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THE MCAT-BIO 2
GENES & VIRUSES
| Question | Answer |
|---|---|
| Purines? | adenine / guanine |
| Pyrimidines? | cytosine / thymine |
| Repetitive sequence DNA | noncoding DNA |
| Old strand has more ____ groups than new strand | methyl |
| semi-conservative replication | heavy --> intermediate --> intermediate and light |
| replisome | -protein that governs DNA replication |
| Site of transcription, DNA replication, translation, recombination for prokaryotes? | Protplasm |
| Site of transcription, DNA replication, recombination for eukaryotes? Translation? | -Nucleus -cytoplasm |
| DNA gyrase / topoisomerase | relieves overwound DNA with negative supercils |
| RNA Primase | Creates RNA primer for DNA polymerase |
| How does DNA polymerase read DNA and make DNA? | Reads 3'-->5' and synthesizes 5' --> 3' |
| What energy drives DNA replication? | hydrolysis of phosphodiester link to free pyrophosphate |
| DNA ligase | fills in gaps of okazaki fragments with nucleotides and sugar phosphate backbone |
| DNA polymerase proofreading activity is also known as? | 3' - 5' exonuclease activity |
| WHich strand is more subject to errors? | lagging strand |
| Replication-origin of replication and chromosome: prok vs. euk | -prok-circular / one origin -euk - multiple origins |
| Telomerase | -enzyme that elongates telomeres by adding nucleotides (5'-->3') -reverse transcriptase activity to elongate 5'--> 3' strand |
| What type of cells are telomerase found in? | cells with high growth potential -early embryonic cell, germ, stem, cancer cells |
| Location of DNA and RNA? | -nucleus and mito matrix -nucleus and cytoplasm |
| Where does transcription take place? Translation? | -nucleus -cytoplasm |
| Monocistronic - what is it and where is it found? | -eukaryotes - each mRNA translates to only one product |
| polycistronic - what is it and where is it found? | -prokaryotes - each mRNA leads to multiple products |
| What is antisense strand? | template strand with sequence complementary to RNA produced |
| RNA produced is same as ______ | sense strand (coding strand) -protects against degradation |
| How do polymerases act for DNA and RNA | Move in 3'-->5' direction but build new strand in 5'-->3'direction |
| How do the types of RNA polymerases compare between prok and euk? | Prok - one polymerase Euk-3 polmerases |
| What is newly formed RNA called? | hnRNA |
| How does transcription know where to start / end ? | promoters (consensus sequence) and termination sequence -variation from consensus seq causes RNA poly to bind less tightly |
| Difference between promoter and primer. | Promoter - tells RNA poly where to start transcription Primer - short piece of RNA that starts replication |
| What are differences between transcription and replication in terms of speed and proofreading? | -transcription is slower and doesn't proofread |
| How is transcription regulated? | activators / inhibitors bind to DNA close to promoter to activate / repress RNA poly |
| Exons / introns are cut out? How to remove? | -Introns --> only exons code -snRNPs form spliceosome |
| T / F: Post-transcriptional processing occurs in both euk and prok? | TRUE |
| Does the 5'cap and poly A tail added before or after mRNA is completely transcribed? | before |
| What is function of 5'cap? | attachment site for px synthesis and protects against exonucleases |
| Where are introns / exons found? | -introns stay in nucleus -exons exit nucleus |
| Start Codon / stop codons? | -start: AUG -stop: UAA, UGA, UAG |
| How to create sticky ends? | use restriction enzymes to cut at palindromic sequences |
| What does lacZ enable? | enable to digest x-gal sugar |
| PCR steps | -95 degrees: denature DNA -60 degrees: cool to anneal primers -72 degrees: activate heat-resistant polymerase |
| Restriction fragment length polymorphisms | DNA of different individuals have different restriction sites and varying distances between restriction sites |
| Besides cytoplasm, where else can translation occur? What locations on ribosomes? | -mito matrix -free floating ribosome or ribosome attached to rough ER |
| How to make a ribosome? | combine rRNA with protein |
| ____ end of codon lines up with _______ end of anticodon | 5' and 3' |
| tRNA synthetase | enzyme that helps bind a.a. to tRNA (use GTP) |
| Prok vs. Euk ribosomes subunits | Prok: 30 + 50 = 70 Euk: 40+ 60 = 80 |
| Initiator tRNA activates translation at which site? | P-Site --> once filled A-site can now be filled |
| Steps for initiating translation. | 1.) 5'end attaches to small ribosome 2.) start tRNA settles in P-site 3. Signals for large subunit to join |
| How to create a peptide bond and what enzyme used? | -C-terminal attaches to N-terminal through dehydration reaction -peptidyl transferase (ribosome) |
