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114 Cards in this Set
- Front
- Back
Genes that encode proteins necessary for an organism to adapt to a change in environment.
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Inducible Genes
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Genes that encode for proteins that cells need in a day to day fashion.
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Constitutive Genes
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Regulation of constitutive genes in prokaryotes depends on what?
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Number of sigma subunits and their affinity for the promoter region.
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In eukaryotes the GC box identifies the gene as what?
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Constitutive Gene
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Regulation of inducible genes depends on what? (3)
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Protein Factors
Small Molecule Factors Operator Sites |
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Protein Factors
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Activators
Repressors |
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Small Molecule Factors
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Inducers (co-activators)
Co-repressors |
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Operator Sites
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Enhancers
Silencers |
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Which protein factors binds to enhancer operator site?
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Activators
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Which protein factor binds to silencer operator site?
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Repressors
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When a gene is normally under negative regulation; this means
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Transcription of the gene is normally inhibited
Repressor protein is bound to silencer site |
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True or False
Repressor proteins and silencer sites are upstream from the promoter. |
False
downstream |
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Repressor proteins physically block ________. Preventing transcription.
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RNA Polymerase
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Signal molecule that binds to repressor stimulating transcription.
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Inducer
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Describe negative regulation mechanism.
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Co-repressor binds repressor.
Repressor binds silencer site. |
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Gene has to be transcribed very rapidly in order to meet normal conditions.
_________ Regulation |
Positive Regulation
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Protein from a gene that is normally under positive regulation is no longer needed. Mechanism?
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Co-repressor binds activator.
Activator dissociates from enhancer site. |
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Enhancer sites are located
___ stream from the promoter region. |
Upstream
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Activators can affect transcription by: (2)
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Altering the conformation of DNA in the promoter region
Interacting with RNA Pol altering its conformation. - higher affinity |
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Gene is not normally regulated.
External condition needs it to transcribe. Mechanism |
Inducer binds activator.
Activator binds enhancer site. |
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The lac operon encodes polycistronic DNA for three enzymes:
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Beta Galactosidase
Galactoside Permease Thiogalactoside Transacetylase |
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The lac operon is normally under ______ control.
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negative control
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Permits the uptake of galactose into the bacteria.
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Galactoside Permease
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What role does beta galactosidase play inside bacteria?
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Breaks down lactose into glucose and galactose
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What is the name of the side product formed during the break down of lactose.
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Allolactose
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What function does the I gene serve?
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Transcription of the lac repressor
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When the lac repressor is synthesized it binds to its silencer sites:
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O1
O1O2 O1O3 |
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The lac operon is a ______ protein, meaning it has 4 subunits.
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tetrameric
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O1 is found ______ stream from promoter
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downstream
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How does the lac repressor stop transcription?
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Forms a loop in the DNA downstream of RNA Pol, physically blocking
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Bacterial DNA binding proteins utilize ________ motifs.
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Helix-turn-Helix
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Bases in the major groove of DNA bind to the helix-turn-helix motifs via:
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Hydrogen bonding
Hydrophobicity |
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The lac repressor binds to DNA via the law of ____ ______. Therefore there will always be a time when it is unbound.
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mass action
in equilibrium |
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What is the function of allolactose?
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Inducer that acts to dissociate the lac repressor from its silencer site.
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______ inducer = 1,6- Allolactose
______ inducer = IPTG |
Primary
Synthetic |
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What is the proposed function of Thiogalatoside Transacetylase?
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Thought to start synthesizing a secondary inducer to stimulate transcription.
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Describe why transcription of the lac operon is slow immediately following a decrease in glucose?
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RNA Pol has low affinity for the promoter region until it adapts using cyclic amp to induce CRP to bind the enhacer site upstream of the promoter.
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CRP is also known as ?
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CAP
Catabolite Gene Activator Protein |
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RNA Pol is bound to the promoter region, CRP protein is bound to enhacer site, but lac repressor is bound to silencer site. Control?
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Positive and Negative
If repressor leaves - rapid transcription |
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Transcriptional attenuation occurs in the ___ operon.
