RNA

YUSRON SUGIARTO, STP, MP, MSc

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Central Dogma of Molecular Biology

The flow of information in the cell starts at DNA, which replicates to form more DNA. Information is then transcribed into RNA, and then it is translated into protein. The proteins do most of the work in the cell.

Structure of RNA
A. Chain of nucleotides like DNA B. Parts of an RNA nucleotide 1. 5 carbon sugar: ribose 2. phosphate group 3. nitrogen base

O C HN H2N-C 5 HO-CH2 N O 3 O O P O O C C N CH

N
NH2 1 C N O CH2 C N O CH CH

DNA is a polymer of 2-deoxyribonucleotides

5 end

O C HN C CH N NH2 C N C HC N CH N C O CH2 CH3

2-deoxyribose sugars Phosphodiester linkages Directional chain (5 to 3) 4 Bases purines: adenine & guanine pyrimidines: cytosine & thymine

O O P O O

O
O P O O

C N

CH2 3

3 end

O-PO32

O C HN H2N-C 5 HO-CH2 N O 3 O O P O O 2 OH C C N CH

N
NH2 1 C N O CH2 C N O HN CH CH

RNA is a polymer of ribonucleotides

5 end

O C CH CH N NH2 C N C N CH

ribose sugars Phosphodiester linkages Directional chain (5 to 3) 4 Bases purines: adenine & guanine pyrimidines: cytosine & uracil

O O P O O

OH

C O CH2

O
O P O O

HC C N OH N CH2 3 O

3 end

O-PO32

OH

C. The RNA bases 1. Purines a. Adenine (A) b. Guanine (G) 2. Pyrimidines a. Cytosine (C) b. Uracil (U)

D. Shape of the molecule: several shapes, but all are single stranded E. Differences between DNA and RNA 1. Different sugars: DNA=deoxyribose, RNA=ribose 2. Different base: DNA=thymine, RNA=uracil 3. Different shape: DNA=double helix, RNA=single strand

F. Types of RNA 1. Messenger RNA (mRNA): long, single stranded molecule that carries DNA message to the ribosomes

2. Transfer RNA (tRNA): small clover-leaf shaped molecules that pick up amino acids and take them to the ribosomes

3. Ribosomal RNA (rRNA): makes up the structure of ribosomes along with proteins

rRNA

rRNAribosomal RNA Two subunits Ribosome reads mRNA and produces a polypepide

3 Types of RNA
1.mRNA Messenger RNA Single strand Serves as a template (pattern for translation)

3 Types of RNA
2. tRNA
Transfer RNA

20+ types of tRNA Cloverleaf shape Each tRNA is specific for an amino acid

3 Types of RNA
3. rRNA
Ribosomal RNA

Globular 2 parts compose the ribosome Where are they made?

F.

The roles of RNA

1. RNA is not the genetic material and does not need to be capable of serving as a template for its own replication.

2. RNA functions as the intermediate, the mRNA, between the gene and the protein-synthesizing machinery. 3. RNA functions as an adaptor, the tRNA, between the codons in the mRNA and amino acids.

F.

The roles of RNA

4. RNA also play a structural role, as in the case of the RNA components of the ribosome. 5. RNA is as a regulatory molecule, which through sequence complementarity binds to, and interferes with the translation of, certain mRNAs. 6. Some RNAs are enzymes that catalyze essential reactions in the cell.

The phosphate groups of DNA and RNA are negatively charged

5 HO-CH2 O

O M+ O P O O CH2

N
O

A phosphodiester group has a pKa of about 1, and so will always be ionized and negatively charged under physiological conditions (pH ~7). Nucleic acids require counterions such as Mg2+, polyamines, histones or other proteins to balance this charge.

