the colors cancel out. If a gene is expressed at a higher level than the other sample, that dye will fluoresce brighter. Then computer algorithms quantitate fluorescent and compare relative expression levels.
base excision repair
In ______, DNA glycosidase recognizes and removes damaged base(s). Apurinic/apyrimidinic endonuclease produces a strand break. DNA polymerase re-inserts a new base. DNA ligase seals the nick.
IntraCytoplasmic Sperm Injection (ICSI)
In ______, a holding pipette holds the egg, and a sharp pipette injects the sperm into the oocyte.
in vitro fertilization
In ______, hormonal stimulation to generate mature follicles, eggs are then harvested from female follicles and are placed in a petri dish with husband or donor sperm, and wait for fertilization to take place. Then the first cell division will take place in the petri dish (morula stage) before they are implanted into the mom.
bacterial mismatch repair
In ______, mismatch is recognized by MutS. A second protein, MutL, is recruited to mismatch. The daughter strand is nicked by an endonuclease MutH. Exonuclease digests past the mismatch. DNA polymerase re-synthesizes the patch removed. DNA ligase seals the nick.
real-time RT-PCR
In ______, you use mRNA and reverse transcriptase to make cDNA. Then you monitor the expression of products using 2 primers and performing PCR
homologous recombination
In _______, double strand breaks are recognized. Resection occurs through exonuclease. The 3'-end of the damaged DNA invades the undamaged sister chromatid, which serves as a template for DNA synthesis
microarray gene expression analysis
In ________, DNA spots representing different genes are arrayed on a solid surface. Fluorescent-labeled cDNA is then made from mRNA. Now, cDNA probes anneal to the target sequences. The expression of thousands of genes is determined through this technology.
identical
In a colony, all colony cells are _____.
death due to disease
In a pedigree analysis, a line through the symbol means ______.
women, men
In a pedigree analysis, circles are _____ and squares are _____.
afflicted
In a pedigree analysis, solid/shaded symbols represent a _____ individual.
male
In about 40% of couples, the infertility problem is due to ____ infertility.
uvrABC, either side, DNA polymerase, DNA ligase
In bacterial NER, damage is recognized by the _____ proteins. These proteins put nicks on _____ of the damage to remove the fragment. ____ resynthesizes the patch removed. ____ seals the nick.
MutS, MutL, MutH, digests, DNA polymerase, DNA ligase
In bacterial mismatch repair, mismatch is recognized by _____. A second protein, ____, is recruited to mismatch. The daughter strand is nicked by an endonuclease _____. Exonuclease _____ past the mismatch. ____ re-synthesizes the patch removed. _____ seals the nick.
nucleotide
In exome DNA sequencing, the enriched regions are sequenced using high-throughput _____ sequencing.
exonuclease, 3'-end, sister chromatid
In homologous recombination, double strand breaks are recognized. Resection occurs through ____. The _____ of the damaged DNA invades the undamaged ______, which serves as a template for DNA synthesis
RAD51
In human cells, normal BRCA proteins interact with a DNA repair protein called ____.
restriction digestion
In lamda DNA, the removal of the middle section occurs through _____ digestion.
genes, fluorescent-labeled cDNA, probes, thousands
In microarray gene expression analysis, DNA spots representing different ____ are arrayed on a solid surface. _____ is then made from mRNA. Now, cDNA ____ anneal to the target sequences. The expression of _____ of genes is determined through this technology.
row, column
In microarray gene expression analysis, each ____ represents a single gene and each ____ represents an experimental sample.
mRNA, cDNA
In microchip hybridization, you use a slide or chip with thousands of spots that correspond to single genes. ___ or _____ from two different samples are labeled with two different dyes. If a gene is expressed at similar levels, the colors cancel out. If a gene is expressed at a higher level than the other sample, that dye will fluoresce brighter. Then computer algorithms quantitate fluorescent and compare relative expression levels.
pronucleus, micropipette, zygote, zygote, pseudopregnant
In microinjection of DNA, you take a recently fertilized mouse egg, inject DNA into the male ______ (because it is larger than the female one) using a ____. Then hopefully, the DNA integrates into the male ____. The male and female nuclei will now fuse together to form a ______. Then you implant the ____ (same word as last blank) into a _____ female.
the newly replicated daughter strand
In mismatch repair, which strand has the wrong base?
