Gene Expression: RNA and Protein Synthesis

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Gene Expression RNA and Protein Synthesis
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Gene Expression

• The essential key players in the cells
  moment-by-moment existence are proteins.
  Therefore, we must consider . . .
• How is information coded in the information
  system,
• How is that information decoded and interpreted,
  and
• How are proteins produced?
• That is, we must examine gene expression

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Three Major Classes of Genes

• Regulatory genes are responsible for the
  expression of structural genes
• Promoters
• Terminators
• Structural genes code for proteins
• Variable Sequences
• Short Tandem Repeats (STRs)

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Regulatory Genes

• Promoters are DNA sequences that act like
  switches that turn genes on/off
• Promoters are located upstream of the structural
  gene.
• DNA bases (nucleotides) that indicate the
  presence of a promoter
• TATAATT box
• Termination sequences tell the enzyme where to
  stop transcription of a gene.

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(No Transcript)
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actcaaaaaaaaaacggttgggttgcgccatacatatgaaagagtataga
ataatgatgtatttcccaaatcaaatatcatggtaaaatttaaCAATgac
ccattcggattcattgataatattagttgatggatcatttgtaaaaaggt
tttattaactcctaagttatgtcgagtagaccttgttgttgttgcTATAA
TTcttaatcATGcgttgtagggggagatttatgtcaccacaaacagaaac
gaaagcaaaggttgggttcaaagctggtgttaaagactgaacgtagcagc
tacgatcgatcgactagctgcatcgggctagcgaagcttcgatcgatcga
tcgagctagcgagcccccagttttaggtcgagctttcagctcagctaggc
gcgaaatctcgagcgcagctcactagctgctctagcatcgagctacgatc
gcgatcgagctagctagaattatccgtgaagcttgcaaatggagtcctga
attagctgctgcttgtgaagtctggaaggaaatcaaatttgaattcccag
caatggatactttgTAAtccagtaataatcattcgttctattaatttcca
ttaaactcggcccaatctt
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• RNA resembles DNA
• Sugar-phosphate backbone
• -OH at the 2 C on the ribose, vs. deoxyribose in
  DNA
• U substitutes for T
• Unlike DNA, RNA is single stranded
• Multiple types
• mRNA Messenger RNA carries information
• tRNA Transfer RNA transfers information from
  mRNA into protein
• rRNA part of the ribosome

RNA Structure
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Base-Pairing Rules
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Three Types of RNAs

• Messenger RNA
• mRNA
• Transfer RNA
• tRNA
• Ribosomal RNA
• rRNA

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Gene Expression
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Transcription

• Is the process of making messenger RNA (mRNA)
  from a DNA template
• RNA polymerase
• Very similar to DNA replication
• Remember as in replication, in transcription,
  addition of a new nucleotide occurs at the 3
  end!
• Transcription occurs by base pairing
• A-U 2 H bonds G-C 3 H bonds

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Three Steps of transcription
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Transcription The Sense Strand and Template
Strand DNA

• The sense strand is the coding strand (5 to 3)
• The template strand is the non-coding strand (3
  to 5)
• RNA polymerase slides along the DNA template
  strand in a 3 to 5 direction

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• Nucleotide triphosphates are added to the growing
  mRNA strand at the 3 end
• Phosphodiester bonds are made by RNA polymerases
• Note the antiparallel, complementary strands

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Transcription
Complementary Base-pairing of DNA to mRNA

• If the template strand reads
• T-A-C-C-T-T-A-A-C-C-G-G-T-T-A
• The transcribed mRNA is
• A-U-G-G-A-A-U-U-G-G-C-C-A-A-U

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The structure of mRNA

• 5 Guanine cap (G-cap)
• Leader sequence does not get made into protein
• Protein coding region begins with AUG ends with
  a STOP codon
• Trailing sequence does not get made into protein.
• 3 poly-A tail

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• 5 Guanine cap (G-cap)
• Leader sequence does not get made into protein
• Protein coding region begins with AUG ends with
  a STOP codon
• Trailing sequence does not get made into protein.
• 3 poly-A tail

