• Shuffle
    Toggle On
    Toggle Off
  • Alphabetize
    Toggle On
    Toggle Off
  • Front First
    Toggle On
    Toggle Off
  • Both Sides
    Toggle On
    Toggle Off
  • Read
    Toggle On
    Toggle Off
Reading...
Front

Card Range To Study

through

image

Play button

image

Play button

image

Progress

1/41

Click to flip

Use LEFT and RIGHT arrow keys to navigate between flashcards;

Use UP and DOWN arrow keys to flip the card;

H to show hint;

A reads text to speech;

41 Cards in this Set

  • Front
  • Back
What are the main steps in transcription?
1. initiation
2. Elongation
3. Termination
What direction is RNA synthesized?
5'-->3'
What direction is DNA copied?
3'-->5'
Compare the difference in types of RNA polymerases in prokaryotes and eukaryotes.
Prokaryotes only have 1 RNA polymerase while eukaryotes have 4 types of RNA polymerases: RNA polymerase I (45 S pre-rRNA transcript), RNA polymerase II(mRNA,miRNA,snRNA) RNA polymerase III(tRNA, 5 S rRNA), and mitochondrial polymerase. All are located in the nucleus except mitochondrial RNA polymerase
Describe the subunit composition of prokaryotic RNA polymerase.
1. 2 alpha
2. 1 beta = grasp DNA template and phosphodiester bond formation
3. 1 beta ' = grasp DNA template
4. 1 sigma= promotor recognition and initiation site
What is the difference between core enzyme and holoenzyme in prokaryotes?
The core enzymes of prokaryotes have 2 alpha, 2 beta subunits. It becomes the holoenzyme when sigma binds which has the recognition and initiation sequence
What is the promotor in prokaryotes?
It is the DNA sequence in the template strand to which RNA polymerase binds to. Prokaryotes have 2 consensus sequences that are upstream to the start site of transcription
Describe the initiation of transcription in prokaryotes.
RNA polymerase binds to the DNA and moves along the strand until it comes to the promotor region of the consensus strand. The sigma unit binds to the consensus strand and undergoes helicase activity to unwind the DNA strand to expose the base pairs. It knows now to start transcription. The first phosphodiester bond is formed and the sigma subunit releases from RNA polymerase.
How many base pairs of DNA does RNA polymerase unwind around the initiation site in prokaryotes?
17 base pairs
Describe the promotor specificity
There are specific sigma subunits that bind to specific promotor consensus sequences in DNA
Describe the elongation step in prokaryotes.
The core RNA polymerase generates the transcription bubble and moves towards the 5'end of DNA.
What is the RNA/DNA duplex in prokaryotes?
A region in the transcription bubble where DNA and RNA are connected which is 12 base pairs long
What is the role of Topoisomerases in prokaryotes?
The transcription bubble causes straining overwinding in DNA so Gyrase (topoisomerase II) creates negative supercoils ahead of the bubble to compensate the positive supercoil formations. Type I relaxes the negative supercoils behind the transcription bubble
Describe 2 methods of termination of transcription in prokaryotes.
1. Template-directed termination: In the DNA sequence there is a region very rich in G and C which can cause the newly synthesized RNA to form a hairpin. Following the GC sequence in DNA is a region of U. The torsion of the hairpin disrupts association between the polymerase and DNA
2. Rho Protein= Binds to RNA sequences and has helicase activity so dissociates RNA from DNA template
Describe the 4 components of RNA polymerase in eukaryotes.
Parts of the holoenzyme:

