Exam 2 Flashcards
What is the function of tRNA?
Transfer RNAs; central to protein synthesis as adaptors between mRNA and amino acids
What is the function of siRNA?
Small interfering RNAs; turn off gene expression by directing the degradation of selective mRNAs and the establishment of compact chromatin structures
What is the function of miRNA?
MicroRNAs; regulate gene expression by blocking translation of mRNAs and cause their degradation
What is the function of piRNA?
Piwi interacting RNAs; bind to piwi-proteins and protect the germ line from transposable elements
The 5’ cap of mRNAs is generated by which enzymes?
Phosphatase, a guanyl transferase, a methyl transferase
RNA is?
Composed of 4 nucleotides connected by a phosphodiester backbone (same as DNA)
RNA is less what than DNA?
Less hydrophobic, less stable than DNA
Uracil can?
Base pair with adenine
What synthesizes RNA from a DNA template?
RNA polymerase
Describe initiation of transcription of a eukaryotic gene by RNA polymerase 2.
Through TBP subunit, TF2D binds TATA box. TF2B is recruited next. RNA polymerase 2 recruited next. Phoshporylation of CTD releases RNA polymerase next
RNA polymerase 2 is an RNA factory involved in?
Transcription of DNA and processing of the mRNA it produces
CTD is key for?
mRNA processing by binding proteins required
mRNA splicing does what?
Removes introns and joins exons
What are two types of splicing error?
Exon skipping and cryptic splice site selection
RNA splicing is performed by the?
Spliceosome
SR proteins do what?
Bind and mark exons
SR proteins contain?
Serine and arginine domains
hnRNPs bind to?
Introns
B thalassemia is what and what causes it?
It is anemia with aberrant hemoglobin synthesis caused by abnormal splicing of the b-globin primary transcript
Some major steps in generating the 3’ end are?
CPSF; a cleavage and polyadenylation specificity factor
CstF; a cleavage stimulation factor
PAP; a poly-A polymerase
Poly-A-binding proteins
What is the role of the RNA polymerase 2 CTD and how does its modification affect the activity of the enzyme?
It serves as a scaffold for mRNA processing by binding the proteins required; it is dephosphorylated before starting transcription again
The purpose of the 5’ cap of mRNAs is to?
Distinguish mRNA from other RNA
What are consequences of errors in splicing?
B thalassemia, cystic fibrosis, Parkinsons, retinitis pigmentosa, cancer
What is translation?
The conversion of the genetic information in mRNA to an amino acid sequence within a protein
What are codons?
Three consecutive nucleotides in mRNA that specify which amino acid should be utilized
What acts as stop codons?
UAA
UAG
UGA
What acts as the start codon?
AUG
Inosine is what?
A non-standard nucleotide that makes codon base pairing more flexible if it is pairing in the wobble position
What is a ribosome?
A large protein/RNA complex containing 2/3 rRNA
What do eukaryotic initiation factors (elFs) do?
Assess mRNA quality
What does the Kozak sequence do?
Helps the small subunit correctly identify the start codon
What does elF4G do?
Binds to the 5’ cap and polyA binding proteins
What do proteins called release factors do?
They bind the A site thus releasing COOH the completed polypeptide chain and then dissassembly of the ribosome
What is a polyribosome?
Multiple ribosomes actively translating a single mRNA
Exon junction complexes (EJCs) do what?
Mark successful splicing events
Upf proteins do what?
Bind to EJCs and target defective mRNAs for degradation
Chaperones including the heat shock proteins do what?
Help to guide protein folding
HSP70 proteins do what?
They fold new proteins
What is a proteasome?
An ATP dependent protease in the cytosol and nucleus that digests proteins down into fragments
What are two ways of inducing protein degradation?
Ubiquitin ligases or degradation signals
Degrons do what?
Stimulate polyubiquination of proteins which targets it for proteasomal degradation
Helps to position the RNA polymerase correctly at the promoter, to aid in pulling apart the two strands of DNA to allow transcription to begin, and to release RNA polymerase from the promoter into the elongation mode once transcription has begun.
General transcription factor
Small RNA molecules that are complexed with proteins to form the ribo-nucleoprotein particles involved in RNA splicing.
snRNA (small nuclear RNA)
Nucleotide sequence in DNA to which RNA polymerase binds to begin transcription.
Promoter
A large protein complex containing multiple 3’ to 5’ RNA exonucleases that degrade improperly processed mRNAs, introns, and other RNA debris retained in the nucleus
Exosome
The enzyme that carries out transcription.
