Term
| do viruses have DNA or RNA genomes? |
|
Definition
| Viruses can have DNA or RNA genomes |
|
|
Term
| what enzyme do viruses with RNA genomes need to have? |
|
Definition
| viruses with RNA genomes must have reverse transcriptase to make DNA from their RNA |
|
|
Term
|
Definition
|
|
Term
| zoonosis: what is it and what particular subject did we connect it to? |
|
Definition
| zoonosis: transfer of a virus from an animal to a human, it is best theory (supported by data) for how HIV in humans started |
|
|
Term
| what is most likely way HIV moved from monkeys to humans? |
|
Definition
| HIV most likely moved from monkeys to humans when raw infected monkey blood was accidentally ingested when the monkey was being prepared for food |
|
|
Term
| what is SIV, why do we care about it? |
|
Definition
| simian immunodeficiency virus, similar to HIV, mostly likley precursor to HIV |
|
|
Term
|
Definition
| B cells produce antibodies |
|
|
Term
|
Definition
| cytoxic T cells bind and destroy mutated or infected "self cells" |
|
|
Term
| how are viral genomes notable? |
|
Definition
| viral genomes are compact, efficient, may even have overlap between genes on opposite sides of the double helix |
|
|
Term
| what is the first step of the HIV replication cycle? |
|
Definition
| the first step of the HIV replication cycle is the fusion of the HIV cell to the host cell surface |
|
|
Term
| what sections of an uninfected host cell does HIV look for? |
|
Definition
| there are certain receptors on the membrane of the host cell that connect to proteins sticking out of HIV |
|
|
Term
| what is the importance of the proteins sticking out of the HIV virus |
|
Definition
| those proteins look for certain receptors on the surface of helper T cells |
|
|
Term
| what is the second step of HIV replication? |
|
Definition
| RNA, reverse transcriptase, integrase, and other viral proteins enter the cell |
|
|
Term
| what is the role of integrase in HIV replication? |
|
Definition
| integrase is an enzyme that integrates HIV DNA (from reverse transcriptase) with host DNA |
|
|
Term
| what is the third step in the HIV replication cycle? this is what occurs after HIV injects it's inner contents into the host |
|
Definition
| the third step in HIV replication is construction of viral DNA from reverse transcription. This occurs outside the nucleous |
|
|
Term
| where does HIV's reverse transcriptase act? |
|
Definition
| HIV's reverse transcriptase makes viral DNA outside of the nucleous |
|
|
Term
| what is the fourth step in HIV's replication cycle? it occurs after viral DNA has been created by reverse transcription |
|
Definition
| the fourth step is that viral DNA enters the nucleous and integrates with the host DNA |
|
|
Term
| what is the fifth step in HIV's life cycle? this is what occurs after viral DNA is integrated with host DNA |
|
Definition
| viral DNA → viral mRNA→ viral proteins |
|
|
Term
| what is the sixth step in HIV's replication cycle? this is the second to last step |
|
Definition
| the sixth step is that viral RNA and viral proteins make an immature HIV virus at the cell surface |
|
|
Term
| what is the seventh step in HIV replication cycle? it is the final step |
|
Definition
| a mature HIV virus is formed when protease releases induvidual HIV proteins |
|
|
Term
|
Definition
| an enzyme coded for by HIV-infected cells that cuts up the proteins HIV genome codes for |
|
|
Term
| name the one enzyme that HIV-infected cells make that we have to know, what does it do? |
|
Definition
| protease, it cuts up the proteins that the HIV-infected cell makes |
|
|
Term
| what are three good things to target with anti-HIV drugs? |
|
Definition
3 proteins each with a seperate, vital function:
1. proteins on HIV's surface
2. reverse transcriptase
3. protease |
|
|
Term
| why aren't antibodies effective against HIV |
|
Definition
| because HIV genome is constantly mutating |
|
|
Term
| the human body is initially fairly successful in fighting HIV, but HIV rebounds after nine weeks. Why? |
|
Definition
| HIV rebounds because of mutations in it's genome that makes antibodies ineffective |
|
|
Term
| what does the test for HIV test for? |
|
Definition
| the test for HIV tests for the antibodies for HIV |
|
|
Term
| why does the test for HIV often come up negative a week after infection? |
|
Definition
| a week after infection, no antibodies have been made yet. |
|
|
Term
| what does the term non-progessors mean in relation to HIV? |
|
Definition