genomic library
In order to create a _____, the genomic DNA must be digested or sheared, then randomly ligated into the lambda DNA arms. Phage proteins are then added to package the DNA, then the bacteria is infected to propagate each clone.
lambda DNA, phage proteins, infected
In order to create a genomic library, genomic DNA is fragmented by shearing or enzymatic digestion. Then it is randomly joined to _____ pieces. _____ are added to package the DNA. Then the bacteria must be _____ to propagate each clone.
shearing, enzymatic digestion
In order to create a genomic library, one must first fragment genomic DNA by _____ or _______.
phosphates, thioate
In order to interfere with exonuclease activity, RNA molecules can be modified by replacing ____ with _____ linkages between sugars.
ribose, morpholino
In order to interfere with exonuclease activity, RNA molecules can be modified by replacing _____ with ___ rings.
backbones
In order to interfere with exonuclease activity, RNA molecules can be synthesized with modified _______.
vaginal plug, blastocyst embryo
In order to return a embryo stem cell modified by genetic recombination to its original environment, you check for a _____ in female mice to determine whether breeding occurred. After 3.5 days, the embryo stem cell is injected into the ______.
primers, excess primers, extension
In polymerase chain reaction, you would add excess ______ to the DNA you have, and heat to 100C to separate the complementary strands. Then the temperature is lowered to 50C to allow base pairing to occur, but the _____ will bind to complementary sites, resulting in annealing. Then the temperature will be raised to 72C, the optimal temperature for DNA polymerase, which will allow for _____ to occur, synthesizing new DNA.
base complementarity
In southern blotting, when the autoradiography is performed, you are able to detect the radioactive DNA probe because of the ______.
SMN1
In spinal muscular atrophy, ____ is mutated/lost.
lytic
In the ____ pathway, the middle section of the lambda DNA can be removed by a restriction digestion, spliced with foreign DNA and the recombinant molecule packaged into an infective lambda phage virion that harbors foreign DNA.
Lysogenic
In the _____ pathway the viral DNA integrates into the E. coli genome and replicates normally until activated under stressful conditions.
Lytic
In the _____ pathway, the virus replicates and then lyses the bacteria cell. When done in a petri dish, this results in the dish having clear areas called plaques where the cells lysed.
ex vivo, unaffected, lentiviral, laminin B3 (LAMB3), transgenic
In the _____ treament of epidermolysis bullosa, skin cells were isolated from ______ area of the patients skin and then grown in lab. Cells infected with a ____ vector with a functional ______ cDNA. Cells were then grown into patches of _____ epidermal patches. 3 graft operations were able to replace 80% of the patient's skin with the grafts.
therapy
In the clinical setting, genetic tests can be performed to confirm a suspected diagnosis, to predict the possibility of future illness, to detect the presence of a carrier state in unaffected individuals, and to predict response to _____.
epidermolysis bullosa
In the ex vivo treament of _______, skin cells were isolated from an unaffected area of the patients skin and then grown in lab. Cells infected with a lentiviral vector with a functional laminin B3 (LAMB3) cDNA. Cells were then grown into patches of transgenic epidermal grafts. 3 graft operations were able to replace 80% of the patient's skin with the grafts.
inducer, polycistronic mRNA
In the lac operon, the _____, often lactose, can bind to and change the conformation of the repressor protein. The repressor can no longer bind to the operator, so ______ can be expressed.
repressor encoding
In the lac operon, the transcript of the ______ gene in the absence of lactose or any other inducer binds to the operator and prevents transcription of the polycistronic mRNA
operator, polycistronic mRNA
In the lac operon, the transcript of the repressor encoding gene in the absence of lactose or any other inducer binds to the _____ and prevents transcription of the _____.
RAD51, BRCA, RAD51
In the strand invasion step of homologous recombination _____ binds to the 3' ends of DNA. ____ proteins help load ____ (same as first blank)
from bottom to top
In what direction is an autoradiogram read?
autonomously replicating sequence (ARS)
In yeast artificial chromosomes, the origin of replication is known as the ______.
bone marrow
In_____, a stem cell can give rise to red blood cells, white blood cells, bone and even heart muscle
Miller Syndrome
Individuals who have _____ have eyes that are slanted down, affected development of face and feet, malformed ears, but normal intelligence.
relatives
Investigators use a database to search for near matches to solve crimes committed by ____ of people in the database.
defective sperm, procedure itself
It is unsure of whether karyotype anomalies that occur in intracytoplasmic sperm injection cycles stem from _____ or the _____.
