chat transcript: Molecular biology

[Lorena]

20:15:56 [hutals] name the nucleotides that are purines? what about pyrimidines?

20:16:23 [Lorena] histones have a positive charge confered by which aminoacids?

20:16:38 [medfan] CUT-PY,

20:16:56 [crusher] adenine n thymidine(purine) cytosiine...uracil thymidinePyrimidine

20:17:01 123456 exits from this room

20:17:06 123456 enters this room

20:17:09 [medfan] LYSINE, Arginine

20:17:18 [jwls29] good one,medfan

20:17:26 [crusher] lysine

20:17:32 [jwls29] agree with medfan about the aminoacids

20:17:33 [medfan] thanks jwls

20:18:22 [hutals] mneumonic is "PURe As Gold" and "CUT the PY (pie) for PURines being A,G and PYrimidines being C,U,T

20:19:26 [hutals] arginine and lysine

20:19:30 [Lorena] you meant to say the bases hutals, in your q's

20:20:11 [hutals] yep, you're right.....see, i told you i wasn't very good at this subject ...sorry

20:20:18 [Lorena] yes very good everyone . Lysine and arginine -

20:20:31 [jwls29] what is a nucleotide?

20:20:34 [Lorena] no porblem, thats why it is good to discuss in group

20:20:55 [crusher] base n sugar

20:21:02 [medfan] base+sugar+phosphate

20:21:55 [crusher] yes only base n sugar=nucleoside

20:22:03 [Lorena] agree with medfan

20:22:11 [jwls29] very good

20:22:19 [hutals] At which end of the tRNA is the aa bound?

20:22:21 [jwls29] base+sugar+phosphate

20:22:52 [Lorena] 3' end

20:23:00 [crusher] 3 aa term

20:23:05 [medfan] 3'

20:23:07 [crusher] CAA arm

20:24:00 [hutals] The amino acid is covalently bound to the 3' end of the tRNA....good

20:24:32 [hutals] Can RNA polymerase initiate chains?

20:25:03 [medfan] yes, but dna pol can not

20:25:16 [Lorena] agree

20:25:40 [hutals] yep, can initiate chains

20:26:18 [Lorena] why DNA pol cannot?

20:26:51 [medfan] dna pol needs an rna primer

20:27:08 [jwls29] agree with medfan

20:27:09 [Lorena] very good

20:27:38 [Lorena] DNA polymerase starts synthesis at the 3' end of the primer ...so without it cannot do it

20:28:24 [hutals] which RNA pol makes rRNA? which one makes tRNA? which makes mRNA?

20:28:43 [hutals] choices are I, II, III?

20:28:52 [crusher] agree

20:29:05 [crusher] sorry

20:29:11 [crusher] rmt=123

20:29:17 [Lorena] RNAP 1- rRNA except 5subunit

20:29:28 [Lorena] RNAP2- mRNA

20:29:49 [Lorena] RNAP3 tRNA plus 5 subunit of the rRNA

20:30:03 [hutals] mneumonic is 1,2,3 = RMT (rhymes).....so I for rRNA, 2 for mRNA, and 3 for tRNA.....very good!

20:30:07 [medfan] agree with lor and crusher

20:30:48 [Lorena] and i added at the end : five "s" is a mess ..it also rhymes

20:31:10 [hutals] which RNA is largest? which is smallest? which is the most abundant? choices are tRNA, mRNA, rRNA?

20:31:34 [hutals] good one lor

20:31:42 [jwls29] massive-mRna

20:31:55 [jwls29] tiny-tRNA

20:32:07 [jwls29] rampant-rRNA

20:32:08 [medfan] most abundant rRna

20:32:19 [Lorena] agree with jwls

20:32:25 [medfan] agree with jwls

20:32:32 [hutals] exactly. mneumonic is Massive, Tiny, Rampant....very good

20:32:36 [crusher] ragree abundant=r RNA

20:33:03 [hutals] name the start and stop codons?

20:33:16 [crusher] start=methionine

20:33:22 [Lorena] what would the deamination of cytosine would result in?

20:33:28 OMD93 enters this room

20:33:38 [crusher] stopr=ura urg

20:33:40 [jwls29] uracil

20:33:51 [Lorena] start AUG- augurates . Stp UGA, UAA, UAG

20:34:23 [medfan] deamination - uracil, methylation - thymine

20:34:37 [hutals] AUG=start , UGA, UAA, UAG are the stop codons. mneumonic is inAUGuration, U Go Away, U Are Away, U Are Gone....excellent

20:34:46 [hutals] hey OMD93

20:34:54 [Lorena] excellent jwls and medfan

20:34:56 [crusher] thanks

20:35:04 [OMD93] hey all

20:35:10 [Lorena] hi OMD

20:35:16 [medfan] thanks

20:35:21 [medfan] hi omd

20:35:34 [crusher] hi omd93

20:36:00 [OMD93] hello

20:36:36 [hutals] difference between transition and transversion?

