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BIOL 200 Study Guide - Restriction Fragment Length Polymorphism, T7 Rna Polymerase, Rna Polymerase Iii


Department
Biology (Sci)
Course Code
BIOL 200
Professor
Richard Roy

Page:
of 3
Lecture16- Molecular Genetics
EcoRI
Complementary DNA (cDNA)
Reverse transcriptase
Poly dG adapter (annealed to 3’)
Poly dC primer
Alkali (remove RNA)
RNAase H (remove RNA)
Lac promoter-> T7 RNA polymerase -> T7 promoter-> recombinant gene expression
neor (selection marker)
Green Fluorescnt Protein(GFP)
Nylon support
Nitrocellulose support
Polynucleotide kinase (PNK)
Restriction fragment length polymorphisms (RFLPs)
Breast cancer related 1 (BRCA1)
Lecture17- Eukaryotic Transcription 1
RNA Polymerase I (ribosomal precursor RNA genes in nucleolus)
Promoter:
UPSTREAM element + UPSTREAM activating factor (UAF)
CORE element + trimeric CORE factor (+TBP)
Insensitive to alpha amatin; no need for ATP
RNA Polymerase II (protein encoding genes; RNAs for splicing; small non-coding functional RNAs)
Highly sensitive to alpha amatin; CTD
RNA Polymerase III (ribosomal RNA genes not in nucleolus; tRNAs; small stable RNAs including U6)
Promoter (within transcribed region):
Internal promoter element-A Box- tRNA
Internal promoter element-B Box- tRNA
Internal promoter element-C Box- 5S
TFIIIC (with TFIIIA in 5S), TFIIIB, RNA Pol III (+tbp)
Intermediate sensitivity to alpha amatin; no need for ATP
Carboxy terminal domain(CTD)
TATA box
TATA-box Binding Protein (TBP)
TFIID (+TBP)
TFIIB
TFIIF+RNA Pol II
TFIIE
TFIIH (possesses helicase and kinase activity)
Couples transcription and repair
Holoenzyme
Xeroderma pigmentosum (NER unable to repair Thymidine dimers)
Lecture18- Eukaryotic Transcription 2
GAL 4
UAS-gal4 System
Antennapedia
Zinc-finger DNA binding domains
C2H2
C4 types
C6 types
Leucine zipper proteins
Helix-Loop-Helix proteins
MADS box TFs
APETALA1
APETALA3
PISTILATA
AGAMOUS
SEPALLATA3 (accessory)
Lecture19- RNA Processing 1
Heptapeptide repeat in large subunit of RNA pol II (+capping, splicing, polyadenylating factors)
S5-P
S2-P
Nascent transcript
Maturation of nacent transcript (capping and methylation on 5’)
7’methylguanylate cap (5’-5’ linkage)
GU---APyrimidine rich region---AG (GU-AG conserved border region)
Transesterification reactions
Lariat intron
Spliceosome: 5 snRNPs (each consist of snRNA + 6-10 proteins)
Debranching enzyme
Group I introns (rRNA genes of protozoans)
Self-splicing
Group II introns (some rRNA and tRNA genes in mitochondria and chloroplasts)
Self-splicing
Lecture20- RNA Processing 2
U2AF65
U2AF35
Exonic splicing enhancers
SR proteins with RPM domains
Cross-exon recognition complex (U2, U2AF, SR proteins, U1)
Sex Lethal protein (Sxl)
Transformer protein (Tra)
Rbp1
SR protein
Tra 2
SR protein
Double sex protein (Dsx)
Presumptive exons
AUUUA in 3’UTR
Destabilizing motif for RNAs
Polyadenylation
Slow phase (PAP) -12A
Fast phase (PAP + PABP II- 200A
Not in histones
AAUAAA xxxxx G/U sequence recognition by cleavage and polyadenylation factors
AAUAAA
Polyadenylation signal
Cleavage factor I and II (CFI and CFII)