O P O M+ O

CH2

N
O

O O P O M+ O 3 O-PO32 M+ CH2

N
O

Transcription
A. Transcription: the process in which DNA makes a complementary copy of mRNA B. Steps of transcription 1. DNA untwists and bases separate 2. Only a small section of the DNA is involved and only one strand acts as the template

3. RNA polymerase adds RNA nucleotides in the correct order as indicated by the DNA molecule

4. Base pairing rules apply a. If DNA has a T, RNA will match by adding A b. If DNA has an A, RNA will match by adding U c. If DNA has a C, RNA will match by adding G d. If DNA has a G, RNA will match by adding C

5. Fill in correct mRNA sequence DNA: A T G C C T A G A RNA: U A C G G A U C U

Most RNA molecules consist of a single strand that folds back on itself to form double-helical regions hairpin

single strands
bulge A

internal loop CGU

GCA

A-form double helix

The loops and hairpins have few or no base-pairs

In RNA, G pairs with C and A pairs with U.

Transcription
Enzyme: RNA polymerase (3 kinds in eukaryotes) unzips DNA and adds RNA nucleotides in the 5 3 direction

Transcription
Promotor Site where the polymerase attaches Termination site Site where transcription ends Transcription Unit The stretch of DNA transcribed

Transcription
In eukaryotes, the mRNA is modified after transcription A 5 cap is added (guanine nuicleotide) Poly A tail (adenine) 50-250 nucleotides long

Transcription Graphics

RNA Processing
A. There are large sections of RNA molecules that are not used in making protein. These must be cut out before the RNA leaves the nucleus

B. Sections that are cut out (not used to make the protein) are called introns C. Sections that are used to make the protein are called exons (they are expressed) D. Some parts of RNA molecules may be exons when one protein is made and introns when another protein is made

The Genetic Code

A. Tells the cell how to assemble a protein B. Proteins determine the structure and function of organisms C. Proteins are made of amino acids D. The bases in mRNA (as made from DNA) determine what amino acids will be assembled into a protein

E. 20 amino acids can be assembled into thousands of proteins F. This works similar to the way letters are assembled to make words - 26 letters in English alphabet make thousands of words

G. Codon: a sequence of 3 bases in mRNA that codes for 1 amino acid 1. Examples GUG = valine GUA = valine GUC = valine

GAC = aspartic acid GAU = aspartic acid UCU = serine UCC = serine UCG = serine Which base could vary and still stand for the same amino acid? - 3rd base

2. The genetic code is redundant: more than 1 codon can stand for 1 amino acid 3. The genetic code is NOT ambiguous: 1 codon cannot stand for more than 1 amino acid

4. Special codons AUG = methionine = start = the first codon of every protein UAA = stop UAG = stop UGA = stop these end a protein

Fill in the chart

mRNA codon AAG Amino acid Lysine

CGU
GGG

Argenine
Glycine

Translation
A. Translation: the process in which the mRNA message is decoded and a protein is made. B. Steps in translation 1. mRNA made in the nucleus leaves and travels to a ribosome 2. mRNA attaches to a ribosome

3. The ribosome reads the first codon, which is always AUG 4. A tRNA that has a sequence of three complementary bases to mRNA brings in the appropriate amino acid. The complementary bases on tRNA are called an anticodon.

5. The ribosome reads the second codon and a tRNA with a matching anticodon brings in a second amino acid 6. The ribosome joins the two amino acids with a linkage that is called a peptide bond 7. The ribosome moves down and reads the next codon

8. tRNA molecules keep bringing in the appropriate amino acids 9. The process continues until a stop codon is reached 10. The polypeptide leaves the ribosome and folds to become a protein

Translation
RNA protein Structure of a ribosome Protein and rRNA Most common form of RNA Ribosomes are formed in the nucleolus

Translation
Three stages of translation 1. Initiation 2. Elongation 3. Termination

Initiation
Small ribosomal subunit binds to both the mRNA and the tRNA Large ribosomal subunit attaches

Elongation

Codon recognition--mRNA and tRNA form hydrogen bonds at the A site of the ribosome
Peptide bond forms between amino acid at the A site and the growing polypeptide at the P site Translocation Ribosome moves the tRNA with polypeptide from the A to the P

Exit site

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Termination
Translation continues until stop codon on mRNAUAA, UAG, or UGA Polyribosomes Multiple ribosomes translating the same rRNA (polysomes)

Genetic Code Table codons

Universal for almost all organisms P. 308 in text Use it to decode the base sequence on the next slide

Transcription and Translation in Cells

Prokaryotic Cell

Eukaryotic Cell

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THANK YOU
YUSRON SUGIARTO, STP, MP, MSc

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