Final Exam Flashcards

Question

DNA growth

Answer 1

- DNA grows when a 5' triphosphate reactions with 3' OH of another nucleotide - cleaves the high-energy phosphate bond -- makes this an energetically favorable reaction

Answer 2

5' phosphate group 3' hydroxyl 1' nitrogenous base *all attached to sugar pentose - phosphate attaches to 3' carbona and replaces OH- - 3 bonds between C & G - 2 bonds between A & T

Answer 3

1) dNTPS 2) 3' OH group 3) DNA template

Answer 4

3' OH adds new dNTPS with a primer

Answer 5

- each replication bubble has 2 replication forks... one traveling in each direction AWAY from the origin of replication (ori)

Answer 6

pro: replicate bidirectionality from 1 ori for 1 replication bubble euk: replicate from many oris so many replication bubbles per chromosomes

Answer 7

relieve tension and disentangle the 2 daughter DNA chromosomes when DNA replication is complete

Answer 8

- end of replication problem when final primers are removed --> unfinished section of the lagging strand - linear chromosomes shorten after every cell direction - telomerase counteracts this by extending the telomeres

Answer 9

- ribonucleoprotein that extends telomeres by adding more repeats (repetitive DNA) - contains RNA that serves as a template for extending the overhang - prevent linear chromosomes from shortening after every cell division *primer attaches after initial extension of the overhang so that the other strand can be lengthed too 1) lengthen overhang 2) go back and extend short section

Answer 10

polymerase chain reaction (DNA replication in a test tube) 1) denaturation - breaking of H-bonds for dsDNA to ssDNA (95) 2) annealing primers - DNA primers bind to ss templates (55) 3) extension - Taq synthesizes the DNA (72)

Answer 11

on 3' ends of DNA strands - synthesized in the opposite direction (5' --> 3' at 3' end of DNA along DNA strand toward the 5' end of the template )

Answer 12

1) helicase VS heat for strand separation 2) DNA polymerase VS Taq for elongation 3) RNA primers VS DNA primers 4) Ligase needed for OFs of lagging strand VS no lagging 5) both need nucleotides for elongation; use DNA at a template for new strand synthesized from 5" --> 3'

Answer 13

- many repair mechanisms - mistakes are 1 in a million

Answer 14

fix errors in DNA replication that arent corrected by DNA polymerase --- occurs after DNA replication

Answer 15

recognize mismatches

Answer 16

nicks DNA (cuts backbone)

Answer 17

remove nucleotides around nick (including mismatch)

Answer 18

1) base excision repair 2) nucleotide excision repair -- occurs when BER doesn't work

Answer 19

1) deaminated DNA with uracil (C--> U) 2) glycosylase removes uracil, leaving an AP (apurinic site) 3) AP endonuclease cutes the backbone to make a nick at the AP site 4) DNA exonucleases remove multiple nucleotides near the nick, creating a gap 5) DNA polymerase synthesizes new DNA to fill in the gap 6) DNA ligase seals the nick

Answer 20

1) exposure to UV light 2) thymine dimer forms 3) UvrB and C endonucleases nick strand containing dimer 4) Damaged fragment is released from DNA 5) DNA poly fills in the gape with new DNA 6) DNA ligase seals the repaired strand

Answer 21

proteins that remove improper bases directly off the nucleotide backbone

Answer 22

nick DNA at AP site

Answer 23

recognize DNA distortions

Answer 24

nicks DNA (cuts backbone)

Answer 25

1) homology-directed repair (HDR) -- more accurate than NHEJ bc it uses homologous DNA from sister chromatid 2) non-homologous end-joining (NHEJ) -- variable length indels -- broken ends are joined together --- less accurate than HDR --- can cause mutations * types of gene editing

Answer 26

- PERMANENT alteration in DNA sequence; not repaired - new sources of ALLELES that are acted upon by evolution

Answer 27

changing one nucleotide to another 1) transition: Pu-Pu or Py-Py 2) transversion: Pu-Py or Py-Pu

Answer 28

bases added or removed *structural change to molecular nature (large scale change to chromosome organization - large deletions - inversions - translocations

Answer 29

1) missense - changing from one amino acid to another 2) nonsense - STOP codon (truncation) 3) silent - null mutation with no change of amino acids

Answer 30

- causes by indels - many codons are affected - often causes truncation and disorders * can be fixed if shift is divisible by 3

Answer 31

- less function - recessive (must have homozygous genotype)

Answer 32

complete LOF

Answer 33

new or more function - dominant (homozygous/heterozygous genotype)

Answer 34

- only type of mutation to be passed to offspring via gametes and gonads

Answer 35

S: natural processes or random chance cause mutation I: caused by mutagen

Answer 36

- alternative, temporary configurations of bases - rare forms have different base pairing properties than typical forms (purine pairs with the wrong pyrimidine and vise versa) spontaneous mutation example - not a mutation, BUT can cause mutations - only a temporary shift but can cause base pairing problems

Answer 37

P: ensures assay gives (+) results when it should - protects against false (-) N: ensures that easy gives (-) results when it should - protects against false (+)

Answer 38

Mitosis: - makes somatic cells (asexual) - 2 identical cells as product - no variation - 1 equal division - somatic cells - developmental problems, cancer if goes wrong Meiosis: - makes gametes - 4 non-identical gametes - variation present - 2 divisions (not equal) - cells for gonads (gametes for egg and sperm) - nonviable gametes or chromosome imbalances if goes wrong

Answer 39

- number of chromosomes in a haploid gamete - how many unique chromosomes in one haploid "set" - each unique chromosomes has different genes than the others n = 23 in humans

Answer 40

23 unique types of chromosomes (1-22 + X/Y) - diploid (2n) - somatic cells have 2 homologous sets of 23 chromosomes (1 from egg and 1 from sperm)

Answer 41

the number of homologous sets of chromosomes

Answer 42

- have the same genes BUT could have different alleles

Answer 43

- the amount of DNA in a haploid gamete - c = amount of DNA in a haploid cell before DNA replication

Answer 44

- doubles the amount of DNA in the cell c + (ploidy x # of chromatid per chromosome) 2n x 2 + c = 2c

