Term
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Definition
| Transports glucose in plasma via facilitated diffusion |
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Term
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Definition
| Transports fructose into intestinal epithelial cells via facilitated diffusion |
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Term
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Definition
| Transports 2Na+, glucose into intestinal epithelial cells via secondary active symport |
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Term
| p-ATPases (phosphorylation) in eukaryotes |
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Definition
Ca++-ATPase
H+/K+-ATPase
Na+/K+-ATPase |
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Term
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Definition
| weak acid + conjugate weak base; accept or donate protons to maintain stable pH |
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Term
| what stereoisomeric form of amino acids is most common biologically? |
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Definition
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Term
| phosphorylation by kinases can occur on which amino acids? |
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Definition
| those with hydroxyl groups: threonine, tyrosine, serine |
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Term
| bond between N and alpha-C |
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Definition
| circle slash angle of freedom |
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Term
| bond between alpha-C and C |
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Definition
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Term
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Definition
right-handed turn
H bonds between n and n+4 amino acids
maximal intrastrand H bonding
R groups face outward |
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Term
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Definition
participating strands can be parallel or antiparallel (strongest H bond)
R groups alternate above and below plane of sheet
backbone zigzags |
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Term
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Definition
1. proline is 2nd AA
2. glycine is 3rd AA |
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Term
| super secondary structures |
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Definition
beta-barrel
beta-alpha-beta loop
alpha-alpha corner |
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Term
| nomenclature: endings for nucelosides |
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Definition
| purines: -sine, pyrimidines: -dine |
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Term
| nomenclature: endings for nucleotides |
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Definition
| purines/pyrimidines: -ylate |
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Term
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Definition
| AKA "beads on a string" or 11 nm fiber; transcriptionally active; stabilized by phosphate - charges and histone + charges (Arg, Lys) |
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Term
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Definition
| dispersed, trascriptionally-active DNA |
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Term
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Definition
| condensed, transcriptionally-inactive DNA |
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Term
| what causes DNA condensation? |
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Definition
deacetylation (HDACs)
methylation (prevents acetylation)
repressor proteins ie. H1 (Histone) |
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Term
| what causes DNA decondensation? |
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Definition
acetylation (HATs)
phosphorylation
activator proteins ie SWI, SNF |
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Term
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Definition
may be widespread on multiple chromosomes or clustered together
may arise by tandem gene amplification |
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Term
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Definition
contain to introns
multigene compound clusters on multiple chr.
highly evolutionarily conserved, except H1
genes are duplicated |
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Term
| methods of verifying a cloned insert: |
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Definition
1. PCR
2. RE digestion pattern
3. DNA sequencing
4. radioactive screen |
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Term
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Definition
1. plasmid <10
2. bacteriophage <23
3. cosmid 30-45
4. BAC 100-300
5. YAC 200-2000 |
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Term
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Definition
| antibiotic topoisomerase (relegation) inhibitor |
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Term
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Definition
bacterial
removes primers
repairs
matures Okazaki fragments |
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Term
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Definition
bacterial
main replication polymerase |
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Term
|
Definition
eukaryotic
primes
first DNA synthesis |
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Term
|
Definition
some leading strand synthesis
primarily lagging strand synthesis |
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Term
|
Definition
some lagging strand sythesis
primarily leading strand synthesis |
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Term
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Definition
|
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Term
| DNA Polymerase epsilon complex components |
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Definition
1. DNA Polymerase epsilon
2. Rfc (reloader)
3. PCNA (clamp) |
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Term
|
Definition
1. most common transition 5MeC -> T
2.DNA glycosylase removes base (T)
3. apurinic (AP)endonuclease cuts backbone
4. DNA lyase removes Pi, ribose
5. repair/ seal w/ DNA Pol beta + ligase |
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Term
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Definition
| reciprocal exchange of DNA between homologous chromosomes |
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Term
| site-specific recombination |
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Definition
| requires specific sequences from both segments; bacteriophage DNA insertion into bacterial genome |
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Term
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Definition
| may be caused by transpositions |
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Term
| meiotic recombination model |
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Definition
1. gap created by RecB,C,D complex
2. branch migrates and displaces homologous strand -> extension, additional branch migration (RecA, DNA Pol) -> formation of Holliday Intermediate (RecA) -> cleavage by Ruv proteins |
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Term
| homologous recombination + DNA lesion |
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Definition
bypasses lesion during replication
1. fork collapse (RecA, RecFOR)
2. lagging strand serves as template
3. reverse branch mirgation reestablishes bubble, bypasses lesion
4. lesion repaired later |
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Term
| homologous recombination + DNA nick |
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Definition
repairs nick during replication
1. leading strand stalled at nick
2. strand invasion by lagging strand (RecA, RecBCD)
3. lagging strand serves as template
4. branch migration forms Holliday Int.