| How to terminate translation? | Release factor binds to termination codon so water can be added to stop |
| In what direction does ribosomal assembly move? | 5' --> 3' |
| What does ribosome bind to initiate translation in prokaryotes? Eukaryotes? | -Shine Delgarno and AUG -5'cap and AUG |
| nonsense mutations | change codon to a stop codon for early termination |
| missense mutation and at what position does it occur ? | -one a.a. is substituted for another to produce different a.a. -first or second position in codon |
| silent mutation | no detectable change |
| transposons | DNA segments can excise themselves and reinsert at another location |
| forward mutation | change organism from original state (wild type) |
| backward mutation | revert organism back to wild type |
| Where do px made by free-floating ribosome in cytosol function? | cytosol |
| Where do px made from rough ER become? | injected into ER lumen and become mem-bound px of ER, golgi, plasma mem, etc. |
| Signal peptide | direct ribo to attach to ER or stay on free-floating ribosome |
| translocation | DNA segment inserts into another chromo |
| nucleosome | eight histones wrapped in DNA |
| 4 stags of cell cycle? | G1 (pre-synthetic) S (or Go) (synthesis) G2 (post-synthetic) M (mitosis) |
| What is restriction point not met? What type of cells are in here? | -enter Go phase -liver cells, mature nx, muscle cells |
| What does G1 phase do? | create organelles and double in size |
| What does S phase do? | -duplicate DNA to create 2 identical sister chromatids -centrioles also duplicated |
| How many chromosomes and chromatids at S-stage? | 46 chromo and 92 chromatids |
| When is tubulin px for microtubules made during interphase? | G2 stage |
| During interphase, is DNA condensed or loose? | loose --> transcribe |
| What is chromatin? | DNA wrapped around histone proteins to allow DNA to fit into cell |
| Why is condensed DNA important for cell division? | don't lose any gnetic material |
| 4 stages of mitosis? | Prophase, Metaphase, Anaphase, Telophase |
| What happens during prophase? | -chromatin condenses and centrioles move to opp. ends of cells to form spindle apparatus -nuclear mem breaks down |
| Aster / centrioles / kinetochore / centromere | Aster rays project from centrioles and attach to kinetochore on centromere to pull them apart |
| How does spindle apparatus attach to centromere? | Spindle microtubules attach to kinetochore microtubules |
| Do chromosomes uncoil before cytokinesis? | yes! |
| When does nuclear membrane disappear / reform? | prophase / telophase |
| What is sister chromatid? | identical copies of chromosome |
| What are homologous chromosomes? | -have same genes in different allelic forms -2 pairs of sister chromatids form a tetrad |
| When does synapsis occur? | Prophase |
| Binary fission produces | equal replication with 2 idential daughter cells |
| budding produces | equal replication (same DNA as parent) with unequal cytokinesis |
| How to accomplish regeneration? | mitosis |
| Number of chromosomes will be diploid for parthenogenic animal? | FALSE - parthenogenesis means adult organism develops from unfertilized egg (haploid) |
| How many cells does mitosis / meiosis create? | 2 and 4 |
| Can synapsis occur btwn sister chromatids? | NO --> only homologous chromo |
| Meiosis I produces? | 2 haploid daughter cells |
| What does spermatocyte form at end of meiosis? | 4 sperm cells |
| What does oocyte form at end of meiosis? | single ovum and 3 polar bodies |
| The law of_____ ( segregation or independent assortment) is dependent on the separation of members of homologous pairs. | segregation |
| the law of _______( segregation or independent assortment) is dependent on the random arrangement of homologous chromosomes at the metaphase plate. | assortment |
| When does nondisjunction occur for Down's syndrome? | meiosis 2 |
| Alleles | alternative copies of same gene |
| When do alleles segregate? | meiosis |
| Meiosis I is _____ division | reductional |
| What are linked genes in terms of segregation? | cannot segregate independently |
| What does it mean when 2 genes are 25 map units apart? | 25% of total gametes between 2 genes recombine |
| What creates codominance? | multiple coding alleles for a gene |
| penetrance vs. expressivity | -penetrance: people who straight up express phenotype -expressitivity: varying expression of phenotype |
| Most recessive diseases are _____ acting while dominant diseases are _____ acting. | early / late |
| Who determines the sex of a child? | father |
| Most sex-linked traits are on __ chromosome and recessive / dominant? | X and recessive |
| Can fathers ever be carriers for sex-linked traits? | NO |
| What are viruses made of? | px coat (capsid) and either DNA or RNA (never both!) |
