RNA
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BI270 CELL BIOLOGY Part II

The Cell Cycle: G1 è S è G2 è M
        G0 = no cell cycle occurring
       
Apoptosis = ??

Cyclins and cyclin-dependent kinases
MPF = ??

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synchronized cell cultures; AUTORADIOGRAPHY

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Study the CELL CYCLE in Onion Root Tips here

Evolution of MITOSIS in Eukaryotes
Dinoflagellates --  no HISTONES!                (nuclear) MEMBRANE TUNNELS  
 
Naegleria gruberi --  promitosis                     endosome and polar bodies 

horizontal rule

TELOMERES = ?

rich in G and T bases (species-specific sequence)

LAGGING STRAND SYNTHESIS ??

Telomerase = CATALYTIC ribonucleoprotein

reverse transcriptase activity = ?? = ??  

Elizabeth Blackburn

CA-rich RNA sequence (species-specific)  

and Carol Greider

essential for TELOMERE synthesis

TRANSLOCATION and repeated sequences

SOMATIC vs. GERM CELLS => Cloning Problems??

See TELOMERASE animation here!

See another TELOMERASE animation here!

Carol Greider Awarded Nobel Prize

line5a.gif (1839 bytes)

RIBONUCLEIC ACID (RNA)

NITROGENOUS BASE (URACIL replaces Thymine) + RIBOSE (5C Sugar) + PHOSPHATE

RNA is synthesized as a SINGLE-STRANDED molecule; but can become
DOUBLE-STRANDED RNA
Þ G º C or A = U

varied 3-D conformation and multi-functional

 RNA World??

TRANSCRIPTION = RNA synthesis

DNA:RNA hybrid = heteroduplex

RNA polymerase.gif (313518 bytes)RNA polymerase
Note active site; exit channel; downstream clamp
1) DNA-dependent
2) multi-functional
Þ a) break H-bonds, etc.
b) recognize & insert nucleotides
c) catalyze PPi cleavage
[CLICK on the DIAGRAM]

See RNA Polymerase II animation here

PROKARYOTES: one RNA polymerase + co-factors
Sigma Factor (s ) and the Promoter region            TATAAT consensus sequence
Rho Factor (r ) and the Terminator region              (r in some genes)

E. coli s 70 vs. human RAP 30/74

EUKARYOTIC RNA Polymerases =

RP I -- most rRNA
RPII -- mRNA; snRNA
RPIII -- tRNA; 5S rRNA

Eukaryotic Transcription Control Factors e.g.
ZINC FINGERS, LEUCINE ZIPPERS, etc.

line5a.gif (1839 bytes)

RNA Transcription & Processing in Eukaryotes

The NUCLEOLUS:  rRNA synthesis & processing [except 5S rRNA segment]

MULTIPLE COPIES of rDNA genes with INTERGENIC SPACER SEQUENCES

tandemly repeated genes (» 7,000,000 rRNA copies/day)

processing via snoRNAs (e.g. U3) and snoRNPs  = small nucleolar RNAs
RNPs = RiboNucleoProteins                                           anti-sense RNAs = ??
                                                                                                ribose methylation; pseudouridine

S = SVEDBERG UNITS Þ Coefficient of Sedimentation

  

45S rRNA 

precursor

  

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41S rRNA with

Introns and Exons

   

í   

î

  

18S rRNA+ PROTEINS   

28S rRNA + 5.8S rRNA + PROTEINS + 5S rRNA

  

ê   

ê

  

small (40S) subunit  

large (60S) subunit

Intact EUKARYOTIC RIBOSOME = 80S ribonucleoprotein complex
                                                                            (rRNA + proteins)

Intact PROKARYOTIC RIBOSOME = 70S (50S + 30S)

PRIMARY BINDING PROTEINS and SECONDARY BINDING PROTEINS

POLYSOMES = ??

line5a.gif (1839 bytes)

POLYCISTRONIC vs. MONOCISTRONIC mRNA

SYNTHESIS and PROCESSING of EUKARYOTIC mRNA Þ the genetic message

Eukaryotic RNA Polymerase II Þ “TATA Box”            Many GTFs [general transcription factors]

Heterogeneous Nuclear RNA = hnRNA (= pre-mRNA)

bullet7-Methylguanosine Cap (5’) and Poly-A "Tail" (3’, via poly(A) polymerase)
bulletLeader (5’) and Trailer (3’) segments [Non-coding regions]
bulletIntrons (Intervening Sequences) vs. Exons
       ê                                                     ê
     cleaved out                                         spliced together è mRNA

POST-TRANSCRIPTIONAL MODIFICATIONS

See Animation Here

small nuclear RNAs = snRNAs = U1 - U8 (and counting) ("Uridine-rich")
small ribonucleoproteins =
snRNPs = "snurps"

bulletThe Spliceosome(60S)(Abelson & Brody)
bulletU1 + U2 + U4 + U5 + U6 + proteins

 

conserved Consensus Sequences on Introns Þ
for binding of  5’GU and 3’AG
 
conserved Pyrimidine-rich region Intron/snRNPs
U1 ® 5’GU U5 ® 3’AG U2 ® Branch Point
U4/U6 ® splice exons Lariat formation  

SPLICESOME ANIMATION 1

SPLICESOME ANIMATION 2

SPLICEOSOME ANIMATION 3

 The 5’ (trimethylgauanosine) M3G Cap for snRNP transport into the nucleus.

line5a.gif (1839 bytes)

SYNTHESIS and PROCESSING of EUKARYOTIC tRNA Þ the amino acid carriers

MULTI-GENE CLUSTERS

RW Holley and the "CLOVERLEAF" configuration (3-D)

bulletLoops, Double-stranded Helical regions, etc.
bulletMethylation and other post-transcriptional modifications
bulletCleavage of LEADER segment, etc.

tRNA 215B.gif (3285 bytes)Amino Acid Arm Þ CCA at 3’ end

Nucleotidyl Transferase = ??

Dihydrouridine Arm (DHU) Þ AA recognition

TYC Arm Þ ribosomal recognition

Anticodon Arm Þ complementary to mRNA codon

variable arm Þ [enzyme recognition??]

INVARIANT vs. SEMI-INVARIANT BASES tRNA 215A.gif (23696 bytes)

            SEE 3-D tRNA: CLICK HERE  Þ

Crick: WOBBLE HYPOTHESIS

line5a.gif (1839 bytes)

RNase P (E. coli) Þ precursor tRNA processing: catalytic RNA

snRNA M1 = Human mitochondrial rRNA and catalytic RNP = (ribonucleoprotein)

Altering Amino Acid after tRNA loading Þ ??

RIBOZYMES = catalytic RNAribozyme1.gif (51473 bytes)

Cech et al.      Tetrahymena (ciliate protozoan)

“cyclized” rRNA 
ACTIVE SITE = 2 RNA Domains
Ribozyme 3-D structure Þ lowers the Energy of Activation (Ea)
GUANOSINE and Mg++
POLYMERASE with internal template
PENTACYTIDILIC ACID primer for POLYMERASE activity
Mg++ and Tertiary Structure (3-D)

pre-mRNA  and  pre-rRNA processing; (endonucleases, ligase, kinase, etc.)

pre-mRNA and pre-rRNA processing

snRNPs and petidyl transferase ® catalytic moiety = RNA

Group I - guanosine; "cyclized" rRNA; variable sequence, similar shape

Group II - highly conserved; Lariat formation

GUIDE RNAs in Kinetoplastid flagellates

RNA Þ CATALYTIC and SELF-REPLICATING

Visit the Cech Lab Site

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