genetics exam 3 - chapter 10

the bacterial promoter has 2 consesus sequences that rna polymerase will bind to , to initiate transcription. describe them

*** the promoter is the initiation for transcription as RNA polymerase will bind to the -10 and -35 consensus sequences present in DNA 1. -10 consesus sequence= common written as TATAAT although most prokaryote promoters are not TATAAT. is called -10 because it is found ~10 nucleotides ahead of the transcription start site 2. -35 consesus sequence= about 35 nucleotides ahead of the transcription start site, common written as TTGACA.

describe tRNAS

- first proposed by francis crick tRNAS transport amino acids to the ribosome during translation, are basically RNAS that transport the amino acid to the ribosome - most organisms have 30-40 diff types tRNA ** each tRNA can be in a single copy or in many copies of the genome

in order for transcription to occur , we need 3 major things what are they

1. A DNA template= we need something to make a copy of , RNA grows off of DNA , rna polymerase actually moves down the dna creating rna molecules 2. raw materials to build a new RNA molecule= need RNA nucleotides to join together 3. need the transcription appartus consisting of proteins necessary to catalyze the synthesis of RNA

for bacterial transcription to terminate, there are 4 requirments. state them

1. RNA polymerase must stop synthesizing RNA 2. the RNA molecule must be released from the RNA polymerase 3. the new RNA molecule must dissociate from the template DNA 4. RNA polymerase must detach from the DNA template

splicing is a two step process. describe it

1. a cut occurs at the 5' splice site which attaches to the brain point and forms a LARIAT 2. then a cut occurs at the 3' splice site, freeing the lariat and the exons join together lariat is degraded, a mature mRNA is formed

overall what are the 3 ways mRNA is processed

1. addition of 5' methyl cap 2. poly a tail 3. removal of introns

describe bacterial transcription : Initiation

1. first in order for a gene to be transcibed, RNA polymerase requires a protein called the SIGMA FACTOR to be able to actually bind to the promoter ( when the rna polymerase and sigma factor are together this is called a holoenzyme) 2. then once sigma factor binds to rna polymerase, rna polymerase can bind to the specific sequences of the promoter. 3. this binding of the holoenzyme causes short unwinding of DNA ( SO RNA POLYMERASE IS DOING UNWINDING OF DNA) 4. a rNTP complemenatry to the dna at the start site is the first nucleotide put down 5. sigma factor is released when rna polymerase moves beyond the promoter

what are the 3 steps of bacterial transcription

1. initiation= transcription apparatus binds to promoter and begins RNA synthesis 2. Elongation= RNA polymerase unwinds DNA and adds new nucleotides to the growing RNA molecule, unwinding and transcription occur simutaneously 3. Termination= recognition of the end of the transcription unit and separation of the RNA molecule from the dna TEMPLATE, whole appartus recognzies the end

what are the 3 RNAS that are transcribed in both eukaryotes and prokaryotes

1. mRNA ( messenger rna)= found in nucleus and cytoplasm, carries the genetic code for proteins aka carry instructions for making protein and tells cell which amino acids to join 2. rRNA ( ribosomal rna)= found in cytoplasm, has structural and functional components of ribosome 3. tRNA (transfer rna)= found in cytoplasm, helps incorporate amino acids into polypeptide chain, brings amino acid to ribosome

describe the 3 parts of the transcription unit

1. promoter= DNA sequence recognized by the transcription appartus, promoter tells RNA polymerase which strand is gonna be transcribed and in what direction . IS THE STARTING LOCATION FOR TRANSCRIPTION, while upstream will be sequence of dna actually being transcribed 2. RNA-coding region= DNA sequence that is copied into an RNA molecule, is the part of the DNA that is actually transcribed 3. terminator= DNA sequence that signals where transcription ends , stops whole process is usually apart of the RNA coding region towards the end, transcription stops when RNA polymerase reaches this sequence

what are the 4 steps of initation of transcription in bacteria

1. recognition of promoter= rna polymerase needs to regonize promoter 2. formation of the transcription bubble= unwinding dna 3. creation of the first bonds between ribonucleotides 4. escape of the transcription appartus from the promoter= when rna polymerase binds to promoter it has to escape promoter