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trp Operon
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trp operon encodes __ proteins that combine to subunits to give all of the enzymes necessary to synthesize ______
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5
Tryptophan |
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What happens when tryptophan is in high concentration?
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Acts as a co-repressor to the trp repressor allowing it to bind to the silencer site.
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The trp operon is regulated by varying levels of tryptophan in the cell by ______ _______
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transcription attenuation
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What is found in the trp operon?
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trpE
Start codon AUG Leader Peptide mRNA Stop Codon UAA |
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What is the significance of two codons in the trp operon?
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As mRNA on the leader peptide is converted into protein, depending on concentration of tryptophan in the cell, transcription will continue through entire operon or undergo rho-dependent termination prior to doing so.
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RNAP I transcribes genes for large ______ molecules
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rRNA
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RNAP II transcribes genes for _____ (which encodes proteins)
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mRNA
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RNAP III transcribes genes____, ____ and other small RNA molecules
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tRNA, snRNA
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____carries amino acids to the translation complex and is very stable.
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tRNA
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RNAP II contains ___ ____ ____ ____ ____ ____ called the initiation complex with other
enhancers and mediators. |
TFIID
TFIIE TFIIA TFIIB TFIIH TFIIF |
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The σ subunit used in prokaryotic RNAP is replaced by _____ for inducible genes
(RNAP II = mRNA). |
TFIID
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True or False
RNAP II can recognize the GC box |
False
RNAP I + III |
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Constitutive genes contain _____ boxes that function like prokaryotic promoters.
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GC
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True or False
GTFs are usually required for constitutive genes. |
False
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Inducible genes contain _____ boxes that function like promoters.
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TATA
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GTFs are required for the initiation of transcription of ______ genes.
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Inducible
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The _______ is analogous to the
prokaryotic NusA which binds after the σ subunit leaves. |
The elongator
Accelerates transcription |
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Once RNAP synthesizes an end consensus sequence, an ________ binds to the consensus sequence and
breaks the synthesized RNA into two pieces: |
endonuclease
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What is the purpose of the 5'-end capping and Poly-A tail?
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Protect eukaryotic mRNA from exonucleases, increasing stability over time.
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The _________ adds a chain of adenosines on the 3’ end of the mRNA which
can be removed by exonucleases without changing the structure of the actual mRNA |
Poly-A tail
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___________ prevents nucleases from recognizing the mRNA
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5’-end capping
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Optional step in the protection of mRNA that prevents autohydrolysis involves?
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2'-O-methyltransferase
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4 proteins involved in formation of the 3' Poly-A tail:
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CPSF
Endonuclease PAP PABP |
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_____ are untranslated regions of a gene.
Transcribed but not translated |
Introns
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_____ are translated regions of a gene.
Transcribed and translated. Hold the genetic code for a protein |
Exons
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______ are removed and _____
are spliced together to get the right mRNA to be translated into a functional protein. |
Introns
Exons |
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Small nuclear RNAs bond to proteins form a structure called _________ which associate to form a spliceosome.
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small nuclear ribonucleoproteins
snRNP |
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The actual spliceosome has __
proteins and __ snRNAs. |
45 proteins
5 snRNA's |
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The spliceosome places ______ on the intron near the 5' splice site to form a phosphodiester bond breaking the mRNA.
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adenylate
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The lasso-shaped intron is otherwise known as a ______
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lariat
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The spliceosome makes deliberate errors and through this planned ______ ________
we get many functional variants for one gene. |
alternative splicing
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_______ _________ determines sex in fruit flies.
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Alternative splicing
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Rifamycin B is a natural product and ________ is synthetic
• Both are specific for prokaryotic RNAP and act by preventing RNA ________ downstream of the promoter. |
Rifampicin
elongation |
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What is the function of aminoacyl-tRNA synthetases?
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Generate charged tRNA
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A ________ mutation is usually mediated by a single base substitution in the anticodon of a tRNA.
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Nonsense
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________ means that more than one codon can specify the same amino acid.