9.5 years
It would take about _____ to read out loud without stopping the 3 billion bases in a person's genome sequence.
DNA ligase
Joining of cohesive ends occurs with the enzyme _____; it reseals DNA breaks that were originally caused by restriction enzymes.
SMN, spinal muscular atrophy
Loss of ____ protein causes motor neuron loss, or ________.
replication
MMR repairs ____ errors such as base mismatches and insertion deletion loops.
base mismatches, insertion/deletion loops
MMR repairs replication errors such as ____ and ____.
adenine, guanine
MYH protein is a DNA glycosidase that removes ____ that is mispaired to an oxidatively damaged ______ base.
the 2nd century
Maladies were recognized to occur in families as early as ______.
300, tail
Mice and humans each have about 30,000 genes, yet only _____ are unique to either organism. Both even have genes for a ____, even though its not "switched on" in humans.
placenta-bearing mammals
Mice are a helpful tool to understanding human disease because many aspects of human development and disease are common only to ______.
exonuclease
Mice with a mutation that inactivates the ____ activity of pol delta get cancer.
antisense oligonucleotide (ASO), siRNA
Modifications to RNA to interfere with exonuclease activity should not change the interaction of _____ or _____ with the target mRNA.
they have a functioning SMN1 gene
Most people who have an SMN2 mutation are unaffected because ______.
MLH1, MSH2, MSH6
Mutations in ____, ____ and ____ genes cause Hereditary non-polyposis colon cancer (HNPCC) (Lynch Syndrome).
LIG4
Mutations in the ____ gene are associated with immunodeficiency
XP-D
Mutations in the ____ gene can cause XP with neurological symptoms, combined XP and Cockayne's syndrome, or trichothiodystrophy (TTD).
MutYH (MYH protein)
Mutations in the _____ gene are associated with polyposis of the colon and colon cancer risk
killing of cells, chromosomal aberrations
Patients with xeroderma pigmentosum have a sensitivity to _____ and ______ caused by UV light
UV, thymine dimers
Patients with xeroderma pigmentosum have an inability to repair ___ damage, which is caused by ______.
several thousand, neurological
Patients with xeroderma pigmentosum have cancer rates that are increased ____ fold. Patients may also have ____ issues.
DNA plasmid vectors
circular DNA molecules
BRCA1, BRCA2
high penetrance allele- if you happen to have this particular mutation, you have a high risk of developing cancer. ____ and ____ genes are examples of this
double strand break, interstrand crosslink
homologous recombination can repair damage to both strands of DNA, such as _____ or ______.
sister chromatid
homologous recombination utilizes the _____ to repair damage to both strands of DNA.
Spinraza (Nusinersen)
injectable antisense oligonucleotide (ASO) that treats spinal muscular atrophy
Flanking sequence
known DNA sequence in PCR that the excess primers complement
cDNA, reverse transcriptase
mRNA is converted into _____ by the enzyme _____.
protein
Xeroderma pigmentosum results in cancer susceptibility AND neurodegeneration for some patients because the clinical symptoms depend on which ____ in the NER pathway is affected.
centromere
Yeast artificial chromosomes require _____ since yeast are eukaryotic.
totipotent
___ cells have the capacity to differentiate individuals into any tissue or even into a complete organism.
antenapedia
___ is a condition in which the legs of a fruit fly coming out of where the antennae should be because a Hox gene has been mutated
20%
___% of breast cancers are not detected by mammography screening
mutant
____ alleles differ from the wild-type allele due to a mutation
MSH2, MSH6
____ and ____ proteins are similar in both sequence and function. When they are mutated, they result in hereditary non-polyposis colon cancer (HNPCC) (Lynch Syndrome).
Thymine dimers
____ are infamous "bulky adducts" that would be targeted by NER
CRISPR
____ can introduce mutations in multiple genes in one step, which allows for rapid genome engineering.
Pluripotent
____ cells have the capacity to form all three germ layers but cannot differentiate into a complete organism.
Checkpoint blockade
____ drugs facilitate immune recognition of the cancer cells as "non-self".
allelic heterogeneity
____ heterogeneity is different mutations in the same gene cause different disease
locus heterogeneity
____ heterogeneity is when two different genes are affected but both cause the same disease with varying symptoms
Rucaparib (Rubraca)
____ is a PARP inhibitor that was approved by the FDA to treat ovarian cancer tumors caused by a specific gene mutation (deleterious BRCA). It was approved alongside FoundationFocus CDxBRCA, a NGS test that will be able to predict a patients response to the PARP inhibitor.
