BIOL 111 Chapter 17

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Protein Synthesis

Purpose of this section

  • Bridge gap between DNA and traits. How does DNA affect the phenotype?
  • How are genes and other processes controlled?
  • Show how this information is used in the real world

Central Dogma of Molecular Biology

DNA (Nucleotides) –transcription [vocab 1] → mRNA (Nucleotides) "transcript" –translation [vocab 2] → Protein (Amino Acids)

Eukaryotes

  • DNA is transcribed in Nucleus
  • Added process: RNA Processing (turns Pre-mRNA into mRNA); also inside nucleus
  • Translation occurs outside of Nucleus

Prokaryotes

No nucleus, so transcription and translation occur in same space

Genetic Code

Problems:

  • How many monomers in a molecule of inheritance (DNA)? 4 nucleotides
  • How many monomers in product of translation (Protein)? 20 amino acids
  • 3 nucleotides = 1 Amino Acid

Mathematical solution

nt(4) × nt(4) × nt(4) = 64 possible codon combinations (nt(4)2=16, which is too small)

Threfore, 3 nucleotides = 1 codon [vocab 3] = 1 amino acid

Figure 17.5

BIOL 111 Figure 17.5.png

Open reading frame:

  • sequence AUG means "start" or Met protein
  • sequences UAA, UAG, and UGA all mean "stop"

Example

DNA Template 3' TAC GTA CCG TAA TGC CCC ATC 5'
mRNA Transcript 5' AUG CAU GGC AUU ACG GGG UAG 3'
Protein Translation [start] His Gly Ile Thr Gly [stop]
Met-His-Gly-Ile-Thr-Gly

Transcription: RNA Synthesis

DNA Template must contain promoter [vocab 4] (beginning point) and terminator [vocab 5] (ending point)

RNA Polymerase II makes mRNA from DNA template between promoter and terminator

Initiation

Promoter contains TATA box (sequence TATAAAA)

Transcription factors (proteins) attach to TATA box and serve as flag for location

RNA Polymerase II binds to transcription factors and promotor site, forming transcription initiation complex [vocab 6]

Elongation

Unwinds DNA helix, attaches RNA complements and transcribes "downstream" (5'→3')

Termination

In prokaryotes, RNA Pol II reads terminator and detaches

In eukaryotes, RNA Pol II reads a little past polyadenylation [vocab 7] sequence before detaching

Processing RNA (Eukaryotes)

Modifying the ends

Functions

  • Prevents degradation
  • Helps exportation to cytoplasm
  • Helps ribosomes attach to mRNA

Types

  • 5' Cap [vocab 8] (Guanine + 3 Phosphates)
  • poly-A tail [vocab 9] at 3' end (LOTS of adenines; like 50-250)
  • 5' and 3' UTR [vocab 10]
    • Polyadenylation signal contained inside 3' UTR

Structure

5' Cap — 5' UTR — [start] Protein-coding segment [stop] — 3' UTR — Poly-A tail


Modifying the middle

RNA Splicing

Exons [vocab 11]
expressed portions of transcript
Introns [vocab 12]
in between express portions
Spliceosome [vocab 13]
composed of proteins and snRNPs [vocab 14]
cuts out introns

All of Pre-mRNA is copied from DNA, but Intron sections contain regulatory "meta" information that will not be expressed in the translated protein.

snRNA binds to complementary strand along RNA Intron; spliceosome loops Intron, clips the snRNA-bound ends, and attaches Exons together.

Consequences

Note: a gene is defined between 2 TATA boxes

Alternative splicings possible:

  • Spliceosome can cut out an exon that is between two introns, creating a protein with a "missing" part or "domain"
Example

Troponin T gene has 5 exons: 1, 2, 3, 4, and 5

Sample alternate splicings:

  • 1, 2, 3, 5
  • 1, 2, 4, 5
  • 1, 3, 4, 5


Thursday, November 18, 2010


Translation

Requires 3 components: mRNA, Ribosome, and tRNA

Transfer RNA (tRNA)

  • 3D "L"-shaped Structure; held together by Hydrogen bonds
  • Amino Acid attachment site at top
  • Anticodon (interacts with codons in mRNA) at bottom

