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THE MCAT-BIO 2

GENES & VIRUSES

QuestionAnswer
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
Created by: 507935299 on 2012-06-14



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