20:37:15 [crusher] transversion Purine exchange for pyrimidine (bases

20:37:32 [Lorena] transition is the change by a purine for another purine , or pyrimidine by another pyrimidine. Transversion is change a purine for a pyrimidine or viceversa

20:37:35 [crusher] transition same purine purine bases changes

20:38:29 [hutals] transition is substituting purine for purine or pyrimidine for pyrimidine (same) and transversion is substituting purine for pyrimidine or vice versa (different). very good

20:38:33 [medfan] which group of drugs block the action of topoisomerases, which inhibit dna gyrase?

20:39:06 [jwls29] fluorquinolones

20:39:36 [Lorena] quinolones inihibit DNA gyrase

20:39:59 acestep1 enters this room

20:40:00 [hutals] fluoroquinolones

20:40:05 [hutals] hey ace

20:40:11 [medfan] quinolones block topoisomerases, nalidixic acid inhibits dna gyrase.

20:40:15 [medfan] good

20:40:23 [crusher] flouroquinolone===dna gyrases

20:40:26 [Lorena] eukarytic topoisimerases are inhibited by etoposide

20:40:56 [crusher] quinilone=dna gyrases

20:41:21 [medfan] yest, topoisomerase II is is blocked by etoposide and teniposide

20:41:25 [Lorena] hi ace

20:41:34 [hutals] what is tRNA wobble?

20:42:35 Hanson enters this room

20:42:42 [Lorena] the wobble hypothesis says that a tRNA can translate many aminoacids

20:43:04 [hutals] hey hanson

20:43:40 [Hanson] hi, I got to run. Have a nice chat. Good luck.

20:44:01 [hutals] ok, bye

20:44:08 [Lorena] usually only the 2 first aminoacids have to be the same, the third can be different because they will code for the same protein

20:44:15 [hutals] is that the same hanson that created the site?

20:44:33 [Lorena] i meant the first 2 bases

20:44:46 [medfan] yes, agree with lorena

20:44:55 [hutals] wobble = Accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd 'wobble' position may code for the same tRNA/amino acid.

20:45:15 [hutals] very good!

20:45:19 [crusher] which DNA poly removes the rna primer

20:45:39 [medfan] pol I

20:45:57 [Lorena] agree

20:46:14 [hutals] agree DNA poly I

20:46:37 [crusher] yesw DNA pol1

20:47:06 [hutals] which has DNA proofreading ability?

20:47:27 [crusher] dna poly

20:47:41 [medfan] pol III has 3' exonuclease for proofreading

20:48:03 [jwls29] agree with medfan

20:48:13 [Lorena] agree with medfan

20:48:23 [hutals] yep its poly 3

20:49:43 [Lorena] of the eukaryotic DNA polymerases , which one (s) has/have 3'-5' exonuclease activity?

20:50:04 [medfan] both I and III

20:50:13 [crusher] what is the action of polymerases n nucleases

20:50:15 [hutals] i know 3 does

20:50:53 [Lorena] those are prokaryotic

20:51:31 [Lorena] the choices are: DNAP alpha, beta, gamma , delta?

20:51:55 [hutals] hmmm...good point.....i think i'll observe for answer on this one because not sure

20:52:27 [medfan] oh, i see what you are asking now!

20:53:08 [Lorena] DNAP alpha sx the lagging strand; delta sx leading strand,gamma is for mitochondrial DNA

20:53:56 [Lorena] only delta and gamma have exonuclease activity

20:54:32 [Lorena] the lagging strand is not "checked" !!

20:55:22 [Lorena] only the leading strand in prokaryotes

20:55:25 [hutals] thanks, didn't know that well enough to answer

20:55:32 [medfan] very good question lor

20:55:58 elb enters this room

20:56:07 [Lorena] yw, just to be careful when they talk about prokaryotes or eukaryotes

20:56:16 [hutals] Describe Euchromatin, are they very condensed or not? are they active or not? (as compared to heterochromatin) .....this seems like a histo question, but its with my biochem stuff???

20:56:26 [OMD93] You all are doing good. Good Luck! Bye

20:56:26 [hutals] hey elb

20:57:21 [medfan] by omd

20:57:24 [kmonica26] eu is loose and active

20:57:39 [Lorena] euchromatin is loosely packaged, active, not as condensed as heterochromatin

20:57:43 [medfan] euchromatin are looselypacked, very active

20:58:10 [hutals] Euchromatin Less condensed (vs. Heterochromatin), transcriptionally active. Heterochromatin Condensed, transcriptionally inactive....good job.

