Biochemfinal cornell Word Scramble
|
Embed Code - If you would like this activity on your web page, copy the script below and paste it into your web page.
Normal Size Small Size show me how
Normal Size Small Size show me how
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 |
Created by:
zideutsch
Popular Biochemistry sets