describe the 6 classes of RNA that are only found in eukaryotes

1. snRNA ( small nuclear rna)= found in nucleus, function is processing of pre-mRNA, so removes introns 2. snoRNA ( small nuclelolar rna)= in nucleus, function is processing and assembly of rRNA, so rna that processes other rns 3. miRNA ( microRNA)= in cytoplasm, inhibitions translation of mRNA 4. siRNA ( small interfering rna)= in ctyoplasm, triggers degragation of other rna molecules 5. piRNA ( piwi interacting RNA)= found in nucleus and cytoplasm, suppresses transcription of transposable elements in reproductive cells 6. lncRNA ( long noncoding RNA)= in nucleus and cytoplasm, has variety of functions ** OVERALL ALL THESE RNAS DO NOT ENCODE PROTEIN ARE JUST FUNCTIONAL AS RNAS THEMSELVES

in bacteria... there are 2 ways transcription can end and is it based on the presence of a special protein. explain

RHO-dependent terminators= - a protein called RHO can bind to RNA being synthesizd and follow the RNA polymerase in 5 to 3'. as RHO catches up, a secondary structure of the RNA can form. rna hits a sequence that causes it so slow/pause, so rho can catch up. when rho catches up, it causes RNA polymerase to release RNA and causes RNA to release from DNA RHO- indepedent terminators= - does not include rho, is spontaneous. these terminators have 2 things included in the DNA sequences: first they have inverted repeats. a series of nucleotides repeated in opposite order. because of that, they are complemenatry and form secondary structures, ususually a string of adenines resulting in a string of uracils in the RNA. once rna reaches the inverted repeat, inverted sequences form HAIRPIN shape. so rna is only associating with DNA by uracils ( week h bonds), so rna and rna polymerase release the DNA

describe key features of bacterial transcription: elongation

RNA polymerase progressively unwinds the DNA as it synthesis RNA, making a complement rna copy of template strand - transcription takes place when the strands are separated in the TRANSCRIPTION BUBBLE RNA polymerase adds nucleotides slower than DNA polymerase, so RNA synthesis slower than DNA synthesis ** there are topiomerases that are probably involved to relieve pressure ahead and behind transcription bubble similar to gyrase

what is transcription and what is true about it

TRANSCRIPTION= is the synthesis of an RNA molecule from a DNA template, aka reading a dna strand, and making a complement using RNA nucleotides ** only PARTS of the DNA are transcribed, and usually only a single gene bc not all gene products are needed at the same time... we can access specific genes to repsond to different situations and only make rna copies of parts of the genome, not the whole thing like DNA replication

describe the structure of a tRNA

all tRNAS from a complex seondary structure called a CLOVERLEAF: tRNAS have a very distinctive shape, sequences fold in on each other and are complemenatry so form a hair pin shape 3 charatertics of tRNA essential to their function: 1. 3' acceptor arm where there amino acid attachment site is and is always CCA 2. anticodon= 3 nucleotides that interact with the mRNA to put the correct amino acid on the mRNA 3. rare bases= after tRNA is transcribed, some nucleotides are chemically modified to make different nucleotides, but not normal ones like a g c or t, these rare bases ALLOW CELLS TO TELL DIFF TRNAS APART

is transcription of archae more similar to eukaryotes or prokaryotes

archae have one RNA polymerase ( like eubacteria), but its sequence is more similar to eukaryotic rna polymerases - some archae trnascription factors are more similar to eukaryotes, while others are similar to eubacteria ** OVERALL : more similar to eukaryotes

