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Biochemfinal cornell
| Term | Definition |
|---|---|
| Central Dogma | DNA->RNA->PROTEIN |
| DNA replication, transcription and translation all take place in the same space at the same time | PROKARYOTE |
| Compartmentalization of transcription and translation | EUKARYOTE |
| PURINES | ADENINE + GUANINE |
| PYRIMIDINES | CYTOSINE, THYMINE +URACIL |
| 5'-3' ENDS | PHOSPHATE- HYDROXY |
| DNA VS RNA | 2 STRANDS VS 1 STRAND THYMINE VS URACIL N-GLYCOSIDIC BONDS OF DNA ARE SUSCEPTIBLE TO ACID HYDROLYSIS 2'OH OF RNA IS SUSCEPTIBLE TO ALKALI HYDROLYSIS |
| NUCLEASE | CLEAVES PHOSPHODIESTER BOND (Rnase or Dnase) |
| RESTRICTION ENDONUCLEASE | CLEAVE AT SPECIFIC INTERNAL BASE SEQUENCES |
| G-?-C | 3 H BONDS |
| A-?-T(U) | 2 H BONDS |
| A FORM OF DNA | right-handed, short and broad, 2.6 A, 11 bp per turn. Formed in dehydrated DNA fibers, RNA/DNA hybrids, and RNA/RNA duplexes. 2’OH of ribose causes puckering of sugar |
| B FORM OF DNA | right-handed, longer, thinner, 3.4 A, 10.5 bp per turn. Natural form of DNA found in prokaryotes and eukaryotes |
| Z FORM | YOUR DRUNK DNA GO HOME LEFT HANDED, ~18A, 12 bases/turn only occurs in synthetic super high salt concentrations in runs of GC UNLESS most of the C's are methylated, then will form Z at physiological conditions |
| HOOGSTEEN PAIRING | WEIRD FUCKING 3-STRANDED HELIX (formed by mirror repeats) rare to form (temp, ph, strand osmolarity dependent) |
| G4 DNA | GUANOSINE TETRAPLEX DNA, SUPER STABLE, WITHSTANDS BOILING |
| 2 FACTORS (of dna) AFFECTING MELTING TEMP | G-C CONTENT, LENGTH |
| DNA HYBRIDIZATION | measure of the relatedness between species |
| HUMAN GENOME SIZE | 3200 MB |
| # OF GENES (HUMAN) | 25,000 |
| GENE DENSITY OF HUMANS | 1/100 KB |
| # HUMAN CHROMOSOMES | 23 |
| "SHOTGUN" SEQUENCING APPROACH | (VENTER) Requires >10x coverage to sequence 90 % of genome. Possible only if cost of sequencing is low and computer software is sophisticated. |
| "SYSTEMATIC" SEQUENCING APPROACH | (COLLINS) 1 DNA IS DIGESTED, FRAGMENTS INSERTED INTO BACS 2. (LONGEST STEP) CONTIGS ARE MAPPED 3.BAC FRAGMENTS SEQUENCED 4 SEQUENCE OVERLAPS REVEAL OVERALL SEQUENCE |
| HUMAN GENOME SEQUENCE TYPES | TRANSPOSONS=64.7%, PROTEIN CODING GENES= 1.5%, INTRONS= 25.9% |
| EXON | PROTEIN CODING SEQUENCE OF EUKARYOTIC RNA, often encodes a single domain of a larger, multidomain protein. |
| INTRON | eukaryotic RNA sequence removed during post transcription |
| HAPLOTYPE | – groups of SNPs close to each other that are inherited together are compiled into haplotypes. Linkage of haplotypes with diseases can be used to map disease genes |
| TAG SNP | a subset of SNPs that define the entire haplotype. By sequencing just these tag positions in human populations, can identify which haplotypes are present in each individual |
| SNP | SINGLE NUCLEOTIDE POLYMORPHISM (lots of variation in humans) |
| CHIMP CHROMOSOME | 3.29x109 bp (VS 3.2), 96% identical genome sequences, one extra pair of chromosomes (2p + 2q) corresponding to the two arms of the human chromosome 2 (BARRIER TO REPRODUCTION WITH THEM) |
| MESELSEN- STAHL DENSITY EXCHANGE EXPERIMENT | HEAVY DNA+ NORMAL NUCLEOTIDES =SEMICONSERVATIVE DNA REPLICATION |
| ARTHUR AND TOM KORNBERG | DISCOVERED DNA POL 1,2 +3 |
| DNA POL 1 | 1. 5’-3’ DNA dependent DNA polymerase activity (CANNOT INITIATE) 2. 3’-5’ exonuclease activity or proof reading function 3. 5’-3’ exonuclease activity 4. 10-20 nucleotides polymerized/second 5. 1 subunit |
