From DNA to Proteins

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From DNA to Proteins

• Chapter 15

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Functions of DNA

• Heredity passing on traits from parents to
  offspring
• Replication
• Coding for our traits by containing the
  information to make proteins
• Protein Synthesis
• Transcription
• Translation

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Genes

• Genes are units of DNA that code to make a single
  polypeptide (protein)
• Found within specific location on the chromosomes
  (loci)
• Humans have gt30,000 genes
• How do we make a protein from the information in
  a gene?

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Steps of Protein synthesis

• Same two steps produce all proteins
• Transcription
• DNA (Gene) is transcribed to form messenger RNA
  (mRNA)
• Occurs in the nucleus
• 2) Translation
• mRNA is translated to form polypeptide chains,
  which fold to form proteins
• Occurs in ribosomes which are in the cytoplasm

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Transcription and Translation
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RNA vs. DNA
DNA RNA
Number of strands Two One
Nucleotides A T G C A U G C
Sugar Deoxyribose Ribose
Location Nucleus only Nucleus and Cytoplasm
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Three Classes of RNAs

• Messenger RNA (mRNA)
• Carries protein-building instruction
• Ribosomal RNA (rRNA)
• Major component of ribosomes
• Transfer RNA (tRNA)
• Delivers amino acids to ribosomes

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A Nucleotide Subunit of RNA
uracil (base)
phosphate group
sugar (ribose)
Figure 14.2Page 228
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Transcription

• DNA ? RNA
• Occurs in the nucleus
• Requires the enzyme RNA Polymerase
• Consists of 3 steps
• Initiation
• Elongation
• Termination

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RNA Polymerases

• No primers needed to start complementary copy
• RNA is made in the 5? 3 direction
• DNA template strand is 3? 5

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Steps of Transcription Initiation

• RNA Polymerase binds to Promoter
• Promoter A base sequence in the DNA that signals
  the start of a gene
• DNA is unwound
• i.e. hydrogen bonds are broken

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Transcription Initiation
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Steps of Transctription Elongation

• RNA ploymerase adds complementary RNA nucleotides
  to one strand of DNA Template strand
• Forms Pre-mRNA

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Transcription Elongation
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Steps of Transcription Termination

• When mRNA synthesis is complete, RNA Polymerase
  falls off of DNA, RNA is released from DNA, and
  DNA rewinds

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Transcription Termination
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Transcription vs. DNA Replication

• Like DNA replication
• Nucleotides added in 5 to 3 direction
• Unlike DNA replication
• Only small stretch is template
• RNA polymerase catalyzes nucleotide addition
• Product is a single strand of RNA

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Production of mRNAs in Eukaryotes

• Eukaryotic protein-coding genes are transcribed
  into precursor-mRNAs that are modified in the
  nucleus
• Introns are removed during pre-mRNA processing to
  produce the translatable mRNA
• Introns contribute to protein variability

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Messenger RNA

• Prokaryotes
• Coding region flanked by 5 and 3 untranslated
  regions
• Eukaryotes
• Coding region flanked by 5 and 3 untranslated
  regions (as in prokaryotes)
• Additional noncoding elements

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Eukaryotic Pre-mRNA

• Precursor-mRNA (pre-mRNA)
• Must be processed in nucleus to produce
  translatable mRNA
• 5 cap
• Reversed guanine-containing nucleotide
• Site where ribosome attaches to mRNA
• Poly(A) tail
• 50 to 250 adenine nucleotides added to 3 end
• Protects mRNA from RNA-digesting enzymes

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Eukaryotic Pre-mRNA

• Introns
• Non-protein-coding sequences in the pre-mRNA
• Must be removed before translation
• Exons
• Amino acid coding sequences in pre-mRNA
• Joined together sequentially in final mRNA

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RNA Processing
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mRNA Splicing

• Introns in pre-mRNAs removed
• Spliceosome
• Pre-mRNA
• Small ribonucleoprotein particles (snRNP)
• Small nuclear RNA (snRNA) several proteins
• Bind to introns
• Loop introns out of the pre-mRNA,
• Clip the intron at each exon boundary
• Join adjacent exons together

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mRNA Splicing
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Why are Introns Present?