5. Ruv proteins cleave |
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Term
|
Definition
afforded by transposition
1. RSS (Recombo Signal Sequences)cleaved by RAG1 and RAG2 protein
2. this removal of intervening DNA sequences (+ differential mRNA splicing) produces variable light chains |
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Term
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Definition
| TA-rich sequence in prokaryotic DNA that stimulates transcription |
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Term
| TATAAT and TTGACAT regions |
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Definition
| sequences in prokaryotic DNA that help define transcription start (+1) |
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Term
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Definition
| factor in prokaryotic transcription that brings RNA Pol to start sequences |
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Term
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Definition
| prokaryotes; group of polycistronic genes that shares the same start sequences |
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Term
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Definition
| recruits TBPs (TATA Binding Proteins) which bind MINOR GROOVE of TATA Box, binding site for PIC, -30 from +1 start site |
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Term
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Definition
| Inr, sequence on eukaryotic DNA within or near +1 site; where DNA is initially unwound |
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Term
| Transcriptional Activators |
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Definition
| DNA binding regions and activation domains; can be located near or far from transcribed sequence; chromatin remodeling and mediator effected by |
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Term
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Definition
| repressor motif that binds to 2 adjacent DNA major grooves in a sequence-specific manner; bends DNA slightly |
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Term
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Definition
| transcription factor; binds to DNA via basic residues (Arg, Lys); 2 proteins assoc. via hydrophobic interactions of Leu (looks like zipper); ex: fos-jun TF |
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Term
| basic helix-loop-helix motif |
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Definition
| 2 such molecules interact via 1 leucine; interact w/ DNA via basic residues (Arg, Lys) |
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Term
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Definition
| 2 loop structures wrap around major grooves; loops formed by 2 cysteine molecules assoc. w/ zinc ion |
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Term
| enhancers in eukaryotic DNA sequences |
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Definition
| usu. far from TATA Box; may be upstream, downstream, or in an intron; do not interact directly with the PIC |
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Term
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Definition
| Binds after TBPS, interacts w/ TBPs, TATA Box; recruits RNA Pol II/ TFIIF complex |
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Term
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Definition
| docking site for TFIIH, which completes PIC assembly |
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Term
|
Definition
| helicase activity powered by ATP hydrolysis, phosphorylates serines of CTD of RNA Pol II, starting transcription; also recruits nucleotide excision repair proteins |
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Term
|
Definition
| TATA Binding Protein- locate TATA Box |
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Term
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Definition
| stabilizes TBPs and TFIIB |
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Term
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Definition
| initiates PIC assembly in absence of TATA Box |
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Term
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Definition
| transcribes pre-rRNA; does not require ATP to start; has own TFs; uses specific polymerase terminator sequence |
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Term
|
Definition
| transcribes mRNA, snRNA, and miRNA; requires ATP to start; termination somewhere after polyA signal site |
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Term
| what does RNA Pol III do? |
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Definition
| transcribes tRNA, 5S rRNA; does not require ATP to start; has own TFs; uses Box A, B, and C as promoter; termination after poly U sequence (A-U combo unstable-released) |
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Term
|
Definition
| Tat, Cyclin T activate CDK9, phosphorylates CTD to prevent termination |
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Term
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Definition
| "heterogenous nuclear RNA" contains introns and exons |
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Term
|
Definition
| site of intron splicing during hnRNA processing; starts with "GT" |
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Term
|
Definition
| end of intron to be spliced during hnRNA processing; "AG" |
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Term
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Definition
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Term
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Definition
| binds to 40S subunit first |
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Term
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Definition
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Term
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Definition
| w/ GTP binds to Met-tRNAi, brings it to 40S subunit during initiation |
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Term
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Definition
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Term
|
Definition
| Poly-A Binding Proteins; bind to poly A tail of mRNA during formation of initiation complex |
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Term
|
Definition
| binds eIF4E/PABS to bring 5' and 3' ends of mRNA together |
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Term
|
Definition
| has helicase activity towards mRNA |
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Term
|
Definition
|
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Term
|
Definition
| complex that includes eIF4A,B,E,and G; binds to 40S subunit to bring mRNA over to it |
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Term
|
Definition
| elongation factor; binds GTP to aa-tRNA to allow for paptide bond formation |
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Term
|
Definition
| exchanges GDP for GTP on eEF1alpha, recharging it for use in elongation |
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Term
|
Definition
| AKA "translocase"; eEF2 + GTP moves ribosome one codon towards 3' end of mRNA, shifting contents of various sites |
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Term
|
Definition
| release factors bind to stop codon in A site -> activate ribosome to hydrolyze polypeptide -> results in ribosome disassembly |
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