| where does virus get lipid-rich envelope? | borrowed from hose mem or made in host cyto (envelope has virus-specific px) -virus buds off host |
| Do viruses have ribosomes or proteins? | NO and yes (enzymes like integrase and reverse transcriptase) |
| DNA/RNA + capsid = ? and does it have to kill host cell? | nucleocapsid (naked virus) and yes |
| nucleocapsid + lipid mem. with glyco px = ? and does it have to kill host cell? | enveloped virus and NO |
| Why are viruses non-living | -require host-cx machinery to reproduce -do not metabolize organic nutrients -no cx wall /mem -never possess both DNA and RNA -can be crystallized and still infect |
| What do viruses absolutely need on host to infect? | specific glycopx chemical receptor |
| How do bacteriophages and euk viruses compare? | -bacteriophages inject nucleic acid through tail after viral enzymes digest hole in cx wall -euk viruses are engulfed by endocytotic process |
| How do lytic vs. lysogenic infections compare? | -lytic-virus takes over host machinery to make new viruses -lysogenic-viral DNA incorporated into host with reverse transcriptase |
| Prions | naked px that can reproduce without DNA or RNA |
| Viroids | rings of naked RNA with no capsid that can only infect plants |
| Plus strand RNA and example | -virus mRNA is same sense as mRNA so px can be directly translated from RNA -AIDS |
| minus strand RNA and example | -virus RNA is complementary to mRNA and must be copied to plus RNA before being translated -flu |
| What is vaccine? | -injection of non-pathogenic virus with same capsid and envelope that forces immune system to create own antibodies -OR injection of antibodies |
| What are difficulties with viral infections? | -rapidly mutating spike proteins -more than one animal acts as carrier population |
| T/F: Viral genomes are more diverse than euk? | TRUE - can be single or double stranded DNA or RNA |
| Can a virus infect cell with no glycoprotein receptors? | NO |
| What is it called when viral DNA is incorporated into host DNA during lysogenic cycle? | dormant, latent, provirus |
| Do euk. have the enzyme to replicate RNA? What do viruses do? | NO --> viruses bring RNA replicase into cell |
| Do retroviruses have proteins? | YES --> bring in reverse transcriptase |
| Why don't antibodies always work? | RNA poly doesn't proofread so changes in spike proteins are common ->spike proteins are what antibodies recognize when fighting infection |
| What are 2 ways body fights viral infections? | -antibodies -cytotoxic T-cells |
| What are 4 forms of genetic recombo for bacteria? | -binary fission -conjugation -transformation -tranduction |
| transformation | bacteria integrates foreign DNA from environment into host genome |
| conjugation | -2 cells form cytoplasmic bridge (sex pili) so + --> - genetic material -one bacterium must have plasmid that codes for sex pilus |
| What is best-studied sex factor? | F-factor |
| transduction | when bacteriophages infect new bacterium, inject harmless bacterial DNA fragments |
| binary fission | 2 DNA polymerases begin at single origin of replication to create 2 DNA-double-stranded circles |
| What is the lac operan about? | regulation of genes that control the digest of lactose -no glucose --> turn on genes -glucose --> turn off genes |
| Constitutive genotype? | always on |
| What are operator and promoter part of operon? | -operator: binds repressor px -promoter: binds RNA poly |
| What is the process for fixing NItrogen? | N2 --> ammonia --> nitrate |
| What type of genetic material do prok have? | single, circular double strand DNA |
| What are the main differences btwn prok. and euk. in terms of cell wall and membrane? | -cell wall with peptidoglycan -plasma mem. without cholesterol |
| What regulate fluidity in membrane? | -hopanoids in prok -cholesterol in euk |
| periplasmic space | space btwn cx wall and plasma membrane with many px |
| hydrostatic pressure vs. osmotic pressure | -pressure fluid exerts on wall vs. pressure required to prevent flow of water across semipermeable mem. via osmosis |
| peptidoglycan | -disaccharide polymer chain connected by a.a. cross-links |
| gram positive bacteria are what and stain what color? | -thick peptidoglycan cell wall and purple |
| gram negative bacteria are what and stain what color | -thin peptidoglycan cell wall and pink |
| capsule + peptidoglycan cell wall + plasma mem = | gram positive |
| capsule + phospholipid bilayer + cell wall + plasma mem = | gram negative |
| Differences in flagella between prok and euk? | -prok: made of flagellin -euk: made of microtubules (9 +2) |
| Fungi | eukaryotic multicx. heterotrops made of hyphae that obtain food by absorption than ingestion |
| When do fungi perform sexual vs. asexual reproduction? | -bad conditions vs. good conditions |
| Does diploid / haploid dominate in fungi? | haploid stage dominates and is growth stage |