Cleavage and polyadenylation specificity factor (CPSF)
Poly A polymerase (PAP)
PABP II
RNA editing: Deaminating enzyme (A->I; C->U)
Apolipoprotein B
Lecture21- Nucleo-Cytopl Transport
Hydrophobic FG domains
FG repeats
FG nucleoporins
Nuclear Pore Complex (NPC)
Nuclear Localization Signal (NLS)
Lysine, arginine rich
Nuclear Export Signal (NES)
Leucine rich
Pyruvate kinase
Ran GTPase
Importin alpha
Binds NLS
Importin beta
Binds FG repeats
GTPase acceleration function protin (GAP)
Guanine exchange factor (GEF)
Exportin 1
For regular cargo
Tri-molecular cargo complex
Exportin t
For tRNAs
mRNA exporter (Tap+ Nxt1)
For mRNAs; Ran-independent
mRNP remodeling
Insect polytene chromosomes
Balbiany rings
Lecture22- Protein Synthesis 1
Genetic code
Codon
Anticodon
Start codon- AUG
Stop codon- UAA,UAG, UGA
mRNA+tRNA+rRNA= RNAs in protein synthesis
Aminoacyl-tRNA synthetase
High energy ester bond
Prokaryote ribosome:
50S large subunit-5S+23S +31proteins
30S small subunit-16S +21 proteins
Eukaryotic ribosome:
60S large subunit-5S +5.8S + 28S+ 50proteins
40S small subunit-18S+ 33 proteins
+eIF6
+eIF3
eIF6
eIF3
eIF1A
eIF2A-GTP + MET-tRNAiMet
Chinese Hamster ovary (CHO)
Formyl group on 1rst methione in bacterial tRNAs
eIF4:
eIF4A
eIF4B
eIF4E
eIF4G
RNA helicase
important for structure
Cap-binding protein
Affinity for eIF3
Shine-Dalgarno sequence
Pairs with 16S in prokaryotes
Kozak sequence (ACC-AUG-G)
Lecture23- Protein Synthesis 2
CCA
Added to 3’ of tRNA
Aminoacy tRNA synthetase
rRNA
eIF6 and eIF3
tRNAiMet
Formyl group
On 1rst met in bacteria
ACCAUGG
Kozak sequence
eIF4A/B/E/G
eIF2-GTP
EF1alpha-GTP+aa
23S RNA
Rybozyme
Peptidyl transferase activity
eRF1
eRF3-GTP
PABPI
Lecture24- Protein Folding and Quality
Control
Hsp70
Hsp40
GroEL
GroES
PrPc state
Conformer state
PrPsc state
Non-conformer state
Rough ER
Lecture25- Transl and Post-Transl
regulation of gene expression
SRP
SRP receptor
Translocon
Signal peptidase
Disulfide bridges
Protein Disulfide Isomerase (PDI)
Ero1
Bip
Calnexin
Ire1
Hac 1
Ferritin
Iron response (IRE) elements
IRE-BP
Inactive at high iron
Transferring receptor
Nanos
Hunchback
Kinase
Ubiquitin
E1 ubiquitin activating enzyme
E2 Ubiquiting conjugating anzyme
E3 ubiquitin ligase
Substrate specification
proteosome
Lecture26- Proteins: Structure, Function,
Strategies
GFP
Aequores Victoria
deltaG
Km
Kd dissociation constant
Amphilates
Isoelectric focusing (IEF)
GST
Glutathione
His
Nickel
HA
Myc
FLAG
Lecture27- Chromatin Modifications
Histones
Nucleosomes
Chromatin
HMLalpha
HMRa
MATa or alpha
RAP1
SIR1
SIR234
SIR3 colocalizs with telomeres
URS1
Ume6 [DBD+RD]
Sin3
Rpd3
HDAC
UAS
Gcn4 [DBD+AD]
Gcn5
HAT
H3 K4 methylaion
Active
H3 K9 methylation
Inactive
Histone deacetylase (HDAC)
Histone acetytransterase (HAT)
Barr bodies
XIST RNA
No-coding; estinguishes gene expression on X
Lecture28- New Roles for mRNA
Centromeric region
Swi6p
Clr4p
Rdp1
T7 promoter
T7 polymerase
Dicer
RNAaseIII like enzyme
RNA-induced silencing complex (RISC)
Helicase and slicer activities
Lin 4
Lin 4 small miRNA
Argonaute
Lecture29-
Trypsin proteolysis
Lecture30-
kanMX
tkHSV
Thymidine kinase
ganciclovir
Nucleotide like molecule