1. Core RNA polymerase: main enzyme consisting of multiple subunits
2. General Transcription Factors: proteins required for transcription
3. Specific transcription factors: differ depending on the gene
4. Mediator protein: facilitate interaction between components of the holoenzyme.
What is the difference between cis-acting elements and trans-acting factors?
Cis-acting elements are the specific genes on the DNA template while trans-acting factors are outside proteins that bind to the DNA strand
Differentiate between the closed and open promotor complex.
The Closed promotor region is when sigma binds to the promotor sequence and the open promotor complex is when the sigma releases from the promotor sequence when initiation is over and elongation can commence.
Describe the structure and function of RNA polymerase I
Function: transcribes rRNA genes to generate 45 S pre-rRNA in the nucleolus which is processed into 18 S, 28 S, and 5.8 S rRNA
Components:
1. Core Polymerase I: multimeric enzyme of 10-12 subunits
2. General transcription factors: (selective factor I) 1 TATA-binding protein and 3 TBP associated factors
3. Specific transcription factors
Describe rRNA genes in humans.
Diploid cells contain 400 rRNA in tandem repeats on 5 different chromosomes. each rRNA gene is separated by nontranscriber spacer DNA (where the core promotor for rRNA is located)
Describe the structure and function of RNA polymerase II.
Function: transcribes mRNA genes, miRNA genes, and snRNA genes in the nucleus
Structure:
1.Core polymerase: multimeric enzyme consisting of 12 subunits
2. General Transcription Factors: includes TFIID and TFIIH
3. Specific transcription factors: have activator, deactivator, coactivator and codeactivator proteins
4. Mediator: interacts with the c terminus domain of RNA polymerase II
What sequence elements does the core promotor have?
1. Transcription start site (+1)
2. TATA Box (TATA(A/T)A)= consensus cis-acting sequence upstream of transcription start site
3. Initiator sequence (Ins)= short sequence in the transcription start site
4. TFIIB recognition elements (BRE)= consensus sequence upstream of transcription start site
What role does TFIID have?
It is general transcription factors that direct recruitment of RNA polymerase II (TBP associated factors) to the TATA box (TATA-Binding protein) in the core promotor.
What role does TFIIH have?
It is a general transcription factor that have helicase activitiy and unwinds DNA in the promotor region and phosphorylates the C terminus of the Core RNA polymerase II
What does polymerase III synthesis?
Transcribes genes for tRNA, 5 S rRNA, and U6 snRNA in the nucleus
Specify the major components of the Lac operon and describe the their corresponding functions in the controlling transcription.
1. regulator gene: codes for repressor or activator protein
2. operator: DNA regulatory sequence of the operon
3. operon: set of coordinately regulated target genes
4. inducer: nutrient or metabolite like lactose
The presence of lactose induces the transcription of galactosidase genes. What happens when no lactose is present? When glucose is present?
When lactase is not present, Transcription of the operon is repressed because the binding of RNA polymerase to the promotor region is blocked by the binding of a repressor protein to the operator. Glucose causes glucose repression and doesn't allow transcription because it reduces cAMP
The presence of lactose induces the transcription of galactosidase genes.What happens when lactase is present?
When lactose is present, it binds to the repressor protein so the repressor can't bind to the operator. Low glucose causes activation of Adenylyl Cyclase to make cAMP. cAMP binds to CAP which both bind to the consensus sequence near the promotor region. Cap allows binding of RNA polymerase holoenzyme to the promoter of the Lac operon
What are the main types of cis-elements in a eukaryotic gene and explain how they function in regulating transcription.
Transcription by RNA polymerase II is regulated by:
1. Core promotor: Contains the TATA box
2. Proximal promotor elements: 300bp upstream that function of activators or repressors
3. enhancers: activate transcription independent of location from promotor
4. silencers= repress transcription independent of location from promotor
5. insulators=binding sites for proteins that block interaction with enhancers or repressors
What are the main type of trans-activating factor in a eukaryotic gene and explain how they function in regulating transcription?
They bind to cis-acting sequences of the target gene to either:
1. general transcription factors like TFIID and TFIIH recruit RNA polymerase II to the promotor genes
2. Specific transcription factors: proteins that regulate transcription of specific target genes by modifying the activity of the RNA polymerase II holoenzyme by either having a transactivation domain or a transrepression domain
3. repressor protein competes with an activating protein for the cis-elements
4. prepressor protein binds to the specific transcription factor and prevents it from activation transcription
(combined actions of multiple factors can happen at once)
Name the 2 classes of specific transcription factors.
1. Leucin zipper family
2. zinc finger family
What are the domains and functions of leucine zippers?
1. leucine zipper = holds the dimer protein together, which the DNA strand between each subunit
2.Basic amino acid = lots of + charge AA (K, R) which binds to the consensus sequences in cis-acting elements
3.transactivation/transrepression= interacts with other proteins in the RNA plymerase II holoenzyme complex
What are the domains and functions of zinc finger?
1. hormone binding and dimerization= steroid hormone binds to hormone receptor which activates the receptor which forms a dimer
2. zinc finger= DNA binding domain of alpha helix and 2 beta sheets that binds directly to cis-acting elements in steroid-responsive genes
3. Transactivation= interacts with RNA polymerase II holoenzyme complex
How does methylation of cis elements silence transcription of a gene and what is an example of methylation?
ex)5-methlycytosine

Methylation of cis-acting elements in the promotor region of a gene decrease or silences transcription by inhibiting binding of activator proteins, promote recruitment of repressor proteins,
What is the sequence for methylation of DNA?
5'-->CpG--3'
What are CpG islands?
high frequency of CpG sequences in parts of the genome which regulatory sequences of genes are found. This is significant because methylation inhibits transcription
When DNA is replicated, is methylated DNA present in the daughter stands if present in the paternal gametes?
Yes
How can covalent modifications of histones such as actetylation affect transcription?
Acetylation by Histone acetyltransferas (HAT) causes K to lose its charge and become loosed around the histone which can increase gene activation. But deacetylation by histone deacetyltransferases (HDAC) causes transcriptional repression
Give 2 examples of antibiotics that inhibit transcription.
1. actinomycin D: blocks RNA polymerase from copying DNA
2. Rifampicin (rifamycin): prevents the 1st phosphodiester bond from forming by RNA polymerase
What is alpha-amanitin?
Toxin produced by mushrooms that binds to RNA polymerase II that inhibits elongation
How can you detect hypersensitive sites in DNA?
The sites have more DNase I digestion which produces small fragments of nucleosomes because the euchromatin is stretched out more.
What do remodeling factors in chromatin do?
stretch the strand out which affects accessibility to transcription factors.