LEC22: Chromatin and Gene Structure Flashcards
(51 cards)
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
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?
complementarity
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
