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BIO |! 351 |! exam |! 4 |! with |! precise |!
detailed |! solutions
general |! DNA |! packaging |! process |! - |! Correct |! answer |! ✔-packaging |! motor |! attaches |! to |! the |! prohead -packaging |! of |! viral |! DNA |! into |! the |! phage |! head -scaffolding |! proteins |! discarded -other |! assembly |! steps -packaging |! motor |! discarded -once |! head |! is |! filled, |! packaging |! motor |! detaches |! and |! tail |! components |! are |! added lambda |! phage |! packaging |! process |! - |! Correct |! answer |! ✔-translocation -cos |! Binding -Terminal |! cos-cleavage -results |! in |! a |! DNA |! filled |! capsid |! and |! the |! formation |! of |! complex |! I function |! of |! terminase |! complex |! in |! lambda |! dna |! packaging |! - |! Correct |! answer |! ✔is |! responsible |! for |! recognizing |! the |! cos |! site, |! which |! is |! a |! specific |! sequence |! of |! DNA |! that |! is |! present |! at |! both |! ends |! of |! the |! lambda |! DNA |! molecule what |! happens |! with |! the |! cos |! site |! is |! recongnized |! by |! the |! terminase |! complex |! - |! Correct |! answer |! ✔the |! terminase |! complex |! binds |! to |! it |! and |! begins |! to |! cleave |!
the |! dna |! at |! the |! cos |! site. |! the |! cleavage |! generates |! a |! 12 |! base-overhang, |! called |! the |! "sticky |! end". |! it |! then |! proceeds |! to |! package |! the |! DNA |! into |! the |! viral |! capsid |! in |! a |! headful |! packaging |! mechanism. |! here, |! the |! terminase |! complex |! fills |! the |! capsid |! with |! DNA |! until |! the |! capsid |! is |! full. |! once |! the |! capsid |! is |! full, |! the |! terminase |! complex |! cleaves |! the |! DNA |! at |! the |! other |! end |! of |! the |! cos |! site, |! releasing |! the |! DNA |! filled |! capsid complex |! I |! in |! lambda |! dna |! packaging |! - |! Correct |! answer |! ✔the |! excess |! DNA |! compressed |! and |! organized |! in |! this |! complex. holin |! - |! Correct |! answer |! ✔creates |! holes |! in |! cell |! membrane; |! produced |! in |! the |! cytoplasm; |! functions |! by |! forming |! small |! membrane |! pores |! in |! the |! bacterial |! cell |! membrane, |! allowing |! the |! lambda |! phage |! endolysin |! enzyme |! to |! access |! and |! degrade |! the |! cell |! wall, |! leading |! to |! the |! lysis |! of |! the |! bacterial |! cell relationship |! between |! holin |! and |! the |! peptidoglycan |! layer |! - |! Correct |! answer |! ✔the |! holin |! is |! responsible |! for |! creating |! small |! pores |! or |! hole |! in |! the |! bacterial |! cell |! membrane, |! allowing |! the |! endolysin |! enzyme |! to |! access |! and |! degrade |! the |! peptidoglycan |! layer. Endolysin |! - |! Correct |! answer |! ✔attacks |! peptidoglycan; |! cleaves |! the |! bond |! between |! the |! sugar |! and |! amino |! acid |! subunits |! in |! the |! peptidoglycan |! layer is |! holin |! formation |! and |! lysis |! immediate |! or |! gradual? |! - |! Correct |! answer |! ✔it |! is |! a |! fast |! process CRISPR |! name |! - |! Correct |! answer |! ✔Clustered |! Regularly |! Interspaced |! Short |! Palindromic |! Repeats
