an introduction to molecular biology and rna motifswangj/rna/slides/dimitri.pdf13 why is rna...
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1Dimitrios Palitskaris
An Introduction to Molecular Biology
and RNA motifs
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What is life?Metabolize, Reproduce, Evolve
…viruses?
Life and its cornerstone
…the cellNucleic acidsProteins
PolysaccharidesLipids
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Nucleic Acids
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1. DNA
Sugar + base + P
Deoxyribose A,C,G,T
Nucleotides
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1. DNA
• Double stranded
• 5’ P 3’ OH
• A-T & C-G (complementary bases)
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1. DNA
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2. RNA
Sugar + base + P
Ribose A,C,G,U
Nucleotides
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• Single stranded
2. RNA
• 5’ P 3’ OH
• A-U & C-G (complementary bases)
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Central Dogma of Biology
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Let’s Review…
DNA
RNA
Proteins
Transcription
Translation
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Why is RNA important?
RNA only can do both!
RNA-World Hypothesis
act as enzymes (catalysts)
DNAcarries genetic information
Proteins
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Types of RNA• mRNA (messenger)• tRNA (transfer)• rRNA (ribosomal)• snRNA (small nuclear)• snoRNA (small nucleolar)• scaRNA (small cajal body-specific)• miRNA (micro)• siRNA (small interfering)• gRNA (guide) • eRNA (efference)• tmRNA
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Non coding RNA (ncRNA)
Includes: tRNA, rRNA, snRNA, snoRNA, miRNA, gRNA, efference RNA, Signal recognition particle RNA,pRNA, tmRNA
RNA genes
Any RNA that isn’t translated into proteins
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What about mRNA?
5’-methylated cap
5’-UTR
CDS Poly-A tail
3’-UTR
UTR= UnTranslated RegionsCDS= CoDing Sequence
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ncRNA vs. mRNA
*However UTRs are not considered ncRNA*
ncRNA
Any RNA that isn’t translated into proteins
mRNA
Contains untranslated regions (5’UTR, 3’UTR)
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StructureIn proteins we have:
• Primary structure (sequence itself)• Secondary structure (general 3d form of local
segments)• Tertiary structure (overall shape, fold)• Quaternary structure (multi-subunit complex)
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Example:MSVHSILFSSEHSEHV
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RNA structureLikewise, we have:• Primary (sequence)• Secondary (direct base pairing)• Tertiary (3d shape in space)
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RNA motifsor RNA elements or regulatory elements
or binding sites or RNA signals
Small RNA segments required for a certain interaction of the RNA with its environment.
They allow a controlled release of informationin the cell from an RNA.
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Functions include:• Protein binding• Basepairing to another RNA• Modifying a nucleic acid bond
RNA motifsFunction of motif depends on:• Sequence • Secondary structure (specific bp)
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Types of RNA motifs
• Single-strand regions• Helices (or stems)• Bulges• Hairpin loops• Internal loops• Junctions
Result of :•WC bp
•non WC bp(mismatch)
•unpaired bases
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A comprehensive example
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Let’s make it more
interesting…
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RNA motifsRegulatory effects:• Regulation of translation• Processing of RNA• Catalytic modification of other RNAs• Transport & position in the cell• Stability of the RNA-transcript• Expression of the encoded protein
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References:• P. Bengert, T. Dandekar, D. Ostareck, A.
Ostareck-Lederer, Thomas Dandekar, RNA Motifs and Regulatory Elements, 2nd
edition, Springer, 2002• http://en.wikipedia.org/
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Picture Resources:• Nicolle Rager Fuller, National Science Foundation • http://genetics.gsk.com/graphics/• http://www.kazusa.or.jp• www.accessexcellence.org• http://employees.csbsju.edu/hjakubowski• http://kvhs.nbed.nb.ca• http://rrna.uia.ac.be• www.genomenewsnetwork.org
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Animation Resources:
• Molecular and Cellular Biology Learning Center, Virtual Cell Animation Collectionhttp://vcell.ndsu.nodak.edu/
• http://www.pbs.org/wgbh/nova/genome/dna.html#• http://www.pwc.k12.nf.ca/wadey/biotech/dna1.swf• http://en.wikipedia.org/
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ENDTHE