Oncotype Dx
____ is a clinically validated multigenerational RT-PCR test used in clinical practice to quantify the likelihood of breast cancer reoccurrence for an individual
Nuclear transfer (cloning)
____ is a method in which the nucleus from an adult somatic (differentiated cell) is inserted into the emptied cytoplasm of an egg cell. The egg cell then reprograms the adult cell's genes so that it behaves like an all-purpose stem cell.
Fruit fly (Drosophila melanogaster)
____ is a model organism for developmental biology.
yeast
____ is a model organism for single celled organisms.
lac operon
____ is a model system that helps us understand how gene expression is regulated.
Cas9
____ is a nuclease that uses guide RNA with short sequences complementary to the targeted sequence.
Gel Electrophoresis
____ is a procedure used to separate DNA fragments by size.
genotype
____ is a set of alleles that make up a person's genetic constitution. Usually, we are talking about a single locus.
infertility
____ is a sub-specialty dealing with the diagnosis and treatment of conditions that prevent women from getting pregnant.
Spinraza (Nusinersen)
____ is an antisense oligonucleotide (ASO) drug with two major modifications- the bases have 2'-O-(2-methoxyethyl) nucleosides and the phosphates are replaced with a thioate linkage.
Ki-67
____ is an expression marker that indicates how aggressive/fast-growing a tumor is
autoradiography
____ is another word for X-ray. It is used for imaging in southern blotting
Eomaia scansoria
____ is the common ancestor of mice and humans that lived alongside the dinosaurs, looking like a creature about the size of a small rat. It is the earliest known representative of the Eutheria lineage, which gave rise to all modern placental mammals
Gene therapy
____ is the introduction of exogenous genetic material to connect or modify the function of a cell
recessive
____ is the phenotype only observed when both chromosomes of a pair carries a mutant allele.
glucose
____ is the preferred energy source for E. coli, but other sugars can also be used as nutrients
SMN2, SMN2
____ is the survival motor neuron protein that has a mutation that causes inefficient inclusion of exon 7, which causes little or no ____ protein to be made.
Homozygous
____ is when a person has a pair of identical alleles
Heterozygous
____ is when a person has different alleles and is sometimes referred to as a genetic carrier
1, 10
____ out of ____ Americans has a rare disease
MYH
____ protein prevents mutations associated with oxidative DNA damage.
BRCA
____ proteins help load RAD51 to the 3' ends of DNA in homologous recombination, so if there is a mutation in the ____ (same as first blank) proteins, then the proteins can't help with the strand invasion function and then there would be difficulties repairing double strand breaks.
a-BRCA2, a-RAD51
_____ and _____ co-localize, are in the same neighborhood, travel together and repair DNA damage together and are associated with each other
nonviral
_____ approaches of gene therapy are unsuccessful so far because they were not efficient at getting into the DNA.
Alleles
_____ are alternative variants of genetic information at a specific location.
Embryo stem cells
_____ are cells that have the potential to turn into every kind of cell that make up the 100 trillion cells of an adult human
YACs, BACs
_____ are large molecules that are also transgenes. The entire chromosomes can be injected into the male pronucleus
Antisense oligonucleotides (ASOs)
_____ are modified RNA drugs that are complementary to an endogenous RNA.
wells
_____ are the sections in gel electrophoresis in which the DNA fragments separate by size
genetic tests
_____ are used as a health care tool to detect gene variants associated with a specific disease or condition, as well as for non-clinical uses such as paternity testing and forensics
Zolgensma (AVXS-101)
_____ by AveXis/Novartis is the gene therapy drug treatment of spinal muscular atrophy.
Chemically competent
_____ cells are treated with calcium and then can punch holes in the cell wall/cell membrane of bacteria. This allows for DNA to ligate into a plasmid, creating a recombinant plasmid.
