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transcription
RNA synthesis; the nucleotide sequence (DNA language) is transcribed into the nucleotide sequence of an RNA molecule
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translation
protein synthesis; nucleotide sequence of RNA (& DNA) is translated into amino acid sequence language of proteins
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the 5' end of a nucleic acid sequence has:
a hydroxyl or phosphate group on the 5' carbon of its terminal sugar;
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the 3' end of a nucleic acid sequence has:
a hydroxyl group attached to the 3' carbon of its terminal sugar
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nucleic acid strand directionality
synthesis proceeds from 5' to 3' (as in new bases are ADDED to the 3' end) so sequences are usually read from 5' to 3'
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phosphoanhydride bonds
A type of high-energy bond formed between two phosphate groups, such as the γ and β phosphates and the β and α phosphates in ATP; used to drive reactions inside the cell
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phosphodiester bonds
the chemical linkage between adjacent nucleotides; actually consist of two phosphoester bonds, one on the 5' side's phosphate and the other on the 3' side's OH group
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A = T
C is triple hydrogen bonded to G
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B form of DNA
stacked bases are .34 nm apart; and the helix makes a complete turn every 3.4 nm therefore there are about 10.1 base pairs per turn
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A form of DNA
structure of B form changes when most of the water is removed from the double helix; is wider and shorter than the B form and the bases are tilted rather than perpendicular to the helix axis; RNA-DNA and RNA-RNA helices exist in this form in the cell
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Z form of DNA
short DNA molecules composed of alternating purine-pyrimidine nucleotides (especially G's and C's) adopt an alternative left handed helix (instead of the usual right handed one)
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DNA is flexible around it's axis:
unlike in proteins, there are no hydrogen bonds parallel to the axis of the DNA helix; this property lets the DNA bend when complexed with a DNA binding protein; this is critical for when it is packed within chromatin
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why is DNA not RNA the genetic information carrier?
because the Hydrogen at the 2' position of the deoxyribose makes it much more stable than the -OH (hydroxyl group) at the 2' position of the ribose; the -OH at the 2' end of an RNA's ribose catalyzes the hydrolysis of phosphodiester bonds at a neutral pH
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hyperchromicity
am abrupt increase in UV light absorption due to stacked base pairs in duplex DNA being denatured into unstacked bases in a single-stranded DNA
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nucleic acid hybridization
technique used to study the relatedness of two DNA strands & to detect and isolate specific DNA molecules in a mixture containing many different DNA sequences
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when part of the DNA helix becomes underwound, the remainder of the helix becomes:
overwound; supercoils are what form
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topoisomerase I/topoisomerase II
- -I is an enzyme that relieves torsional stress that develops in cellular DNA as a result of replication or any other processes; it does so by breaking a phosphodiester bond in one strand (a one-strand break = a nick); I also ligates the strand back together
- -II makes nicks in both strands of double stranded DNA and can then religate them
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secondary structures in RNA
formed by pairing of complementary bases within a linear sequence
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'hairpins'
formed by pairing of bases within 5-10 nucleotides
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stemloops
pairing of bases that are separated by more than 10 to several hundred nucelotides; these folds can cooperate to form more complicated tertiary structures, one of which is called a pseudoknot
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ribozymes (ribonucleic acid enzyme)
an RNA molecule with a tertiary structure that enables it to catalyze a chemical reaction; many catalyze either the hydrolysis of one of their own phosphodiester bonds (self-cleaving ribozymes), or the hydrolysis of bonds in other RNAs; ex. hammerhead ribozyme, and hairpin ribozyme
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pyrophosphatase
makes chain elongation the state of equilibrium; it catalzes cleavage of the reased PPi into two molecules of inorganic phosphate; acid anhydride hydrolases (enzymes that catalyze the hydrolysis of a acid anhydride bond) that act upon diphosphate bonds
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RNA polymerase
joins rNTPs (ribonucleoside triphosphates) that have base paired complementarily to a template DNA strand; involves a nucleophilic attack by 3' oxygen on the RNA strand to the α phosphate of the next nucleotide base being added; results in a release of pyrophosphate and the formation of a phosphodiester bond
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+1
the site on the DNA where RNA polymerase beings transcription; downstream is the direction in which the RNA is transcribed (denoted by positive or higher numbers); upstream = the opposite direction (denoted by negative or lower numbers)
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RNA polymerase
an enzyme that produces RNA from DNA in a process called transcription; nucleotidyl transferase that polymerizes ribonucleotides at the 3' end of an RNA transcript
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RNA synthesis occurs at about ____ nucleotides per minute
1000! (At 37 degrees celcius)
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bacterial RNA polymerase
composed of two large subunits (β' and β), two copies of smaller subunits (α) and one copy of a 5th subunit (ω) useful for stabilization and assembly of subunits
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(bond) dipole moment
measures the polarity of a chemical bond within a molecule; the product of magnitude of charge & distance of separation between the charges
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TATA-binding protein (TBP)
a transcription factor that binds specifically to a DNA sequence called the TATA box; TATA box is found about 35 base pairs upstream of transcription start site in some eukaryotic promoters; TBP (+ associated factors) make up a general transcription factor that in turn makes up part of the RNA polymerase II preinitiation complex; helps position RNA polymerase II over the transcription start site of the gene
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CTD
c-terminal domain; distinguishes RNA polymerase II from every other type of RNA sequence
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What are the differences between RNA I, II, and III?
