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pre-implantation screening
Embryos generated by in vitro fertilization, at 8-cell stage, one cell from each embryo is taken for testing, only embryos that pass are implanted
does not
pre-implantation screening _______ create a novel or different genetic make-up of offspring
double stranded DNA
AAV has a ______ genome
nuclues
When AAV infects a cell, its genome is transported to the _____ where viral genes are expressed
does not integrate
The AAV genome is not replicated by the host DNA replication process and __________ into the host genome
therapeutic
AAV gene therapy replaces the bulk of the AAV genome with ______ DNA
Complementation
when loss of gene activity is compensated for by adding a functional copy of the gene
complementation
AAV is a form of _______
RNA
What type of genomes do retroviruses have in RTV
copied, integrated
In RTV, upon infection, the RNA genome is ___ into DNA and the DNA copy is randomly ______ into the host genome
complementation
RTV is a form of _____
Dominant mutation
What type of genetic disease cannot be fixed by AAV, RTV gene therapy
CRISPR
allows you to target a specific location for fixing in genome because it uses an RNA molecule that you design to base-pair with your sequence of interest
Guide RNA, Cas9 protein, Donor DNA template
What are the three things you need for CRISPR
Cas9 protein
Holds the guide RNA, helps it basepair to DNA, and cuts the genomic DNA during CRISPR
fix, inactive, add
CRISPR can be used to __ a mutant gene, _____ a gene
Somatic cell transformation
attempt to change the genetic make-up of somatic cells in an adult or child
consent, no germline, some cells
Somatic cell therapy is an ethical
more difficult
germline
Any changes made to the ______ will be a permanent, heritable change
mutations
Challenge : if you are editing the germline of the genome, CRISPR can induce _____ if the guide RNA basepairs with a related sequence elsewhere in the genome
efficient, precise
CRISPR editing is getting more ___ (a higher percent of cells subjected to it have edits), and more ___ (changes at off-site locations happening less frequently)
prime editing
CRISPR ______ works without cutting the DNA - removing any potential negative side effects
constitutive, growth hormone
The aquabounty salmon uses a ____ enhancer from ocean pout and a _____ gene from chinook salmon to gain constant expression of growth hormone to drive faster growth
1 acre
How much farmland is available to grow all the food you eat all year long
lower
organic farming has significantly _____ yields than conventional farming
Bt
___ is a species of bacteria that synthesizes a protein (Cry) toxic to certain classes of insects
enhancers
Corn will express CRy2 in locations based on the ____ you chose, and the protein will go where you direct it
photosynthetic tissues
rice normally makes beta-carotene, but only in _______, not in developing seed
not expressed
the genes encoding the biosynthetic enzymes needed to make beta-carotene are present in the rice genome, but _______ in developing seed cells (the location we want them to be expressed in)
seed enhancer
to get the phytoene synthase gene expressed in seed cells, we would need a ________
obligate parasites
viruses are not organisms, they are ______
obligate parasites
entirely depends upon a host for its nourishment, reproduction, habitat, and survival
are not
viruses ____ alive
take over
viruses enter a host cell and ______ its biosynthetic machinery
overlapping reading frames
two proteins are encoded by a segment of DNA read in different reading frames
protease
in viruses, multiple proteins are encoded by a single open reading frame: the long polypeptide must be cut by a ____ to release the different proteins
lytic
viral genome enters host cell, gets transcribed + translated, viral genome is replicated, and the viruses are released, killing the host cell (infection then spreads to other cells/hosts)
lysogenic
viral genome enters the host cell and is inserted into the host genome (when the host cell divides, the viral genome is replicated as well)
herpes
what disease has both a lytic and lysogenic lifecycle
epithelial
what cells in the herpes virus have a lytic lifecycle
neuronal
what cells in the herpes virus have a lysogenic cycle
lytic, recognized
when a virus is engaged in a __ lifecycle, the viral particles are presented on the surface of the cell, meaning they are ____ by the immune system (infected cell can then be killed preventing viral replication)
lysogenic
what lifecycle has a cell that is metabolically indistinguishable from an uninfected cell making them nearly impossible to cure
coronaviruses
large family of viruses that infect animals and humans
COVID-19
refers to the human disease state in reference to SARS2
positive, single strand RNA
What type of genome does SARS2 have
ACE2
To gain host cell entry, the SARS2 spike protein binds to _____, once bound, the virus is endocytosed into the host cell
furin cleavage site
without the ____, SARS2 is not infectious -- _____ is cleaved by a human protease, releasing the head group and allowing the fusion machinery to function efficiently
positive strand
RNA strand that contains the open reading frame for proteins (like an mRNA -- has a polyA tail, 5’ cap, etc)
translated
The SARS2 viral +RNA genome is immediately ______ upon entry into the cytoplasm, leading to viral proteins being produced
RNA dependent RNA polymerase (RdRp)