| non-progessors are people who are HIV-positive and have functioning immune systems |
|
|
Term
| how does risk of transmission change over time? |
|
Definition
| risk of transmission is highest right after infection, is lowest while one is asymptomatic, and then goes up once symptoms are developed |
|
|
Term
| name three tests for HIV, and name what they do |
|
Definition
1. ELISA: looks for antibodies for HIV genes
2. Western Blot: uses antibodies which
bind to proteins on HIV membranes
3. PCR: uses primers specific to HIV genes |
|
|
Term
| viral load, what is it and what important attribute is it connected to? |
|
Definition
| viral load is how much of a virus one is carrying, and high viral load leads a higher chance of transmitting the virus |
|
|
Term
| what process "turns on" HIV in T-Cells? |
|
Definition
| there is a promoter sequence in HIV that is activated by transcription factors in T-Cells. When these transcription factors try and induce transcription (and eventually gene expression) in T-Cells, the HIV promoter sequence recognizes the transcription factors and activates HIV |
|
|
Term
| what makes HIV evasive to vaccines? |
|
Definition
| HIV's genome is always randomly changing due to mutations, making it very evasive to vaccines |
|
|
Term
| what would an optimal HIV vaccine target? |
|
Definition
| an optimal HIV vaccine would target the unchanging proteins on HIV |
|
|
Term
| define antigenic variation |
|
Definition
| when a pathogen changes it's surface proteins to avoid host antibodies |
|
|
Term
| how can we inhibit HIV like we inhibit an enzyme? |
|
Definition
| if we design a molecule that acts as a competitive inhibitor and binds to the "active site" of HIV |
|
|
Term
| what did the first class of HIV drugs target, and why did they stop being effective? |
|
Definition
| the first class of HIV drugs targeted reverse transcriptase, and after some time HIV's reverse transcriptase evolved around the drugs |
|
|
Term
| what is a the drug regimen that is best at keep HIV viral load very very low (non-dectable). What does this drug regimen involve, and why is it successful? |
|
Definition
| the HAART drug regimen uses a cocktail of three drugs at the same time. It is sucessful becuase HIV is much much less likley to evolve around three drugs at once. The HAART regimen uses effective protease and integrase inhibitors |
|
|
Term
| what HIV proteins does the HAART regimen target? |
|
Definition
| the HAART regimen inhibits protease and integrase, HIV proteins that are vital for replication |
|
|
Term
|
Definition
in various parts of the body, HIV hides in
non-T-cells. |
|
|
Term
| when HIV is in non-T-cells, why is it "hiding" |
|
Definition
| if the promoter regions of HIV don't see transcription factors specific to T-cells, HIV doesn't replicate, and simply sits there inactive |
|
|
Term
| what causes HIV to be isolated in regions of the body and stay dormant? What can cause HIV to re-activate? |
|
Definition
| a sucessful anti-HIV drug regimen will inhibit HIV's ability to replicate, forcing it to stay dormant in non-T-cells. If the drug regimen is stopped, HIV can start replicating again |
|
|
Term
| what is the cause of HIV's genome constantly randomly changing? |
|
Definition
| HIV's reverse transcriptase makes many mistakes |
|
|
Term
| protease inhbitors work by what mechanism? |
|
Definition
| protease inhbitors for competitive inhbitors that bind to the active site of protease more readily than the normal substrate |
|
|
Term
| if viral levels of HIV are indectable, is the body free of HIV? |
|
Definition
| no, there are still latent resvoirs of dormant HIV hiding in lymph nodes, brain, liver, etc |
|
|
Term
| what is the nucleous of a eukaryotic cell? |
|
Definition
| the nucleous is where the DNA stays |
|
|
Term
|
Definition
| when an eukaryotic cell envelops but doesn't digest a bacterial cell, and the bacteria cells lives in the eukaryote and helps it |
|
|
Term
| what two organelles have thier origins in endosymobiotic thoery? |
|
Definition
| both mitchondria and chloroplasts come from endosymbiosis |
|
|
Term
| what is wrong about picture of mitochondria we see drawn? |
|
Definition
| inner memebrane of mitchondria looks like tubes. The inner mitchondrial memebrane is drawn as folds |
|
|
Term
| the phosolipid bilayer has two parts, what is each half and what is important about each half? |
|
Definition
| the phosphate groups touch the cytoplasm and the environment outside the cell, they are charged and hydrophobic. The lipid part is comprised of hydrophobic hydrocarbon chains and makes up the middle of the memebrane |