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Gene Expression Translation

• Central Dogma DNA ? RNA ? Protein
• Proposed by Frances Crick
• DNA 3' ACC AAA CCG AGT
• mRNA 5' UGG UUU GGC UCA
• Protein Trp Phe Gly Ser
• The string of amino acids has a direct
  relationship to nucleotide bases in RNA and DNA
• Every three nucleotides is called a Codon
• Each Codon corresponds to ONE amino acid

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• Amino acid subunits are added at the carboxyl
  terminus of the growing protein

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(No Transcript)
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dsDNA
5-ATGGAATTCGATCAGTCCAATGCATGACAAGTACCTT-3
3-TACCTTAAGCTAGTCAGGTTACGTACTGTTCATGGAA-5
transcription
mRNA
5-AUGGAAUUCGAUCAGUCCAAUGCAUCAAAGGUACCU-3
translation
protein
NH4 -Met- Glu- Gly-Asp- Gln- Ser- Asn- Ala- Ser-
Lys- Val- Pro-COOH
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The Code of Life

• The code indicated here is nearly identical in
  all organisms, prokaryotes and eukaryotes
• Note that there is redundancy in the genetic code
• Often four, and up to to six (can you find it?)
  codon sequences encode one amino acid

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Translation Transfer RNA (tRNA)

• Each tRNA has
• An amino acid
• An amino acid is added at the 3 end of the tRNA
• Each has a unique anticodon
• Each tRNA is unique and can be attached to only
  one amino acid

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• Transfer RNA Structure Function
• Some areas, AU Hydrogen bonding as well as GC
  Hydrogen bonding
• Each tRNA just picks up one amino acid
  

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Translation Ribosomes

• Ribosomes are made of protein and rRNA

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Translation Ribosomes

• Ribosomes are made of protein and rRNA
• The ribosome clamps over the tRNAs and mRNAs to
  make new protein
• A site receives new tRNA
• P site receives peptide-bearing tRNA after
  peptide bond formation
• E site is where tRNAs exit

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• The mRNA passes through a groove between the
  large and small subunits
• The tRNAs enter at the aminoacyl site, A site
• rRNA catalyzes the production of the peptide bond
  at the peptidyl site, P site
• The tRNA exits at the E site

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Protein Synthesis
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The New Polypeptide

• Just like nucleic acids have directionality (5
  to 3)
• Polypeptides also have an orientation
• New amino acids are always added to the carboxyl
  end of the growing chain.

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Summary of Gene Expression
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Bacterial Gene Expression
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Eukaryotic RNA Processing

• The parts of the mRNA that actually code for
  protein are called exons
• Parts of the mRNA segments that are cut out are
  called intervening sequences or introns
• At the end of the process, RNA is modified
• Capping A 7-methyl G (G-cap) is attached
  BACKWARDS to the 5 end
• Splicing Introns are cut out of the mRNA
• Tailing RNA has a string of As (poly A) added to
  the 3 end
• Both modifications protect RNA from degradation
• Thus, the mature mRNA contains less material than
  the DNA.

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mRNA processing in eukaryotic cells
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mRNA Processing Capping and Tailing
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mRNA Processing Splicing
FYI
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(No Transcript)
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Exon Shuffling

• Reason for noncoding regions (exons) is becoming
  clear.
• They could be important to the evolution of
  complex organisms.
• Different exons are mixed to form proteins with
  different domains
• Allows for rapid evolution of proteins
• Evolution by exon shuffling
• Introns might have come about as leftover pieces
  of DNA from symbiosis

FYI
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Genes

• A modern definition of the gene
• A gene is a nucleotide sequence that carries the
  information needed to produce a specific RNA or
  protein product

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Prokaryotic and Eukaryotic Gene Expression

• Prokaryotes make RNA and protein in cytoplasm
• Eukaryotes make RNA in the nucleus, protein in
  cytoplasm

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Genomes and Proteomes

• The genetic code is universal and found virtually
  unchanged in all organisms
• Evolution of the genetic code must have occurred
  very early in evolution
• The genetic sequences of components important to
  transcription and translation are conserved.