Chapter 4

RNA synthesis; the nucleotide sequence (DNA language) is transcribed into the nucleotide sequence of an RNA molecule

protein synthesis; nucleotide sequence of RNA (& DNA) is translated into amino acid sequence language of proteins

a hydroxyl or phosphate group on the 5' carbon of its terminal sugar;

a hydroxyl group attached to the 3' carbon of its terminal sugar

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'

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

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

C is triple hydrogen bonded to G

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

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

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)

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

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

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

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

overwound; supercoils are what form

• -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

formed by pairing of complementary bases within a linear sequence

formed by pairing of bases within 5-10 nucleotides

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

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

makes chain elongation the state of equilibrium; it catalzes cleavage of the reased PP_i into two molecules of inorganic phosphate; acid anhydride hydrolases (enzymes that catalyze the hydrolysis of a acid anhydride bond) that act upon diphosphate bonds

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

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)

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

1000! (At 37 degrees celcius)

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

measures the polarity of a chemical bond within a molecule; the product of magnitude of charge & distance of separation between the charges

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

c-terminal domain; distinguishes RNA polymerase II from every other type of RNA sequence

-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!

a unit of DNA that contains the information to specify synthesis of a single polypeptide chain or functional RNA

the entire complement of DNA of an organism (i.e., all the DNA contained in one cell of an organism)

-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)

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

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

any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene

Because transcription/processing occurs inside the nucleus and then the mRNA is transported into the cytoplasm for translation; all happens simultaneously in prokaryotes

the internal cleavage of a transcript to excise introns, followed by ligation of the coding exons

present in the 5' and 3' ends of funcitonal mRNAs; UTRs are longer in eukaryotes, and longer at the 3' end of function mRNAs

• •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)

• -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

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

• -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

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

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

form ribosomes by associating with a set of proteins; ribosomes move along an mRNA molecule to catalyze the formation of polypeptides from amino acids

when a tRNA becomes chemically linked to a particular amino acid via a high-energy ester bond

• 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

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