BCMB 3100: TEST 3
59 Cards in this Set
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topoisomers
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adds/ removes supercoils in DNA
cleaves 1 or noth DNA strands- unwinds/ overwinds cleaved ends- rejoins ends
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chromatin
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association of DNA w/ proteins= compact / manageable
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histones
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major protein of chromatin
5 basic histones in euks= H1/ H2-A/ H2-B/ H3/ H4
histones bind to sugar phosphates
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nucleosome
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chromatin structural unit- segment of DNA wrapped around histones
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solenoid
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higher level chromatin structure
coil wound in tightly packed helix
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nuclease
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hydrolyzes phosphodiester bonds
RNases= RNA substrate
DNases= DNA substrate
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exonuclease
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starts at ends of chains
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endonuclease
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hydrolyze sites within a chain
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restriction endonuclease
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site specific
cleaves both DNA strands w/ in or near specific site recognize by enzymes
- Type 1 RE= catalyze methylation of host DNA/ cleavage of non-methylated DNA at recognition site
- Type 2 RE= cleaves non-methylated DNA
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DNA polymerase
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primer needed
activities:
5-3 polymerase
3-5 exonuclease (proofreading)
5-3 exonuclease (editing)
1= repairs DNA/ DNA synthesis
2= DNA repair
3= DNA replication enzyme
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DNA photolyase
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directs DNA repair
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excision repair pathway
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alkylation/ methylation/ demination
excision repair enzymes detect damaged DNA
1. endonuclease cleaves damaged DNA
2. 12-13 nuc gap occurs
3. filled by DNA poly 1 and nick is ligated by ligase
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PCR
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1. heat melts DNA duplex- primers added
2. DNA polymerase extends primers
3. repeat
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RNA polymerase
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no primer required
sigma subunit= finds site where transcription begins - intiates RNA synthesis then dissociates
- leaving core enzyme (aBB'w)= contains active site
B= binds DNA template
w= restores denatured polymerase
a= required for core enzyme assembly
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intiation
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1. promoters direct RNA poly to correct initiation sites- sigma unit helps find it
2. shifts to open complex- DNA unwinds
3. RNA chain is initiated
4. core enzyme binds- elongates
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elongation
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unwinds DNA - closed promoter to open promoter complex
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termination
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RNA-DNA hybrid dissociates- RNA poly releases DNA
stop signal terminates elongation
some sites require rho (p) protein= binds RNA so that breaks DNA-RNA
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transcription factors
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required for formation of transcription complex
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housekeeping genes
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encode proteins required for metabolism
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activators
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regulatory proteins that bind DNA and increases rate of transcription
interacts with RNA poly- increases RNA poly binding/ bubble formation
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repressors
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regulatory proteins that bind DNA to repress transcription
-prevents RNA poly from binding promoter
- inhibition of initiation reactions
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inducer
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ligate that binds/ inactivates repressors
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corepressor
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ligand that binds/ activates repressors
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catabolite activator protein (CAP)
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stimulates transcription of lac operon
binds to site near promoter
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cis-acting element
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DNA sequences that regulate expression of genes located on same DNA molecule
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INR
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initiator element
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DPE
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downstream core promoter element
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transcription initation
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TFII opens double helix and phosphorylates CTD- allows RNA poly 2 to leave promoter
CTD= carboxyl terminal domain of RNA poly II
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transacting elements
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proteins that recognize cis-acting elements/ regulate RNA synthesis
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nuclear hormone receptors
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bind to specific regions of DNA called response elements
2 domains
1. DNA binding domain= toward center- specific DNA binding
2. ligand binding domain= toward carboxyl terminus- changes structure- enables receptor to recruit other proteins to regulate transcription
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agonists
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ligands that activate NHR
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antagonists
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ligands that inhibit NHR
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chromatin remodeling agents
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use hydrolysis of ATP to shift nucleosomes- opens up regions for transcription
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histone deactelylases
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transcription repression
genes need to be repressed at certain times
catalyze removal of acetyl groups from histones- results in inhibition of transcription
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mRNA processing
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1. 5' capping
2. 3' polyadenylation
3. splicing
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formation of 5' cap
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1. phosphohydrolase
2. guany transferase
3. methylation
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3' polyadenylation
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poly A polymerase--- poly A tail
begins when RNA poly II transcription complex synthesizes a polyad signal
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splicing
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takes place on splicesomes= complexes of proteins and snRNA
snRNPs= small ribonuclear proteins
intron removal
- splicesome positions adenylate residue near 5' splice site
- 2'-OH attahces to 5' end on intron- 3'-OH attacks 3' splice site
- ends of exons are joined- intron is released…
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CTD
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recruits enzymes to synthesize 5' cap
recruits componentsof splicing complex
recruits endonuclease that cleaves pre-mRNA to expose site for poly A adenylation
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wobble
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recognition of 3rd base is less discriminating then first 2
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isoacceptor tRNA
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diff tRNAs that attach to same aa
-recognize synonymous codons
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aminoacyl tRNA synthetases
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specific aa covalently attached 3' end of tRNA
high energy when aa is activated
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initiation complex
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assembles at 1st mRNA codon- deassembles at termination site
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polysomes
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group of ribosomes bound to mRNA/ carry out translation
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3 tRNA binding sites
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A= amino site- binds incoming tRNA
P= peptidyl site- binds tRNA w/ growing peptide chain
E= exit- binds uncharged tRNA before it leaves ribosome
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initiation of translation
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1st codon= AUG= MET
initiation complexes assemble at sites
initiation factors required= IF-1/ IF-2/ IF-3
GTP required
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Elongation of translation
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insertion of aa-tRNA by EF-TU during chain elongation
-EF-TU positions correct amino-tRNA in A site- contacts w/ ribosome in P-site
-formation of correct complex causes EF-TU to dissociate
formation of peptide bond catalyzed by peptidyl transferase
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translocation step
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peptidyl tRNA moves from A site to P site
elongation factor (translocase) bound to GTP competes for partially open A site
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termination of Translation
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stop codons= UGA/ UAA/ UAG
release factors (RF-1/ RF-2/ RF-3) bind and cause peptidyl tRNA to release chain
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signal recognition particle (SRP)
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GTP binding
binds signal sequence as it exits ribosome
binding of SRP to ribosome stops protein synthesis
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translocon
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protein conducting channel
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transferrin
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blood protein that transports iron
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transferrin receptor
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membrane protein
binds iron rich transferrin= helps it into cell
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ferritin
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iron storage protein in cell
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IRE
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iron response element
in absence of iron- IRE binding proteins bind to IRE- prevents translation
iron present= iron binds to IRE-BP dissociates transferrin receptor mRNA is degraded
IRE-BP= iron sensor
iron is high= ferritin is synthesized to store iron
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small interfering RNA (siRNA)
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bound by proteins to form RNA induced silencing complex (RISC)
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RISC
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...
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RISC
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locates mRNA to siRNA and degrades mRNA
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microRNAs
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target specific mRNA for cleavage
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BCMB 3100: Test 1