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Biochemistry
Midterm 4
| Term | Definition |
|---|---|
| what is semiconservative DNA replication? | each daughter cell has a parent strand and a daughter strand |
| what is the process of DNA replication initiation? (Prokaryote) | one origin of replication and origin recognition protein that recruits a helicase loader, DNA helicase unwinds in AT rich regions, single-stranded DNA binding protein prevents reannealing, circular DNA |
| what is the process of DNA replication initiation? (Eukaryote) | multiple origins of replication and origin of replication complex protein that recruits a helicase loader, DNA helicase unwinds in AT rich regions, single-stranded DNA binding protein prevents reannealing, linear DNA |
| what is the process of DNA replication elongation? (Prokaryote) | primase synthesizes a piece of RNA (10 nt), DNA polymerase III extends from primer (lead), or backwards from the primer (lagging), Polymerase I removes 5' RNA NMPs and inserts DNA, Ligase forms bonds between 5' phosphate and 3'hydroxyl Okazaki fragments |
| what are the ends of eukaryotic DNA called? | telomeres 5'-AGGGTT-3' repeat in the 3'-overhang |
| where do telomeres come from? | telomerase RNA template (CAAUCCCAA) that creates DNA ends (AGGGTT) |
| what result from deamination of adenine? | hypoxanthine |
| what result from deamination of guanine? | xanthine |
| what result from deamination of cytosine? | uracil |
| what result from deamination of methyl cytosine? | thymine |
| what do you need to run a PCR? | template DNA, primer DNA, deoxynucleotides, and Taq Polymerase -Polymerase Chain Reaction |
| what is needed for transcription initiation? (Prokaryote) | RNA polymerase attaches to the sigma factor, the sigma factor binds to the -35 DNA promoter region, and then moves to the -10 promoter region (TATA box), opening up the DNA starting transcription |
| what is the process of transcription termination? | rho-dependent: rho helicase pulls RNA from the DNA, recognizes c-rich sequences (hexameric ATP-dependent helicase) rho-independent: no enzyme, GC-rich hairpin followed by poly-u sequence pulls RNA |
| what RNA is modified? (Prokaryote) | unmodified: mRNA (cotranscriptional translation) modified: tRNA and rRNA |
| what is needed for transcription initiation? (Eukaryote) | RNA polymerase, promoter region, family of TF II |
| what is needed for transcription elongation? (Eukaryote) | 5' cap occurs after initiation |
| what is needed for transcription termination? (Eukaryote) | 3' poly-A tail after termination (AAUAAA) |
| what is the process of mRNA splicing? | step 1: 2' hydroxyl of the branch site reacts with 5' phosphate of the intron, forming a 2'-5' lariat intermediate and release the 3' hydroxyl of exon 1 step 2: 3' hydroxyl of exon 1 reacts with the 5' phosphate of the exon 2, releasing the 3'OH lariat |
| what does rifampin do? | inhibits RNA polymerase in prokaryotes, TB treatment |
| what does actinomycin D do? | inhibits RNA polymerase in eukaryotes by blocking translocation, cancer treatment |
| what is aminoacyl-tRNA synthetase? | carboxyl group of an amino acid connected to the 3' hydroxyl of tRNA (connected to a carbonyl group that charges tRNA) |
| Process of Aminoacyl-tRNA Synthetase | step 1: activate amino acid by reacting the aa carboxyl group with the first phosphate of ATP to form aminoacyl-AMP and PPi step 2: 3' hydroxyl of the tRNA reacts with the carboxyl carbon on the aminoacyl anhydride releasing AMP creating aminoacyl-tRNA |
| what are the prokaryote ribosome units? | Whole: 70s Large: 50s - 23s and 5s Small: 30s - 16s |
| what are the eukaryote ribosome units? | Whole: 80s Large: 60s - 28s, 5.8s, and 5s Small: 40s - 18s |
| what is needed for protein translation initiation? | start codon: AUG which codes for methionine (methionyl tRNA) 16s RNA subunit recruits and binds the mRNA and facilitates positioning of the AUG codon into the P site |
| what delivers methionyl tRNA? | IF2-GTP |
| what is the process for protein translation elongation? (Prokaryote) | EF-Tu-GTP (GAR/GAP) delivers amino acids to the next site, EF-Ts (GEF) recycles, peptide bond forms between P and A sites; catalyzed by 23s and 50s, EF-G-GTP causes a site shift |
| what is the process for protein translation termination? | release factors recognize stop codons (UAA, UAG, UGA) that enter the A site and hydrolyze GTP, tRNA, and releases proteins |
