Enzymes
What is the function of an enzyme?
What is lower the Activation energy by stabilizing the transition state and increasing the rate of reaction
What is the final electron acceptor in the ETC?
What is oxygen
Where do the light-dependent reactions take place?
What is the thylakoid membrane?
What is a virus?
What is an obligate (not alive) parasite that has ss/ds DNA or RNA for genetic material. They also may have a protein outer coating and enzymes.
What are GMO crops and what are some of their bioengineered traits?
GMOs are genetically modified organisms that are widely present in agriculture. Traits include herbicide resistance, pesticide resistance, viral resistance and climate resistance. They may also contain increased nutritional density
What are cofactors and coenzymes?
What are molecules that bind to an enzyme and increase the range of reactions able to be catalyzed
Cofactors are inorganic molecules, coenzymes are organic molecules
What are the products of glycolysis? What is substrate level phosphorylation and how is it used in this process?
What is ATP, NADH, and pyruvate
What is using a high energy molecule to directly transfer an inorganic phosphate to ADP, making ATP
What is the primary function of the light-dependent reactions of photosynthesis?
What is to convert light energy into chemical energy in the form of ATP and NADPH?
What is an overlapping reading frame? What is proteolytic cleavage?
What is using one single open reading frame to code for multiple polypeptides
What is the cleavage of one long polypeptide into multiple different protein subunits
What is the function of the Cry protein in Bt corn? From what organism domain is it from?
What is kill corn borer insects and increase corn yield
What is bacteria (Bacillus thuringiensi)
What is Vmax for an enzyme? What is Km? Would an enzyme with a low affinity for a substrate have a low or high Km?
What is the maximum velocity in which an enzyme is processing substrates (saturation of enzymes)
What is the substrate concentration at 1/2 Vmax
Low affinity = high Km bc takes more substrate to reach half the max reaction velocity
Energy stored by proton gradient is coupled with the production of ATP by what enzyme? What is this process called?
What is ATPase and Chemiosmosis
What is the importance of the Calvin Cycle in the context of the worlds ecosystem?
It fixes inorganic CO2 into usable, organic C in the form of glucose, which allows the global ecosystem to function.
What is the full mechanism in which Sars-2 COVID infects a host cell?
1) Sars 2 spike protein binds to ACE2 receptor proteins
2) Binding triggers receptor mediated endocytosis and the virus enters the cell
3) The Furin cleavage site is cleaved releasing the “head group” and allowing the fusion machinery to function
4) The virus fuses its membrane with the endocytic membrane and its genome is released into the cytoplasm
What are reporter constructs?
The process of testing enhancer activity: Place the suspected enhancer upstream of a promoter and a gene encoding a protein that is easily detected (Reporter Genes) Then introduce the Reporter Construct (promoter + reporter genes) into cell and look for gene expression
What are the factors that affect the rate of reaction and how does each do this?
What is:
Temperature: denaturation of enzyme structure
pH: denature enzyme and increase activation energy
Substrate concentration: increase rate of reaction bc more enzyme substrate binding
Enzyme concentration: increase rate of reaction and Vmax bc more enzyme present to bind with substrate and create product
What are the products of the Krebs Cycle? What molecule is oxidized during this process?
What are NADH, FADH2, ATP and CO2
What is acetyl CoA
What is the role of photosystems II and I in the ETC of light-dependent reactions? What about NADP+ Reductase?
Photosystem II: use energy to strip electrons from water (electron donator) and excite them to another energy level
Photosystem I: use light energy to re-excite the electrons, increasing free energy of the electrons
NADP+: synthesizes NADPH from NADP+ using electrons donated during the ETC
What are the 5 sources of antibiotic resistance?
1. Missense mutation in the antibiotic target protein so that the protein doesn't binds to the antibiotic.
2. Enzyme degradation of the antibiotic.
3. New gene replacement for nucleotide biosynthesis provides resistance to sulfonamides
4. Antibiotic cannot access the bacteria due to changes in biofilm
5) Evolution of antibiotic exporters in bacteria
What is the process for how Golden Rice is engineered with beta-carotene?
Cut out the leaf enhancer and replace with rice seed enhancer upstream of the promoter. Put back into rice seed. Regulatory seed transcription factors bind to this seed enhancer and begin transcription of the Phyotene Synthase, Crt1 and Lycopene Cyclase genes in developing seed cells.
What are the differences between a competitive and non-competitive inhibitor? Distinguish between binding mechanism, binding sites, and effects on Vmax and Km
Competitive inhibitor: inhibitor is structurally similar to substrate, competes with it. Binds directly to active site, increases Km but no change in Vmax
Non Competitive inhibitor: inhibitor alters shape and function of active site. Binds away from active site, decreases Km and Vmax
Name each cellular location where the process occurs:
1) Glycolysis
2) Pyruvate Processing
3) Krebs Cycle
4) ETC
1) cytosol
2) b/t the cytosol and mitochondria
3) mitochondrial matrix
4) inner mitochondrial membrane/intermembrane space (where H+ are pumped)
What are the three steps of the Calvin Cycle? Describe what happens in each
Carbon fixation: addition of CO2 to a 5 carbon sugar to produce a 6 carbon sugar by Rubisco
Reduction: energy from ATP and NADPH is used to reduce the 6 carbon sugar made by Rubisco into G3P
Regeneration: the remaining 5 G3P are made back into 5 Carbon sugar, RuBP to get back the carbon fixation substrate
What is the lytic and lysogenic viral life cycle? Why can't immune cells recognize lysogenic (latent) infections?
Lytic: Virus enters host cell, genome translated and replicated, viral proteins assembled and are released killing the host cell. Infection spreads to other cells
Lysogenic: Virus enters host cell, viral genome inserted into host genome using reverse transcriptase and integrase. Viral genome is replicated using host machinery and lies latent until later activated
When a virus is in the lysogenic (latent) life cycle, it is not actively infecting other host cells. It does not express viral surface proteins that would be recognized by immune cells.
What would be needed to transcribe and translate the Cry gene in corn plants? What could be kept the same in this process for both corn and bacteria?
Transcription: A corn promoter, corn enhancer (corn regulatory transcription factors), corn transcription terminator sequence.
Translation: A 5' UTR sequence with one AUG start codon, 3' UTR sequence for mRNA stability
The amino acid sequence for the Cry gene could be kept the same, since bacteria and plants use the same amino acid code (A, U, C, G)