Answer 45

1.) prophase I = crossing over of alleles 2.) metaphase I = independent orientation leading to independent assortment

Answer 46

generates variation by generating new combinations of alleles on a particular chromosome

Answer 47

generates variation by generating new combinations of chromosome homologs in a particular gamete

Answer 48

extra or missing chromosomes leading to an unbalanced chromosome complement 2n+1 = trisomy 2n-1 = monosomy

Answer 49

Anaphase I: failure of homologs to seperate Anaphase II: failure of sister chromatids to segregate into different daughter cells

Answer 50

MI: - heterozygous duplicate - homologs don't seperate - all aneuploid gametes (2 n+1; 2 n-1) MII: - homozygous duplicate - sister chromatids don't segregate - 1/2 aneuploid gametes ( 1 n+1, 1 n-1, 2 2n)

Answer 51

1) mutation generates new alleles 2) in sexually-reproducing organisms, meiosis generates gametes with new haploid combinations of alleles by crossing over or independent assortment 3) fertilization brings together new 2n allele combos

Answer 52

WT appears as most common trait dominant allele appears in heterozygote phenotype *Alleles themselves are not dominant/recessive rather they have dominant/recessive relationships

Answer 53

whether a single WT allele can produce a WT phenotype - determined by examining the phenotype of a hemizygote (an organism containing only 1 allele for a gene)

Answer 54

- aneuploidy - heterozygous for a chromosomal deletion (deficiency) - sex chromosomes (found on X, but not on Y) - 2n with monosomy by nondisjunction - deletion on homolog (1 copy only of effected genes)

Answer 55

- threshold of WT phenotype when WT allele is haploinsufficient will be HIGHER than the threshold when WT allele is haplosufficient

Answer 56

LOF: 1. amorphic (null) - less (none) 2. hypomorphic (leaky) -less (some) GOF: 1. hypermorphic - more 2. neomorphic - new 3. antimorphic (dom-neg) - new, but antagonizes WT

Answer 57

DNA --> RNA --> protein LOF - reduces transcription (less RNA and protein) - reduces translation (less protein) - reduces protein activity GOF - increase transcription (more RNA and protein) - increase translation (more protein) - increase protein activity OR cause new activity

Answer 58

reduced transcription

Answer 59

reduced translation

Answer 60

- proteins bind to inititator protein - initator protein attracts helicase which unwinds DNA - DNA unwinds into replication bubble with 2 Y shaped area called replication forks - SSBPs stabalize DNA and keep them seperated - DNA poly III adds nucleotides to 3' end of preexisiting DNA strand - RNA primer initates DNA synthesis with primase

Answer 61

- DNA poly III catalyzes polymerization - DNA grows 5 to 3 - DNA poly moves 3 to 5 - DNA poly moves in the same direction as the fork to synthesize the leading strand - the new DNA strand is the lagging stand and replicated 5 to 5 away from Y-fork in Okazaki fragments - DNA poly I replaces the RNA primer of OFs with DNA - Ligase bonds fragments

Answer 62

replicated continuously 5' to 3' toward the unwinding y-fork synthesized continuously toward the 5' end of the template strand from (5'->3') - arrow points to 5' end

Answer 63

the new DNA strand is the lagging stand and replicated 5 to 5 away from Y-fork in Okazaki fragments synthesized discontinuously toward the 5'prime end of template strand (closest to the 3' of template)

Answer 64

relax supercoils by nicking DNA strands and cleaving the sugar-phosphate backbone between 2 adjoining nucleotides - supercoiling is when chromosomes accommodates strain of distortion by twisting back upon itself

Answer 65

screen for chemicals that cause mutations in bacterial cells - Many His- -- His+ will grow without histidine look for high number of revertants (suggests that mutation occurred)

Answer 66

G1: new cell birth S: synthesize DNA and cells duplicate genetic material (chromosomes double to produce sister chromatids) G2: grow more; synthesize proteins for mitosis mitosis: 2 identical d. cells form

Answer 67

chromosomal rearrangement where the number of DNA copies increases (paired with duplications often) occur on homologous chromosomes

Answer 68

2 breaks 1 in each of 2 homologous chromosomes -- fragments switch places and attach on the nonhomo chromo

Answer 69

pulse: pulse of radioactive dnTPS are used up for synthesis quickly and then cells are killed -- dna is extracted and denatured and separated by size --**many small pieces bc ligase doesn't have time to mend pieces pulse chase: - allows some time for DNA synthesis to occur (chase) -- less pieces and larger sizes bc ligase had time to mend pieces together

Answer 70

Base excision repair is a pathway that repairs replicating DNA throughout the cell cycle. Nucleotide excision repair is a pathway that repairs constantly damaging DNA due to UV rays, radiation and mutagens.

Answer 71

mismatch repair

Answer 72

anaphase I

Answer 73

both built 5 to 3 with a mix of leading and lagging

Answer 74

44 chromatids 22 chromosomes

Answer 75

may be PCR primer

Answer 76

Tetrad" or "Bivalent" or Chiasmata

Answer 77

2 alleles of each gene separate/segregate during gamete formation, and then unite at random (1 from each parent) at fertilization - MI separates homologs; then MII separates sisters. Each gamete ends up with 1 copy of each allele - Homologous chromosomes align in metaphase I and segregate into separate daughter cells

Answer 78

During gamete formation, different pairs of alleles segregate independently of each other 50% chance of receiving alleles from mother vs father Homologous chromosomes align in MetaphaseI with independent orientation; the orientation of 1 tetrad does not influence the orientation of another

Answer 79

- alleles on different chromosomes = always independently assort - alleles on the same chromosome may/may not independently assort

Answer 80

cross recessive genotype with mystery genotype - all dominant --> homozygote dom - half dominant --> heterozygote dom ** figure out the genotype of an individual

Answer 81

homozygous individuals whose line produces the same phenotype when selfed 100% of the time **can assume genotype is homozygous

Answer 82

look at heterozygous -cross 2 pure-breeding individuals to get all heterozygous F1 generation and analyze the phenotypes

Answer 83

heterozygotes of 1 gene crossed with each other Ex/ Aa x Aa 1:2:1 genotypic ratio 3:1 phenotypic ratio

Answer 84

/ - alleles on different homologs of the same chromosome ; - alleles on different chromosomes

Answer 85

2 genes controlling 2 traits -heterozygotes crossed with recessive homozygotes Ex/ A/a;B/b x a/a;b/b genotypic: 1:1:1:1 phenotypic: 1:1:1:1

Answer 86

selfing of dihybrid genotypic: 9:3:3:1 phenotypic: 9:3:3:1 9 - both dom 3 - 1 dom; 1 rec 3 - 1 rec; 1 dom 1 - both rec

Answer 87

product - AND - the probability that 2 or more independent events occurring together is the product of the probabilities that each will occur by itself addition - OR - the probabilities of 2 mutually-exclusive events occurring is the sum of their individual probabilities

Answer 88

testable and is falsifiable. *null hypothesis must make a testable prediction. ex/ IA will occur.