transcription |! process |! of |! CRISPR |! - |! Correct |! answer |! ✔produced |! pre-crRNA |! which |! is |! a |! long, |! single |! stranded |! RNA |! molecule |! that |! contains |! the |! spacer |! sequence |! as |! well |! as |! the |! repeat |! sequence processing |! process |! of |! CRISPR |! - |! Correct |! answer |! ✔pre-crRNA |! is |! processed |! into |! mature |! crRNA |! which |! happens |! using |! Cas |! proteins |! that |! recognize |! and |! cleave |! the |! pre-crRNA |! at |! specific |! sites |! within |! the |! repeat |! sequences, |! which |! generates |! individual |! crRNA |! that |! contain |! only |! the |! spacer |! sequence |! and |! a |! short |! sequence |! derived |! from |! the |! repeat silencing |! process |! of |! CRISPR |! - |! Correct |! answer |! ✔-crRNA |! recruits |! Cas9 |! protein |! and |! binds |! to |! desired |! target |! DNA |! sequence(invading |! phage |! or |! plasmid |! DNA). |! this |! is |! called |! the |! effector |! complex. |! the |! Cas |! will |! cut |! and |! at |! the |! cut |! site, |! the |! DNA |! can |! either |! be |! ligated |! or |! used |! or |! inserting |! new |! DNA genome |! insertion/DNA |! insertion |! - |! Correct |! answer |! ✔An |! SgRNA |! is |! synthesized |! to |! bind |! to |! a |! single |! target |! site |! on |! the |! genome |! through |! complementarity. |! The |! Cas9 |! binds |! to |! sgRNA |! and |! this |! stimulates |! the |! Cas9 |! cleaves |! the |! genome |! at |! the |! target |! site. |! A |! foreign |! DNA |! with |! homologus |! ends |! is |! then |! inserted |! and |! reparirs |! the |! DNA |! cleavage genome |! deletion/DNA |! deletion |! - |! Correct |! answer |! ✔Two |! separate |! target |! sites. |! The |! sgRNA |! attaches |! to |! the |! target |! sites/DNA |! to |! be |! deleted. |! The |! Cas9 |! protein |! attaches |! to |! the |! sgRNA |! to |! these |! sites |! which |! results |! in |! a |! double |! stranded |! break |! in |! the |! target |! chromosome |! and |! a |! free |! piece |! of |! DNA. |! The |! double |! stranded |! break |! is |! then |! ligated |! while |! a |! free |! piece |! of |! genomic |! DNA |! is |! degraded. |! This |! results |! in |! genomic |! deleted.
phage |! titering |! - |! Correct |! answer |! ✔The |! number |! of |! phages |! in |! a |! given |! solution |! is |! determined |! using |! "plaque |! forming |! units" |! (PFU) phage |! therapy |! - |! Correct |! answer |! ✔the |! use |! of |! bacteriophage |! to |! treat |! infections, |! first |! used |! in |! 1919 |! France |! to |! treat |! a |! boy |! with |! severe |! dysentery |! who |! recovered |! from |! the |! infection bacteriophage |! v. |! antibiotics |! advantages |! - |! Correct |! answer |! ✔-very |! specific |! -replicate |! at |! the |! site |! of |! infection -occur |! naturally -safe -active |! against |! antibiotic-resistant |! bacteria bacteriophage |! v. |! antibiotics |! disadvantages |! - |! Correct |! answer |! ✔-additional |! research |! required -development |! of |! phage |! resistance |! and |! phage-neutralizing |! antibodies -not |! accessible |! to |! intracellular |! pathogens -difficult |! to |! administer -can |! transfer |! toxin |! genes |! between |! bacteria dsDNA |! virus |! - |! Correct |! answer |! ✔Herpes |! Simplex |! Virus |! (HSV) symptom |! of |! HSV-1 |! - |! Correct |! answer |! ✔mainly |! cold |! sores
HSV |! Replication |! - |! Correct |! answer |! ✔- |! once |! HSV |! replicates |! to |! a |! few |! copies/cell |! the |! viral |! DNA |! is |! then |! replicated |! by |! rolling |! circle |! replication