| IS POLYMERIZATION THERMODYNAMICALLY FAVORABLE? | YES |
| Shape selectivity | TEMPLATE STRAND BINDING TO DNA POL 1 INDUCES CONFORMATIONAL CHANGE ENSURING BASE PAIR FIDELITY |
| 3’/5’ exonuclease activity of dna pol 1 | Proof reading improves accuracy by 10^2-10^3 folds. Repair mechanisms improves accuracy by another 10^2-10^3 folds. |
| 5’/3’ exonuclease activity of DNA POL 1 | Pol&I can resynthesize a stretch of DNA by chain elongation at the nick and removing nucleosides ahead to clear the way for polymerization. |
| DNA POL 2 | 1. 7 subunits 2. 3'-5' exonuclease proofreading 3. no 5'-3' proofreading 4. 40 nucleotides/second |
| DNA POL 3 | 1. more than 10 subunits 2. 3'-5' proofreading 3. no 5'-3' proofreading 4. 250-1000 nucleotides/second (highest) |
| PRIMASE | creates short RNA primer strands during DNA replication |
| REPLISOME | HELICASE, PRIMASE, DNA POL1, DNA POL 3, DNA LIGASE, TOPOISOMERASE 2 |
| OriC | E. coli replication origin secquence |
| Dna A protein | Recognizes OriC sequence, initiates replication bubble (@ AT rich region, by overwinding adjacent region) |
| Helicase (DnaB) | unwinds DNA in replication |
| DnaC protein | assists helicase with unwinding |
| SSB | single stranded binding protein, necessary to keep DNA from rewinding during replication |
| DNA gyrase (topoisomerase 2) | relieves torsional strain during DNA replication |
| Dam Methylase | methylates GATC sequence necessary for mismatch repair in E. coli |
| SUPERCOILNG | WHEN (in B form) Dna is wound more or less than 10.5 bp/turn |
| LINKING NUMBER | # of times one strand of DNA winds around the other (L) L = T + W |
| TWISTING NUMBER | (# of turns resulting from base-pairing in B form DNA or # of bp divided by 10.5 bp (Lo) T in: L=T+W |
| WRITHING NUMBER | # of superhelical turns (W) L=T+W |
| TOPOISOMERS | different forms of a DNA molecule that differ only in their topological property such as linking number. |
| TOPOISOMERASE | introduce or remove supercoils by increasing or decreasing the linking number |
| TYPE 1 TOPOISOMERASE IN E.COLI | relaxes DNA by removing negative supercoils (TOPO 1+3) |
| TYPE 2 TOPOISOMERASE IN E. COLI | TOPO 2 (GYRASE): introduce negative supercoils (ANTIBIOTIC TARGET)( REQUIRES ATP) TOPO4: decatenates daughter DNA molecules at the completion of DNA replication |
| EUKARYOTIC TYPE 1 TOPOISOMERASE | (1+3) relaxes negative OR positive supercoils |
| EUKARYOTIC TYPE 2 TOPOISOMERASE | relax both positive AND negative supercoils (IIa+IIb) |
| POSITIVE SUPERCOILING TOPOISOMERASE | STOP. THIS IS WRONG. THIS MAKES NO SENSE AND DOES NOT EXIST IN NATURE OR EVER. WE DONT LIKE POSITIVELY SUPERCOILED DNA. GO HOME. |
| NUCLEOSOMES | unit of organization of chromatin = one bead plus adjoining DNA that leads to the next bead or 200 bp DNA plus 2 |
| HISTONE | protein core of nucleosome with DNA wrapped around found in an octomer form |
| amino-terminal tail | NH2 terminal tails of one nucleosome extrude from the paticle and interact with adjacent nucleosomes, helping to define higher order DNA packaging. highly conserved across species |
| SMC | structural maintenance of chromosome proteins |
| CONDENSIN | introduces positive superhelical tension into DNA in an ATP-hydrolysis-dependent manner (SMC) |
| COHESIN | (SMC) protein complex that regulates the separation of sister chromatids during cell division |
| MISMATCH REPAIR | POL 3 (10^2-10^3 IMPROVEMENT) 1. MUTL-MUTS BINDS TO MISMATCH 2. MUTH BINDS TO MUTL AND NEAREST METHYLATED GATC SEQUENCE 3. MUTh CUTS UNMETHYLATED STRAND 4. DNA POL 3 TRIES AGAIN |
