Experiment where mixture of living IIR and heat-killed IIIS bacteria produced living IIIS Griffith's Transformation Experiment Griffith's experiment proved this Genetic material was transferrable Experiment that proved DNA and not RNA was the genetic material Avery's Transformation Experiments Experiment tested each component (lipids, polysaccharides, proteins, nucleic acids) individually to see if it could transfer R bacteria derived from IIS into IIIS Avery's Transformation Experiments Experiment that marked T2 virus with 32P DNA and 35S protein radioactive isotopes, then infected E. coli to see what resultant T2 offspring propagated (32P DNA); proved DNA was genetic material Hershey-Chase Bacteriophage Experiments By stripping off the protective protein subunits of the tobacco mosaic virus, and using what was left to successfully infect tobacco leaves, Gierer and Schramm proved That RNA could also be genetic material for some organisms Purines Double ringed (6 + 5 membered) nitrogenous bases; includes adenine and guanine Pyrmidines Single ringed (6 membered) nitrogenous bases; includes cytosine, thymine, and uracil Nucleotide five-carbon sugar + nitrogenous base + phosphate group Nucleoside five-carbon sugar + nitrogenous base 5' - 3' linkages between nucleotides Phosphodiester bonds Experiment that found that A:T = C:G = 1 Chargaff's experiments Experiment that found that DNA was a helix Rosalind Franklin's and Maurice Wilkins' X-Ray diffraction experiments Watson & Crick's DNA model has these features Two chains in a right-handed helix; two chains are anti-parallel (one 5' - 3', other 3' - 5'); bases are in the inside of helix and stacked flat; bases are H-bonded according to Chargaff's rules; base pairs are 0.34 nm apart; helix chains contain minor and major grooves Oligomers Short DNA sequences A-DNA B-DNA without water B-DNA Biological form of DNA Z-DNA Left-handed form with zigzag shape Number of base pairs per turn of DNA 10 base pairs Chromosome or set of chromosomes that contains all DNA of an organism Genome A prokaryote's genome A single circular chromosome Robert Sinsheimer found that the ratio of bases in Phi X174 was 25A:33T:24G:18C. This proved that Its DNA was single-stranded In bacteria and archaea, the chromosome is found here Nucleoid A-T has this many H-bonds 2 G-C has this many H-bonds 3 Plasmids Plasmids are molecules of DNA that are found in bacteria separate from the bacterial chromosome Reason a long strand of DNA can fit within a cell It's supercoiled When a strand has more 360¡ turns it is positively supercoiled When a strand has less 360¡ turns it is negatively supercoiled These cause supercoiling Topoisomerases Number of human chromosomes 46 chromosomes C value Total number of base pairs in DNA Chromatin The complex of DNA and chromosomal proteins in the chromosome These help DNA compact itself by forming "beads on a string" Histones Nonhistones All proteins associated with DNA except for histones Nucleosome The first-level packing of DNA with histones 30-nm chromatin fiber Chromatin fiber of packed nucleosomes; second-level packing Euchromatin This is the chromosomes or region of chromosomes that show the normal cycle of de/condensation in the cell cycle; more importantly, it contains genes that are expressed Heterochromatin This is the chromosomes or region of chromosomes that remain condensed throughout cell cycle and do not express genes The centromere regions are Constitutive heterochromatin These families of DNA patterns are 100 to 500 bp long short interspersed repeated sequences (SINES) These families of DNA patterns are around 5000 bp long long interspersed repeated sequences (LINES) This experiment demonstrated that DNA replicates by the semi-conservative model. 15N marked DNA allowed to replicate in a 14N medium produced DNA with one strand of 15N and the other of 14N. Meselsohn-Stahl Experiment Kornberg found that these minimal ingredients were required for DNA synthesis All four dNTPs; a template DNA fragment; DNA Polymerase I; Mg2+ ions An exonuclease can do this Proofreading This can do proofreading in the 5' - 3' direction DNA Polymerase I In E. coli, this enzyme the bulk of DNA synthesis DNA Polymerase III In E. coli, there this is the single location of replication oriC This relaxes the supercoiled DNA so that replication can start Gyrase (a topoisomerase) This unwinds the DNA Helicase Primase Binds to helicase and synthesizes a short RNA primer SSBs Bind to the single-stranded DNA, to stabilize it and prevent it from reforming the helix. They are displaced automatically by DNA Polymerase III. Leading strand The new strand being made in the same direction the