Viruses
Are viruses living organisms? Explain why/why not. Do they have genetic material?
Viruses are not organisms but instead obligate parasites because they require host machinery to replicate. They have double stranded/single stranded DNA or RNA
What are GMO crops? What are some engineered traits of GMO crops?
GMOs are genetically modified organisms, which have been transformed to have a recombinant genome from another organism
Engineered traits: herbicide resistance, insect resistance, drought tolerance, viral resistance, increased nutritional value
What type of enzyme inhibition are antibiotics most commonly an example of? What are some differences between antibiotic classes
Enzyme inhibition: competitive inhibition bc enzyme binding to active site; structurally related
Differences: Half-life, affinity for enzyme (km), solubility, effectiveness
Describe the characteristics of viral genomes. What is the function of overlapping reading frames and proteolytic cleavage in viral cells?
Viral genomes are compact, with no parasitic junk DNA such that is in humans (transposons, introns)
Overlapping reading frames are when a single DNA sequence codes for multiple protein reading frames.
Proteolytic cleavage is a related, yet separate mechanistic process that cuts a long single polypeptide produced by the single ORF into multiple smaller peptides
What gene components form Golden Rice? What precursor compound is found in Golden Rice?
Golden rice is made from three biosynthesis genes: Phyotene Synthase, Crt1, and Lycopene, along with a seed enhancer and a rice promoter.
Beta-carotene (Vit A precursor)
Describe the common prokaryotic factors/toxic conditions targeted by antibiotics
1) Folic acid biosynthesis (required for nucleotide anabolism)
2) RNA Polymerase (blocks bacterial transcription)
3) Ribosome (blocks translation)/causes the making non-functional proteins (energy wasting
4) Peptidoglycan synthesis enzymes (blocks cell wall formation)/energy utilization to "fix" cell wall
5)
Describe the lysogenic and lytic viral lifecycles. What two enzymes are needed within the lysogenic phase for Retroviruses & what are their functions?
Lytic viral lifecycle: Virus enters host cell --> viral genome transcribed + translated --> viral replication and growth --> new virus particles release from host cell killing it
Lysogenic viral lifecycle: viral genome enters host cell --> inserts into host genome --> latency period (viral genome replicating but no active growth) --> viral sequences reactivated and lytic stage commences
Retroviruses need Reverse Transcriptase & Integrase
Reverse Transcriptase: catalyzes RNA into DNA
Integrase: put viral genome within host genome for further replication
Explain the process of using reporter constructs to find seed enhancers. What are reporter genes and tissue-specific enhancers?
Reporter genes encode proteins that are easily detected and are often translated in order to find specific genes
Tissue-specific enhancers bind to regulatory transcription factors and make transcription happen in specific cell types.
Reporter constructs: Creates a synthetic gene consisting of the suspected enhancer, promoter and reporter gene. Put into cells and look for expression of reporter gene (whichever is expressed has correct enhancer).
How does antibiotic resistance influence bacterial fitness? Through what evolutionary process is this done?
Environmental pressures for survival induce natural selection, or the physiological advantage of some bacterial organisms with specific traits. These traits confer increased fitness, and are therefore passed along through reproduction of surviving organisms
Antibiotic resistance confers large increases in bacterial fitness, as bacteria can better survive antibiotic treatments and environments. This allows them to continue reproducing and selection for this trait continues to occur when antibiotics are being used (in vivo conditions ONLY).
Describe the infection process of COVID-19
(Break it into two parts: Viral Entry and Genome Replication)
Viral Entry
1) SARS-2 Spike Protein binds to human cells with ACE2 receptors and triggers receptor mediated endocytosis of viral particles
2) Furin site is recognized and cleaved by a protease, allowing fusion machinery with host cell to function
Genome Replication
1) Viral +RNA genome is immediately translated + viral proteins are produced
2) Genomic copies of viral genome are made via making the viral ss+RNA into complementary ss-RNA with RdRp
3) ss-RNA is used as a template to synthesize more ss+RNA through complementary RNA base pairing
Explain the process of creating Aquabounty Salmon. What genetic components are expressed that transform the salmon genome?
Aquabounty Salmon involves genes from two different organisms: Chinook Salmon and Ocean Pout.
The constitutive (always expressive) enhancer was put into salmon, replacing the season specific enhancer. This constitutive enhancer was put in front of the IGF-1 gene which codes for growth associated proteins.
This recombinant DNA allowed for the growth gene (IGF-1) to be constitutively expressed increasing development
Explain how antibiotic resistance is spread from bacteria to bacteria (two main ways discussed in lecture)
1) Horizontal Gene Transfer: genetic material transferred between two different species (ex: ecoli resistance gene is transferred to gonorrhea --> both species now have the same resistance characteristic)
2) Plasmids: bacterial antibiotic resistance genes are often located on plasmids. These are accessory genes seperate from the bacterial chromosome. Undergo HGT with other bacterial species.
Compare and contrast the four methods of immunizations. What are advantages and disadvantages for all of them?
1) Attenuated Vaccine- weakened version of the pathogen created through mutating the viral pathogen such that it cannot cause disease. Disadvantage includes potential virulence for immunocompromised individuals
2) Inactivated Virus- dead version of pathogen. Advantages are incorporated into other vaccines, confers protect against multiple pathogens. Disadvantages include exposure to only surface proteins
3) Purified Protein Vaccines- Viral protein created in lab that would normally be created in host. Advantages are no virulence/pathogen cultures. Disadvantages are protection conferred against only one pathogen, pathogen evading immune response via missense mutation.
4)mRNA- injection encodes the pathogenic protein such that host cells take up mRNA and synthesize the viral protein. Only one pathogenic protein used as vaccine (confers protection against one pathogen)
Explain the process of creating Bt Corn. What genetic components are needed to express the Cry protein in corn?
The Cry protein originates from bacteria which produce it as defense against insects
Genetic components: Corn promoter and enhancer
5'UTR and 3'UTR for translation initiation/mRNA stability
Cry gene with same coding region in corn AND bacteria (triplet codon sequence doesnt change) that has been transformed into corn via CRISPR
List and describe the five sources of antibiotic resistance
1) Missense mutations in target enzyme active site: causes both the enzyme active site and substrate to have decreased affinity for each other
2) Antibiotic degredation: chemical neutralization of the antibiotic structure/components
3) Gene replacement: bacterial acquisition of a new gene that can perform the same essential function without effect by antibiotic
4) Biofils: bacteria organizing in a community have mechanisms to protect against antibiotics --> lower antibiotic effectiveness
5) Antibiotic exporters: cell membrane transporters pushing antibiotics out of the bacteria cell