Prediction: At least 61 tRNAs (one for each codon permutation; not including stop codons)

Reality: 45 tRNAs: 3rd base is "wobble base" (3rd base doesn't particularly matter and allows more room for error)

tRNA Synthesis

Aminoacyl-tRNA synthetase

  1. binds to a specific amino acid; requires 1 ATP (Recall Metabolism: ATP makes amino acid more reactive)
  2. binds to the matching tRNA
  3. releases "charged tRNA"

20 types of Aminoacyl-tRNA synthetases: one for each amino acid

Ribosomes

  • 4 locations:
    1. Rough ER
    2. Cytoplasm
    3. Chloroplasts
    4. Mitochondria
  • Made in the Nucleolus inside the Nucleus
  • Composed of rRNA and protein
  • Two subunits: large and small
  • Binding sites for mRNA and multiple tRNAs (E, P, and A)


Protein Synthesis

Similar to steps involved in transcription

Initiation

  1. Small ribosomal subunit bonds to mRNA binding site
  2. Start codon (AUG — Met) added by Initiator tRNA (requires {{tooltip|GTP, which is similar to ATP, and initiation proteins)
  3. Large ribosomal subunit attaches to the complex, with Initiator tRNA at P-site

Elongation

10 cycles/second

  1. The next tRNA binds to the A-site (requires GTP)
  2. Peptide bond forms between P-site amino acid and A-site amino acid
  3. Polypeptide chain moves to tRNA in A-site
  4. tRNA's shifted left (E ← P; P ← A) (requires GTP)

Termination

Release factor binds to stop codon (UAG, UAA, UGA) in A-site Polypeptide released and ribosome dissociates (requires 2 GTP)


NET RESULT: Primary structure of Protein


Signal peptide (20 amino acids) at beginning of protein (N-terminus[vocab 15]) read by SRP and transported to wherever it needs to go


Overview

BIOL 111 Figure 17.25.png


Mutations

Any change in DNA sequence (See BIOL 111 Chapter 15#Mutations: Altered Chromosome Structure→)


Large Scale Mutations caused by radiation, chemicals, viruses, etc.

Point Mutations

also called Small Scale Mutations

Substitution
replacement of one nucleotide with a different nucleotide
silent (no amino acid change)
missense (new code is for different amino acid; e.g. sickle-cell anemia)
nonsense (new code is for stop codon)
Insertion/Deletion
addition or removal of one nucleotide causes entire RNA sequence to shift
causes nonfunctional protein


Vocabulary

  1. ↑ transcription is the process by which a DNA template sequence is copied/replicated into mRNA
  2. ↑ translation is the process by which proteins are made from sequences of mRNA
  3. ↑ a codon is a three-nucleotide sequence of DNA/mRNA that specifies a particular amino acid or termination signal
  4. ↑ the promoter of a DNA sequence tells the RNA Polymerase II molecule where to begin RNA synthesis
  5. ↑ the terminator of a DNA sequence tells the RNA Polymerase II molecule where to stop RNA synthesis and detach
  6. ↑ the transcription initiation complex is the completed assembly of transcription factor proteins and RNA polymerase bound to a promoter
  7. ↑ the polyadenylation sequence of Eukaryotic DNA acts as the terminator for RNA synthesis.
  8. ↑ a 5' Cap end-modification is a Guanine with 3 Phosphates (similar in structure to ATP) that attaches to the 5' end of mRNA to prevent degradation
  9. ↑ a poly-A tail is a LONG string of adenines attached to the 3' end of mRNA
  10. ↑ the 5' and 3' Untranslated regions (UTR) are partes of mRNA that will not be translated into protein, but contain other information
  11. ↑ exons are parts of mRNA that persist all the way until they are expressed in protein translation
  12. ↑ introns are parts of mRNA in between exons that are normally cut out before translation
  13. ↑ spliceosomes are complexes composed of snRNPs and other proteins that cut out introns
  14. ↑ snRNPs ("snurps") are small protein and snRNA (small nuclear RNA) complexes that bind to certain sequences found in introns
  15. ↑ the n-terminus end of a protein is the "beginning"; associated with the 5' end of mRNA
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