RNA polymerase
RNA molecule that specifies the amino acid sequence of a protein.
mRNA (messenger RNA)
Process in which intron sequences are excised from RNA transcripts in the nucleus during the formation of messenger and other RNAs.
RNA splicing
Signal in bacterial DNA that halts transcription
Terminator
Segment of a eukaryotic gene consisting of a sequence of nucleotides that will be represented in mRNA or other functional RNAs.
Exon
Large multiprotein structure forming a channel through the nuclear envelope that allows selected molecules to move between nucleus and cytoplasm.
Nuclear pore complex
Large protein complex in the cytosol and nucleus with proteolytic activity that is responsible for degrading the proteins marked for destruction.
Proteasome
Set of rules specifying the correspondence between nucleotide triplets in DNA or RNA and amino acids in proteins
Genetic code
Special tRNA that carries methionine and is used to begin translation
Initiator tRNA
Sequence of three nucleotides in a tRNA that is complementary to a three nucleotide sequence in an mRNA molecule
Anticodon
RNA molecule with catalytic activity
Ribozyme
Surveillance system in eukaryotes that eliminates defective mRNAs before they can be translated into protein.
Nonsense mediated mRNA decay
The three-nucleotide phase in which nucleotides in an mRNA are translated into amino acids in a protein.
Reading frame
Enzyme that attaches the correct amino acid to a tRNA molecule to form the activated intermediate used in protein synthesis.
Aminoacyl-tRNA synthetase
Protein that helps other proteins fold correctly.
Molecular chaperone
Regulates which RNAs are exported from the nucleus
RNA transport control
Regulates when and how often a given gene sequence is made into RNA
Transcriptional control
Regulates which mRNA molecules are selectively destabilized in the cytoplasm
mRNA degradation control
Regulates which mRNAs are selected to be used for protein synthesis by ribosomes
Translational control
Regulates the splicing and modification of RNA transcripts
RNA processing control
Nucleotide sequence in DNA to which RNA polymerase binds to begin transcription
Promoter
The whole expanse of DNA involved in regulating and initiating transcription of a gene
Gene control region
The segment of DNA that is transcribed into RNA
Gene
Cell derived from a fibroblast, by artificial expression of specific transcription regulators, that looks and behaves like an embryonic stem cell
Induced pluripotent stem cell
The property that allows a proliferating cell to maintain its identity through subsequent cell divisions
Cell memory
Antibody secreted by a hybridoma cell line
Monoclonal antibody
Cell line used in the production of monoclonal antibodies; obtained by fusing antibody secreting B cells with cells of a lymphocyte tumor
Hybridoma
General term for purification technique in which a mixture of proteins is passed through a cylinder containing a porous solid matrix
Column chromatography
Type of chromatography that uses columns packed with special chromatography resins composed of tiny spheres that attain a high degree of resolution, even at very fast flow rates
High performance liquid chromatography
Artificial product generated by linking the coding sequences for two different proteins, or protein segments, and expressing the hybrid gene in cells
Fusion protein
Technique for protein separation in which the protein mixture is run first in one direction and then in a direction at right angles to the first
Two dimensional gel electrophoresis
Technique in which a protein mixture is separated by running it through a gel containing a detergent that binds to and unfolds the proteins
SDS polyacrylamide-gel electrophoresis
The main technique that has been used to discover the three dimensional structure of molecules, including proteins, at atomic resolution
X-ray crystallography
Technique by which proteins are separated by electrophoresis, immobilized on a paper sheet, and then analyzed, usually by means of a labeled antibody
Western blotting (immunoblotting)
Fluorescent protein (from a jellyfish) that is widely used as a marker for monitoring the movements of proteins in living cells
Green fluorescent protein
The minimal separation between two objects at which they appear distinct
Limit of resolution
The normal light microscope in which the image is obtained by simple transmission of light through the object being viewed
Bright field microscope
Computer treatment of images gained from microscopy that reveals information not immediately visible to the eye
Image processing
Similar to a light microscope but the illuminating light is passed through one set of filters before the specimen, to select those wavelengths that excite the dye, and through another set of filters before it reaches the eye, to select only those wavelengths emitted when the dye fluoresces
Fluorescence microscope
Type of light microscope that produces a clear image of a given plane within a solid object. It uses a laser beam as a pinpoint source of illumination and scans across the plane to produce a two dimensional optical section
Confocal microscope
Technique for monitoring the closeness of two fluorescently labeled molecules in cells
Fluorescence resonance energy transfer
Piece of fine glass tubing, pulled to an even finer tip, that is used to inject electric current into cells
Microelectrode