|
|
Term
| does transporting something across a cell membrane require energy? |
|
Definition
| sometimes transporting something across a membrane takes energy, sometimes it doesn't |
|
|
Term
| uniporter transport protein |
|
Definition
| an uniporter transport protein moves one thing in one direction |
|
|
Term
| symporter transport protein |
|
Definition
| a symporter transport protein moves two things in one direction |
|
|
Term
| antiporter transport protein |
|
Definition
| antiporter transport proteins switch two things (one thing goes in, another thing goes out) |
|
|
Term
what type of transport protein would you use to:
1. move one thing across a cell membrane
2. move two things across a cell membrane
3. move one thing into and move another one out of a cell |
|
Definition
1. uniporter is used to move one thing
2. symporter is used to move two things
3. antiporter is used to switch two things |
|
|
Term
|
Definition
| the nucleolus is a concentration of DNA in the nucleous |
|
|
Term
|
Definition
| the system of two membranes, the inner and outer nuclear membranes, that sorround the nucleous |
|
|
Term
| what would an optimal HIV vaccine target? |
|
Definition
| an optimal HIV vaccine would target the unchanging proteins on HIV's surface |
|
|
Term
|
Definition
| DNA is in the nucelous of the cell |
|
|
Term
| what organelle serves as the site of transport and processing? |
|
Definition
| the endoplasmic reticulum serves as the site of transport and processing |
|
|
Term
| what organelle is vital for proteins being packaged into vesicles and transported to other cells |
|
Definition
| the function of the golgi appartus is to process proteins and package them in vesicles so they can be transported to other cells |
|
|
Term
|
Definition
| scaffolding within the cytoplasm |
|
|
Term
| why is the cytoskeleton made out of globular monomer? |
|
Definition
| to make the cytoskeleton easy to assumble and dissamble one monomer at a time |
|
|
Term
| what structure is responsible for physically halving the mother cell during mitosis/cytokensis? |
|
Definition
| the contractile ring physically cuts at center, splitting the mother cell |
|
|
Term
| mitosis is specifically dividing of what structure? compare to cytokensis |
|
Definition
| mitosis is division of nucleus, whereas cytokeneis is division of cytoplasm |
|
|
Term
| what is the function of the cytoskeleton? |
|
Definition
| the function of the cytoskeleton is to provide structure for the cell and transport things within the cell |
|
|
Term
| when DNA condenses into chromosomes during prophase, what change does this bring around in terms of the DNA's functionality? |
|
Definition
| when DNA is condensed into chromosomes, transcription almost completley stops |
|
|
Term
|
Definition
| every part of cell divison that isn't mitosis |
|
|
Term
| what is the contractile ring made of? |
|
Definition
| the contractile ring is made of myosin and actin |
|
|
Term
| what is created during G2 phase? |
|
Definition
| RNA and proteins are made in G2 phase as preperation for mitosis |
|
|
Term
| how many copies of each chromosome does a cell have during prophase |
|
Definition
| during prophase, a cell has two copies of it's genome, meaning it has four of each chromosome, two from each parent |
|
|
Term
| what occurs during prometaphase |
|
Definition
| during prometaphase, the chromosomes begin to move towards/line up along the spindle |
|
|
Term
| what occurs during metaphase? |
|
Definition
| during metaphase, chromosomes line up along the middle of the cell, and connect to the spindle |
|
|
Term
| during metaphase, chromsomes line up along and connect to a spindle. what is this spindle? |
|
Definition
| this spindle is a bunch of actin molecules going across the cell |
|
|
Term
|
Definition
| during anaphase, sister chromosomes (which are identical chromosomes) are pulled apart towards opposite ends of the cell |
|
|
Term
| what occurs in telophase? |
|
Definition
| the two halves of the genome are seperated, the nuclear membrane reforms, and contractile ring begins to cleave cell |
|
|
Term
| what would be a more efficient way to do meiosis compared to how it actually happens? |
|
Definition
| a more efficient way to do meiosis would be to simply halve one cell. The way it is done is double everything and make four haploid cells |
|
|
Term
| what is different about metaphase 1 in meiosis compared to metaphase in mitosis? |
|
Definition