Answer 89

there is no significant difference between the observed and expected frequencies - must be very certain that you can reject the null hypothesis (5% error; 95% confidence)

Answer 90

determine p-value using a formula total = (observed - expected)^2 /expected compare values in chart expected values: - look at total and use ratio expected based on the type of cross - ex/ monohybrid self cross = 3:1 out of 400 300 and 100 are expected values

Answer 91

represents the probability that the null hypothesis is TRUE p > 0.05 - fail to reject the null p < 0.05 - reject the null

Answer 92

the number of groups of observed/expected minus 1 n -1

Answer 93

display characteristic inheritance patterns *though most traits are not controlled by a single gene

Answer 94

1. males and females equally affected 2. unaffected individuals can have affected children via heterozygous carriers 3. can skip generations 4. rare 5. becomes more common with inbreeding (homozygous recessive)

Answer 95

when discussing diseases, you can assume these traits are rare so people entering the pedigree do NOT carry the disease allele - unless you have info to suggest otherwise

Answer 96

1. males and females are equally affected 2. affected individuals always have an affected parent (no heterozygous carriers bc they are affected too) 3. does not skip generations

Answer 97

1. males inherit Y from their father and MUST inherit X from their mother 2. females inherit one X from father and one X from mother

Answer 98

1. males more frequently affected 2. never transmitted from fathers to daughters 3. All sons of affected mothers will also be affected by the trait 4. can "skip generations" via female carriers

Answer 99

1. females more frequently affected 2. ALL of the daughters and NONE of the sons of affected fathers have the trait 3. does not "skip generations"

Answer 100

- the percentage of individuals with a particular genotype that demonstate the expected phenotype - complete penetrance = 100% - incomplete penetrance = 1-99%

Answer 101

overestimate - there could be other nonpenetrant individuals that we are not certain about - the demoninator is larger so the overall fraction/percentage will be smaller than originally estimated

Answer 102

for individuals with the same genotype, there is a range of phenotype severity/expression ** the degree with which a genotype is expressed as a phenotype (how much phenotype is shown)

Answer 103

heterozygous phenotype = 1) complete - same as homozygous dominant 2) incomplete - intermediate between the 2 homozygotes 3) codominance - mix of 2 homozygotes (shows both homo) * same genotypic but different phenotypic rations

Answer 104

Monomorphic: have single "wild type" allele Polymorphic: multiple common allele variants (no single WT allele)

Answer 105

- classifications can change - a mutant allele can become a common varient over time or a common varient can be lost from the population

Answer 106

AB: express 2 variants of the A and B enzymes [polymorphic] - IAIB O: null version/non-functional enzymes - ii B: enzyme adds B sugars - IBIB - IBi A: enzyme adds A sugars - IAIA - IAii

Answer 107

codominant to IB and dominant to i

Answer 108

single alleles affects multiple properties/parts of an organism

Answer 109

recessive for pelger is lethal phenotype lethal means that they have severe defects or are never born changes the phenotypic ratios - nuclear morphology: pelger allele is dominant - lethality phenotype: pelger allele is recessive

Answer 110

the effect of one gene masks the effect of another - often occurs when 2 genes encode members of the same biochemical pathway - indicated by fewer phenotypic classes than expected - gene-gene interaction

Answer 111

recessive epistasis hh genotype - overrides the blood type for an O blood type - doesn't matter what parental blood types are - 2 recessive h alleles mask the IA alleles phenotypic effect

Answer 112

collapse all phenotypic categories with 1+ dominant allele for either gene 15:1 ratio

Answer 113

- when 2 individuals with the same mutant phenotype but different homozygous recessive genotypes produce offsprng with the wild-type phenotype when crossed only works for recessive mutants - always cross homo recessive mutants that are mutant for only one gene -no complementaion if mutant trait appears (same gene) - complementation if mutatnt trait does not appear (mutations in different genes) - failure to complement with itself bc if has mutant and crosses with itself, the mutant phenotype will remain.

Answer 114

can produce different doses of eumelanin vs phenomelanin depending on the available receptor variants - melanocytes are cells found in skin that produce pigmented melanosomes that give skin its color

Answer 115

individual that is heterozygous at 2 different genes

Answer 116

P: phenotypes that reflect a previously existing parental combination of alleles that is retained during gamete formation R: phenotypes reflecting a new combo of alleles that occurred during gamete formation via crossing over during prophase

Answer 117

genotype for genes present in only one copy in an otherwise 2n organism ex/ x-linked genes in a male

Answer 118

an allele that is advantageous in one environment may be disadvantageous in another - UV damages folate for neural birth defects --- alleles that increase pigmentation would be advantageous - UV is required for vitamin D production and without causes rickets in bone --- alleles that increase pigmentation would be disadvantageous in a sunny environment --- alleles that decrease pigmentation would be advantageous in a less sunny envt.

Answer 119

so >50% of gametes will be parental. Fewer offspring will be recombinant.

