Bcd Cell Bio 4 -_-

Front 1

2 functions of DNA polymerase

Back 1

5' -> 3' polymerase

3' --> 5' exonuclease

Front 2

how often does DNA polymerase make a mistake?

with DNA mismatch repairrepair?

Back 2

1 in 10^7

1 in 10^9

Front 3

DNA polymerase can only join a nt to a _______ of a base associated with a double helix

Back 3

3'-OH

Front 4

makes short stretch of RNA using DNA as template

Back 4

DNA primase

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primers are removed by _____
gaps filled in DNA during replication by _______________
completed fragments joined by _________

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nuclease

DNA repair polymerase

DNA ligase

Front 6

connects okazaki fragments

Back 6

DNA ligase

Front 7

adds additional nt repeats at the end of the chromosome

in what direction?

Back 7

telomerase
5'-->3'

Front 8

somatic cell mutation aka _______ contributes to ____ of deaths in europe and north america

Back 8

cancer 30% of deaths

Front 9

DNA damage- releases G and A from DNA
phosphodiester backbone maintained

Back 9

depurination

Front 10

DNA damage- spontaneous loss of amino group from cytosine

Back 10

deamination

Front 11

DNA damage- caused by radiation, covalent linkage between two adjacent pyrimidines

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thymine dimers

Front 12

happens if deamination goes uncorrected

depurination

thymine dimers

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substitution of one base for another

deletion of nt/base pair
incorrect nt places at site of deletion by G-T pairing

stall DNA replication machinery at site of damage

Front 13

way to spread favorable alleles and eliminate unfavorable

where and when does homologous occur?

Back 13

DNA recombination-

homologous region
during meiosis prophase 1

Front 14

characteristics of mobile genetic elements

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- in most organisms
- short sequences of DNA
- site specific recombination
- may be considered parasitic DNA
- generate genetic variation
- encode enzyme that mediates its movement
- may act as a mutagen

Front 15

the enzyme that mediates the movement of the mobile genetic element it resides in

Back 15

transposase

Front 16

2 mechanisms by which transposons move

Back 16

cut and paste (non-replicative)
replicative

Front 17

in what organisms are retro-transposons found?

what do they require?

Back 17

eukaryotes

reverse transcriptase (RNA dependent- DNA polymerase)

Front 18

disease that involves an L-1 retrotransposon inserting into gene encoding Factor VIII

Back 18

hemophilia

Front 19

RNA type:

proteins coding

form the core of ribosome and catalyze proteins synth

regualte gene expression

serve as mRNA/ AA adaptors

used in RNA splicing, telomere maintenance, etc

Back 19

mRNA

rRNAs

miRNA

tRNA

other small RNAs

Front 20

DNA has an OH group at this C

H at this C

Back 20

OH at 3'

H at 2'

Front 21

enzyme that carries out transcription

Back 21

RNA polymerase

Front 22

which is shorter- DNA or RNA?

Back 22

RNA

Front 23

how fast is transcription? can it repair its mistakes?

Back 23

40 nt/sec
cannot correct mistakes

Front 24

mistake rate in RNA polymerase

does it need a primer?

Back 24

1 in 10^4

can start without a primer

Front 25

components of prokaryotic transcription

how does it know where to start?

Back 25

RNA plymerase/ sigma factor
promoters: -35 and -10 start signals

Front 26

primarily respoinsible for recognizing promoter sequence on DNA in prokaryotes

how long does it stay attached?

Back 26

sigma factor

first 10 nts

Front 27

terminator for prokaryotic transcription

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stop signal of repeated Ts

Front 28

what the 3 RNA polymerases in eukaryotes transcribe

I
II
II

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I: most rRNA genes
II: protein-coding genes, miRNA genes, smoe small RNAs

III: tRNA genes, 5s rRNA gene, genes for other small RNAs

Front 29

RNA in prokaryotes mono or polycistronic? eukaroytes?

Back 29

prok: polycistronic
euk: monocistronic

Front 30

RNA in eukaryotes is transcribed ________ and translated in _________

Back 30

the nucleus

cytoplasm

Front 31

RNA capping happens at the ___ end and consists of what

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5' end

guanine NT with methyl group
after production of ~25 nts

Front 32

polyadenylation happens at the ____ end of the transcript

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3' end

trimming of end of transcript by enzyme that recognizes particular sequence
then addition of AAA stretch by another enzyme

Front 33

4 purposes of RNA modification in euks

Back 33

- increases stability
- aids in export to cytoplasm
- IDs molecule as mRNA
- used by the protein synthesis machinery to indicate that both ends of transcript are present

Front 34

is eukaryotic transcript colinear? prok?

Back 34

not colinear

prok is

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splices intron sequences out

occurs after:

Back 35

snRNP complexes (small nuclear ribonucleoproteins)

after capping

Front 36

% of genes that undergo alternative splicing

why is it favorable

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60%

makes genetic recombination between exons of different genes more likely

Front 37

if the anticodon of tRNA is 5'-ACG-3' then what is its corresponding codon on mRNA

Back 37

3' - UGC- 5'

5' -CGU- 3'

Front 38

the machinery of translation

Back 38

mRNA
tRNA
ribosomes
AAs
aminoacyl tRNA synthetases
protein factors
ATP and GTP

Front 39

small subunit of ribosome does what?

large subunit function?