| in metaphase 1, the mother/father chromosomes are mixed up so each daughter cell doesn't have the exact same genome |
|
|
Term
| how many useful haploid cells are created from one cycle of meiosis |
|
Definition
| only one useful haploid cell is created from one cycle of meiosis |
|
|
Term
| what is the role of a "timer" in cell cycle control? |
|
Definition
| a "timer" in cell cycle control can control how long a cell spends doing each step/each event and know when to move on |
|
|
Term
| how do cells know when they are supposed to do each step in cell divison? (very general answer) |
|
Definition
| cells have mechanisms to control the order of events, for example cell division must come after DNA replication |
|
|
Term
| what are 3 necessary features of effective cell cycle control? |
|
Definition
1. a timer to make sure that each step is done for the
correct amount of time
2. a mechanism to make sure that steps happen in the correct order, example: that cell divison happens after DNA replication
3. a mechanism to make sure any one step is done only once
|
|
|
Term
| what is an example of a time the cell cycle is changed based on enviroment/development? |
|
Definition
| after a fertilization of an egg, the cell divides into many smaller cells without ever growing |
|
|
Term
| what organism do we use to study cell cycle controls and why? |
|
Definition
| we study the cell cycle controls of yeast because they are similar to the cell cycle controls of humans. Human cell cycle control proteins functioned in yeast cells |
|
|
Term
| start of the cell cycle is controlled by ____ (3 things) |
|
Definition
1. nutrients
2. mating factors
3. cell size
all affect if a cell will undergo divison |
|
|
Term
| how do we study genes that control the cell cycle? |
|
Definition
|
|
Term
| how do we study genes that regulate the cell cycle? |
|
Definition
| we design temperature sensitive mutations on the genes so that we can switch the gene expression between wild and mutant by changing the temperature |
|
|
Term
| what was the big picture result of the study that used temperature sensitive mutations to study what genes controlled the cell cycle? |
|
Definition
| the result was that there are many genes that control the cell cycle |
|
|
Term
| what was one gene that was discovered to play a role in the cell cycle from the temperature sensitive mutation experiment? |
|
Definition
| cdc 28 is a gene whose mutant phenotype stops the cell cycle at S phase. This is evidence that normal-functioning, non-mutant cdc 28 plays a role in making sure the S phase is done correctly |
|
|
Term
|
Definition
| cell-cycle promoting factor that starts cell cycle in frog embryos |
|
|
Term
|
Definition
| kinases take phosphate groups from high-energy molecules like ATP and put them on specific molecules |
|
|
Term
| cell cycle control in eukaryotes uses what two types of molecules? |
|
Definition
| cyclins and cyclin-dependent kinases |
|
|
Term
| what factor in cell cycle control is responsible for turning on proteins that are used to proceed in the cell cycle? |
|
Definition
| cyclin-dependent kinases are responsible for phosphorylating proteins to turn them on |
|
|
Term
| pyruvate dydrogenase catalyzes what reaction? |
|
Definition
pyruvate dydrogenase cataylzes this reaction:
pyruvate → Acetyl-CoA + CO2
NAD+ is turned into NADH in this reaction |
|
|
Term
| why can't fatty acid chains turn into acetyl-CoA and then glucose? |
|
Definition
| because the krebbs cycle involves emitting 2 CO2 molecules, so we lose 2 molecules of carbon every time we add two from a fatty acid chain |
|
|
Term
| what is the first enzyme used in the krebbs cycle? |
|
Definition
| the first enzyme used in the krebbs cycle is citrate synthase |
|
|
Term
| what is special about the last step in glycolysis? |
|
Definition
| the last step in glycolysis has a large negative ΔG, so there is a detour for this step with a additonal intermediate for gluconeogenesis |
|
|
Term
| what is changing about DNA sequencing? |
|
Definition
| DNA sequencing is getting cheaper, easier, and requires less human involvement. However, the size of the sections of DNA we read are getting smaller |
|
|
Term
| what makes telomers hard to sequence? |
|
Definition
| telomers are hard to sequence because they are so repepitive |
|
|
Term
| what is functional genomics and what is one thing is focuses on? |
|
Definition
functional genomics looks at effects of DNA code down the line, i.e. transcription, protein building, protein-protein interactions, etc.