- |! the |! linear |! DNA |! is |! cut, |! packaged |! and |! then |! the |! virus |! buds |! from |! the |! nucleus |! (process |! happens |! in |! the |! nucleus) immediate |! early |! proteins |! - |! Correct |! answer |! ✔synthesized |! immediately |! after |! infection; |! typically |! function |! to |! activate |! expression |! of |! early |! genes delayed |! early |! proteins |! - |! Correct |! answer |! ✔key |! proteins |! synthesized, |! necessary |! for |! viral |! DNA |! replication late |! proteins |! - |! Correct |! answer |! ✔primarily |! viral |! structures |! replicated the |! viral |! envelope |! is |! added |! during |! budding |! through |! the... |! - |! Correct |! answer |! ✔inner |! nuclear |! membrane process |! of |! HSV |! replication |! - |! Correct |! answer |! ✔-penetration |! and |! uncoating |! of |! the |! cell -absorption |! of |! the |! virus |! into |! the |! cell -circularization |! of |! genome |! and |! transcription |! of |! immediate |! early |! genes |! once |! the |! cell |! has |! released |! its |! DNA |! into |! the |! nucleus -circularization |! of |! genome |! and |! transcription |! of |! immediate |! early |! genes -immediate-early |! proteins |! (products |! of |! immediate-early |! genes) |! stimulate |! transcription |! of |! early |! genes
-early |! proteins |! (products |! of |! early |! genes) |! function |! in |! DNA |! replication, |! yielding |! concatemeric |! DNA. |! Late |! genes |! are |! transcribed -late |! proteins |! (products |! of |! late |! genes) |! participate |! in |! virion |! assemblyHS HSV |! exit |! from |! the |! cell |! - |! Correct |! answer |! ✔-nucleocapsid |! buds |! through |! inner |! nuclear |! membrane |! to |! form |! an |! enveloped |! virus -loses |! its |! envelope |! when |! it |! fuses |! with |! the |! outer |! nuclear |! membrane |! -naked |! capsid |! is |! released |! into |! the |! cytoplasm |! and |! buds |! into |! the |! Golgi |! where |! it |! is |! modifed -the |! modified, |! enveloped |! virus |! exits |! the |! cell |! when |! the |! Golgi |! vesicle |! fuses |! with |! the |! plasma |! membrane |! (exocytosis) HSV |! latency |! and |! reactivation |! - |! Correct |! answer |! ✔During |! latency, |! the |! host |! exhibits |! no |! symptoms -virus |! enters |! sensory |! neurons |! near |! the |! site |! of |! productive |! infection |! and |! remains |! in |! neurons |! for |! a |! lifetime -does |! not |! integrate |! into |! cell During |! reactivation |! event |! (host |! cell |! immune |! suppression), |! the |! host |! has |! symptoms -virus |! leaves |! sensory |! neurons -copy |! of |! viral |! DNA |! remains |! in |! nucleus -virus |! returns |! to |! site |! of |! initial |! infection |! (epithelial |! cell) |! and |! undergoes |! productive |! replication
5.PCR |! process |! (polymerase |! chain |! reaction |! which |! are |! tests |! used |! to |! detect |! HIV/s |! genetic |! material) |! 6.multiple |! copies |! of |! HIV |! genomes |! are |! made poor |! prognosis |! vs |! good |! prognosis |! - |! Correct |! answer |! ✔poor |! prognosis: |! decrease |! in |! CD4 |! cells |! and |! an |! increase |! in |! viral |! RNA |! would |! lead |! to |! earlier |! death good |! prognosis: |! higher |! number |! in |! CD4 |! cells |! and |! a |! drop |! in |! viral |! RNA |! that |! leaves |! to |! extended |! survival HIV |! Structure |! - |! Correct |! answer |! ✔HIV |! is |! an |! RNA |! retrovirus. |! The |! virus |! consists |! of |! -RNA, |! reverse |! transcriptase |! enzyme |! inside |! a |! capsid -capsid |! inside |! a |! matrix -lipid |! membrane -proteins |! on |! the |! outside |! of |! the |! cell |! (gp120 |! and |! gp41) HIV |! genome |! consists |! of |! - |! Correct |! answer |! ✔gag, |! pol, |! and |! env Gag |! encodes |! what? |! - |! Correct |! answer |! ✔gag |! polyprotein gag |! can |! be |! broken |! down |! to... |! - |! Correct |! answer |! ✔matrix, |! capsid, |! nucleocapsid pol |! encodes |! for |! - |! Correct |! answer |! ✔Pol |! polyprotein