20:59:40 [Lorena] which one is sensitive to nucleases?

20:59:52 [medfan] euchromatin

21:00:31 [hutals] agree

21:00:40 [Lorena] yes, very good

21:01:28 [hutals] i'm sweating every time a biochem question comes up....how many days of biochem are left

21:01:43 [Lorena]

21:02:13 [jwls29] lol...i'm not very confident so i don't answer

21:02:15 [hutals] Describe the method by which introns are removed from primary mRNA transcript?

21:02:44 [hutals] i'm not very confident and i try to answer anyway....but i probably shouldn't

21:03:06 [Lorena] you are doing great

21:03:27 [medfan] you always do good hutals

21:04:06 [hutals] i'm hoping not too many biochem questions on the exam

21:04:17 [Lorena] me too

21:05:11 [medfan] intorn are removed by spliceomsomes or snRNP (snurp)

21:05:36 [crusher] splicosomematod introns are remove and exons join together within nuclues

21:05:48 [Lorena] the intrins are removed by splicing and then the fragments-lariat- are degraded and the exons joined together

21:05:59 [hutals] yep, very good all

21:07:58 [crusher] where does transcription n translation occur (part of a cell)

21:08:13 [Lorena] what does prevent euchromatin to be degraded by endonucleases then?

21:08:46 [Lorena] transcription in nucleus and translation in cytoplasm

21:09:18 [crusher] yes good lor ..correct

21:09:23 [hutals] transcription=nucleus, translation=cytoplasm

21:10:46 [medfan] H1? I know H1 protects heterchromatin but not sure about euchromatin

21:11:17 [Lorena] Single stranded binding proteins - the ones in replication, the ones that bind to the single strand of the DNA so prevents reassociation of the strands and also destruction

21:11:28 [hutals] restriction endonucleases

21:11:35 [Lorena] good thinking medfan

21:12:02 [medfan] very nice question!

21:12:38 [Lorena] euchromatin doesnt have H1

21:13:06 [hutals] what is a palindrome? give an example

21:13:13 [medfan] yes, you are right, that's why it's loosely associated

21:13:15 [crusher] which rna poly inhibted by alpha amatin and rifampin

21:14:09 [Lorena] RNA polymerase II?

21:15:05 [Lorena] palindrome is a sequence of DNA that if folded will be like a mirror of the bases or something like that

21:15:38 [crusher] rna poly 2 (eukar)inhibit alpha amanitin.....only onr RNA poly(prok) inhibit rifampin

21:15:40 [hutals] yep, a palidrome reads the same forward and backwards. ex: XANAX

21:16:13 [Lorena] thanks crush

21:16:30 [hutals] what are the number of bonds per purine-pyrimidine pair. Which is stronger?

21:16:34 [medfan] good questions

21:16:49 [crusher] whts the role of shine darganlo sequnce

21:17:07 [medfan] Pyramidine have 3 , Purines 2. Pyramidines are stronger

21:17:11 [crusher] cg=3 stronger

21:17:45 [Lorena] C-G have 3 bonds, U or T with A have only 2

21:17:46 [medfan] CG have 3, AT have 2, sorry, my bad

21:17:47 [hutals] G-C bond (3 H-bonds) A-T bond (2 H-bonds). G-C bond is stronger....good

21:18:43 [Lorena] shine dalgarnho sequence in prokaryotes is the one that will bind to the 16 s subunit of the ribosome to start translation

21:18:53 [crusher] shine dargano is on 5 UTR on which ribosome binds..

21:19:14 [medfan] SD is found in the 5' UTR

21:20:25 [crusher] which organelle prot synth start which aa seq start n stop

21:21:26 [crusher] whts the role of TATTA n CAAT box

21:21:33 [Lorena] methionine starts ...in ribosome?

21:21:53 [medfan] sorry everyone, i have to take off and give a friend a ride. see you all tomorrow night.

21:22:07 [jwls29] bye medfan

21:22:12 [Lorena] thanks for coming medfan, see you tomorrow

21:22:22 [hutals] ok medfan....see ya tomorrow

21:22:22 [crusher] yes protein syntheisis in ribosome....in NH2-------COOH

21:22:25 [medfan] bye

21:23:02 [Lorena] thanks crush

21:23:31 [Lorena] TATA AND CAAT are promoter regions in eukaryotics

21:24:56 [hutals] if you all dont mind, i will just observe from this point on because i'm outta questions and i didn't reach the end of this section

21:25:49 [Lorena] yes, jump whenever you feel comfortable

21:26:32 [Lorena] RNA pol recognize these areas-promoters ...and start doing its job

21:27:07 [crusher] yes they are promotor regions

21:27:43 [Lorena] what does monocystronic mean?

