An Introduction to Molecular Biology and RNA motifs Dimitrios - - PowerPoint PPT Presentation

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An Introduction to Molecular Biology and RNA motifs Dimitrios - - PowerPoint PPT Presentation

Nov 11, 2023 340 likes •656 views

An Introduction to Molecular Biology and RNA motifs Dimitrios Palitskaris 1 2 What is life? Metabolize, Reproduce, Evolve viruses? Life and its cornerstone Nucleic acids the cell Proteins Lipids Polysaccharides 3

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Dimitrios 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 cell

Nucleic acids Proteins Polysaccharides Lipids

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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) DNA carries 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 Regions CDS= 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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Structure

In 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 structure

Likewise, we have:

  • Primary (sequence)
  • Secondary (direct base pairing)
  • Tertiary (3d shape in space)
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RNA motifs

  • r RNA elements or regulatory elements
  • r 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 information in the cell from an RNA.

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Functions include:

  • Protein binding
  • Basepairing to another RNA
  • Modifying a nucleic acid bond

RNA motifs

Function 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 motifs

Regulatory 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 Collection http://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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