| Can fungi have diploid stage? | YES - sexual reproduction when 2 hyphae grow towards each other to form zygospore |
| What are four main types of connective tissue? | blood, lymph, bone, cartilage |
| What is most common extracx matrix structural protein? | collagen |
| most proteins used by mito are from? | nuclear DNA |
| What are desmosomes? | join 2 cells at a point but do not create watertight seal |
| What are microtubules used for? | mitotic spindle, flagella, cilia |
| Where are cilia found? | fallopian tubues and respiratory tract |
| What are microfilaments used for? | muscle, phagocytosis, cytokinesis |
| In muscle, smooth ER is known as ____ and controls? | sarcoplasmic reticulum and controls calcium |
| What do secretory vesicles do? | supply cx membrane with integral px and lipids |
| What is the ER contiguous with? | cell membrane and nuclear membrane |
| What is an axoneme? | major part of cilia / flagella with 9+2 arrangement connected by dynein |
| What end does DNA polymerase add to in growing strand? | 3'-OH end |
| nucleoside vs. nucleotide | -base + sugar -base + sugar + phosphate |
| What gives DNA its acidity? | phosphate group |
| What unwinds DNA and relaxes supercoils ahead of replication fork? | DNA gyrase (class II topoisomerase) |
| What unwinds DNA at replication fork? | helicase |
| Replication occurs _____ every cell generation during ___ phase. | -once -S phase |
| DNA polymerase III can add new deoxyribonucleotides only to a free ____ | 3' OH end |
| Which DNA polymerase adds new deoxyribonucleotides and which removes the RNA primer? | -DNA poly 3 -DNA poly 1 |
| If DNA replication were completely conservative, what would be seen? | Only heavy and light DNA |
| If DNA replication were dispersive, what would be seen? | everything intermediate weight |
| If DNA replication is semi-conservative what would be seen? | intermediate weight after first round, intermediate and light weight after second round |
| DNA polymerase has what kind of proofreading activity? | 3' - 5' exonuclease -scans and backs up to fix mistake |
| The DNA polymerase that replaces the RNA primer has what kind of activity? | 5'- 3' activity |
| What leads to DNA damage? | -attack by water, chemical damage, radiation damage |
| Mismatch repair | enzymes cut out stretch of DNA with mismatch -polymerase adds correct nucleotides |
| How does enzyme know which strand of DNA to cut during mismatch repair? | methylation |
| Base-excision repair | -damaged base gets cut out and replaced |
| Nucleotide excision repair | -similar to mismatch repair -used for damages like thymine dimers |
| nick translation | -5'--3' exonuclease activity coupled to polymerase activity -polymerase chews off bad nucleotides and replaces with new nucleotides |
| SOS response in E.Coli | -so much DNA damage that instead of correcting DNA damages during replication, polymerase replicates over damaged DNA as if it were normal |
| What is benefit / disadvantage of SOS response? | -better than not replicating at all but high error rates |
| restriction enzymes / endonucleases | - cut double stranded DNA at palindrome sequences |
| Can sticky / blunt ends hybridize? | sticky ends only |
| What does the plasmid need to have for gene cloning? | -restriction site to insert gene -origin of replication to clone gene -antibiotic resistant gene to kill competing, useless bacteria -replicate independently of genomic DNA of bacteria |
| Steps for PCR | -denature - heat to 90C to separate DNA -anneal - cool so primers can anneal to ss DNA -elongation - use heat stable polymerase to extend primers |
| Why don't the separated strands reanneal in PCR? | excess amount of primers used |
| What is the amplification of DNA after "n" cycles? | 2^n |
| Where is mRNA made? Where does translation occur? | nucleus / cyto |
| What are characteristics of codons? | continuous, non-overlapping, and degenerate |
| Where is start codon AUG located? | downstream of Shine Dalgarno sequence in prokaryotes -Kozak sequence for eukaryotes |
| Is there a tRNA codon complementary to stop codon? | NO |
| Where does wobble exist? | on anticodon on 5' position --> creates degeneracy |
| Does prok mRNA have 5' cap or polyA tail? | NO |
| What does 5'cap and 3'poly A tail for? | protects against exonuclease degradation |
| What is structure of tRNA | -anticodon at the tip -amino acid at 3' tail |
| How is amino acid attached to 3'OH end of tRNA? | ester linkage |
| What are mRNA, tRNA, rRNA made of? | nucleotides |
| What catalyzes peptide bond formation in translation? | rRNA of large ribosomal subunit |
| How does transcription initiate? | RNA poly binds to promoter (TATA box) of ds DNA and dsDNA opens up |
| What are 2 ways that transcription can terminate? | 1. intrinsic termination 2. rho dependent termination |