21:27:58 [crusher] single gene

21:27:59 [hutals] i found a question dealing with that......How does RNA polymerase II open DNA?

21:28:50 [Lorena] yes crush

21:28:58 [crusher] via topiso 2

21:28:59 [hutals] RNA polymerase II opens DNA at promoter site (A-T rich upstream sequence- TATA and CAAT)

21:29:58 [Lorena] and how does DNA polymerase opens DNA?

21:30:07 [hutals] in eukaryotes, all mRNA is moncistonic

21:30:22 [crusher] by unwinding the double strand

21:30:37 [Lorena] tricky q's

21:31:07 [kmonica26] helicase?

21:31:20 [Lorena] yes, it requires helicase to do so, very good monica

21:31:40 [kmonica26] thks

21:32:59 [crusher] give somename of dis with large seg deletion?

21:33:43 [hutals] by the way, excellent free question source here http://www.valuemd.com/start.html

21:34:03 [Lorena] why prokaryotic cells dont require the action of a telomerase at the end of DNA replication?

21:34:19 [Lorena] thanks hutals

21:34:37 [hutals] no prob

21:35:05 [Lorena] cri du chat crush?

21:35:52 [crusher] yes cridu chat n alpha thalsemia

21:37:24 [Lorena] what is a telomere? function of telomerase?

21:38:48 [Lorena] are you guys there?

21:38:50 [crusher] it removes the terminal part i guess something good tom prevent fromcancer

21:39:42 [Lorena] telomere is practically the tip of the linear DNA in eukaryotes

21:40:24 [Lorena] eveytime DNA is replicated , the tips become shorter cauze DNAP cannot complete the sx of the whole DNA

21:41:10 [Lorena] telomerase is an enzyme that maintain the telomeres but only in embryonic cells, stem cells, not in all cells so thats why we get old

21:41:32 [Lorena] cancer cells have a high activity of telomerase and thats why they are immortal

21:42:09 [Lorena] prokaryotic cells dont require telomerase because their chromosome is circular and not linear like ours

21:42:42 [Lorena] so dont loose the tips like ours everytime they replicate their DNA

21:42:43 [jwls29] ty,lorena

21:42:53 [crusher] very good thanks

21:43:00 [hutals] thanks lor, great info

21:43:12 [Lorena] yw

21:43:58 [crusher] What does the statement, 'the genetic code is commaless' mean? What is the exception to this rule?

21:44:48 [hutals] non-overlapping ??

21:45:14 [crusher] The code is non-overlapping. The exception are some viruses

21:45:40 [crusher] What does the statement, 'the genetic code is degenerate' mean?

21:45:49 [Lorena] ok

21:46:19 [hutals] >1 codon can code for same aa

21:46:45 [Lorena] agree

21:46:58 [hutals] that part i studied

21:47:13 [crusher] correct

21:47:32 [crusher] What is a frameshift mutation? What is usually the effect on the encoded protein?

21:48:28 [hutals] change downstream. truncated proteins

21:48:55 [Lorena] frameshift mutation is deletion or adition of a base so it is not multiple of three anymore and read all wrong downstream

21:49:36 [crusher] change in DNA resulting in misreading of all nucleotides downstream. Usually results in a truncated protein

21:49:56 [hutals] give example of frameshift dz

21:51:18 [hutals] duschene MD and tay sachs are examples

21:51:34 [Lorena] thanx , didnt remember

21:52:13 [crusher] What is a silent mutation? What usually causes a silent mutation

21:52:55 [Lorena] the last base is changed but nothing happens cauze the first 2 code for the same aa

21:53:20 [hutals] new codon for same aa....usuallly 3rd position

21:53:38 [crusher] Mutation results in the same aa encoded. Often the base change is in the 3rd position of the codon

21:54:23 [crusher] What is an enhancer

21:54:51 [jwls29] i'm gonna go.....goodnite...i will see u tomorrow

21:55:06 [crusher] good nite jwls

21:55:16 [hutals] good nite jwls

21:55:33 [Lorena] see you tomorrow

21:55:33 [Lorena] see you tomorrow

21:56:34 [Lorena] enhancer is .i dont remember

21:57:24 [crusher] Stretch of Dan that alters gene expression by binding transcription facts. May be located close to, far from, or even within (an intron) the gene whose expression it regulates

21:58:03 [Lorena] thanks