Chapters 11

1
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.

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Structure of RNA

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

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DNA is a polymer of2-deoxyribonucleotides
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RNA is a polymer of ribonucleotides
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• The RNA bases
• 1. Purines
• a. Adenine (A)
• b. Guanine (G)
• 2. Pyrimidines
• a. Cytosine (C)
• b. Uracil (U)

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• Shape of the molecule several shapes, but all
  are single stranded
• Differences between DNA and RNA
• 1. Different sugars
  DNAdeoxyribose, RNAribose
• 2. Different base DNAthymine, RNAuracil
• 3. Different shape DNAdouble helix,
  RNAsingle strand

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

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

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

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rRNA

• rRNAribosomal RNA
• Two subunits
• Ribosome reads mRNA and produces a polypepide

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3 Types of RNA

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

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3 Types of RNA

• 2. tRNA
• Transfer RNA
• 20 types of tRNA
• Cloverleaf shape
• Each tRNA is specific for an amino acid

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3 Types of RNA

• 3. rRNA
• Ribosomal RNA
• Globular
• 2 parts compose the ribosome
• Where are they made?

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• The roles of RNA
• RNA is not the genetic material and does not need
  to be capable of serving as a template for its
  own replication.
• RNA functions as the intermediate, the mRNA,
  between the gene and the protein-synthesizing
  machinery.
• RNA functions as an adaptor, the tRNA, between
  the codons in the mRNA and amino acids.

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• 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.

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The phosphate groups of DNA and RNA are
negatively charged
5
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.
3
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Transcription

• Transcription the process in which DNA makes a
  complementary copy of mRNA
• 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

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

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• 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

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• 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

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Most RNA molecules consist of a single strand
that folds back on itself to form double-helical
regions
The loops and hairpins have few or no base-pairs
In RNA, G pairs with C and A pairs with U.
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Transcription

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

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Transcription

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

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Transcription

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

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Transcription Graphics
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RNA Processing

• 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

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

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The Genetic Code

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

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

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

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• 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

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• 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

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

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(No Transcript)
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Fill in the chart
mRNA codon Amino acid
AAG Lysine
CGU Argenine
GGG Glycine
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Translation

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

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• 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.

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• 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

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• 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

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Translation

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

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Translation

• Three stages of translation
• Initiation
• Elongation
• Termination

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Initiation

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

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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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(No Transcript)
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Termination

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

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Genetic Code Tablecodons

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

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Transcription and Translation in Cells
Prokaryotic Cell
Eukaryotic Cell
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THANK YOU
YUSRON SUGIARTO, STP, MP, MSc