Back 39

matches tRNA to codon on mRNA

links aa by peptide bonds

Front 40

size of eukaryotic ribosome

prok?

Back 40

80s (40 and 60S)

70 (30 and 50S)

Front 41

antibiotic that blocks binding of aminoacytl-tRNA to A-site of riosome (step 1)

Back 41

tetracycline

Front 42

antibiotic that blocks peptidyl transferase reaction on ribosomes (step 2)

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chloramphenicol (toxic- can cause aplastic anemia)

Front 43

antibiotic that blocks translocation reaction on ribosomes (step 3)

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erythromycin

Front 44

antibiotic that prevents transition from initiation complex to chain-elongating ribosome
causes miscoding

Back 44

streptomycin

Front 45

antibiotic that blocks initiation of RNA chains by binding to RNA polymerase

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rifamycin

Front 46

4 DNA-binding protein motifs

Back 46

helix-turn-helix

basic helix-loop-helix

zinc finger

leucine zipper

Front 47

special class of HTH- regulatory proteins

Back 47

homeo-domain proteins (in proks and euks)

Front 48

makes up a helix-turn-helix

Back 48

two perpendicular alpha helices joined by a short strand of AAs

Front 49

makes up a basic helix-loop-helix

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two alpha-helices containing basic AAs linked by a loop (usually dimers)

Front 50

zinc fingers are made up of these two AAs bound by zinc to cause the protein to pucker

Back 50

cysteine and histidine units

Front 51

how far away are each DNA binding protein from one another?

Back 51

3.4nm aka 10bps aka 1 turn apart

Front 52

creates amphipathic area between its dimer

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leucine zipper

Front 53

where do DNA binding proteins bind?

Back 53

inverted palindromes

Front 54

how do repressors work?

Back 54

bind to operator
block RNA polymerase from binding to promoter

Front 55

how do activators work?

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help initiate transcription by interacting with RNA polymerase, allowing it to bind to otherwise weak promoters

Front 56

the _____ the promoter is to the start site the stronger it is

Back 56

closer

Front 57

transcription is controlled by these 2 things

Back 57

DNA-binding proteins
regulatory sequences

Front 58

site where transcription begins and
binding site for RNA polymerase

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promoter

Front 59

recognized by regulatory proteins and where is it?

Back 59

regulatory DNA sequences ~50 nts upstream

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tryptophan operon repressor can only bind if:

Back 60

bound to tryptophan

Front 61

tryptophan operon repressor falls off if:

Back 61

tryptophan concentration is low, operon is expressed to make tryptophan

Front 62

needed for CAP to be able to bind to DNA

Back 62

cAMP binding first

Front 63

when is cAMP present? what is the overall affect?

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when glucose is lower.
cAMP binds to CAP activator which can then bind to the operon, turning it on

Front 64

situation in which the lac operon is turned on

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no glucose present (CAP bound)
lactose present (lac repressor off)

Front 65

situations in which the lac operon is turned off

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in the presence of glucose (CAP won't bind)

in the absence of lactose (lac repressor is bound) no lactose to breakdown

Front 66

where is the cap binding site?

Back 66

upstream of the RNA polymerase binding site (promoter)

Front 67

where are enhancer regions located? do they use energy?

Back 67

1000+ bp upstream. energy used to fold

Front 68

there are multiple sigma factors for specific:

implications

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promoters recognized

bacteria can make its own sigma factors that are specific for the promoters in its own genome

Front 69

rho-independent termination depends on this

Back 69

G-C rich palindrome that forms hairpin loop before stretch of U residues

Front 70

how does rho-dependent termination work?

energy dependent?

what does rho function as?

Back 70

Rho binds newly transcribed RNA, uses ATP to move, catches RNA polymerase stalled at termination site, breaks RNA_DNA-hybrid by working as a RNA_DNA helicase

Front 71

ribosome binding site on RNA

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shine-dalgarno sequence (usually 4-7 nts 5' of the initiator AUG)

Front 72

protein binding at a hairpin before the start of translation does what?

Back 72

stops binding of translation components

Front 73

3 translational termination steps

Back 73

release factors recognize stop codons
causes addition of water molecule instead of aa
polypeptide chain terminated

Front 74

caused by Mutations of CBFA1

what is common?

Back 74

cleidocranial dysplasia

absent clavicle, late primary dentiton, supernumeray teeth

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caused by Mutations of CBFA1

what is common?

Back 75

cleidocranial dysplasia

absent clavicle, late primary dentiton, supernumeray teeth

Front 76

caused by mutations in the FGFR2 gene

Back 76

crouzon's

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caused by mutations in the FGFR2 gene

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crouzon's

Front 78

oligodontia is caused by defects in which genes?

Back 78

PAX9
MSX1

Front 79

oligodontia is caused by defects in which genes?

Back 79

PAX9
MSX1