It focuses on levels of mRNA |
|
|
Term
| how much of human genome by volume has that DNA codes for something? |
|
Definition
| only 1-2% of our genome actually codes for anything |
|
|
Term
| what percent of our genes are transposable elements? |
|
Definition
| about 50% of our genome is transposable elements |
|
|
Term
| what is the name of the membrane protein that moves two things across the membrane in the same direction |
|
Definition
|
|
Term
| antigenic variation helps HIV dodge what? |
|
Definition
| antigenic varitation helps HIV dodge antibodies |
|
|
Term
| why does binding to a histone prevent DNA from being expressed? |
|
Definition
| because the DNA binds to the histone instead of RNA of polymerase |
|
|
Term
| what are the two halves of epigenetic inheritance? |
|
Definition
1. histone acetlyation
2. DNA methlyation |
|
|
Term
| what is the result of histone actylation on transcription |
|
Definition
| more actetyl groups on histones means more expression of DNA |
|
|
Term
| what is the physical affect of acetylation of histones |
|
Definition
| more acetlyation of histones means less histone-DNA interaction |
|
|
Term
| methylation of paternal allele favors what (general), and competes with what |
|
Definition
| methylation of paternal allele favors what is best for child with no regard for mother, it competes with the maternal allele, whose biasas is for preservation of the mother as the well as the offspring |
|
|
Term
| regulation of metabolism often uses what mechanism? |
|
Definition
| negative feedback loop, where the products of a process slow down the production that makes them |
|
|
Term
| which line of genes, paternal or maternal, is it easiest to study epigenetics along |
|
Definition
| it is easiest to study paternal, as maternal passes along so much non-genetic stuff it is hard to differentiate |
|
|
Term
| does methlyation get reset every generation? what tests was done on this? |
|
Definition
| methylation doesn't reset every generation, mice were taught to fear a scent and then offspring for 2 generations feared that same scent |
|
|
Term
|
Definition
| intersection of many sex-determining mechanisms |
|
|
Term
| 3 cell cycle checkpoint controls |
|
Definition
1. during G1 to see if DNA was damaged
2. end of G2 to see if DNA is fully replicated before mitosis starts
3. during metaphase to make sure chromosomes are aligned on the spindle |
|
|
Term
| what is a good way to make sure transposable elements aren't expressed? |
|
Definition
| methylation is a good way to make sure transposable elements are not expressed |
|
|
Term
| what is special about complex 2 in the e- transport chain? |
|
Definition
| complex 2 is an enzyme that puts e- on FAD to make it FADH2 |
|
|
Term
| what is special about complex 2 in the e- transport chain? |
|
Definition
| complex 2 is an enzyme that puts e- on FAD to make it FADH2 |
|
|
Term
| what happens to methylation of DNA during meiosis? |
|
Definition
| methylation is mostly wiped clean, but some goes on to kids |
|
|
