LEC22: Chromatin and Gene Structure Flashcards Preview

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Flashcards in LEC22: Chromatin and Gene Structure Deck (51):

what are the molecules that make up chromatin?

DNA + histone octamer core (H2A, H2B, H3, H4) + H1


what is the direction of nucleic acid synthesis? 

in which direction is the template strand read? 

strand is read 3' to 5' 

synthesis is 5' to 3' 


name the types of sequences that are present in a pre-mRNA transcript

exons, introns


how can DNA in double strand be bound by proteins? 

1) binding between amino acid side chains of alpha helices of a DNA binding protein, which sit on DNA, bind to DNA bases; this is protein a.a. sequence has high specificity, plugs into DNA sequence w/ its available H-bonding 

(specific amino acid - base sequence pairing)

2) a homotetram (4 identical proteins that are binding a particular DNA sequence) have a specific binding site on DNA, it's kinky, they bind in a specific spot therefore

(overall DNA sequence is recognized by DNA binding proteins)


what is RNA's secondary structure? 

how does it form? 

what is it called? 

what base pairs form? 

RNA usually = single stranded

can have 2ndary linear, single strand of RNA fold up on itself via complementary base-pairing within the strand

this forms a stem-loop structure of intramolecular double stranding

A-U, G-C, G-U also possible



what is this 


Q image thumb

RNA secondary structure - stem-loop

intramolecular double stranding


what kind of genome does HIV have? why is this significant re: structure of that genome?

RNA genome 

lots of secondary structure required for proper functioning of this RNA genome 



what is DNA denaturation?

heating up a double stranded DNA molecule separates the 2 strands b/c they are only held together by H-bonds


what happens if you denature 2 strands of double stranded DNA molecules in a test tube and then lower the temperature?

why does this occur?

raise temperature: strands come apart

lower temperature: complementary strands will find each other again, get renaturation back to what you had originally

this is bc of complementary base pairing


what is hybridization?

complementary base pairing between 2 nucleic acid strands which are not naturally together 



how does a probe work?

probe = complementary piece of nucleic acid (DNA usually, can be RNA though) 

make it complementary to the sequence that you are trying to locate in your sample 

if put probe in with mixed up sample, denature, and then renature, it will bind if its complement is present; and can have it signal if binding occurs 

this is nucleic acid hybridization


what is the nucleosome

packing mechanism that allows 2 meters of DNA to get into a 10 micron nucleus 

nucleosome = double stranded DNA (150 bp) + histone proteins core 


what is teh structure of the histone proteins of the nucleosome?

2 molecules each of H2A, H2B, H3, H4, and 1 H1 that staples DNA to that core protein octamer 


what comprises a nucleosome

DNA-histone protein unit


what is chromatin 

DNA in its bound form to histones in the nucleus


what is euchromatin vs heterochromatin? where is each found? 

euchromatin: transcriptionally active region of chromosome 

heterochromatin: tightly wound, dense structures of chromosome that're inaccessible to RNA polymerase 


what is centromere

connects chromatins


what is telomere

at end of chromosome


what are the processes of nucleic acid synthesis?

1) DNA replication 

2) Transcription


in DNA replication, which strand(s) is/are used as template(s)? 

what does the replication? 

what direction is the new product synthesized? which direction is the unit being replicated read? 

what do you end up with?

both strands are used as templates 

DNA polymerase (DNA dependent DNA polymerase) reads nucleotide sequence of template strand in the 3' to 5' direction, and synthesizes new DNA in the 5' to 3' direction

result: 2 identical double stranded DNA molecules



what is teh basis of DNA replication?





what does transcription? are both strands templates? how is the template read, how is RNA synthesized? what is the product resulting?

done by RNA polymerase, a DNA dependent RNA polymerase

only 1 template strand, 1 is non-template

RNA polymerase reads template strand from 3' to 5', makes RNA in 5' to 3' direction 

product: 1 single stranded RNA molecule 


newly synthesized RNA transcript has same sequence as what?

same as the non-template strand of the DNA that was transcribed, but has U's not T's 


what problem does the tight packing of DNA present? 

what determines if DNA will be expressed?

generates problem of accessibility to the DNA by proteins that regulate transcription or are engaged in replication 

histone modifications - acetylations, methylations, phosphorylations - determine if DNA info will be expressed


what are the substrates of DNA polymerase?

the end of the previously replicaed DNA 


incoming deoxyribonucleoside triphosphates (dATP, dCTP, dGTP, dTTP) 


what are ribonucleoside triphosphates?


are what RNA polymerase incorporates into growing RNA chain as it transcribes DNA info into RNA 


what's another name for the DNA non-template strand? why?