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Degenerate
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________ contain several different proteases that degrade proteins.
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Proteasomes
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Which nucleotide found in the wobble position could lead to a non-functional or incorrect protein?
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Inosine
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In bacteria, the peptidyl transferase activity that catalyzes peptide bond formation is found in
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23S ribosomal RNA
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The _____________ sequence is a translation initiation signal in bacteria mRNAs that guides the __S ribosome to the initiating (5′) AUG of the mRNA
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Shine-Dalgarno
30S |
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EF-G can bind the A site of the ribosome because its structure resembles
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EF-Tu / tRNA complex
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Upon termination of polypeptide synthesis the ribosome dissociates into
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30S + 50S subunits
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True or False
Translation and transcription are coupled only in prokaryotes |
True
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Proofreading occurs in the __ ____ of the ribosome.
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A site
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True or False
Transcriptional attenuation is common to prokayotes and eukaryotes. |
False
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Antineoplastics such as Actinomycin D are __________ agents.
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Intercalating
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_______ alter the conformation of RNAP II preventing it from moving along the template.
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Toxins
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The sequences of nucleotides that identify the positions of amino acids in the primary
structure of a protein are known as the |
genetic code.
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AUG =
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Start
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UAA
UAG UGA |
Stop Codons
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Stop and look over the structure of tRNA.
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Okay
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______ _____ is an enzyme that covalently attaches an amino acid to
its corresponding tRNA molecule • Creates ________ ____ |
Aminoacyl-tRNA synthetase
aminoacyl tRNA |
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The 3’ end of tRNA has a highly conserved sequence of
nucleotides: |
ACC
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True or False
Each amino acid has its own aminoacyl synthetase |
True
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There are __ amino acids
There are __ codons There are __ tRNAs (some tRNAs bind >1 codon) |
20
61 32 |
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_______ is often found at
the 5’ wobble position • I can form H bonds with A, C, or U |
• Inosinate
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Ribosomes are composed of both _____ and _____.
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rRNA
Protein |
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____ rRNA (establishes the reading
frame in prokaryotic translation) |
16S
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____ rRNA (catalyzes the formation
of the peptide bond) |
23S
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The following histone modifications weaken DNA-histone bond
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• Trimethylation of Lys
• Acetylation of Lys • Phosphorylation of Ser/Thr • Ubiquitination of Lys |
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_________ are sequences of nucleotides in DNA that define the boundaries of
transcriptionally functional DNA – They may act by preventing methylation of key histone residues |
Insulators
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____ methylation is reversible
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DNA
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Methylation of DNA on cytosine by ____ __________ turns off eukaryotic gene expression
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DNA Methyltransferases
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____ ________ is a process in which double-stranded RNA triggers the fragmentation of
complimentary mRNA and thereby prevents gene expression by preventing translation. |
RNA interference
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Similar to the situation in plants,
in eukaryotes a _____ _____ cuts microRNA into short interfering RNA (siRNA) which is still double stranded |
dicer enzyme
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_____ binds siRNA and causes the two strands of the siRNA to separate
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RISC
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Epigenetically RISC promotes DNA _________.
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methylation
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These proteins act as intermediaries between the transcription activators and the GTF-RNAP II complex.
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Co-activator Protein Complexes
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The principle co-activator protein complex is called the _______
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mediator
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Mediator complex binds to ___ domain of RNAP II and stimulates phosphorylation by ____
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CTD
TFIIH |
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True or False
Methylation of DNA is reversible |
True
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Three main classes of regulatory RNA:
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siRNA
miRNA piRNA |
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pri-miRNA is endonucleased by ____ into pre-miRNA which is processed by ______ into miRNA
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Drosha
Dicer |
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Eukaryotic Transcription:
TBP recruits _____ which places active site at +1 start site. Indicates binding for _____. ___ and ___ act as helicase to unwinds DNA, _____ phosphorylates ___ domain of RNAP II which breaks away from promoter then elongator binds. |
TFIIB
RNAP II TFIIH + TFIIE TFIIH CTD |