-RNA pol I: the only enzyme that transcribes ribosomal RNA, a type of RNA that accounts for over 50% of the total RNA synthesized in a cell; important for PROTEIN SYNTHESIS
-RNA pol II: enzyme found in eukaryotic cells that catalyzes the transcription of DNA to synthesize precursors of mRNA (& most snRNA and microRNA); important for PROTEIN ENCODING, RNA SPLICING, POST-TRANSCRIPTIONAL GENE CONTROL
- -RNA pol III: genes transcribed by RNA Pol III fall in the category of "housekeeping" genes whose expression is required in all cells/most
- environments; transcribes genes that encode small RNAs that are themselves functional (ex: tRNA); [the regulation of Pol III transcription is primarily tied to the regulation of cell growth and the cell cycle, thus requiring fewer regulatory proteins than RNA polymerase I]; important for PROTEIN SYNTHESIS, RNA SPLICING, MANY FUNCTIONS UNKNOWN, SIGNAL RECOGNITION!
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gene
a unit of DNA that contains the information to specify synthesis of a single polypeptide chain or functional RNA
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genome
the entire complement of DNA of an organism (i.e., all the DNA contained in one cell of an organism)
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Operon v. Eukaryotic DNA
-trp operon contains proteins which are all needed for cells to create tryptophan (for example); probable explanation for why genes are organized in operons like this/next to each other because if the cell is deciding to make tryptophan it’s going to need all 5 proteins; you get the same number of proteins and the cell gets them all at the same time; coordinate expression
-eukaryotes lack operons; each gene has to be turned off and on independently
-(other important difference between pro and eukaryotes = RNA processing; in between transcription and mature mRNA is RNA processing; in prokaryotes most processing happens as transcription is still taking place)
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operon
a functioning unit of genomic DNA containing a cluster of genes controlled by a single promoter; the genes are transcribed together into an mRNA strand; genes contained in the operon are either expressed together or not at all
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exon
nucleic acid sequence that is represented in the mature form of an RNA molecule either after introns have been removed by cis-splicing or when two or more precursor RNA molecules have been ligated by trans-splicing
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introns
any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene
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why can't transcription and translation happen at the same time in eukaryotic cells?
Because transcription/processing occurs inside the nucleus and then the mRNA is transported into the cytoplasm for translation; all happens simultaneously in prokaryotes
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RNA splicing
the internal cleavage of a transcript to excise introns, followed by ligation of the coding exons
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UTR (untranslated regions)
present in the 5' and 3' ends of funcitonal mRNAs; UTRs are longer in eukaryotes, and longer at the 3' end of function mRNAs
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Functions of the 5’ cap (3)
- •protects the mRNA from enzymatic degradation •assists in export of mRNA to the cytoplasm
- •bound by a protein factor required to initiate translation in the cytoplasm
(hehehehe 7-methylguanylate)
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there are 5 nucleotides that define an intron:
- -all of these factors are called a consensus sequence
- 1) GU at the beginning of intron
- 2) AG at the end
- 3) branch point: an A somewhere in between those; not required just happens to be there
- *95% of the time the base after the beginning GU
- is a G or A
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Do I have to know the figure on page 330?
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spliceosome
a large ribonuclear protein complex (composed of 5 snRNPs + other proteins that attach to the pre-mRNA) that removes introns from a transcribed pre-mRNA segment
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The Deal with Fibronectin:
- -good example of alternative splicing
- -function: long adhesive protein secreted into extracellular space that binds proteins together
- -what and where it binds depends on which exons are spliced together
- -if certain domains are coded for, fibronectin binds to fibrin causing blood clots
- -if certain domains are not coded for, it doesn't act as a proponent of blood clots
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mRNA (messenger RNA)
carries genetic information transcribed from DNA in a linear form; it is read in sets of 3 nucleotide sequences, called codons, each of which specifies a SPECIFIC amino acid
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tRNA (transfer RNA)
deciphers the codons in mRNA; each amino acid (building block of proteins) has its own tRNA, which bind the amino acid and carry it to growing end of polypeptide chain; each tRNA has a 3-nucleotide sequence (ANTI-CODON) that base pairs to complementary mRNA codon
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rRNA (ribosomal RNA)
form ribosomes by associating with a set of proteins; ribosomes move along an mRNA molecule to catalyze the formation of polypeptides from amino acids
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aminoacyl-tRNA
when a tRNA becomes chemically linked to a particular amino acid via a high-energy ester bond
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in animal and plants cells 50-100 tRNAs have been identified:
- significance = the number of tRNAs used is greater than
- a) the number of amino acids that compose proteins (20)
- b) the number of amino acid codons in the genetic code (61)
-if perfect watson/crick pairing existed between codons and tRNA's anticodons then there would need to be 61 tRNAs...but there aren't: this is because multiple tRNAs can recognize a single codon corresponding to an amino acid
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wobble position
the 3rd (3') base in an mRNA codon and the 1st (5') base in it's tRNA anticodon; pairing will shift and be flexible
·sequences ending in U & C, and A & G (respectively) tend to code for the same amino acids
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