Pol |! can |! be |! broken |! down |! to |! - |! Correct |! answer |! ✔reverse |! transcriptase, |! integrase, |! and |! protease env |! encodes |! for |! - |! Correct |! answer |! ✔gp160 |! polyprotein Gp160 |! can |! be |! broken |! down |! to |! - |! Correct |! answer |! ✔gp120 |! and |! gp41 |! protease HIV |! genome |! picture |! - |! Correct |! answer |! ✔env: |! encodes |! a |! precursor |! glycoprotein |! (g120), |! which |! is |! cleaved |! into |! 2 |! parts, |! defined |! g120 |! and |! g41. |! they |! form |! enveloped |! structural |! proteins |! in |! the |! extra |! and |! intra |! cellular |! parts |! of |! the |! cell gag: |! gene |! encodes |! for |! the |! viral |! structural |! proteins |! that |! are |! involved |! in |! assembly |! and |! release |! of |! new |! virus |! particles. |! gag |! protein |! is |! synthesized |! as |! a |! precursor |! protein |! that |! is |! cleaved |! into |! smaller |! proteins, HIV |! Entry |! - |! Correct |! answer |! ✔-HIV |! gp120/gp41 |! protein |! binds |! CD4 |! receptor |! and |! CCR5 |! receptor -Interaction |! of |! the |! virus |! with |! a |! receptor-corereceptor |! pair |! on |! the |! host |! cell -The |! viral |! envelope |! and |! host |! membrane |! fuse -The |! nucelocapsid |! is |! inserted |! into |! the |! host |! cell, |! beginning |! the |! viral |! infection reverse |! transcriptase |! is |! a |! _____ |! dependent |! _______________________ |! - |! Correct |! answer |! ✔RNA |! dependent |! DNA |! polymerase |! (remember, |! it |! makes |! DNA |! frommmm |! RNA)
Protease |! & |! Polyprotein; |! the |! smaller |! RNA |! transcriptase |! encode |! what? |! - |! Correct |! answer |! ✔more |! than |! 1 |! protein/transcript. |! generate |! a |! "polyprotein": |! a |! peptide |! chain |! that |! contains |! more |! than |! 1 |! protein the |! polyprotein |! is |! digested |! by... |! - |! Correct |! answer |! ✔HIV |! protease, |! in |! order |! to |! separate |! the |! polyprotein |! into |! the |! individual |! proteins |! needed What |! does |! HAART |! stand |! for |! and |! what |! is |! used |! in |! it? |! - |! Correct |! answer |! ✔- Highly |! active |! antiretroviral |! therapy. |! The |! use |! of |! three |! or |! more |! drugs |! (drug |! cocktail) |! in |! combination |! to |! decrease |! the |! viral |! load. what |! is |! the |! HAART |! entry |! drug |! and |! what |! does |! it |! do |! - |! Correct |! answer |! ✔enfuvride, |! blocks |! the |! entry |! of |! HIV |! into |! human |! cells |! by |! inhibiting |! the |! fusion |! of |! the |! virus |! with |! the |! host what |! are |! the |! HAART |! reverse |! transcriptase |! (NRTI |! and |! NNRTI) |! drugs |! and |! what |! do |! they |! do |! - |! Correct |! answer |! ✔NRTI: |! tenovir, |! false |! nucleotide |! which |! once |! incorportated |! into |! the |! DNA |! chain, |! it |! terminates |! further |! elongation NNRTI: |! efavirenz, |! directly |! inhibits |! the |! activity |! of |! reverse |! transcriptase |! by |! binding |! to |! the |! catalytic |! site what |! is |! the |! HAART |! integrase |! drug |! and |! what |! does |! it |! do |! - |! Correct |! answer |! ✔raltegravir, |! works |! by |! inhibiting |! the |! activity |! of |! integrase, |! thereby |! preventing |! HIV |! from |! integrating |! its |! genetic |! material |! into |! the |! host |! cell's |! DNA. |! This |! stops |! the |! virus |! from |! replicating |! and |! reduces |! the |! amount |! of |! HIV |! in |! the |! bloodstream
