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Genetic Information Flow: RNA Structure . YILDIRIM BEYAZIT UNIVERSITY FACULTY OF MEDICINE THE DEPARTMENT OF MEDICAL BIOLOGY ASST. PROF. DR. ENDER ŞİMŞEK. Central Dogma. Nucleic Acids. DNA ( Deoxyribonucleic acids ). RNA ( Ribonucleic acids ). NUCLEIC ACIDS. RNA .

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genetic information flow rna structure

Genetic Information Flow: RNA Structure

YILDIRIM BEYAZIT UNIVERSITY FACULTY OF MEDICINE

THE DEPARTMENT OF MEDICAL BIOLOGY

ASST. PROF. DR. ENDER ŞİMŞEK

nucleic acids

NucleicAcids

DNA

(Deoxyribonucleicacids)

RNA

(Ribonucleicacids)

NUCLEIC ACIDS
slide4
RNA

3 Hydrogen Bonds – more stable

2 Hydrogen Bonds

  • RNA bases: A,G,C,U
  • Canonical Base Pairs
    • A-U
    • G-C
    • G-U

“wobble” pairing

different bases in rna and dna
Different bases in RNA and DNA

RNA

only

DNA

only

DNA and RNA

slide12

HairpinStructure

RNA Structures in Different RNA Viruses

slide13

RNA

mRNA

(messengerRNA)

tRNA

(transfer RNA)

rRNA

(ribosomalRNA)

Three RNA Molecules

slide14

RNA structure

RNA

Pyrimidine (C4N2H4)

Purine (C5N4H4)

Adenine

Uracil

Cytosine

Guanine

Thymine (DNA)

Uracil (RNA)

Nucleoside

Nucleotide

base

+ sugar (ribose)

base

+ sugar

+ phosphate

3 major types of RNA

messenger RNA (mRNA); template for protein synthesis transfer RNA (tRNA); adaptor molecules that decode the genetic coderibosomal RNA (rRNA); catalyzing the synthesis of proteins

ribonucleic acid

4 bases

A =

U =

C =

G =

slide16

Base interactions in RNA

Base pairing:

U/A/(T) (2 hydrogen bonds)

G/C (3 hydrogen bonds)

RNA base composition:

A + G = U + C

/ Chargaff’s rule does not apply (RNA usually prevails as single strand)

slide17

A) single stranded regions

B) duplex

C

C) hairpin

D) internal loop

D

E) bulge loop

G

E

F

F) junction

B

A

G) pseudoknot

RNA structure

Primary structure

formed by unpaired nucleotides

Secondary structure

double helical RNA (A-form with 11 bp per turn)

duplex bridged by a loop of unpaired nucleotides

nucleotides not forming Watson-Crick base pairs

unpaired nucleotides in one strand,other strand has contiguous base pairing

three or more duplexes separated by singlestranded regions

tertiary interaction between bases of hairpin loopand outside bases

slide18

RNA structure

Primary structure

Secondary structure

Tertiary structure

C

D

G

E

F

B

A

slide19

RNA

1. mRNA

(messengerRNA)

2. tRNA

(transfer RNA)

3. rRNA

(ribosomalRNA)

Three RNA Molecules

slide20

1- Messenger RNA (mRNA):

  • comprised only 5% of total cellular RNA.
  • Function: Carry genetic information from DNA in the nucleus to ribosomes (in cystol) where it is used as template for protein biosynthesis.
slide22

mRNA is synthesized in thenucleus

Singlestrandedhelix in shape

Carrygeneticinformationfrom DNA tocytosol

Copiedgeneticinformationcalled as transcription

Containsno H bonds

slide23

EukaryoticmRNAcodesfor a single protein-Monosistronic

ProkaryoticmRNAcodesformanyproteins-Polysistronic

slide24

mRNAProcess

in Eukaryotes

mRNA is synthesized as a pre-mRNA form. Processstepsare:

After capping of 5’ end of mRNA, 20-30 ntmRNA is synthesizedand 7-metylguanosine is added on thisend. The role of thisstructure is tobindtoribosomes.

slide25

mRNAProcess

in Eukaryotes

  • mRNA is synthesized as a pre-mRNA form. Processstepsare:
  • After capping of 5’ end of mRNA, 20-30 ntmRNA is synthesizedand 7-metylguanosine is added on thisend. The role of thisstructure is tobindtoribosomes.
  • PolyA tail (50-250 A nt) is added on to 3’ end of mRNA. Thisstructure is importantfortermination of transcriptandstability of mRNA.
slide27

The pre-mRNA molecule undergoes three main modifications.