Answer 120

cis - dominant alleles are on the same homolog [AB/ab] trans - dominant alleles are on different homologs [Ab/aB] - cis and trans dihybrids differ in...what allele combinations are parental vs recombinant (parental vs recombinant combos swap with cis and trans switch)

Answer 121

- the father apart genes are on a chromosome (mu), the more likely that they are able to be affected by a crossover event (recombination is more common)

Answer 122

1. do a test cross of dihybrid (heterozygous with recessive genotype) 2. determine which offspring are recombinant 3. add up recombinants and divide by the total offspring

Answer 123

- RF = 0% (complete linkage; only parental genotypes) - RF = <50% (linkage; parental genotypes are more common) - RF = 50% (unlinked; parental and recombinant are equally likely; independent assortment) * RF will never exceed 50% * 1 m.u./cM = 1% RF

Answer 124

6 mu = 6% will be recombinant - do a test cross and determine the parental and recomb genotypes - divide % by 2 and assign % to each recomb. - remaining % out of 100% divided by 2 will be the parental types ex/ 3% each recomb 47% each parental 1/2 of each recombinant will be of each recombinant type.

Answer 125

an allele that prevents survival of homozygotes - although heterozygotes carrying the allele survive - decreases the denominator for a larger fraction/probability

Answer 126

phenotypic ratios NOT genotypic ratios

Answer 127

function depends on the environmental temperature (permissive conditions allows for allele; restrictive does not)

Answer 128

gene (and its genotypic effects) that is being masked by the epistatic allele

Answer 129

R: the effects of recessive alley at one gene hid the effects of alleles at another another gene D: the effects of a dominant allele at one gene hide the effects of alleles at another gene

Answer 130

variable expressivity

Answer 131

2/3 crested 1/3 non-crested

Answer 132

The genes independently assort...cannot be linked because they are on different chromosomes

Answer 133

DNA (nucleic acids) --> RNA (amino acids) --> protein

Answer 134

- start codon is translated and found within the transcribed region - stop codon is not translated and is found outside the amino acid sequence (not encoded within the protein)

Answer 135

(indicated often with an arrow) - indicates the transcription start site and first nucleotide to be transcribed *not necessarily before the AUG start codon

Answer 136

coding 5' to 3' (codons) template 3' to 5' (antiparallel) see the codons within the coding strand (look for ATG)

Answer 137

directions of transcription this is bc different strands of dsDNA are used as the template for different genes (might be coding for one gene but template for another)

Answer 138

- recruit RNA polymerase to a gene CIS: regions of DNA that are required for gene expression/regulation *part of the same molecule as the genes they regulate TRANS: diffusible molecules (proteins) that bind cis elements - separate molecules from the genes they regulate!

Answer 139

key trans-factor that helps RNAP associate with promoters in prokaryotes many subunits functions together as 1 enzyme

Answer 140

a sequence of DNA having similar structure and function in different organisms. (same sequence in the same location) -10 and -35 consensus sequences are found in nearly all bacterial promoters

Answer 141

1) no sigma subunit 2) different consensus sequences (TATA box most common) 3) additional cis-reg. elements besides promotor (enhancer/silencer) common. Enhancer often required!

Answer 142

hairpin/stem loop - complementary base pairing with itself - strong C-G bonds hold structure together causing the stalling of RNAP - When stalling occurs, the weak AU bonds cannot hold mRNA and DNA complex together

Answer 143

snRNA and proteins - functions in recognizing introns and removing them - recognizes specific sequences in the DNA that will determine the sites of splicing - via BPing, the RNA component of splicesome recognizes the splice site sequences - found in nucleus

Answer 144

would be degraded

Answer 145

2 ore more types of mRNA from the same transcript

Answer 146

1) Initiation - complex of ribosome, first charged tRNA enters with mRNA 2) Elongation - peptide bonds formed as charged tRNAs bring appropriate amino acids to site 3) Termination - stop codons signal release factors and complex dissociates at the A site

Answer 147

- ribosome binding site - positions ribosomes by start codon - found only in prokaryotes

Answer 148

transfers the peptide in the P site to the amino acid in the A site

Answer 149

- catalyzed by ribosomes in order to form a peptide (covalent) bond between 2 amino acids - loss of a water molecule

Answer 150

N to C amino acid to carboxylic acid

Answer 151

indicate regions that could potentially encode for a protein - sequence of codons within the same reading frame starting with 5'-AUG and ending with STOP-3' ** the longer the ORF, the more likely its a true protein-coding ORF

Answer 152

translated and untranslated regions

Answer 153

- use coding strands that look like mRNA 1) locate potential start codons (ATGs in any direction if coding strand is unknown) 2) identify the ORFs by finding inframe STOP codons 3) Determine polypeptide length 4) Determine directionality 5) Determine mRNA sequence 6) Translate!

Answer 154

translate codons into amino acids - speak both languages bc can bind to codons that are both complementary and antiparallel -function is to base pair with the codon on a strand of mRNA during translation. ***ensures that the correct amino acid will be added to the growing polypeptide chain.

Answer 155

64 total 61 encode for amino acids

Answer 156

enzyme that carries out the charging of the tRNA with its specific amino acid - attaches an a.acid to its tRNA - highly specific for a given amino acid and for a given tRNA ** product = charged tRNA

Answer 157

- allows for a single anticodon of tRNA to interact with more than one mRNA codon - 61 codons but not 61 tRNAs

Answer 158

- metabolize organisms - bacteria only produce the proteins needed for lactose metabolism when lactose is present - saves energy and resources only to transcribe/translate when a protein is needed

Answer 159

removing repressor

Answer 160

I: auto OFF - transcription is turned ON R: auto ON - transcription is turn OFF

Answer 161

always on - expression even when there is no lactose around and the operon should be turned off

Answer 162

1) add activator 2) remove repressor

Answer 163

transcription

Answer 164

mRNAs that code for more than one protein under the control of a single promoter. (share a promotor) (prokaryotic only)

Answer 165

group of prok. genes that share a promoter and get regulated and transcribed as one unit (energy/resource saver)

Answer 166

Regulatory: 1) promoter (P) 2) operator (O) Ensures Lac Y/Z expression: 3) LacI Genes encoding metabolism proteins: 4) LacZ 5) LacY

Answer 167

DNA site where RNA polymerase initially binds

Answer 168

the site where the repressor binds

Answer 169

gene that encodes the repressor protein ****gene itself is NOT part of the lac operon - has its own promoter and its regulated seperately - still relevant bc protein it encodes regulated the lac operon