• Alternative splicing
• Different versions of mRNA can be produced
• Exon shuffling
• Generates new proteins

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Alternative Splicing

• Exons joined in different combinations to produce
  different mRNAs from the same gene
• Different mRNA versions translated into different
  proteins with different functions
• More information can be stored in the DNA

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Alternative mRNA Splicing

• a-tropomyosin in smooth and striated muscle

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The next step Translation

• Translating from nucleic acid (DNA/RNA)
  language (nucleotides) to protein language
  (amino acids)
• Occurs in the ribosome within the cytoplasm
• Requires tRNA transfer RNA
• How does the mRNA (and DNA) code for proteins?
• The Genetic Code

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Genetic Code

• Information
• 4 nucleotide bases in DNA or RNA sequences
• DNA A,T,G,C RNA A,U,G,C
• 20 different amino acids in polypeptides
• Code
• One-letter words only 4 combinations
• Two-letter words only 16 combinations
• Three-letter words 64 combinations

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Genetic Code

• DNA
• Three-letter code triplet
• RNA
• Three-letter code codon

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Genetic Code
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Features of the Genetic Code

• Sense codons
• 61 codons specify amino acids
• Most amino acids specified by several codons
  (degeneracy or redundancy)
• Ex CCU, CCC, CCA, CCG all specify proline
• Start codon or initiator codon
• First amino acid recognized during translation
• Specifies amino acid methionine

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Features of the Genetic Code

• Stop codons or termination codons
• End of a polypeptide-encoding mRNA sequence
• UAA, UAG, UGA
• Commaless
• Nucleic acid codes are sequential
• No commas or spaces between codons
• Start codon AUG establishes the reading frame

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The Genetic Code
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Genetic Code is Universal

• Same codons specify the same amino acids in all
  living organisms and viruses
• Only a few minor exceptions
• Genetic code was established very early in the
  evolution of life and has remained unchanged

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Translation Overview
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Translation

• Purpose
• To translate from nucleic acid language to
  protein language
• RNA?protein
• What is needed for translation?
• mRNA transcript (processed)
• tRNAs
• Ribosomes

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tRNAs

• Transfer RNAs (tRNA)
• Bring specific amino acids to ribosome
• Cloverleaf shape
• Bottom end of tRNA contains anticodon sequence
  that pairs with codon in mRNAs

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tRNA Structure
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Ribosomes

• Made of ribosomal RNA (rRNA) and proteins
• Two subunits large and small

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Translation Stages

• Initiation
• Ribosome assembled with mRNA molecule and
  initiator methionine-tRNA
• Elongation
• Amino acids linked to tRNAs added one at a time
  to growing polypeptide chain
• Termination
• New polypeptide released from ribosome
• Ribosomal subunits separate from mRNA

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Initiation

• Initiator tRNA (Met-tRNA) binds to small subunit

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Initiation

• Complex binds to 5 cap of mRNA, scans along mRNA
  to find AUG start codon

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Initiation

• Large ribosomal subunit binds to complete
  initiation

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Elongation

• tRNA matching the next codon enters A site
  carrying its amino acid
• A peptide bond forms between the first and second
  amino acids, which breaks the bond between the
  first amino acid and its tRNA
• Ribosome moves along mRNA to next codon
• Empty tRNA moves from P site to E site, then
  released
• Newly formed peptidyl-tRNA moves from A site to P
  site
• A site empty again

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Elongation
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Termination

• Begins when A site reaches stop codon
• Release factor (RF) or termination factor binds
  to A site
• Polypeptide chain released from P site
• Remaining parts of complex separated

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Termination
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What Happens to the New Polypeptides?

• Some just enter the cytoplasm
• Many enter the endoplasmic reticulum and move
  through the cytomembrane system where they are
  modified

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Gene ExpressionSummary
Transcription
mRNA
rRNA
tRNA
Mature mRNA transcripts
ribosomal subunits
mature tRNA
Translation
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Gene Mutations

• Changes in genetic material
• Base-pair mutations change DNA triplet
• Results in change in mRNA codon
• May lead to changes in the amino acid sequence of
  the encoded polypeptide

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Gene Mutation Types

• Missense mutation
• Nonsense mutation
• Silent mutation
• Frameshift mutation

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Missense Mutation

• Changes one sense codon to one that specifies a
  different amino acid

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Sickle-Cell Anemia

• Caused by a single missense mutation

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Nonsense Mutation

• Changes a sense codon to a stop codon

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Silent Mutation

• Changes one sense codon to another sense codon
  that specifies the same amino acid

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Frameshift Mutation

• Base-pair insertion or deletion alters the
  reading frame after the point of the mutation

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Mutation Rates

• Each gene has a characteristic mutation rate
• Average rate for eukaryotes is between 10-4 and
  10-6 per gene per generation
• Only mutations that arise in germ cells can be
  passed on to next generation

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Mutagens

• Ionizing radiation (X rays)
• Nonionizing radiation (UV)
• Natural and synthetic chemicals