| what is the process for protein translation initiation? (Eukaryote) | methionyl-tRNA is put into the subunit then mRNA is brought to the tRNA, eIF2 is needed for initiation |
| what is the process for protein translation elongation? (Eukaryote) | eEF1-alpha-GTP delivers amino acids to the next site, eEF1-beta recycles, peptide bond formation between P and A site; catalyzed by 28s and 60s, eEF2-GTP causes shift to next site |
| what is the response to stress? | phosphorylation of the initiation (IeF2) and elongation factor (eEF2), GEF is bonded to phosphate and can't recycle |
| what are the prokaryote protein translation inhibitors? | streptomycin, tetracycline, chloramphenicol, puromycin, erythomycin |
| what are the eukaryote protein translation inhibitors? | cyclohexamide, puromycin |
| what is the process of DNA replication elongation? (Eukaryote) | primase (pol-alpha) makes short piece of RNA and DNA, DNA polymerase (pol-epsilon) makes the leading strand, DNA polymerase (pol-delta) makes the lagging strand, ligase binds the Okazaki fragments |
| TCA Cycle/Matrix Enzymes Facts | nuclear encoded DNA (23 chromosomes), N-terminal amphipathic basic helix targets mitochondrial matrix, translocased through the outer and inner membrane |
| Membrane Proteins | mitochondrial encoded genes, translated and end up in the inner membrane, make up the ETC, no signal sequence |
| a nuclear encoded protein with N-terminal hydrophobic signal sequence results in what? | delivery or insertion into the ER |
| what does the ER produce? | proteins delivered/incorporated in lysosomes, plasma membrane proteins (transporters/receptors), proteins secreted by cells (insulin) |
| N-Linked Glycosylation Process | oligosaccharide synth. onto dolichol PPi in the cytoplasm, flipped into the membrane, then oligosaccharide is attached to amide nitrogen of asparagine; mannose 6-phosphate is targeted by lysosomes (mannose 6-P deficiency =no proteins in lysosome/membrane) |
| Nuclear Import | GAP outside: hydrolyzes GTP, causing Ran-GTP to release the importin, importin binds to the target to bring it into the nucleus GEF inside: generates Ran-GTP, displacing the target, binds to importin to bring it out of the nucleus |
| Ubiquitin-Proteasome System | C-terminus of ubiquitin in a secondary amide linkage with an amino-nitrogen of lysine, ubiquitin chains are is the c-terminus of ubiquitin connected to the amino nitrogen of lysine 48 |
| Phosphorylation Facts | Residues: Side Chain -OH of Ser, Thr, Tyr Enzyme: Kinases Donor: ATP Reversible: Phosphatases Note: Intracellular |
| Sulfation Facts | Residues: Side Chain -OH of Tyr Enzyme: sulfotransferases Donor: PAPS Note: extracellular |
| Acetylation Facts | Residues: Side Chain -NH3+ of N-term and Lys Enzyme: acetyltransferases Donor: acetyl-CoA Reversible: deacetylases Note: Intracellular |
| Methylation Facts | Residues: Side Chain -NH3+ of Lys and Arg Enzyme: methyltransferases Donor: SAM Reversible: demethylases |
| Myristylation Facts | Residues: Side Chain -NH3+ of N-term Enzyme: myristoyltransferases Donor: myristoyl-CoA Reversible: No |
| Palmitoylation Facts | Residues: Side Chain -SH of Cys Enzyme: palmitoyltransferases Donor: palmitoyl-CoA Reversible: thioesterases |
| Farnesylation Facts | Residues: Side Chain -SH of Cys near C-term Enzyme: farnesyltransferases Donor: farnesylpyrophosphate (FPP) Reversible: No |
| Geranylgeranylation Facts | Residues: Side Chain -SH of Cys near C-term Enzyme: geranylgeranyltransferases Donor: geranylgeranylpyrophosphate (GGPP) Reversible: No |
| what is a nucleosome? | histone core: histone octamer, 8 subunits, 2 pairs of histone heterodimers, wraps around histones 1.7 turns -histone 2A and 2B (never apart) and histone 3 and 4 (never apart) |
| what is euchromatin? | active DNA, 10 nm fibers + 30 nm filament |
| what is heterochromatin? | inactive DNA, 30 nm filament |
| ATPase Subunit | two helicase domains and any number of different interaction domains N-terminal helicase domain has DExx domain which hydrolyzes ATP and C-terminal HELICc domain assembles/disassembles nucleus zones |
| DNA Methylation | occurs in CG islands in DNA gene promoters, 5-methyl C enzyme is DNA methyltransferase (DNMT) |
| what binds acetylated lysine? | bromodomains |
| DNA Binding Domains | zinc fingers, homeodomain, basin leucine zipper (bZIP) -alpha helix binding in the major groves of DNA |