Answer 170

gene that encodes B-galactosidase, an enzyme that breaks down lactose into monosaccharides

Answer 171

gene that encodes permease, an enzyme that makes it easy for lactose to enter the cell

Answer 172

with: allolactose binds to repressor protein and changes shape so that it cannot bind to the operator - transcription DOES occur without: repressor protein binds to operator and RNA poly cannot pass - transcription DOES NOT occur

Answer 173

Lac I- Lac Oc

Answer 174

changes the shape of the Lac repressor DNA binding domain - prevents lac repressor from being made

Answer 175

changes DNA sequence (operator) that Lac repressor recognizes - prevents lac repressor from binding - constitutive expression

Answer 176

prevents binding of allolactose - prevents transcription (default OFF) *** uninduciable transcription super repressor

Answer 177

produces nonfunctional B-gal protein - cannot metabolize lactose - does not prevent transcription

Answer 178

produces a nonfunctional permease protein - stop the metabolism of lactose as it will not be able to enter the cell without permease.

Answer 179

Lac I- is recessive to Lac I+ - heterozygote is inducible, not constitutive (Lac I+/I- => merozygote)

Answer 180

- controls expression of genes - directly influences whether RNAP transcribes a gene

Answer 181

alleles are in cis not trans (on same DNA molecule) DOMINANT (O+ will falil to rescue the constiutive phenotype)

Answer 182

adding (+) regulation

Answer 183

glucose for carbon energy source - therefore, beneficial to transcribe lac operon only when glucose is absent

Answer 184

trans-regulatory factor that binds the promoter and helps to recruit RNAP - w/o CRP, RNAP is inefficient for finding and binding to promoter (trans. levels LOW)

Answer 185

effector that causes allosteric changes to CRP to allow it to bind to the promoter cAMP levels are HIGH when glucose levels are LOW

Answer 186

1. metabolizes glucose for low level transcription 2. runs out of glucose, changes gene expression, and plateaus 3. metabolizes lactose instead for higher levels of transcription

Answer 187

G + L = low transcription No G + L = max transcription G + no L = no transcription No G + No L = no transcription

Answer 188

catabolic (break down): inducible [auto OFF] anabolic (build up): recessive [auto ON]

Answer 189

controls the expression of tryptophan synthesis of genes (anabolic) contains: - trp promoter - trp operator - repressor protein binding to operator (trpR) - structural genes for tryptophan biosynthesis (trpE/B/C/D/A)

Answer 190

transcription does not occur (operon is turned off) - repressible (auto ON) - adds (-) regulation) - anabolic operon repressed in the presence of their metabolic end products (turned off when end product formed)

Answer 191

Regulation of: 1. chromatin remodeling 2. transcription -------- post-translational 3. splicing and processing 4. transport (out of cell) 5. degradation of mRNA 6. translational 7. protein modification

Answer 192

- the same DNA - same genes and cis elements - DIFFERENT trans elements **Therefore, the same gene in different cell types will have the exact same DNA (promoter and cis regulatory elements)

Answer 193

has different TFs that may or may not bind to cis reg. elements of different genes **Therefore, a gene will be off unless cis-elements are accessible to bind to TF

Answer 194

cis-elements that are packed into inaccessible chromatin

Answer 195

Euchromatin: loosely packed open accessible transcription ON Heterochromatin: condensed closed inaccessible transcription OFF

Answer 196

1. histone modifications - acetylation increases accessibility (opens DNA) 2. DNA methylation - decreases accessibility (closes DNA) 3. Nucleosome sliding/reorganization

Answer 197

if/how a gene is transcribed 1) basal factors 2) TFs binding to enhancers/silencers 3) Tfs+cofactors

Answer 198

bind to promoters to recruit RNA poly to the gene LOW LEVEL TRANSCRIPTION if only factor bound to DNA

Answer 199

enhancers or silencers increases rate of transcription in addition to basal factors

Answer 200

increase or decrease the rate of transcription

Answer 201

Promoter: gene is NOT transcribed Enhancer: cis/trans factors can usually still complex and function normally

Answer 202

on the same chromosome (in cis) to genes they regulate - nearby but can be far away (few hundred/thousand bp away on coding gene)

Answer 203

type of enhancer that decreases transcription by binding to repressor proteins (trans-acting regulatory element)

Answer 204

context-specific if they interact with TFs present/active only in those specific contexts (cell type, envt.)

Answer 205

enhancers and silencers

Answer 206

encode TFs that specify the formation of specific parts of the body Ex/ front leg hox gene produces... front leg hox protein (TF) that binds....to cis regulatory elements on gene - If body part in wrong spot...the body part will still be found in correct location - promoter = where - coding region = what

Answer 207

design: link eyeless cis elements to reporter gene (GFP) methods: add this hybrid transgene to normal early embryo results: look for GFP expression as flyes develop - indicates where eyeless is being expressed and functioning!

Answer 208

green fluorescent protein - reporter gene we can see in living tissues

Answer 209

a gene that has been transferred naturally, or by any of a number of genetic engineering techniques, from one organism to another. can change phenotypes !!

Answer 210

- RNA poly binds to dsDNA at promoter - RNAP unwinds dsDNA to expose unpaired bases on template strand

Answer 211

- sigma subunit is released and RNAP looses its affinity for promoter and gains affiinity to DNA - mRNA extended 5' to 3' antiparallel to template strand

Answer 212

terminator RNA sequences signal the end of transcription - forms hairpin loops - releases both RNA polymerase and mRNA chain from DNA

Answer 213

ssRNA folds back on itself and comp. base pairs with C/G's

Answer 214

single strand of RNA resulting from transcription Pro: primary transcript is the mRNA used for synthesis Euk: primary transcript undergoes RNA processing before protein synthesis

Answer 215

sequences located just after the methylated cap and before poly-A-tial - encoded by exons and don't include codons

Answer 216

deletes introns in euk. pre-mRNA and joins together adjacent exons to form mature mRNA

Answer 217

transcribe genes that encode major RNA components of ribosomes (rRNAs)

