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PCB 3063

Exam 4

TermDefinition
transformation takes place when a bacterium takes up DNA from the medium in which it is growing, which may lead to recombination between the introduced genes and those of the bacterial chromosome.
transduction takes place when bacterial viruses (bacteriophages) carry DNA from one bacterium to another; the newly introduced DNA may undergo recombination with the bacterial chromosome.
Griffith experiment on in vivo transformation (1927) live virulent cells=dead mouse; live avirulent cells=live mouse; heat killed virulent cells=live mouse; live avirulent cells and heat killed virulent cells=dead mouse
Avery, MacLeod & McCarty in vitro Transformation (1944) experiment showed that DNA is what was transforming the cell; used R and S cells
Hershey & Chase (1952) experiment on phages experiment showed that DNA is the genetic material and not protein
Nucleoside nitrogenous base & sugar
nucleotide nitrogenous base, sugar, and phosphate
pyrimidines one 6-membered rings
purines 5-membered and 6-membered rings attached
stability of DNA is due to hydrogen bonding between the bases and base stacking
B DNA most abundant in nature; right-handed; 10.4 bp/turn
A DNA right-handed; 11 bp/turn; bases tilt
C, D, and E DNA only occur in laboratory settings; D and E DNA lack guanine
Z DNA left-handed, zig zag; 12 bp/turn; occurs GC-rich alternating regions; major groove almost absent
Tm the temperature at which 50% is the DNA unwound or denatured; important to understand when working with primers;
higher GC content = higher Tm
palindrome nucleotides read the same forward and backward on the complimentary and antiparallel strands
DNA electrophoresis run to red (electrode) because DNA backbone is negatively-charged whereas cathode is positively charged; smaller fragments will move further;
positive supercoiling overwound DNA; helps resist denaturing at high temperatures
negative supercoiling underwound DNA; helps with unraveling during DNA replication
heterochromatin highly coiled regions of DNA, normally inactive predominantly located at centromeres and telomeres; inactivated X’s and most of Y; not transcribed, does not replicate and lacks crossovers
euchromatin non-coiled active DNA regions, condense and decondense during cell cycle; are capable of being replicated and transcribed
histones interact with DNA to form nucleosomes; H1 is the linker histone; H2A and H2B form two dimers; H3 and H4 form a tetramer
nucleosomes made up of an octamer of H2A, H2B, H3, and H4; about 147 bp wrapped around the histone; roughly 200 bp between nucleosomes; humans have about 25 million nucleosomes per cell
chromatosome nucleosome plus the linker H1 histone
acetylation addition of acetyl group to + charged amino group of lysine; “opens” chromatin and thus increases gene activity
methylation Methyl added to lysine or arginine; causes low levels of transcription (silencing of genes); possible helpful in cancer diagnosis; methylation may activate certain histones
cytogenetics study of chromosome banding
unique repetitive DNA 50-60% of DNA
satellite DNA short sequences repeated thousands to millions of times
Meselson and Stahl experiment on DNA replication (1958) E. coli first grown on N15 in Generation 0 (G0), then bacteria washed and transferred to the lighter isotope N14 for both Generation 1 (G1) and Generation 2 (G2). Results showed two bands when centrifuged
DNA Poly I removes primer and replaces it with DNA; needs free 3‘-OH
DNA Poly II main proof reading and repair
DNA Poly III main synthesis; elongation (extends DNA from RNA primer); holoenzyme with 10 different parts that needs ATP to assemble
ori C E. coli origin of replication; composed of 245 base pairs of repeated 9mers and 13mers
DNA-A Protein binds to several 9mers, which facilitates binding of DNA-B and DNA-C
DNA-A, -B, and -C are helices and thus require ATP
Primase synthesizes a 5-15 nucleotide RNA called the RNA Primer to allow DNA synthesis to begin
Single stranded binding proteins (SSBs) complex DNA to keeps strands separated