DESCRIBE the one class of RNA that is found only in prokaryotes

crRNA ( CRISPR RNA)= assists in the destruction of forgein DNA, can destory viruses is almost like an immune system

describe the transcription appartus : eukaryotes

eukaryotes have AT LEAST 3 different RNA polymerases 1. RNA polymerase I= transcribes larger rRNAS 2. RNA polymerase II= transcribed pre-mRNA, some snRNAS, snoRNAS, some miRNAS 3. Rna polymerase III= transcribes tRNAS, small rRNAS, some snRNAS, some miRNAS ** all 3 eukaryotic RNA polymerases are large enzymes with 12+ subunits aka 12 gene products to preform the process - there are accessory proteins called transcription factors that will bind to the core enzyme and affect its function and affect how RNA polymerase works

describe small RNA molecules: RNA interference

fire, mello, collegaues were trying to affect gene expression -expresion of genes could be inhibited by antisense RNA - they realized there was more inhibition resulting from DOUBLE STRANDED RNA - this lead to realzing that small RNAS occur in the genome and regulate gene expression ** these 2 types are small intergeging rna ( siRNA) and micro RNA ( miRNA)

bacterial transcription: describe what happens first

first, RNA polymerase needs to recgonize the location of the promoter and does so based on specific sequences... does so by recognziing speciifc sequences on the DNA called -10 consesus sequence and -35 consesus sequence, which is upstream the transcription start site where the first rna nucleotide will be put down

the transcription appartus : bacteria

in bacteria, 1 RNA polymerase transcribed ALL the RNA in the cell, being termed just RNA polymerase - this core rna polymerase doing all the transcription has 5 subunits, so this one RNA polymerase is built by 5 genes working together - for bacteria, SIGMA FACTOR, is necessary for promoter binding, aka sigma factor is needed for RNA polymerase to bind the promoter and start transcription

in chapter 9 we discussed dna replication.. what are we looking at in chapter 10

in chapter 10 we are looking at how we get the info that is stored in our genome ( dna) out of the genome, and make copies of parts of the genome into RNA

what is required for introm splicing by the spliceosome to occur

intron splicing requires 3 consesus sequences: 1. 5' splice site 2. branch point ( A) 3. 3' splice site ** snRNP proteins will recognize the consesus sequenes and use them as markers for where introns needed to be chopped and join exons

what are some true statements about introns

introns are common in eukaryotes but rare in bacterial genes ( pro) introns vary in size and number all types of RNAS can have introns

how is transcription similar to DNA replication

like DNA replication, transcription occurs 5' to 3', cell reads one strand , so unravelling DNA to create a TRANSCRIPTION BUBBLE, rna is built 5' to 3' , instead of completely unravelling strands of DNA like in DNA replication, is a small unravelling which moves across dna as is, making the rna molecule

what is true about alternative splicing?

mRNA cells processed in different ways result in different cell types ex: having exon 1,2,3,4, makes calcition but 1,2,3,5, 6 makes caliciton gene related peptide

describe mRNA aka messenger mRNA

mRNA encodes for a protein product aka mRNA provides instructions for making a protein - a mature mRNA in both prok and euk have the 3 following structures: 1. 5' untranslated region- this is where the ribosome binds and the start point. this is the FIRST NT of a mature mRNA 2. protein-coding region= has instructions for assembling the amino acid in translation with a start codon 3. 3' untranslated region= which also affects the ability of the ribosome to bind to mRNA and involved in the lifespan of mRNA

what is different about mRNAs in eukaryotes compared to prokaryotes

mRNA molecules are modified after transcription in eukaryotes: 1. there is pre-mRNA processing of the 5' cap= is the only time a nucelotide is added in the backward direction. a guanine is attached backwards 1' to 5' to the 5' end of the mRNA. methyl groups are also added to the guanine and the sugars of 2nd and 3rd nucleotides WHY THIS IS NECESSARY: the 5' cap is necessary for binding the ribosome aka for ribosome to recognize mRNA, increases stability of the mRNA ( making it live longer), and has an influence/signal on removing introns 2. there is pre-mRNA process of the Poly(A) Tail= the poly a tail is added to mRNA and has consesus sequences called POLYADENYLATION SIGNAL which is recognized by proteins that chop part of the 3' end off and cuts nucleotides about 11-30 nucleotides away, these proteins add a string of adenine to the mRNA after transcription. WHY THIS IS NECESSARY: the poly a tail affects stability of the mRNA and facilitates attachment of the ribosome