Answer 218

transcribes genes that encode proteins

Answer 219

transcribes genes that encode tRNAs/other small noncoding RNA molecules

Answer 220

cis-acting regulatory element that regulates from nearby promoters --- function by acting as binding sites for TFs and are responsible for spatiotemporal specificity of transcription

Answer 221

TF that binds to specific DNA seq. with enhancer elements (CpG islands) and increases the level of transcription of a nearby promoter

Answer 222

protein that binds to a transcriptional activator and plays a role in increasing transcription levels

Answer 223

no other genes will function

Answer 224

it is bound to the operator

Answer 225

epistastic -- makes the effects of I

Answer 226

no ----- requires beta-galactosidase

Answer 227

within eukaryotic genes

Answer 228

- not regulated as part of the same operon - must not be expressed in the same area - must not be expressed at the same time - do not have differnet enhancers in diffrent cell types

Answer 229

no translation (normal transcription)

Answer 230

GOF hypermorphic

Answer 231

Promoter Transcription start site Shine-Dalgarno sequence start codon stop codon 3' UTR transcription termination site

Answer 232

uninducible

Answer 233

constitutive

Answer 234

- GH deficiency was treated by injected by cadaver-derived human GH - pool pituitary glands have GH - GH extracted with Wilhemi preparation - c-hGH is injected into hGH deficient humans - requires a lot of cadavers bc method only produces TINY amounts of hGH --- prevented clinical testing for additional treatment uses --- many people were denied due to scarcity - some were contaminated with prions giving people CJ disease

Answer 235

exact genetic copies of entire organism

Answer 236

groups of genetically-identical cells

Answer 237

identical molecules (e.g. DNA)

Answer 238

1) isolate the DNA of the hGH gene 2) clone the gene -- make many copies of the hGH gene in vivo 3) Make bacteria transcribe and translate the gene to make a ton of hGH

Answer 239

- chops up one genome into millions of restriction fragments - still don't know where the gene is and may only have a few copies total in the sample

Answer 240

- allows us to make many copies of the exact sequence we want - replicate target DNA into may copies (2^n) (n = number of cycles)

Answer 241

- large dark band show many copies of the amplified DNA region - no band for the template (genomic) DNA on gel because there is not enough present to be seen

Answer 242

- Primer is the exact same sequence as the 5' to 3' next to the region of interest (on both sides) - The PCR product will extend from the 5' end of one primer to the 5' end of the other

Answer 243

- When bacteria replicates, linear DNA will be lost - need cloning vector that will be replicated when cell replicates DNA during mitosis

Answer 244

1. origin of replication -- so plasmid can be replicated 2. multiple cloning site (MCS) -- many different restriction enzyme sites so things can be inserted into plasmid (often LacZ gene) 3. antibiotic resistace gene -- any cells that uptake this plasmid will be resistant to a particular antibiotic

Answer 245

5' end of primers for isolation of the region of interest

Answer 246

- EcoRi addition creates identical sets of sticky ends on both the plasmid and GH gene - sticky ends by EcoRi allows for recombination and GH gene to be added to the plasmid after annealing of primers and ligase

Answer 247

- transformed into bacteria which replicate it with its endogenous DNA replication machinery - the plasmid replicates with the bacteria and we now have a lot of recombinant molecules inside the bacteria if transformation worked - even if it did...there may be some untransformed bacteria mixed in!!!

Answer 248

is used to identify bacteria that contain the plasmid colonies = transformants (have plasmid) no colonies = non-transformants (no plasmid)

Answer 249

- know the Amp-resistant colonies have a plasmid but we do NOT know if they have a plasmid that contains the GH gene

Answer 250

B-galactosidase activity can be visualized using X- gal (blue colored reporter gene) *If B-gal is functional, X-gal is converted into a blue chemical - MCS doesn't disrupt LacZ alleles and functional B-gal is produced (blue color) - If gene is inserted at MCS, it does disrupt LacZ allele so NO B-gal is produced (white color)

Answer 251

so functional lacZ is from the plasmid

Answer 252

1) genomic DNA PCR 2) hGH gene and restriction sites + cloning vector (plasmid) digest 3) complementary sticky ends pair ligate 4) final vector 5) transform into bacteria 6) look for white colonies

Answer 253

1) pick colonies 2) grow each colony in individual culture 3) Isolate plasmid DNA 4) Cut with EcoRi 5) Run gel Blue: one band of DNA White: one DNA plasmid band and one band for GH gene --- GH gene travels farther bc it is smaller than plasmid DNA

Answer 254

1) Pick colonies 2) Grow each colony in individual culture 3) Isolate plasmid DNA 4) Run PCR with primers specific to GH gene one large band representing the PCR product

Answer 255

promoter - prokaryotic if end goal is to make protein in bacteria (bacterial RNA polymerase won't recognize eukaryotic promoter) - same for eukaryotic promoter - prokaryotic and eukaryotic ==> recombinant DNA

Answer 256

- cDNA does not contain introns and will have a shorter length of bp - no extra material

Answer 257

- prokaryotes don't splice (so introns are still present) - they do not have the proper machinery to splice a eukaryotic gene

Answer 258

- Genetically Modified Organisms - recombinant organism - any organism that contains DNA that has been recombined from multiple sources What do people not support GMOS? - can pass transgenic DNA to you - unanticipated ecological effects if released into the environment - Organic foods are more nutritious - There is not a consensus among scientists (though 88% believe they are safe)

Answer 259

- corn borers are small caterpillars that eat and destroy corn - farmers often spray corn with Bacillus thuringiensis toxin (Bt) - toxin considered an organic pesticide when purified directly from bacteria that normally produce it - Bt toxin unfortunately degrades in the sun and other concerns about affects on pests/bugs - INSTEAD... -- Agrobacterium tumefaciens can insert pieces of its Ti plasmid into plant genomes -- Recombinant DNA allows plants to have new trait eliminating the need for pesticide *** typically pathogenic but Ti plasmid is altered to remove harmful part and still include gene of interest

Answer 260

1. isolate DNA from the Bacillus thuringiensis 2. Amplify (PCR) the Bt toxin gene 3/4. Digest (RE) vector/plasmid and digest gene of interest 5. Create recomb. DNA molecule 6. Transform bacteria 7. Select for transformed Agrobacteria 8. Transform corn plant 9. Select for transformed corn plants