B-galactosidase
_____ cleaves lactose into galactose and glucose.
Hox (homeotic)
_____ genes that are transcription factor regulators in the fruit fly. They specify organs/appendages and their locations.
micro-RNAs
_____ in our bodies suppress mRNA
exonic reads
_____ indicate the number of times that sequences occurred in RNA-seq.
Olaparib (Lynparza)
_____ is a PARP inhibitor that the FDA approved to treat BRCA-defective ovarian and breast cancer. It was approved along with the genetic test, BRACAnalysis CDx (Myriad genetics) which can determined if a patient can be treated effectively with this PARP inhibitor.
bithorax
_____ is a condition in which the fruit fly has two sets of wings because of a mutated Hox gene
operon
_____ is a coordinated unit of gene expression with common functions in the same location along the DNA
RNAi (RNA interference), posttranscriptional gene silencing
_____ is a degradation mechanism that prevents mRNA from being translated into protein, also called _____.
BRCA1 mutation
_____ is a deletion of 4 base pairs in chromosome 17 which results in a frameshift mutation.
onpattro
_____ is a drug that modulates RNA by targeting the RISC complex to degrade the message.
coding region
_____ is a feature of mRNA that is made up of exon that are spliced together.
Exome DNA sequencing
_____ is a method that is more affordable than whole genome sequencing and permits large numbers of samples to be analyzed
real-time RT-PCR
_____ is a method to prove that a gene identified by microarray or RNA-seq is actually expressed in your sample.
Bacteria (may have foreign DNA introduced)
_____ is a model organism that can be used to understand the structure of promoters, and therefore gene expression
uRA3
_____ is a selective marker that is placed in yeast artificial chromosomes that lack the ability to produce uracil. This marker gives the chromosomes that ability. Otherwise they would not be able to grow in the absence of uracil
Nitrocellulose membrane
_____ is a substance similar to paper that is used to make a replica of the gel electrophoresis in southern blotting.
RNAi (RNA interference)
_____ is a very powerful technique to silence gene expression because it appears to broadly work for nearly all genes in many cell types.
Mammaprint
_____ is an FDA-approved 70-gene microarray assay that is used to prove important prognostic information for individuals with primary invasive breast cancer with lymph node negative disease of either positive or negative ER status.
transgenic animal
_____ is an animal that carries a foreign DNA sequence that has been stably inserted into its genome
Mismatch repair (MMR)
_____ is an extra proofreading function in addition to the exonuclease of the polymerase
phenotype
_____ is an observable expression of a genotype as a morphological, clinical, biochemical or molecular trait. It may be normal or abnormal in a given individual
BRCA2
_____ is located on chromosome 13 in humans, and can predict its location on chromosome 5 in mice.
Sequencher
_____ is software that is able to sequence complete genomes. This technology was used to identify 9/11 victims
dihydroorotate
_____ is the enzyme encoded by DHODH, the same gene that causes Miller Syndrome.
reverse transcriptase
_____ is the enzyme used to generate cDNA.
dominant
_____ is the phenotype observed when only one chromosome of a pair carries the mutant allele
transcriptome
_____ is the sum of all the RNA molecules produced in a cell under a given set of conditions
30
_____ million people in the US are living with a rare disease.
Knockout mutation
_____ occurs by replacement of a gene segment by homologous recombination that normally results in a nonfiction or "null" allele.
Wild type, normal
_____ or ____ alleles are the sequence present in a majority of individuals.
MYH
_____ protein is a DNA glycosidase that removes adenine that is mispaired to an oxidatively damaged guanine base.
polycistronic
_____ refers to multiple proteins encoded by a single mRNA
Nucleotide excision repair (NER)
_____ repairs "bulky adducts", including intrastrand crosslinks and helix distorting adducts.
Mismatch repair (MMR)
_____ repairs replication errors such as base mismatches and insertion/deletion loops
Palindromic
_____ sequences are the same going forward as they are going backwards, when the template strand is used to make a complementary strand.
RNAi (RNA interference)
_____ silences the expression of the target gene
CRISPR
_____ utilizes a Cas9 protein and specific guide RNAs to either disrupt host genes or insert sequences of interest.
homologous recombination
_____ utilizes the sister chromatid to repair damage to both strands of DNA.
Ambry Genetics
_____ was the first company to offer exome sequencing service
Clarence Cook Little
_____, a Harvard biologist from William Castle's lab, developed the first inbred mouse train, known as DBA (dilute brown non-agouti). He is convinced that studying a genetically pure breed will unlock the secretes of human disease such as cancer. This event is subsequently hailed as the birth of the modern lab mouse, and DBA mice are still used in genetics labs today.