Looping of template for the lagging strand enables a dimeric DNA polymerase III holoenzyme at the replication fork to synthesize both of the daughter strands
DNA Ligase joins Okazaki fragments by sealing nicks in the sugar-phosphate backbone of newly synthesized DNA
In eukaryotes, the origin of replication is ARS (Autonomously replicating sequence); multiple
DNA polymerase alpha 5'->3' polymerase activity but no exonuclease activity; initiation of nuclear DNA synthesis and DNA repair
DNA polymerase delta 5'->3' polymerase and exonuclease activity; lagging-strand synthesis of nuclear DNA, DNA repair, and translesion DNA synthesis
DNA polymerase epsilon 5'->3' polymerase and exonuclease activity; leading strand synthesis
Kinases are involved in the actual activation of the replication signal during S phase
Licensing factors are proteins that stick up in eukaryotes that basically will allow DNA replication forks to open up; must be put down in G1 phase
DNA; codons; anticodons; DNA is the code; Codons are on the mRNA; Anticodons are on the tRNA
template strand Is the 3'->5' side of the DNA; strand used as the template for transcription of mRNA, which is synthesized in the 5'->3' direction
promoter is the control mechanism that determines if you’re allowed to undergo transcription, replication, etc.
codon table quick way to get from mRNA to proteins
Degenerate code A genetic code in which some amino acids may be encoded by more than one codon each. This offers a selective advantage since most single nucleotide alterations will result in some amino acid included in polypeptide.
sickle cell anemia A Single nucleotide alteration resulted in glutamic acid being replaced with valine; leads to a resistance of malaria
coding or "mRNA-like" strand is the 5'->3' strand
+1 on consensus sequence the first base in the RNA transcript
-35 on consensus sequence is where the promoter has to bind so it can get ready for transcription
RNA polymerase III holoenzyme involved in making mRNA; this is a SEPARATE process from DNA transcription, which uses primase
Sigma of RNA polymerase is the reading head, scans promoter so that the RNA polymerase can recognize and bind to promoter regions (TATA boxes)
cis promoter location adjacent on the same DNA strand
trans promoter location across from on the opposite strand
Termination site for RNA polymerase in bacteria stop codon; RNA hairpin loop of GC sequences and section of U residues or attachment of Rho protein
hnRNA heterogeneous nuclear RNA; is the cap that is added to mRNA before it leaves the nucleus
polyA tail up to 250 adenosines added to the end of the mRNA before it leaves the nucleus; length of tail determines the half life of the mRNA before nucleases degrade it
The more important and conserved the gene is, the less introns it will have because it can't afford for mistakes to occur when the spliceosomes splice out the introns
Translation Derivation of amino acid sequence of a polypeptide from the base sequence of an mRNA molecule in association with a ribosome.
mRNA is made from the anti-sense/template strand (3'->5')
tRNA is made from the mRNA strand (5'->3')
Shine-Dalgarno sequence the sequence that helps the ribosomal subunits to bind to mRNA; involved in translation
IF1 Factor stabilizes the 30S subunit of the ribosome
IF2 Factor binds fmet-tRNA to 30S-mRNA complex; binds to GTP and stimulates hydrolysis
IF3 Factor binds 30S subunit to mRNA; dissociates monosomes into subunits following termination
EF-Tu Factor binds GTP; brings aminoacyl-tRNA to the A site of ribosome
Ef-G Factor stimulates translocation; GTP-dependent
DNA synthesis results in 10% tRNA; 5% mRNA; and 85% rRNA
Fragile-X 250+ repeats that occur in the promoter region; the more repeats, the earlier onset of disease; mostly caused by mothers; fathers won't pass it to son; when fathers pass to daughter, it usually doesn't fully expand
Ataluren translarna makes ribosomes translate over premature stop codon; makes ribosomes less sensitive to premature stop codons
Gamenin signals that its been replicated and stops replication
Created by: JacobGant