Answer 261

eukaryotic promoter must be upstream the gene of interest - RNA polymerase does not recognize a prokaryotic promoter

Answer 262

1. a cloning vector to be replicated and selected for in bacteria (agrobacterium) 2. serve as an expression vector once in plants 3. carry info for "selection" of transformed plants

Answer 263

prokaryotic

Answer 264

bacterial defense system against viruses. - Bacteria integrate bits of viral genetic material into their genomes. - encode for RNAs that can bind to viral genomes by complementary base pairing, allowing the bacteria to detect and destroy viral DNA **cut DNA at precise location using guide RNA and Cas9 - SPECIFIC & PROGRAMMABLE

Answer 265

enzyme that cuts DNA to form single-stranded breaks

Answer 266

- guide RNA directs Cas9 to cut at specific locations based on base pairing - sgRNA functions the same as 2 separate RNAs

Answer 267

- Cas9 will only cut a particular DNA sequence - DNA sequence can be determined by the guide sequence

Answer 268

- restriction enzymes have specific DNA sequences and are NOT programmable Ex/ EcoRi will always cut at a specific point (GAATTC) *cannot be used for targeted gene sequencing

Answer 269

A short DNA sequence, the protospacer-adjacent motif (PAM), is frequently used to mark proper target site NGG (N= any nucleotide) * found in the non-complementary strand *N is adjacent to 3' end of guide on the opposite strand

Answer 270

1. sgRNA 2. PAM sequence - sgRNA does not contain the PAM - sgRNA found right before PAM - sgRNA contains the same sequence (Us instead of Ts) as the bottom strand (where PAM is found)

Answer 271

1) non-homologous end joining (NHEJ) - repair double-stranded break by doing 2 ends directly together * could ADD or REMOVE nucleotides to the sequence first before ending joining 2) homology directed repair (HDR) break is repaired using homologous chromosome as template to ensure proper sequence - homologous template "fills in the blank" of what was lost

Answer 272

- random change (indel) will be introduced at the targeted site - if break is repaired correctly, it will be recognized by sgRNA and cut again! (used to create knockouts/loss-of-function mutations) *random mutation is likely a loss-of-function mutation -Two cells edited with the same guide could end up with a different repair. (null, hypomorphic, silent)

Answer 273

-relies on homologous chromosomes/sister chromatids -- UNLESS scientists provide a repair template with homology arms (regions of homology to the L/R of break site); the cell can be used instead **used to generate gene knock-ins

Answer 274

1) mouse embryonic stem (ES) cells are genetically modified 2) edited stem cells are injected into a blastocyst (cells are pluripotent and totipotent 3) mosaic pups are born (cells are mix of original blastocyst cells and edited stem cells) 4)mosaic pup are crossed to WT

Answer 275

- cells can develop into any kind if cell type given the proper cues P: adult T: embryo and adult (all stages)

Answer 276

occurs when a person has two or more genetically different sets of cells in his or her body.

Answer 277

- 0% homozygous for edited DNA - 25% homo for transgene - 50% hetero for transgene - 25% homo for WT * always heterozygous for edited gene bc only female or male is affected most often

Answer 278

- selfing of edited gene heterozygotes 50/50: heterozygotes/homozygous dominant

Answer 279

- germline may be derived from the blastocyst rather than the ES cells injected --- if no pups inherit the genome edit when crossing WT and mosaic

Answer 280

- BCL11A is a TF that promotes the switch from expressing y-globin(fetal) to b-globin(adult) -Casgevy introduces mutations in an ENHANCER that normally turns BCL11A on after birth - gene that produces BCL11A has its own promoters and enhancers that are controlled by other TFs! - Casgevy mutates an enhancers of the BCL11A gene so that it is not made and affects how the globin genes are regulated - preventing BCL11A expression means that y-globin can be expressed

Answer 281

- regulate gene expression - TFs themselves are encoded by the genes - genes that produce TF have its own promoters and enhancers that are regulated by other TFs

Answer 282

1) causing a gene knockOUT is easier than a gene knockIN --> it doesn't not require HDR with a template (you just break the gene) 2) Casgevy works for multiple kinds of b-globin disorders regardless of what specifically is wrong with a particular patient's B-globin gene 3) using a patient's own (edited) marrow cells makes rejection of a transplant unlikely

Answer 283

- DNA synthesis for Sanger sequencing includes ddNTPs, so synthesis will stop whenever one is added even though only 1 primer is used - dNTPS - ddNTPS - primer

Answer 284

- top to bottom - use separate lanes OR one lane with dyes

Answer 285

- capillary gel electrophoresis (used laser through DNA sample and detector) - automated detection (sequence analysis and reconstruction on computer)

Answer 286

reads that are 100s or 1000s of base pairs long human genome is billions of bp long

Answer 287

the sequence determined by a single sequencing reaction

Answer 288

a set of DNA segments/sequences that overlap in a way that provides contiguous (touching) representation of a genomic region

Answer 289

identification of overlapping reads (reads are like sentence fragments that need to be assembled into contigs like sentences)

Answer 290

2000s - competition and collaboration between the government (Human Genome Project) and the private sector (Celera Genomics)

Answer 291

- the genome of a single individual - synonymous with wild type or normal - 100% perfectly assembled or complete (it may improved over time!)