Restriction enzymes
_____, because of their actions, may be used to determine the order of genes on chromosomes, to analyze the chemical structure of genes and of regions of DNA which regulate the function of genes, and to create new combinations of genes.
Restriction enzymes
______ are endonucleases that cut/digest DNA at specific recognition sequences.
Genetic markers
______ are used to track the inheritance of a nearby gene that has not yet been identified but whose approximate location is known.
ionizing radiation
______ causes double strand breaks.
Promoter regions
______ drive gene expression in prokaryotes and are responsible for the transcription factor binding to the promoter to drive the expression of mRNA.
Pedigree analysis
______ has been used since the mid-1800s to track human heredity.
Bacteriophage Lambda
______ is a model organism that provided fundamental understanding of regulation of gene expression and genetic recombination
exome DNA sequencing
______ is a strategy to selectively sequence the 180,000 exon coding regions of the human genome (approximately 1% of the entire genome) to identify novel mutations
Pharmacogenomics (PGx)
______ is a study of inter-individual variations in whole-genome to candidate gene single-nucleotide polymorphism maps, haplotype markers and alterations in gene expression or inactivation that might be correlated with pharmacological function and therapeutic response
Piebald Syndrome
______ is a syndrome in which both affected mice and humans have the same white patch on the stomach and forehead resulting from a mutation in the same (c-kit) gene.
polymerase chain reaction (PCR)
______ is a technique to amplify specific DNA sequences
pulsed-field gel
______ is a type of gel electrophoresis that pulses an electrical field around the gel, it can separate very large DNA fragments.
Bacterial artificial chromosomes (BAC)
______ is a vector that works the same as and has the exact same features as the bacterial vectors, but can incorporate very large pieces of DNA.
RNA-seq
______ is an alternative to microarray technology
Chimeric embryo
______ is an embryo made from tissues from the original mom and the genetically modified embryonic stem cells.
quality control
______ is essential for forensics and polymerase chain reaction (PCR)
Mus musculus (mouse)
______ is physiologically similar to humans.
Recombinant DNA technology
______ is the basis for: -understanding biochemical, cellular and physiological function (and dysfunction) of proteins -tests for prediction, diagnosis, and treatment of disease (pharmacogenomics) -producing biopharmaceutical drugs
Lactose
______ is the inducer of gene expression for B-galactosidase.
Pharmacogenetics (PGt)
______ is the study of inter-individual variations in DNA sequence related to drug absorption and disposition (pharmacokinetics) or drug action (pharmacodynamics)
therapeutic cloning
______ is the use of somatic cell nuclear transfer to regenerate different cell types
Base Excision Repair (BER)
______ repairs many types of base damage, including base loss and single strand breaks.
endonucleases, exonucleases
_______ and ____ chew up foreign DNA as an immune response
multiple cloning site
_______ can also be referred to as a polylinker.
BRCA2 defective
_______ cancer cells are the most sensitive to PARP inhibitors, they require a much lower concentration to kill cancer cells
somatic cell nuclear transfer (SCNT)
_________ can be used for reproductive OR therapeutic cloning.
BRCA
____tumor cells are extremely sensitive to PARP inhibitors.
Stem cell
a cell that carries the potential to develop into several different types of cells
adult stem cell
a cell that has the ability to differentiate into a limited number of cells (multipotent)
trichothiodystrophy
a disease associated with brittle hair and brittle skin
c-kit
a mutation in the ____ gene causes Piebald Syndrome.
acrylamide
a neurotoxin but also used as a gel in gel electrophoresis; not as hazardous as a solid
Xeoderma Pigmentosum
a patient with ____ would have severe and extensive lesions in exposed areas of skin. The lesions have a high risk of developing into cancer. Patients have severe photosensitivity- only a few minutes in the sun cases 3rd degree burns.
recombinant plasmid
a plasmid with foreign DNA inserted into it
pUC18 vector
a vector with a cloning site, origin of replication, ampicillin resistance gene and a multiple cloning site, B-galactosidase (also known as the lacZ gene)
non-homologous end joining
a way of repairing a DNA double-strand break that reconnects broken ends, sometimes imprecisely
pre-implantation embryos
an embryo stem cell is derived from _______.