These modifications are

5' capping,

3' polyadenylation, and

RNA splicing,

which occur in the cell nucleus before the RNA is translated.

slide28

2- Ribosomal RNA (rRNA):

  • In the cell, 80 % of total RNA are rRNA.
  • rRNA are found in combination with several proteins as component of the ribosome which is the site of protein synthesis.
slide29

RNA

1. mRNA

(messengerRNA)

2. rRNA

(ribosomal RNA)

3. tRNA

(transfer RNA)

Three RNA Molecules

slide30

2- Ribosomal RNA (rRNA):

  • In Eucaryotic(mammals):
  • There are 4 size types of rRNA (5S, 5.8S, 18S and 28S) representing 2/3 particle mass of the ribosome.
  • In procaryotic (bacterias):
  • There are 3 size species of rRNA (5S, 16S and 23S)
slide31

Ribozomal RNA

  • Synthesized in nucleus.
  • 80% of total RNA in the cytoplasm.
  • The main structural element of the ribosomes (approximately 65%).
  • Decoding the genetic codes of mRNA in ribosomes.
  • Play a role in all kinds of protein synthesis.
  • Re-used many times.
  • There are weak hydrogen bonds in its structure.
rrna ribosomal rna
rRNA (RibosomalRNA)

Svedberg Units

slide37

RNA

1. mRNA

(messengerRNA)

2. tRNA

(transfer RNA)

3. rRNA

(ribosomalRNA)

Three RNA Molecules

slide38

3- Transfer RNA (tRNA): tRNA represents 15% of total RNA in the cell.

Structure:

1- amino acid attachment site or amino acid acceptor: which terminates with the triplet CCA.

slide39

3- Transfer RNA (tRNA): tRNA represents 15% of total RNA in the cell.

Structure:

1- amino acid attachment site or amino acid acceptor: which terminates with the triplet CCA.

2- Anticodon loop or anticodon triplet

slide40

3- Transfer RNA (tRNA): tRNA represents 15% of total RNA in the cell.

Structure:

1- amino acid attachment site or amino acid acceptor: which terminates with the triplet CCA.

2- Anticodon loop or anticodon triplet.

3- D loop and T loop: contain unusual bases e.g. dihydro-uracil, ribothymidine or methyl guanine.

slide41

Functions of tRNA:

1- transport amino acids to ribosome for protein synthesis. Each tRNA carry only one amino acid. The specific amino acid is attached enzymatically to 3' end of tRNA.

slide42

Functions of tRNA:

2- recognize the specified codon on mRNA to ensure the insertion of the correct amino acid in the growing polypeptide chain. This function is due to anticodon triplet which binds to codon on mRNA by base pairing.

slide43

(Three nucleotide bases on mRNA form a codon which is then translated into specific amino acid.)

slide45

The smallest RNA.

  • Specificforoneaminoacid.
  • Re-usedfordifferent protein synthesis.
  • At least 20 kinds of tRNA in cells.
rna structure 3 levels of organization
RNA structure:3 levels of organization

Primary:

Covalent bonds

  • Secondary/Tertiary
  • Non-covalent bonds
    • H-bonds
    • (base-pairing)
    • Base stacking
common structural motifs in rna
Common structural motifs in RNA
  • Helices
  • Loops
    • Hairpin
    • Interior
    • Bulge
    • Multibranch
  • Pseudoknots
slide50

Pseudoknot. Thepseudoknotstructure is formed by base pairingbetweennoncontiguouscomplementarysequences.

(a) hairpin (b) bulge (c) loop