"coding strand' because it has the same sequence as the RNA that is transcribed from the DNA template strand


what is the +1 site?

the base pair where txn initiation occurs 

aka "TSS" "transcription start site" 



what is the transcription unit?

what are its boundaries? 

what happens to it and does it result in?

the piece of DNA that is transcribed by RNA polymerase 

from +1 site to terminator sequence 

acted on by RNA polyermase 

makes pre-mRNA


what are the steps of pre-mRNA processing? what is the result?

1) splicing: exons are knit together, introns are spliced out 

2) capping: 5' CAP is put on pre-mRNA 

3) poly-adenylation: poly-AAAAA tail put on 3' end of pre-mRNA


what's splicing

during pre-mRNA processing, pre-mRNA is spliced

introns are spliced out ("intervening"); exons stay in ("expressed") to the mRNA 

no functional consequence of this for the DNA, only for the pre-mRNA and mRNA


what does poly adenylation onto what?

a DNA-independent RNA polymerase adds a poly-A tail on to the 3' end of mRNA


where does mature mRNA go?



what is the open reading frame?

what are its features?

the part of the mRNA that ribosome will actually translate, code for a protein

begins w/ AUG, codon for methionine

ends w/ UAA, UAG, UGA, stop codons 



what are the ends of the mRNA?

5' untranslated region, 3' untranslated region poly-A tail 


whole thing is: 

5'UTR, coding sequence (ORF), 3'UTR, poly-A tail


what is a codon

a string of 3 nucleotides 

encodes for an amino acid 



what does it mean that the code is degenerate?

multiple codons code for the same amino acid


what do RNA Pol I, II, and III transcribe for?

RNA Pol I: rRNA genes 

RNA Pol II: protein-coding genes! 

RNA Pol III: tRNA genes 


what is a silent mutation?

occurs b/c code is degenerate so 1 base change may still code for same amino acid

does not effect function 


what is a missense mutation?

single nucleotide change results in codon that codes for a different amino acid 

may or may not effect function depending on how different amino acid that's put in is 


what is a nonsense mutation?

point mutation that results in premature STOP codon in coding sequence

results in truncated (shorter), nonfunctional protein

almost always effects function


what is a frameshift mutation?

insertion or deletion of a nucleotide/nucleotides in a DNA sequence that isn't divisible by 3, so shifts entire ORF 

resutls in totally different translation from original

the earlier in the sequence the deletion/insertion occurs, the more altered the protein 

causes reading of codons after the mutation to code for different amino acids


what is the first nucleoside in pre-mRNA? why? 

a nucleoside 5' triphosphate 

b/c RNA synthesis can begin de novo 


how does RNA pol II know where to start txn?

needs help of general transcription factors (TFII complexes of TFIIB, D, E, F, H) and mediator which guide RNA Pol II to sit down on DNA, start txn 

guide the RNA Pol II to the TATA region


what is a cis vs. trans element?

cis: something on teh DNA itself, intrinsic pt of DNA 

trans: soemthing that binds DNA from outside, has an effect on it


what is the promoter?

a cis element of the DNA 

where txn begins 

TATA sequence of promoter is notable


what is a consensus sequence?

an example?

a sequence that is most often found at a particular position

TATA is an example of this


where is the TATA sequence located?

-25 or -30 location, upstream of +1 site where txn begins


what is TBP? what does it do?

TBP: TATA box binding protein 

recognizes the TATA sequence and so binds, has TFIID attached and allows binding of TFIID to DNA at initiation site

causes a bend when binds



what is characteristic of the carboxyterminal domain of RNA Pol II's largest subunit?

multiple repeats of a short sequence highly enriched in serine 

gets phosphorylated by TFIIH, a protein kinase 

this phosphorylation singals a switch to elongation mode


how does RNA Pol II get recycled? why?

gets recyled for repeated rounds of txn

protein factors rearrange elongating txn complex such that RNA Pol II is released from DNA template, is returned to its hypophosphrylated state by a CTD phosphatase

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