Biology Exam Three

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