| Type 1 Receptor Facts | examples are estrogen, androgens, glucocorticoid; located in cytoplasm; binds the ligand to homodimerize; and translocate to the nucleus |
| Type 2 Receptor Facts | examples are vitamin A, D, and thyroid hormones; located in the nucleus, binds to the ligand to heterodimerize |
| cAMP Pathway | G-protein coupled receptor binding (GTP on alpha) activates adenyl cyclase that catalyzes ATP to cAMP + PPi (3' to 5'), cAMP binds regulatory subunits and releases PKA, PKA phosphorylates and activates PDE, catalyze hydrolysis of cAMP + H2O into AMP; CREB |
| JAK-Stat Pathway | cytokine storm and inflammation cytokine receptor activates Janus kinase which phosphorylates the receptor tail recruiting the stat transcription factor which gets phosphorylated, dimerizes, and activates transcription, basic leucine zipper |
| MAPK Pathway | adaptor protein activates RAS, RAS G-protein activates (GDP to GTP) the mitogen activated protein kinases, phosphorylates the transcription factor AP1, dimerizes, and activates transcription. basic leucine zipper |
| what do you expect to happen when cancers are placed in serum with growth factors and nutrients? | phosphorylation, G-protein activation (GEF), transcription, and translation |
| what do you expect to happen when cancers are washed and deprived of serum? | dephosphorylation, G-protein hydrolysis (GAP) |
| what are painkillers? | opioid agonist receptors (pain relief, euphoria) |
| what are amphetamines? | adrenergic agonist receptors (stimulants) |
| what is Benadryl? | H1 histamine antagonist (allergy relief) |
| what is Zantac? | H2 histamine antagonist (stomach acid relief) |
| what are glucocorticoids? | anti-inflammatory and immunosuppressant anything with -one |
| ER Recognition | N-terminal hydrophobic recognized by SRP (G-protein) opens translocon |
| N-Linked Glycosylation | oligosaccharide transferred to the side chain amide nitrogen of asparagine, comes from dolichol pyrophosphate (dolichol-PPi) |
| H2A Variants | macroH2A: inactive x chromosome H2A.Bbd: active x chromosome |
| what binds to chromodomains? | methylated lysine |
| what does RISC do? | argonaut bound with miRNA that recognizes mRNA transcripts with complementary regions to the guide miRNA blocking translation by degrading the RNA |
| what is a mTOR inhibitor? | transplant immunosuppressant; rapamune (FBP12 target) |
| what is a EGFR inhibitor? | cancer treatment; mainly lung and breast |
| what is a BCR-Abl inhibitor? | leukemia treatment; Gleevec |
| what is a JAK inhibitor? | anti-inflammatory; Xeljanz |
| Elongation Facts | parental strand is read 3' to 5' and new strand is synthesized 5' to 3' |
| DNA Polymerase III | 5' to 3' polymerase, stand elongation 3' to 5' exonuclease, proofreading and excision of mispaired bases |
| DNA Polymerase I | 5' to 3' exonuclease, RNA primer excision 5' to 3' polymerase, gap filling with DNA 3' to 5' exonuclease, proofreading during gap filling |
| DNA Ligase | catalyzes 3' to 5' phosphodiester bond (phosphate + hydroxyl) |
| S Phase | the time when DNA replication or synthesis occurs |
| what is the process of DNA replication elongation? (Eukaryote) | primase and DNA polymerase (pol alpha subunits) synthesizes a piece of RNA and DNA, DNA polymerase (pol epsilon) (lead), DNA polymerase (pol delta) (lag), ribonuclease removes RNA, DNA polymerases inserts DNA, Ligase forms bonds between Okazaki fragments |
| Ribonuclease H | ribonucleases used for excision of RNA primer |
| RNA Nucleotides | AUGC |
| DNA Nucleotides | ATGC |
| what is needed for transcription elongation? (Prokaryote) | RNA polymerization proceeds in the 5' to 3' direction, dsDNA enters core-RNAP and is separated |
| 30 nm filament | a single linker histone H1 binds to each linker region of DNA, which induces nucleosomes to condense into a coil of coils |
| Chromatin Modification: Histones | lysine methylation/acetylation |
| DNMT | known to silence expression of tumor expression genes |
| TET dioxygenase | cytosine demethylation |
| LKB1/AMPK | represents the AMP-activated kinase complex, which responds to low nutrient and low energy conditions |
| Oncogene | anything that stimulates growth through hyperactivation, RAS mutation, receptors, kinases, GEFs |
| Tumor Suppressor | contributors to inactivation, phosphatases and GAPs |
| Peptide Bond Formation | deacylated tRNA goes from P to E site peptidyl-tRNA goes from A to P site |
Created by:
Hopethisworks
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