Answer 292

NO there will be millions of differences to check because the genome is so BIG - extracting useful into from genome data remains a challenge - most of the human genome is shared yet we still have a tremendous amount of genetic variation

Answer 293

- MAYBE...we can check what differences we can find in the regions of the genome that have been annotated as the disease gene or one of its known regulatory elements

Answer 294

- common differences between genomes (single nucleotide variant will be considered a SNP if it becomes a frequency of at least 1%) - every SNP begins as a substitution mutation (rare variant that becomes COMMON) - may or may not be the cause of a mutation - can only change protein if in coding region

Answer 295

no effect on protein production or function (just bc a SNP is in an exon does NOT mean it must be causative)

Answer 296

- in the regulatory region = changes the amount of protein produced - in coding region/protein = changes amino acid sequence

Answer 297

one that is completely linked to whatever causes the trait of interest (recombination frequency is ~0%)

Answer 298

- take advantage of known associations between easily genotyped SNPs and whatever linked variant is responsible for a phenotype even if we do NOT know what the causative nearby variant !!! *may not know what allele is responsible for the trait, but linked SNPs can sometimes still help us make predictions about phenotype (haplotype presence can show commonality)

Answer 299

- sets of SNPs that do not independently assort (inherited as one unit * many SNPS are completely linked to all other nearby SNPS

Answer 300

- SNPs not located in recomb. hot spots are almost never separated from each other by recombinations - not all regions of the genome are equally likely to undergo recombination

Answer 301

1. Locate SNPs in a region of DNA - (examine DNA in and around gene) 2. Create haplotype group (create groups with certain SNPs and determine people that fall into certain groups) 3. Test haplo response to certain condition/treatment

Answer 302

- pre-implantation genetic diagnosis tests embryos for genetics traits before implantation in uterus 1. mothers eggs are collected 2. each is fertilized with sperm 3. fertilized eggs are placed on Petri dish to grow 4. embryos divide for 3 days 5. blastomere is removed from each embryo 6. blastomere is tested to see if its embryo contains the defective gene carried by one or both parents 7. defective gene discarded or donated to reserach 8. good genes are implanted or frozen for later use

Answer 303

immoral and pseudoscientific theory that claims it is possible o perfect people and groups through genetics and the scientific laws of inheritance - use incorrect and prejudiced understanding of Charles Darwin and Gregor Mendel to support the idea of "racial improvement"

Answer 304

- relies on highly variable SSR loci. - 13 different loci are tested - each person has 2 alleles for each locus and there are many differently sized alleles for each locus the population *** fingerprinting looks at the sizes of PCR products made from all 13 loci

Answer 305

- size standard added to every lane - other lanes are fluorescently labeled PCR products - compare the fragments to see if relatives DNA fingerprints match relatives * babies have STR loci from each parent

Answer 306

genomic: represent all regions of DNA equally and show what the intact genome looks like in the region of each clone cDNA: reveal which parts of the genome are transcribed in specific tissues and how those transcripts are processed into mRNAs

Answer 307

homozygous for an amorphic allele of a gene induced by gene targeting

Answer 308

SSRS, indels, CNVs DO change the number of base pairs in a sequence SNPs do NOT [PCR/gel cannot differentiate between fragments]

Answer 309

the 5' end of one primer to the 5' end of the other primer

Answer 310

NHEJ can be used to make a random insertion or deletion in a specific location

Answer 311

- directly upstream of the region we want to utilize - sticky ends > blunt ends

Answer 312

the size of the band on the gel will be larger than the original sequence due to the addition of RE

Answer 313

industrial production of Bt toxin in bacteria for use by organic farmers

Answer 314

false -can use genomic DNA bc prokaryotes do NOT have introns

Answer 315

- doesn't change phenotypic ratios for crosses and offspring

Answer 316

all cells arise from preexisting cells

Answer 317

Meiosis: generating heritable genetic variation Mitosis: growth by cell division

Answer 318

somatic mutations that arise in development

Answer 319

- generate clones of genetically distinct cells - most cancers have more than 1 somatic mutation - all mutated cells will contain the first mutation

Answer 320

- cancer cells continue to divide when normal cells stop - genetic changes lead to inappropriate growth or survival

Answer 321

S: mutation after the embryonic stage somewhere during development G: mutation occurs before sperm and egg fertilize

Answer 322

- loss of apoptosis cell death - loss of contact inhibition that stops growth of cells when cells of certain type come in contact with one another

Answer 323

- angiogenesis (blood vessel development) - metastasis (changing skin cells) - growth in areas of the body away from the primary initiation of cancer

Answer 324

- WT function is to promote growth (at appropriate times and locations) - GOF mutation in a proto-oncogene can promote cancer

Answer 325

- WT function is to restrict growth OR maintain genome stability - LOF mutation in a tumor suppressor can promote cancer

Answer 326

* proto-oncogene - promotes cell proliferation when active - normally, activation is regulated by cell signaling - mutation causes Ras to be stuck in active form regardless of signaling with growth factor

Answer 327

* proto-oncogene -Bcr and Abl genes are on separate chromosomes - Abl promotes cell proliferation but does so in a way that is tightly regulated - A reciprocal translocation generates a fusion protein that retains the pro-proliferation abilities of Abl, but it cannot be regulated properly "Philidelphia chromosome"

Answer 328

*tumor-suppressor - Rb normally functions to restrict the expression of cell cycle genes

Answer 329

*tumor-suppressor - prevents cells from dividing when there is DNA damage - makes sure DNA is repaired so replication errors or damage don't become permanent mutations - anti-growth gene - does not directly promote growth, but increases the likelihood of more mutations occurring within tumor suppressors or proto-oncogenes

Answer 330

- cancerous tumors associated with LOF mutations in the Rb tumor suppressor - recessive LOF - WT are haplosufficient (but are at high risk for cancer bc already have one allele disabled in every cell - autosomal dominant inheritance pattern with high penetrance (~90%)

Answer 331

S: requires 2 mutations (very unlikely) F: rb1 allele is inherited for heterozygosy and another mutation occur *converting a SINGLE retina cell from WT phenotype to Rb-/- phenotype can initiate a tumor (random mutation)

Answer 332

* nearly all familial - spontaneous RB in 2 eyes is highly unlikely - loss of heterozygosy is more statistically likely to happen in 1 or more retinal cells unilateral - tumor in 1 eye bilateral - tumor in 2 eyes

Answer 333

- can mutagenize already-destabilized cancer cells - precise spatial targeting gives high mutagenic dose to tumor , with much less exposure to healthy tissues * genomic instability drives cancer progression but also can make cancer cells more vulnerable to catastrophe - use cancer-causing radiation to stop radiation

Answer 334

- knocking which mutations cause a person's cancer can enable targeted chemotherapy - often target DNA replication that happens a lot in fast-dividing cells *therefore affects rapidly growing cells like hair and stomach cells

Final Exam Flashcards

(371 cards)