Overview of Module 7

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Overview of Module 7

• By the end of module 7, you will be able to
• Describe the structure of DNA and identify its
  components.
• Describe how DNA is replicated in prokaryotes and
  eukaryotes.
• Describe the process of transcription and give
  the role of RNA polymerase in transcription.
• Define mRNA, tRNA and rRNA and give their roles
  in translation.
• Describe the initiation, elongation and
  termination stages of translation.

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Module 7Fundamentals of Protein Synthesis
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Sections In This Module

• I. DNA, the Chromosome the Gene
• II. Transcription
• III. Translation/Protein Synthesis

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I. DNA, The chromosomes the gene
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Review of DNA--Nucleotides

• DNA, deoxyribonucleic acid, is a nucleic acid and
  so is made of nucleotides.
• A nucleotidephosphate 5-carbon sugar
• nitrogenous base
• DNAs nucleotides are adenine (A), thymine (T),
  cytosine (C) and guanine (G)
• Complementary Base Pairing
• They are paired AT (2 hydrogen bonds)
• And CG (3 hydrogen bonds)
• The paired bases form the rungs of the double
  helix.

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Review of DNA--Backbone

• The backbone of each half of the double helix is
  made of
• Sugardeoxyriboseattached to nucleotide
• Phosphate attached to 3 carbon of 1 sugar
• and 5 carbon of the next sugar
• Backbones are anti-parallel to each other so that
  the 3 end of 1molecule is across from the 5 end
  of the other molecule.

5 end
3 end
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Structure of 1 Strand of DNA
5 end
The backboneblueshowing the alternating
phosphates and sugars.
The nucleotides T, A, C and G. Note that T and C
are smallerthe pyrimidines, and A and G are
largerthe purines.
3 end
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The Double Helix
Note that the 2 strands are anti-parallel and A
T and CG are always paired.
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Nuclear DNA

• Most eukaryotic DNA in the nucleus.
• Humans have about 5 feet of DNA in every nucleus!
  This is over 1 billion pairs of nucleotides or
  base pairs long.
• DNA is the same in every cell of an individual.
• A gene is a short stretch of DNA that is
  transcribed to RNA(see next section).
• Humans have about 20,000 - 25,000 genes.

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Chromosomes

• Segments of nuclear DNA are arranged into
  chromosomes.
• Humans have 46 chromosomes in their cells 23
  from each parent.
• So humans have 2 similar copies of each gene

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Mitochondrial DNA

• The mitochondria of the cell each have a small
  circle of DNA.
• Contains 37 genes needed for normal mitochondrial
  function.
• All mitochondria come from our mothers
• Can use mitochondrial DNA to trace human movement
  in history.
• All people on earth descended from 18 ancestral
  Eves.

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DNA Replication

• In order for a cell to divide by mitosis, it must
  first double the DNA.
• This doubling of DNA, DNA Replication, occurs
  during the S part of the cell cycle
• S stands for Synthesis of DNA
• The DNA is copied exactly resulting in 2
  identical molecules.

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DNA Replication, Briefly

• DNA double helix opens to single strands.
• DNA Polymerase attaches to short RNA primer and
  replicates the DNA
• Reads the old base and adds complementary new
  base,
• Then attaches the new backbone and proofreads
  the result.
• Then moves to the next base.
• 3. Continues until all the DNA has been
  replicated.

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Limitations of the DNA Polymerase

• DNA polymerase can only read the old strand in 3
  ? 5 direction
• Can only make new DNA in 5 ? 3 direction
• Since the 2 strands are anti-parallel, this
  results in replication where
• One strand of the old DNA is copied quickly, the
  leading strand
• Other strand of the old DNA is copied more
  slowly, the lagging strand

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Concept Check

• Below is part of one strand of DNA. Give the
  other strand.
• 3 -A T T C G G A G C T T C C- 5
• 2. What does anti-parallel mean?
• What is the main enzyme used in replicating DNA?
• What stage of the cell cycle does replication
  occur?

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Concept Check Answers

• 1. If 3 -A T T C G G A G C T T C C- 5
• Then 5-T A A G C C T C G A A G G- 3
• 2. Anti-parallel means that the 2 strands of DNA
  are arranged head-to-tail or opposite each other.
• 3. The main enzyme is DNA polymerase.
• 4. Replication takes place in the S part of the
  cell cycle.

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II. RNA and Transcription
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Structure of RNA

• RNA is a nucleic acid, but with some differences
  from DNA
• Also, RNA is copied from DNA, the master
  molecule.

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RNA in Protein Synthesis--rRNA

• rRNA (ribosomal RNA) is a structural component of
  the ribosomes of all cells.
• Ribosomes are structures in cells where protein
  synthesis occurs.
• Free in cytoplasm or attached to rough ER.
• Has large and small subunits fit together.

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RNA in Protein Synthesis-mRNA

• mRNA (messenger RNA) is a copy of a gene that
  codes for making a protein.
• Used as template for making a protein in the
  cytoplasm.
• mRNA is modified in the nucleolus of eukaryotic
  cells
• Cap of modified G added to 5 end
• Poly A Tail of up to 250 As added to 3 end
• Sections of the new mRNA, the introns, are
  removed and the remaining exons are spliced
  together for the final mRNA.

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Processing the mRNA
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RNA in Protein Synthesis--tRNA

• tRNA (transfer RNA) brings an amino acid to the
  mRNA in the ribosome.
• Has 2 important regions
• Anticodon3 bases that are
• complementary to mRNA
• Amino acid binding site for
• binding a specific amino acid

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Other Types of RNAs

• A very hot research area is looking at other
  types of RNA molecules such as RNAi and snRNA.
• These appear to be involved in regulating how
  genes are turned on or off and in fine tuning
  protein synthesis.