| intrinsic termination | termination sequences create stem-loop structure on RNA that causes to slip off template |
| rho-dependent termination | -rho factor travels along synthesized RNA and bumps off polymerase |
| Prok: transcription factors bind to ______ and ________ to affect transcription. | enhancers / silencers (DNA) |
| Where are enhancers and silencers located in prok. transcription? | close to core promoter |
| operon | cluster of genes under control of single regulatory signal or promoter |
| transcription attenuation | -Trp operon -needed - made, not needed - not made |
| alpha factors | -how phages control transcription in bacterial host -by making different alpha factors at different times, phage controls correct sequence of early, middle, and late genes |
| What does small subunit of ribo do? | -recognize mRNA and bind to Shine-Dalgarno / Kozak sequence |
| What is initiation complex for translation? | mRNA, start tRNA (fmet), ribosome, initiation factors, and GTP |
| In what direction is protein made? | N terminus --> C-terminus |
| In what direction is mRNA codons read to make proteins? | 5' --> 3' |
| HOw to attach a.a. to tRNA? What is required? | -enzymes called aminoacyl-tRNA synthetases attach correct a.a. to tRNA -ATP |
| For tRNA with a.a. to enter A site, what is required? | GTP and elongation factor |
| Peptidyl transfer occurs in which site? | A site |
| Translocation from P site to E site requires? | GTP --> basically, any mvmt requires GTP |
| Translation termination requires what? | water, release factors, and GTP |
| histones | responsible for compact packing and winding of DNA -DNA winds itself around histone octamers |
| centromere | links sister chromatids |
| What is difference between chromatin and chromosome? | -chromatin is "stuff" chromosomes are made of |
| What is difference between euk transcription factors and prok transcription factors? | -euk's can be far away, upstream, or downstream from promoter -DNA must look back so transcription factor bound to enhancer / silencer can make contact with promoter -prok's must be at promoter |
| angiogenesis | cause new blood vessels to grow to nourish cancer cell |
| Proto-oncogen --> oncogene | harmless --> harmful |
| Example of oncogene and example of tumor suppressor | -src -p53 |
| mass of hyphae is called | mycelium |
| fungi cell wall is made of | chitin |
| what are lichens? | fungi + algae |
| How do fungi reproduce? | spores or mycelial fragmentation |
| What are the types of viral nucleic acid? | DNA or RNA / ss or ds |
| Why do certain viruses not have envelope? | cause host cx to burst |
| What are 3 structural components to bacteria? | head to store genetic info, sheath to provide way for injection, tail to attach to host |
| Viruses are ______ times smaller than bacteria and _______ times smaller than eukaryotic cells | 100 / 1000 |
| Does the virus provide anything to replicate? | NO - host provides ribosomes, ATP, nucleotides, and a.a. |
| How do new viral particles assemble together? | self-assembly --> no effort required |
| What type of nucleic acid do retroviruses have? | ss RNA |
| What is process of transduction? | virus infects cx, host DNA fragments packaged by accident, virus progeny infects other cells, fragment enters cells and crosses over |
| What type of growth do bacteria exhibit? | exponential and then slows down |
| facultative anaerobe | doesn't need oxygen for growth, but grows better with oxygen |
| Commensalistic relationship | one benefits while other has no effect |
| Plasmids are _______stranded DNA and are _____ essential for growth and reproduction | -double stranded -not essential |
| What does F+ bacteria transfer to F- bacteria? What can it also transfer? | -plasmid with pillus genes -genomic DNA because F+ plasmid can integrate into chromo |
| Where do prok mostly regulate gene expression? | transcription level (i.e. operons) |
| Is there any RNA processing in prok? | NO |
| When cx if full of TRP, translation occurs fast / slow? When cx is starved of Trp, translation occurs fast / slow? | -fast - causes termination -slow - causes Trp mRNA to be made to completion |
| What causes growth arrest? | -too much genomic mutation / damage causes cx to arrest in M phase -contact inhibition (too crowded) -lack of food |
| apoptosis | cx death that is clean and healthy --> activation of caspases that digest cx from within |
| How is apoptic cell engulged? | -apoptosed cell releases chemicals that attract macrophages -gets engulfed |
| What causes apoptosis? | -development -immune response |
| What type of bacteria does conjugation occur in? | gram negative |
| Virions are obligate____ | parasites |
| Are viruses bigger than bacteria? | DEFINITELY NOT |
| Viral px are produced by translation of viral or host nucleic acid? | viral nucleic acid |
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