cleavage site
the position where restriction enzyme/endonucleases will cut the DNA
Hereditary non-polyposis colon cancer (HNPCC) (Lynch Syndrome)
this syndrome is characterized by mismatch repair associated cancer. uterine, stomach, breast, ovarian, urinary tract, pancreatic cancers....
uracil
uRA3 is a selective marker placed in yeast that lack the ability to produce ______.
holoclones
undifferentiated skin cells (stem cells) that have self-renewal capacity
multiple cloning site
A DNA fragment is ligated into the ______ to generate a recombinant plasmid.
enzyme
A _____ is used to digest DNA so that only a specific DNA fragment is left and it can be inserted into a plasmid.
enzyme
A _____ is used to digest part of the plasmid so that a DNA fragment can be inserted into that plasmid.
genetic marker
A ______ is a DNA sequence with a known physical location on a chromosome.
F1 hybrid
A ______ mouse results from 2 inbred strains mixed together to make a 1st generation.
foreign
A challenge of gene therapy is that bodies and cells have aggressive defense mechanisms against any ____ DNA/RNA
pseudopregnant female, 18
A chimeric embryo in which embryonic stem cells were genetically modified to have a targeted mutation are implanted into a _________. A single incision is made to the mouse under a mild anesthetic. A needle punches a hole in the wall of the uterus and the embryo is implanted. About _____ days later, she will give birth to chimeric mice.
17
A dangerous mutation on chromosome _____ that puts a woman at a higher risk for developing breast cancer.
integrated
A disadvantage of viral-based gene therapy is not knowing where in the genome the DNA would be _____.
Cockayne's syndrome
A disease characterized by developmental delay, short stature, and neurological abnormalities (and severe photosensitivity when combined XP)
200,000
A disease is defined as orphan in the US when it affects fewer than _____ people.
0.1%
A fraction, ___%, of DNA differs from person to person
Dolly
A lamb (number 6LL3) that was made from reproductive cloning of the mammary gland of a Finn Dorset ewe
Sanger sequencing
A method in which dideoxynucleotides halt DNA polymerization at each base, generating sequences of various lengths that encompass the entire original sequence. Terminated fragments are electrophoresed and the original sequence can be deduced.
Oligonucleotide-directed mutagenesis
A primer containing a single mismatched nucleotide is used to produce a desired single change in the DNA sequence
RISC (RNA-induced silencing complex)
A protein complex that is responsible for the actions of RNAi (RNA interference)
screened
A random genomic library must be _____ to identify a specific genomic fragment.
recombinant plasmids
A type of transgene, ____ are genes or cDNAs linked to promoters that allow altered expression
reporter construct
A type of transgene, ______ are desired gene promoters linked to expression cassette that can be assayed. Ex: Green Fluorescent Protein
99%, 81%
About ____% of genes in humans have counterparts in the mouse. ___% have identical, one-to-one counterparts.
1, 1000
Acrylamide, when used in gel electrophoresis, can separate DNA into fragments from ____ to _____ bases long.
self-renewal, differentiation
Adult stem cells have two functions: _____ and _____.
SMN2, exon 7
After injection, Spinraza (Nusinersen) binds to the ____ primary transcript which prevents ____ from being spliced out.
Spinraza (Nusinersen)
After injection, _____ binds to the SMN2 primary transcript which prevents exon 7 from being spliced out. The SMN2 mRNA containing exon 7 is now translated into protein. The SMN2 protein substitutes for the missing SMN1 protein.
100, 100
Agarose, when used in gel electrophoresis, can separate DNA into fragments from ____ base pairs to _____ kilo base pairs
multipotent
An adult stem cell has the ability to differentiate into a limited number of cells, also known as _____.
Poly(ADP-ribose) polymerase (PARP)
An enzyme, ______, promotes repair of single and double strand repair breaks.
homology-directed repair
Another name for homologous recombination (HR)
complementary
Antisense oligonucleotides (ASOs) are modified RNA drugs that are _____ to an endogenous RNA. This gives the drug the specificity needed to bind to one specific message.
15
Approximately ___% of couples either have trouble conceiving or cannot conceive at all.
reporter
B-galactosidase (lacZ) is known as the _____ gene in the pUC18 vector.
lactose, galactose, glucose
B-galactosidase cleaves the sugar ____ into ____ and ____.
base loss, single strand breaks
BER repairs many types of base damage, including ____ and _____.
purines
BER would repair base damage caused by base loss. _____ are lost at a frequent rate, so BER is needed to fix this base damage.