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Transcription

• Transcription is the process of making RNA from
  the DNA template.
• Only 1 strand of DNA is transcribed to make
  single-stranded RNA.
• A genes worth of RNA is transcribed in the
  nucleus, then stored and processed in the
  nucleolus.
• Transcription DNA ? RNA

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Process of Transcription

• The enzyme of transcription is RNA polymerase.
• Step 1 RNA polymerase opens the double helix at
  the start of the gene.
• Step 2 Reads one base on template strand and
  attaches complementary base.
• Step 3 Attaches the ribose to the phosphate of
  the backbone then repeats until the end of the
  gene.

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Transcription Diagrammed
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Regulation of Transcription

• The cell carefully controls transcription of
  genes by several mechanisms.
• Promoter regions before the gene help bind the
  RNA polymerase.
• Activator and enhancer regions will increase RNA
  production.
• Repressors will reduce or shut down
  transcription.
• There are also codes for ending transcription.

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Concept Check

• What occurs in transcription? What is the major
  enzyme of transcription?
• What is the poly A tail and where is it added to
  the mRNA?
• Below is a template region of a gene. Give the
  RNA that would be transcribed.
• 5 C C G A T T A A A C T G T3

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Concept Check Answers

• Transcription is making RNA from the DNA
  template. The major enzyme is RNA polymerase.
• The poly A tail of up to 250 Adenines added to
  the 3 end of mRNA in the nucleolus.
• 3C C G A T T A A A C T G T5 DNA
• 5G G C U A AU U U G A C A3 RNA

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III. Translation or Protein synthesis
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Overview of Translation

• Translation is making a protein from the RNA
  template.
• Occurs on the ribosomes of the rough ER or free
  in the cytoplasm.
• Involves interplay between mRNA, tRNA and rRNA.
  DNA does not play a role in this process!
• Translation mRNA ? Protein

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Translation

• Translation is the process of making a
  polypeptide or protein on the ribosomes using the
  mRNA as a template.
• The 3 Stages of Translation are
• Initiation
• Elongation
• Termination

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1. Initiation of Translation

• In this stage
• The mRNA binds to the ribosome
• The initiator tRNA with its amino acid,
  methionine (met) binds to the mRNA, with the tRNA
  anticodon complementary to 3 bases on the mRNA.

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2. Elongation of Translation

• Step 1 The anticodon of the second tRNA binds to
  the next 3 bases, the codon, of the mRNA.
• Step 2 The first amino acid is transferred to
  the new amino acid (a peptide bond forms).
• Step 3 The ribosome moves down the mRNA to the
  next codon toallow a new tRNA to bind.
• Step 4 The tRNA without an amino acid leaves the
  ribosome.
• The process repeats until the end, lengthening
  the new polypeptide or protein.

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Elongation Diagrammed
Step 1
Step 2
Step 4
Step 3
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3. Termination of Translation

• Step 5 When there is a stop codon in the mRNA,
  a release factor is added instead of a tRNA.
• Step 6 This causes the new polypeptide to be
  released from the complex, ready to be processed
  and used by the cell.
• Step 7 The ribosome-mRNA complex dissociates,
  freeing the mRNA to be translated again.

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Termination Diagrammed
Step 7
Step 5
Step 6
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Table of the RNA-Amino Acid Code
The rows are the first letters, the columns the
second, the boxes are the third. For example,
AUG 3rd row, 1st column, bottom of box ? Met
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RNA-Amino Acid Code

• There are 3 stop codons, UAA, UAG and UGA that
  terminate translation and stop protein synthesis.
• Many amino acids have 2 or even 4 different
  codons.
• This is called the wobble.
• This causes some individual differences in
  organisms.
• For example, you may have AUC and I have AUU, but
  we will both put in Ile into the growing
  polypeptide.

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The DNA Code

• The codon of 3 bases on mRNA are complementary
  for a particular tRNA anticodon. That tRNA
  carries a unique amino acid.
• So 3 bases on mRNA code for 1 amino acid.
• Since mRNA is copied from DNA this means that 3
  bases on the DNA code for a specific amino acid.
• The gene for mRNA codes for making the primary
  sequence of amino acids of a polypeptide.

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Implications of the DNA Code

• The DNA that we inherit from our parents and pass
  down to our children has at its core the specific
  set of instructions for making proteins.
• These proteins do many jobs in the body including
  enzymes, hormones, receptors, structure and
  support.
• Therefore our unique set of DNA codes for the
  proteins to make each individual.

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Concept Check

• Which RNA brings the amino acid to the
  translation complex?
• Look at the table of the code and say which
  codons are the stop codons that terminate
  translation.
• For the following mRNA, give the amino acid
  sequence.
• 5-U A C A C G C G A U U U-3

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Concept Check Answers

• tRNA brings the amino acid to the complex.
• The stop codons for termination are UAA, UAG and
  UGA.
• 5-U A C.A C G.C G A.U U U-3 RNA
• --TyrThrArgPhe
• (Note it helps to separate the codons of
  the RNA so you dont get confuseda type of
  mutation!
• Also, it is preferred to put the covalent bond
  between the amino acids of the polypeptide.)

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Summary For This Module

• DNA is a double helix with a backbone of
  phosphate and sugar and rungs of bases of
• A, T, C and G.
• DNA replicates in S phase using DNA polymerase.
• RNA is transcribed from a genes worth of DNA as
  a single strand with ribose and A, U, C and G.
  RNA polymerase is the enzyme.
• mRNA is the template that is translated into a
  polypeptide on ribosomes.
• 3 bases on DNA code for 1 amino acid of a
  polypeptide.