lecture 5 Flashcards
What are the different types of RNA
mRNA: messenger RNA, specifiv order of amino acid during protein synthesis
tRNA: Transfer rna, during translation mRNA info interpreted into tRNA
rRNA: ribosomal rna: combined with proteins aid trna in translation
Small rna: variety of regulatory functions, can make a complimentary strand that then binds to rna so other things like ribosomes cant bind to it (regulatory function) so cant make the protien
ribozymes: (in splicing, and peptide bond formationg duirng protein syntehsis)
RNA FUNCTIONS
What is the original nucleic acid
RNA
rna is stikk a component in viruses
at the beginning there were no proteins just ribosomes and because ribsome is single stranded it can make lots of shape, so it had different frunction like actuing like enzymes
What are snoRNA used for
small nucleolar rnas that are needed to make rRNA
essentially involved in the rna processing
What are SNrna used for
mrna splicing
Can we get information going from rna to dna
Yes, reverse transcription
done in some rna viruses to make dna that can be replicated into more viruses
you can also have info from rna that acts as enzymes to modulate transcription, so info going the other way as well
What is the only unidirectional way for central dogma
rna-> protein, cant make rna from protein, nature cant make dna from protein, it only stores the info
Is the primary structure of RNA similar to DNA
yes
its phosphate sugar bonded all together, with bases attached to sugar
What are the two main differences in primary structure for dna and rna
1) sugar: deoxyribose for dna (lacks an oh at 2’ c)
2)rna doesnt use t it uses uracil, this allows cell to see the differenc ebetween dna and rna
Primary structure of RNA
1) The hydroxyl group at the 2’ c prevents a B helix from forming for RNA … so A helix is formed, oxygen gets in the way of making the helix tight
2) can be single double stranded, linear or circular
3)can exhibit different conformations, allows it to carry out a variety of specific functions within cell
why is dna more stable than rna
the hydroxyl group can cause rna to chop itself
What is the secondary structure of RNA
single stranded, rna is sticky; has bases sticking out that want tohydrogen bond with something, ie other bases, water, so unhappy (unlike dna), so because of this it tries to BASE PAIR WITH ITSELF TO MAKE a PARTIALLY DOUBLE STRANDED RNA IN SAME MOLECULE (CALLED BASE PAIR SEGMENTS) so u can get alot of conformations that are differnt
so essentially secondary structures: areas with regular helices and discontinous helices with stem loops and hairpins
What are modified bases
-post transcriptional modifications
with the different possibilities of bases there can be new combinations since its not just atcg
Tertiary structure in RNA
Formed through interactions of secondary structures
-lack of constraint of long randge regular helices means that rna has a high degree of rotational freedom in the backbone of its non-base paired regions; so capable of forming teritary structures
-tertiaryy structures are also possible due to triple base pairing
The loop: anticodon is here, these are single strnaded so that they can recognize stuff
How are teritary strucutres in rna possible
1) lack of constraint for long range helices means that rna has rotational freedom on ends with no pairing so it can twist alot on itself
2) triple base pairing is possible ( 3 bases bonded together due to hydrogen bonds)
3) Pseudoknots: sticky ends cause even sections not close together to bond together
There are many types of tertiary structures, name some
a minor motif
tetraloop motif
ribose zipper motif
kink turn motif
kissing hairpin loop motif
How to pack dna into a small thing like an ecoli (prokaryote)
Forms a nucleoid: genome forms this which is a strcuture that has mixture of supercoiled and relaxed regions of dna
What is the bacterial chromosome like
-genome forms a nucleoid
-dna organized into 50-100 loops (domains)
-dna is compacted and supercoiled, it isthen held in place by Polyamines(spermine nad spermidine, +ve charge), and HU proteins (+ve, dimeric) and H-NS (neutral)
Hu and H-NS are dna binding proteins
What are the two ways of supercoiling?
Same idea, wind it (supercoiling)
Restrained Supercoiling: path is supercoiled around a protein, creates no tension, makes it more compact, more proteins we use, the more compact
Unrestrained supercoiling: supercoiled in space, creates tension
What is the average size of a chromosome for a eukaryote
150 million Base pairs
How to calculate the length of dna using basepair
BP x 0.34nm
How long is human dna per cell
51 mm (length of one dna) x 46 chromosomes = 2.5 meters
What is the average size of a euk cell
10-100um so we need to pack in 2.5 meters of dna into a ball of 10 um
Eukaryotic chromatin
-euk genome forms linear chromosomes
-each chromosome contains SINGLE linear dna molecule
-individual chromosomes can be seperated using pulse field gel electrophoresis
Chromatin organization
-beads on a string
-bead is made uo of histones (composed of 8 proteins), dna wrapped around this
-nucleoprotein material of chromosome is this
What is the functional unit of organization of the chromatin fiber
Nucleosome
each nucleosome contains a histone protein, and is wrapped around by dna
takes 146 bp of dna to wrap around one histone
What is the dna wrapped around the histone called
core dna
Nucleosome consists of
core dna and histone
it is positively charged
Facts about histones
-present in all euk nuclei
-small proteins
-rich in lysine and arginine (extra amino grouos become NH3+) so pos charged so that it can bind to dna neg charge, basic proteins
-interact with dna throuhg electrostatic interactions
What is a histone made up of
proteins
H2A+H2B: together form one unit and there is two of these units so there is 4 proteins here
H3 and H4: Togheter form another unit and there is two of these inits so there are another 4 proteins here
total 8 proteins
+ H1( which is a linker protein)
so 5 major subunits BUT the first 4 are the ones that directly make up the histone (h1 does not make up the histone protein, it is seperate)
What does linker protein H1 do
Brings the histones closer together in linker regions, binds two distinct regions together
because it is a linker protein, sits “ on top” so it can bring other histones together to make it all nice and tightly would up
How many times is the dna wrapped around octet
1.65 times
Size of dna that wraps around octect can be analyzed by partial digestion using dNASE (nuclease)
size of the fragments that it cuts ip is dependent on how much of the nuclease is used, the more that is used, the shorter the fragments since more linkers are digested