the viral + ssRNA genome is copied into a complementary - RNA strand by ______ to allow further genomic copies to be made
attenuated vaccine
a weakened version of the pathogen, transient infection is established upon vaccination which boosts and lengthens the immune response
non-human host cells
one way to create a weak pathogen (attenuated) is to culture the pathogen in ________. Pathogen then adapts through mutation and loses ability to grow in a human host
attenuated
what vaccine is not suitable for immunodeficient patients
inactivated vaccine
a dead version of the pathogen that is readily incorporated into other vaccines, contains multiple pathogenic proteins, is easy to ship+store, and has no reversion to virulence
denaturation (heat), cross-linking
how are pathogens killed for an inactivated vaccine
purified protein vaccines
synthesizes all or part of a pathogenic protein in lab
mRNA vaccine
encodes an exposed viral protein to be targeted, coated in delivery liposome that can fuse with cells, human cells take up the _____- and synthesize the protein themselves
mRNA
what type of vaccine is the Pfizer covid
fades very rapidly
The pfizer vaccine starts off with strong vaccine effectiveness, but _______ compared to other vaccines
vaccine avoidance
selecting variants that are no longer recognized by the antibodies
more, less
the omicron strain is __ transmissible, ___ deadly, and a vaccine avoidant
Omicron
SARS2 variant with a large number of missense mutations in the RBD domain and other regions of the spike protein -- antibodies created against original spike to have reduced abiity to bind to this new spike protein
cytosine analog
used by the viral RdRp, once incorporated into viral RNA, it switches between two forms (one read as C, the other U), which creates a very high rate of mutations in the replicating viral genomes
gain of function research
research that would increase the ability of a virus to infect humans (by taking a human-infecting virus and increasing pathogenicity or taking a virus that infects a non-human animal and getting it to infect humans)
humanized mouse
a mouse whose epithelia cells express human ACE2 instead of the mouse ACE2
adapt to a human host
If you take a non-human virus and culture it in human cells or humanized mice, you risk having the virus _______
naturally occurring compounds
many of the first antibiotics are __________ from fungi and bacteria that evolved to kill competing bacteria
antibiotic class
a group of structurally-related compounds that all target the same bacterial protein
beta lactams
class of antibiotics that inhibit bacterial cell wall biosynthesis
selection
_____ drives the evolution and spread of antibiotic resistance when antibiotic use is common
fitness
genotypes increase or decrease in frequency based upon their influence on an individual’s _____
fitness
the number of surviving, fertile offspring that an individual produces
environmental conditions
the fitness of a specific genotype depends on specific ________
biofilms
extracellular structures that can protect the bacteria from the immune system and drugs.
antibiotic exporters
action of a transporter that exports many antibiotics out of the bacterial cell (can lead to antibiotic resistance)
reduced, new gene
Resistance to beta lactams occurs by wither having a mutated transpeptidase gene with ___ antibiotic binding, or they have picked up an entirely ____ that encodes a different protein that will catalyze the same reaction
resistant, sensitive
when antibiotic use is common, the ____ bacterial genotypes are more fit than the ____- genotypes
sensitive, resistance
in the abscene of antibiotics, the ___ version of the bacteria is more fit than the ______ version
horizontal gene transfer
the transfer of genetic material between different species
conjugation
DNA (usually a plasmid) from a donor cell is transferred through a pilus into the recipient cell
transformation
DNA released into the environment by dead cells is taken up by a recipient cell
transduction
DNA is transferred from a donor to a recipient cell by a virus
plasmids
antibiotic resistant genes are often located on ______ and can be easily transferred from one bacterium to another
multiple
a single plasmid can harbor _____ resistance genes
does not
AAV _____ work for germline gene therapy
cell signaling
the ability of cells to perceive signals from outside the cell and alter cellular activities in response
signal, receptor, signaling intermediates, effectors, cell response
what is the outline for cell signaling?
gene expression patterns
when regulatory transcription factors are the effectors for a pathway, the consequence of signaling is to change _____
effectors
the response that a cell has to a signal depends on which _____ get activated in that cell
different
the same signal can activate _____ effectors in different cell types
proteins
In animals and plants, the most common signals used for cell differentiation are _____ encoded by genes
lipid insoluble signal
large hydrophilic molecule that can;t cross plasma membrane on own. Accepted by cell-surface receptors
lipid soluble signal
small, hydrophobic molecule that can cross plasma membrane to enter cell. Accepted by intracellular receptor
lipid insoluble
what type of signal is more common
ligands
signals when bound to receptors are also referred to as ______
enzymes, ATP
protein kinases are ____ that use ___ as a substrate
specific
protein kinases each have a ______ protein substrate
terminal phosphate
the _______ of ATP is transferred to a protein substrate on residues