what is true about eukaryotic genes

many include exons and introns exons=coding regions of gene, end up in final mRNA product introns= intervening noncoding sequences that are removed after transcription. SO ARE TRANSCRIBED THEN REMOVED *** AN MRNA IS NOT COMPLETELY MATURE ENTIRE INTRONS ARE REMOVED, 5' CAP, AND POLY A TAIL

what exactly is a consesus sequence

nucleotides most commonly encounterd at each site... so it is a summary of nucleotides found in that location Y means= either c or t R means= A or G N= means any nucleotide C/G= means c and g are equally common

describe intron splicing

occurs within the spliceosome which is in the nucleus, this spliceosome has 5 small nuclear RNAs and ~ 300 proteins - the snRNAS associated with proteins to form snRNPs ( small ribonucleoprotein particles) that have an RNA componenet and are involved in removing the introns

Describe ribosomal RNA

rRNA= structural and functional part of ribosomes, possibly involved in connection of a.a - have a large and small subunit - they can be present in multiple copies and numbers vary among species - in eukaryotes, rRNA genes are clustered in tandem - in eukaryotes: -one gene encodes 18s, 28s, 5.8 rRNAS -in bacteria, all 3 rRNAS coded by one gene

what is true about the -10 and -35 consesus sequences in the bacterial promoters

rna polymerase is gonna bind to the promoter, and the promoter has these specific consesus sequences that are recognized by rna polymerase.... these consesus sequences determine the location of transcription start site and WHICH strand is being transcribed ** shifting the -10 and -35 consesus sequences also shifts transcription start site, and you get a longer RNA molecule

explain the differenes of the structure of RNA compared to the structure of DNA

similarities: RNA is chemically similar to DNA in the way RNA is a chain of nucleotides joined by phosphodiester linkages differences: rna has a ribose 2'OH sugar instead of a 2'H deoxyribose like dna, rna has uracils instead of thymine, rna also tends to be single stranded, but when it does form double strands, it can form complex structures and the nucleotides within the one strand pair up with itself, forming a hari pin like structure **the ability to form these structures is often critical to function of RNAs. DNA HAS STABLILITY, RNA IS EASILY DEGRADED

how is transcription in eukaryotes different from transcription in prokaryotes

some differences for eukaryotes: 1. dna packaging must be relaxed= so rna polymerase can access the DNA and make a copy. have to have modifications of histones 2. dna sequence of eukaryotic promoters differ from bacterial promoters= the consesus sequences in eukaryotic promoters are called TATA BOX 3. prokaryotes have one rna polymerase doing work, eukaryotes have at least 3 different RNA polymerases

what is the substrate for transcription

substrate is rna nucleotides... is synthesized from ribonuclecoside triphosphates= is a free rna nucleotide with 3 phosphates and enzymes chop off 2 phosphates and join the nucleotide to 3'OH of growing RNA nucleotide chain like dna, this joining creates a phosphidester bond

what was once believed about genes

that all genes were co-linear, and although many are, there are some cases where there is extra dna in the gene that is not present in the mRNA. have been experiments done where dna from a virus was shown, and the DNA had extra loops in it that was not present in the mRNA, sugesstes gene had additional sequences ( introns)

Describe alternative splicing

through the phenonema of alternative splicing, ONE GENE CAN PRODUCE MULTIPLE MRNAS. intron removal allows for a gene to be processed in different ways and produce different mRNAS, aka the same pre-mRNA can be spliced more than one way to yield multile mRNAS that are trnalsated into different amino acid sequences ALTERNATIVE SPLICING ALLOWS 1 GENE TO ENCODE MULTIPLE PROTEINS. is dependet on how intrond are removed, and even some exons can be removed

what is true regarding transcription

with transcription, usually only ONE dna strand is transcribd. only 1 DNA strand is used as the template and when there is separation of the double helix, 1 strand is used as the template to make an RNA molecule BUT... different genes may be transcribed in diff directions, which one the template strand is varies for each gene, it just depends which strand has info in it ,, parts of genome can be trnascribed and genes can be going in different directions