replication fork is proceeding Lagging strand The new strand being made in the opposite direction the replication fork is proceeding Since the leading strand is being made continuously and the lagging strand not Semidiscontinuous The fragments of the lagging strand Okazaki fragments This links together two Okazaki fragments DNA ligase These form checkpoints to prevent the cell from moving to a different phase of the cell cycle until it is ready Cyclins These are multiple start points of DNA replication so it won't take forever Replicons This prevents loss of genetic material by adding on repeats to the end of chromosomes Telomerase At the end of replication, removal of this results in some special activity to fix the ends so that no material is lost. The RNA primer These need nutritional supplements to survive, since they lack the ability to synthesize an important nutrient Auxotrophs These do not need nutritional supplements to survive Prototrophs Beadle and Tatum proposed this One gene, one enzyme (one polypeptide) He proposed the Hypothesis of Inborn Errors of Metabolism Archibald Garrod Transcription Synthesis of a single-stranded RNA copy of a DNA segment Translation Conversion of a messenger RNA into the amino acid sequence of a polypeptide Watson & Crick proposed this as the "Central Dogma" DNA-->RNA-->protein (transcription followed by translation) tRNA Brings amino acids to ribosomes during translation rRNA Along with ribosomal proteins, make up the structure of ribosomes snRNA With proteins, form complexes that are used in eukaryotic RNA processing Catalyzes the process of transcription RNA Polymerase The template strand The 3' - 5' DNA strand that is read to make the RNA strand during transcription Promoter A sequence upstream of the DNA to be transcribed with which RNA polymerase interacts with to begin the transcription Terminator A sequence downstream of the DNA to be transcribed which specifies where transcription will stop Consensus sequence in the -35 region A promoter in E. coli found at about offset -35; 5'-TTGACA-3' Pribnow box A promoter in E. coli found at about offset -10; 5'-TATAAT-3' Holoenzyme A form of RNA polymerase which must bind to the promoter for transcription to proceed Sigma factor A polypeptide bound to the holoenzyme which is responsible for recognizing the -35 and -10 regions of the promoter rho-independent terminators In prokaryotes, these sequences have two-fold symmetry which can fold up on itself to form a termination hairpin rho-dependent terminators In prokaryotes, these sequences lack the AT string found in r-indep and cannot form hairpin structures. Instead, they rely upon the rho-factor protein for termination TATA box A promoter in eukaryotes found at -25 CAAT box A promoter in eukaryotes found at -75 GC box A promoter in eukaryotes found at -90 RNA Polymerase I In eukaryotes, responsible for rRNA synthesis RNA Polymerase II In eukaryotes, responsible for mRNA, snRNA synthesis RNA Polymerase III In eukaryotes, responsible for tRNA synthesis 5' capping In euks, once 20 - 30 nucleotides of pre-mRNA has been made, a methylated guanine nucleotide with 5' - 5' linkage is added; this is required for the ribosome to bind to the 5' end of the mRNA to start translation poly(A) tail In euks, about 50 to 250 adenine nucleotides are added at the 3' end. Helps stabilize the mRNA. pre-mRNA mRNA with introns to be edited out Introns Filler edited out of mRNAs Exons Expressed sequences of mRNAs (non-filler) snRNPs (snurps) bind to pre-mRNAs to form the spliceosome which edit out introns spliceosomes Edit out introns in pre-mRNAs spacers result in splitting into two sequences self-splicing When the RNA intron folds into a secondary structure that promotes its own excision ribozymes Modified self-cleaving RNAs that can be used experimentally to cleave RNA molecules at specific sequences chaperones Act analagously to enzymes in that they help proteins fold but are not consumed charging when a tRNA is attached to its correct amino acid Responsible for charging the tRNA Amino-acyl synthetase Shine-Dalgarno sequence In prokaryotes, helps position the ribosome on the mRNA to find the start codon Start codon AUG Stop codons UAA, UAG, UGA Wobble Hypothesis Proposed by Crick; less than 61 distinct tRNAs are needed for the 61 codons because of less strict behavior at third letter of the codon Polysome Complex of mRNA plus multiple ribosomes doing translation Release factors These help a ribosome recognize a stop codon Cotranslational transport When a protein is injected into the ER while it is still be synthesized Signal recognition particle When present, allows the protein to be injected into the ER