PARP
BRCA-tumor cells are extremely sensitive to ____ inhibitors.
mouse and human genomes
By comparing ____ and _____, you can predict a gene's location in the opposite organism's chromosomes.
die
By using one of the two methods to introduce plasmids into bacteria, when the bacteria does not have the plasmids and is placed into a culture containing an antibiotic, these bacteria will _______.
antibiotic selection
By using one of the two methods to introduce plasmids into bacteria, when the bacteria has the plasmids and is placed into a culture containing an antibiotic, these bacteria will form colonies while bacteria without the plasmids will die. This is known as ______.
form colonies
By using one of the two methods to introduce plasmids into bacteria, when the bacteria have the plasmids and are placed into a culture containing an antibiotic, these bacteria will _______.
Automated DNA sequencing
fluorescence detection of oligonucleotide fragments produced by the dideoxy method
clastogenesis
generation of chromosomal breaks
acrylamide
the gel in gel electrophoresis that is more precise in separating fragments
mRNA, protein
RNAi (RNA interference) is a degradation mechanism that prevents ____ from being translated into ____, also called posttranscriptional gene silencing.
siRNA
RNAi (RNA interference) is also called ______.
RNA viruses
RNAi (RNA interference) is thought to be a defense mechanism against _____.
oligonucleotide probes (baits)
Exome DNA sequencing captures RNA coding regions by hybridizing genomic DNA to _____ that cover the human exome regions.
DHODH
Exome DNA sequencing identified a single candidate gene _____, that is responsible for Miller syndrome. This gene encodes a key enzyme in the pyrimidine de novo biosynthesis pathway.
protein coding
Exome sequencing is a strategy that only sequences the _____ region of the human genome.
10-100
Exonucleases proofreading activity increases fidelity about ___-___ fold
BRACAnalysis CDx (Myriad genetics)
FDA approved the ______, a genetic test for the qualitative detection and classification of variants in the BRCA1 and BRCA2 genes. This allows you to determine if a patient can be treated effectively with Olaparib (Lynparza)
pembrolizumab
FDA granted ______ accelerated approval for first tissue/site agnostic indication.
nivolumab
FDA granted ______ accelerated approval to treat MSI-H or dMMR colorectal cancer (Lynch syndrome).
grow
Feeding mice with the rat growth hormone gene genetically engineered behind the mouse metallothionein promoter cadmium caused these transgenic mice to _____ dramatically compared to mice without the transgene.
morula
Following fertilization, totipotent stem cells make up the _____.
size
Gel Electrophoresis separates DNA fragments by ______.
homologous recombination
Gene disruption can occur by manipulating a gene from an embryo stem cell to create a deletion. You then take a targeted gene with this mutated gene and by ______, the targeted gene will "pick up" the mutation that you created. The embryo stem cell must then be returned to its origin to make an animal.
nucleic acids
Gene therapy and RNA therapies are challenging because they require delivering ____ into cells.
exogenous
Gene therapy is the introduction of _____ genetic material to connect or modify the function of a cell
endogenous
Gene therapy may be used to reintroduce a gene into a cell or organism in which a ____ gene is missing or mutated.
inherited disease
Genetic markers can help link a _____ with the responsible gene.
transcription
Going from DNA to RNA is called _____.
translation
Going from RNA to protein is called _____.
gene expression
RNAi (RNA interface) is used for disrupting ______.
pBR322
One of the first identified plasmid vectors that has an Ampicillin (Amp) resistance gene
RISC, degrade
Onpattro is a drug that modulates RNA by targeting the ____ complex to ____ the message.
prokaryotes
Operons are unique to ____.
Poly(ADP-ribose) polymerase
PARP stands for ______.
lysed
Plaques are the area in which the bacteria cells have _____.
immunity
Pre-existing ______ to the virus would be a disadvantage of viral based gene therapy.
yeast
Pulsed-field gel electrophoresis can separate very large DNA fragments. It can even separate ____ chromosomes.
baker's yeast
RAD proteins were originally studied in _____.
Southern blotting
blotting technique that detects a DNA fragment
Western blot
blotting technique that detects a protein
Northern blot
blotting technique that detects an RNA fragment
Clastogen
something that can cause the breaks of chromosomes