what |! is |! the |! HAART |! protease |! drug |! and |! what |! does |! it |! do |! - |! Correct |! answer |! ✔darunavir, |! Protease |! is |! an |! enzyme |! that |! HIV |! uses |! to |! cleave |! long |! chains |! of |! viral |! proteins |! into |! smaller |! pieces, |! which |! are |! then |! assembled |! into |! new |! virus |! particles. |! Darunavir |! works |! by |! inhibiting |! the |! activity |! of |! protease, |! thereby |! preventing |! the |! virus |! from |! making |! new |! virus |! particles |! and |! reducing |! the |! amount |! of |! HIV |! in |! the |! bloodstream what |! happens |! with |! HIV |! drug |! resistance |! - |! Correct |! answer |! ✔when |! a |! drug |! is |! first |! introduced, |! the |! viral |! diversity |! goes |! down, |! however, |! as |! time |! goes |! on, |! the |! strains |! that |! are |! able |! to |! survive |! the |! drug |! are |! the |! ones |! that |! continue |! to |! survive |! even |! after |! the |! introduction |! a |! drug (-) |! RNA |! virus |! - |! Correct |! answer |! ✔influenza |! virus what |! are |! some |! symptoms |! of |! the |! influenza |! virus |! - |! Correct |! answer |! ✔fever, |! cough, |! runny/stuffy |! nose, |! fatigue prevalence |! of |! influenza |! - |! Correct |! answer |! ✔10%-20% incidence |! rate |! of |! influenza |! - |! Correct |! answer |! ✔~36 |! per |! 100 |! (35-50 |! million |! annually) 1918 |! Influenza |! Pandemic, |! how |! many |! were |! infection? |! how |! many |! died? |! and |! who |! was |! most |! affected? |! - |! Correct |! answer |! ✔-20-40 |! million |! died -infection |! 20% |! of |! people |! on |! earth -most |! deadly |! to |! 20-40 |! year |! olds
influenza |! life |! cycle |! - |! Correct |! answer |! ✔lol Cap |! snatching |! in |! influenza |! - |! Correct |! answer |! ✔lol antigenic |! DRIFT |! - |! Correct |! answer |! ✔mutations |! in |! HA |! and |! NA |! from |! mutations |! during |! replication antigenic |! SHIFT |! - |! Correct |! answer |! ✔large |! antigenic |! change |! resulting |! from |! rearrangement |! of |! 2 |! different |! viruses |! in |! the |! same |! cell mutualism |! - |! Correct |! answer |! ✔a |! reciprocal |! benefit |! accrues |! to |! both |! partners |! (obligatory) example |! of |! a |! mutualism |! relationship |! - |! Correct |! answer |! ✔Buchnera |! aphidicola |! and |! aphids Buchnera |! aphidicola |! are |! gram |! ___________ |! - |! Correct |! answer |! ✔negative where |! do |! Buchnera |! aphidicola |! live |! - |! Correct |! answer |! ✔within |! large |! aphid |! cells, |! called |! "bacteriocytes" |! (also |! mycetocyte) how |! are |! Buchnera |! aphidicola |! transmitted |! - |! Correct |! answer |! ✔vertically |! from |! mother |! to |! daughter
Buchnera |! aphidicola |! are |! ________ |! mutualists |! - |! Correct |! answer |! ✔obligate; |! they |! require |! their |! mutualistic |! partner |! to |! survive |! and |! reproduce what |! does |! the |! aphid |! do |! for |! Buchnera? |! - |! Correct |! answer |! ✔The |! two |! have |! evolved |! together |! millions |! of |! years'; |! 75% |! of |! the |! Buchnera |! genome |! has |! been |! lost; |! aphid |! provides |! Buchnera |! with |! amino |! acids |! that |! Buchnera |! cannot |! make What |! does |! Buchnera |! do |! for |! the |! aphid? |! - |! Correct |! answer |! ✔grow |! normally |! provided |! a |! diet |! supplemented |! with |! amino |! acids; |! aphids |! cannot |! make |! Trp, |! Buchnera |! must |! synthesize |! and |! provide |! Trp |! for |! the |! aphid what |! does |! a |! anotobiotic |! aphid |! mean |! - |! Correct |! answer |! ✔a |! gnotobiotic |! = |! germ |! free what |! is |! the |! result |! of |! low |! trytophan |! levels |! - |! Correct |! answer |! ✔the |! regulatory |! protein, |! the |! trp |! repressor, |! cannot |! bind |! to |! the |! operator |! sequence. |! this |! means |! RNA |! pol |! can |! bind |! to |! the |! promoter |! region |! and |! initiate |! transcription |! of |! the |! trp |! operon what |! is |! the |! result |! of |! high |! tryptophan |! levels |! - |! Correct |! answer |! ✔tryptophan |! moleucles |! bind |! to |! the |! trp |! repressor |! protein, |! causing |! a |! conformational |! change |! that |! allows |! it |! to |! bind |! to |! the |! operator |! sequence |! of |! the |! trp |! operon. |! This |! binding |! of |! the |! trp |! repressor |! to |! the |! operator |! sequence |! prevents |! RNA |! pol |! from |! binding |! to |! the |! promoter |! region, |! thus |! inhibiting |! transcription |! of |! the |! trp |! operon
During |! attenuation, |! when |! tryptophan |! levels |! are |! high, |! the |! ________ |! stem-loop |! forms |! and |! transcription |! _________ |! the |! trpL |! gene. |! - |! Correct |! answer |! ✔ 3 |! and |! 4; |! ends during |! attenuation, |! in |! the |! absence |! of |! Trp, |! what |! happens |! to |! the |! Trp |! ribosome? |! what |! two |! sites |! bind |! - |! Correct |! answer |! ✔a |! 2:3 |! pair |! forms |! and |! there |! is |! no |! termination, |! transcription |! continues if |! region |! 2 |! of |! the |! RNA |! pairs |! with |! region |! 3 |! of |! the |! RNA |! then... |! - |! Correct |! answer |! ✔nontermination |! stem |! loop, |! transcription |! continues If |! region |! 3 |! of |! the |! RNA |! pairs |! with |! Region |! 4 |! of |! the |! RNA |! then... |! - |! Correct |! answer |! ✔terminating |! stem |! loop |! forms, |! transcription |! terminates translation |! of |! the |! leader |! peptide |! affects... |! - |! Correct |! answer |! ✔which |! region |! pairs cooperation |! - |! Correct |! answer |! ✔a |! reciprocal |! benefit |! accrues |! to |! both |! partners |! (not |! obligatory) examples |! of |! cooperation |! - |! Correct |! answer |! ✔1. |! Desulfovibirio |! and |! Chromatium |! 2.Nitrogen |! fixing |! bacteria |! (Azotobacter) |! and |! Cellulose |! degrader |! (Cellulomonas)
commensalism |! - |! Correct |! answer |! ✔one |! symbiont |! (the |! commensal) |! benefits |! while |! the |! other |! (host) |! isn't |! harmed |! or |! helped example |! of |! commensalism? |! where |! is |! it |! commonly |! found |! and |! what |! does |! it |! do |! - |! Correct |! answer |! ✔-staphlyococcus |! epidermidis |! |! commonly |! found |! growing |! on |! skin consumes |! human |! waste |! (oils, |! water, |! salts, |! dead |! skin |! cells) |! and |! usually |! has |! no |! impact |! on |! human |! health predation |! - |! Correct |! answer |! ✔one |! organism |! preys |! on |! another example |! of |! a |! predator.. |! what |! does |! it |! do |! - |! Correct |! answer |! ✔Bdellovibirio; |! it |! is |! a |! gram |! negative |! bacteria |! that |! preys |! on |! other |! gram-negative |! bacteria. |! enter's |! the |! prey's |! periplasmic |! space |! and |! feeds |! on |! the |! cytoplasmic |! contents How |! does |! Bdellovibrio |! divide |! and |! reproduce? |! - |! Correct |! answer |! ✔- elongation |! (initiation |! and |! completion) -synchronous |! septation |! (initation, |! progagation, |! filamentation) |! -maturation |! (progency |! maturation) -lysis |! (escape) Parasitism |! - |! Correct |! answer |! ✔the |! parasite |! benefits |! while |! the |! host |! is |! usually |! harded