| EXCISION REPAIR | damage occured throughout lifetime- POL 1 |
| BASE EXCISION REPAIR | POL 1- removal of damaged base specifically uracil or depurinated bases |
| NUCLEOTIDE EXCISION REPAIR | POL 1- - repairs damage due to environmental mutagens such as ultraviolet rays |
| Direct repair | DNA photolyases (not present in placental mammals) Photoreactivation of cyclobutane pyrimidine dimers induced by UV + methyltransferase repairs alkylated bases |
| ERROR PRONE REPAIR | (BACTERIA) Pol IV and Pol V translesion DNA synthesis (reduces fidelity to one error in ~1000 nucleotides) AT REPLICATION FORK via recombination |
| PYRIMIDINE DIMER DNA ERROR | caused by uv light, fixed by direct repair by dna photolyases |
| HOMOLOGOUS RECOMBINATION | genetic exchanges between any two DNA molecules (or segments of the same molecule) that share an extended region of nearly identical sequence. , |
| 3 FUNCTIONS OF HOMOLOGOUS RECOMBINATION | 1. contributes to the repair of several types of DNA damage 2. a transient link between chromatids that promotes an orderly segregation of chromosomes (EUKARYOTES) 3. enhances genetic diversity in a population |
| RecBCD | helicase/nuclease generates a 3’ end single strand when it reaches a Chi site |
| BACTERIAL HOMOLOGOUS REPLICATION AS DNA REPAIR | 1. 5' ND PROCESSING 2. STRAND INVASION 3. BRANCH MIGRATION 4. HOLLIDAY INTERMEDIATE RESOLUTION +LIGATION |
| SITE SPECIFIC RECOMBINATION | RECOMBINATION LIMITED TO SPECIFIC SEQUENCE (20-200 BP) duh |
| HOLLIDAY INTERMEDIATE | mobile junction between four strands of DNA found during homologous genetic recombination |
| NONHOMOLOGOUS RECOMBINATION | ALLOWS THE MOVEMENT OF TRANSPOSABLE ELEMENTS |
| 2 FACTORS AFFECTING NUMBER OF RESTRICTION ENZYME CLEAVAGE SPOTS | 1. A/T:G/C RATIO 2. THE RECOGNITION SEQUENCE AND ITS LENGTH |
| 4 RESTRICTION ENDONUCLEASE USES | 1. RECOMBINANT DNA 2. CLONING LARGE DNA SEQUENCES (GENOME SEQUENCING) 3. ASSEMBLING GENOMIC SEQUENCES 4. DNA SEQUENCING |
| BAC | bacterial artificial chromosomes- a cloning vector 100-300kb sequences, incorporated with electricity |
| Bacteriophage λ cloning vector | high yield ~100 phage/cell |
| YAC | yeast artificial chromosome, Used for cloning DNA segments of up to 2,000 kb. Important for the human genome sequencing project, less rearranging than BAC |
| STS | sequence tag sites used for ordering clones in a dna library |
| ETS | expression sequence tag used for ordering clones in a dna library |
| dDNA | dideoxynucleotides, used in DNA sequencing, forces termination of sequence (no OH to continue) |
| AUTOMATED SEQUENCING REACTIoN | using 5' radioactively labeled dDNA, can resolve 600-750bp |
| PCR | polymerase chain reaction 1. heat target sequence (90C) to denature 2. add synthetic oligonucleotide primers, cool 3. add thermostable DNA pol 4. repeat- amplifies 10^6 fold |
| DNA GENOTYPING | fingerprinting, forensic use using PCR to analyze multiple STR sequences that together are a unique profile |
| CODIS | combined DNA index system contains >7mil STR sequences for DNA genotyping comparison |
| PHOTOLITHOGRAPHY | This technique for preparing DNA microarray makes use of nucleotide precursors that are activated by light, joining one nucleotide to the next in a photoreaction. |
| tRNA | transfer RNA, Between 73 and 93 bases, Contain many unusual bases, L-shaped, Half base-paired (A form)., unpaired regions that provide the structural diversity so that the tRNAs can be uniquely distinguished, 5’ end is phosphorylated, Amino acid is |
| AMINOACYL TRNA SYNTHETASE | Read mRNA codons, translate to amino acids. each one is responsible for 1 amino acid, multiple codons |
| DEGENERATE CODE | some amino acids are coded for by multiple codons, instead of initiating a stop sequence. minimizes deleterious effect of mutation |
| WOBBLE HYPOTHESIS | Synonymous codons differing in the third base read for same AA, wobble has rules, hypothesis predicts the number of codons recognized by tRNA |
| RIBOSOME | 50s+30s, 23s is not protein, catalyst property |
| 16s rRNA | used to differentiate archea/bacteria/eukaryota/ lots of differenciation |
| AMINO ACID ACTIVATION | step 1 of protein synthesis proofread before and after by aa-tRNA sythetase very accurate |
| PROTEIN SYNTHESIS INITIATION | STEP 2 small subunit binds mRNA and initiator aminoacyl tRNA large subunit binds requires GTP hydrolysis |
| SHINE-DELGARNO SEQUENCE | BINDS 16s rRNA before start codon in prokaryotes |
| EUKARYOTIC INITIATION COMPLEX (translation) | requires 5'cap and 3'polyadenylation of mRNA to initiate eLF's bind to 5' cap and 3' tail to bind to ribosome |
| PROTEIN SYNTHESIS ELONGATION | 1. bind 2nd aminoacyl tRNA 2. form 1st peptide bond with peptidyl transferase 3. translocation (gtp hydrolysis) |
| PROTEIN SYNTHESIS TERMINATION | 1. stop codon enters ribosome A site 2. RF1/2 bind (RF3 promotes) 3. peptidyl transferase hydrolyzes, releasing peptide |
| POLYSOME | ribosome aggregates translating same protein concurrently |
| PUROMYCIN | resembles aminoacyl end of tRNA, terminates peptide chains prematurely. ANTIBIOTIC |
| REVERSE TRANSCRIPTASE | ONLY IN RNA VIRUSES. tRNA primer from previous host is required transcribes RNA to DNA to create RNA:DNA hybrid that can be transcribed by host polymerase degrades the RNA in DNA:RNA hybrid HIV therapy target high error rate (bad for curing/immunity |
| AZT | azido di-deoxy-thymidine HIV reverse transcriptase inhibitor |
| DDI | dideoxyinosine HIV reverse transcriptase inhibitor |
| TELOMERASE | special eukaryotic reverse transcriptase transcribe telomeres backwards to add buffer DNA (chromosomal ends) |
| mRNA | 2-5% of all RNA short lived, heterogeneous |
| tRNA | stable, ~15% of all RNA |
| rRNA | ~80% of all RNA, stable |
| SPIEGELMAN EXPERIMENT | determined makeup/proportions of RNA |
| SECONDARY RNA STRUCTURES | BULGE, INTERNAL LOOP, SINGLE STRAND, HAIRPIN |
| 4 STAGES OF TRANSCRIPTION | 1.RNA pol recognizes promoter region 2. moves along DNA synthesizing RNA 3. stops at termination site 4. releases RNA |
| SIGMA 70 | binds to DNA promoter region in order fo RNA POL to bind, released during transcription TATA BOX/ 10/30 sequence |
| RHO helicase | separates RNA from RNA pol in P-dependent termination |
| INTRON | NONCODING MRNA SEQUENCE IN EUKARYOTES REMOVED DURING PROCESSING |
| 5' MRNA CAP | 7-methylguanosine cap, added to 5'end of mRNA while still being synthesized |
| SPLICEOSOME | attached to RNA pol, removes introns, splices exons |
| POLY (A) TAIL | added to transcribed mRNA sequences when polyadenylate polymerase recognizes bound polyadenylation factors |
| lac OPERON REGULATION | 1. presence of lactose removes the repressor, allowing lactase transcription 2. lack of glucose activates cAMP, activating promoter which promotes high lactase transcriptase |
| DNA FOOTPRINTING | IDENTIFY PROMOTER BINDING SITE - THE DNA SEQUENCE WHERE A PROTEIN BINDS. |
| # OF PROTEINS IN HUMANS | 60,000-100,000 |
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