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Chapter 33. Biochemistry 432/832 Protein Synthesis and Degradation December 05. Announcements. Central dogma of biochemistry: DNA --> RNA --> protein. Transcription Translation. Protein Synthesis and Degradation. Outline. 33.1 Ribosome Structure and Assembly

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chapter 33

Chapter 33

Biochemistry 432/832

Protein Synthesis and Degradation

December 05

protein synthesis and degradation

Central dogma of biochemistry:

DNA --> RNA --> protein

Transcription Translation

Protein Synthesis and Degradation

  • 33.1 Ribosome Structure and Assembly
  • 33.2 Mechanics of Protein Synthesis
  • 33.3 Protein Synthesis in Eukaryotes
  • 33.4 Inhibitors of Protein Synthesis
  • 33.5 Protein Folding
  • 33.6 Post-Translational Processing of Proteins
  • 33.7 Protein Degradation

Proof that polypeptides (hemoglobin) grow by addition of new amino acid residues to the carboxyl end

Direction of chain growth

0 min

4 min

7 min

16 min

60 min



N-terminus C-terminus

Dintzis experiment, 1961, rabbit reticulocytes labeled with leucine

  • Ribonucleoprotein particles
  • Found in the cytosol, mitochondria and chloroplasts of all cells
  • Move along mRNAs and synthesize proteins
  • Bind and orient mRNAs and aminoacyl-tRNAs
  • Organize interactions between codons and anticodons in aminoacyl-tRNAs
  • Catalyze the formation of peptide bonds between adjacent amino acid residues
ribosome structure and assembly
Ribosome Structure and Assembly
  • E. coli ribosome is 25 nm diameter, 2520 kDa in mass, and consists of two unequal subunits that dissociate at < 1mM Mg2+
  • 30S subunit is 930 kDa with 21 proteins and a 16S rRNA
  • 50S subunit is 1590 kDa with 31 proteins and two rRNAs: 23S rRNA and 5S rRNA
  • These ribosomes and others are roughly 2/3 RNA
  • 20,000 ribosomes in a cell, 20% of cell's mass
organization of e coli ribosomes
Organization of E.coli ribosomes
          • Ribosome Small Large
          • subunit subunit
  • Sedimentation 70S 30S 50S coefficient
  • Mass (kDa) 2520 930 1590
  • Major RNAs 16S (1542 b) 23S (2904 b)
  • Minor RNAs 5S (120 b)
  • RNA mass 1664 560 1104
  • RNA proportion 66% 60% 70%
  • Proteins 21 31
  • Protein mass 857 370 487
  • Protein 34% 40% 30%

Ribosomal RNA operons in Escherichia coli. Precursor RNA is cleaved to generate 23S, 16S and 5S rRNA as well as tRNA


The 16S rRNA fits within the 30S ribosomal subunit

The rest of space (peripheral) is occupied by proteins

ribosomal proteins
Ribosomal Proteins
  • One of each per ribosome, except L7/L12 (same proteins that differ at N-terminus) with 4
  • L7/L12 identical except for extent of acetylation at N-terminus
  • Four L7/L12 plus L10 makes "L8"
  • Only one protein is common to large and small subunits: S20 = L26
  • No similarity (Lys, Arg-rich). The largest is S1 (557 aa) , the smallest is L34 (46 aa)
  • Overall fold of proteins was established less than a year ago
ribosome assembly structure
Ribosome Assembly/Structure
  • If individual proteins and rRNAs are mixed, functional ribosomes will assemble
  • Structures of large and small subunits have been determined in 2000/2001
  • A tunnel runs through the large subunit
  • Growing peptide chain is thought to thread through the tunnel during protein synthesis

Comparison of ribosomes and tRNAs (two tRNAs may be bound to a ribosome)

E.coli ribosome

Image reconstruction is based on cryoelectron microscopy

eukaryotic ribosomes
Eukaryotic Ribosomes
  • Mitochondrial and chloroplast ribosomes are quite similar to prokaryotic ribosomes, reflecting their supposed prokaryotic origin
  • Cytoplasmic ribosomes are larger and more complex, but many of the structural and functional properties are similar
  • Complexity and size of ribosomes are increased from prokaryotes to lower eukaryotes to higher eukaryotes
  • Conservation of overall RNA structure as well as specific segments of primary sequences
properties of eukaryotic ribosomes
Properties of Eukaryotic Ribosomes
          • Ribosome Small Large
          • subunit subunit
  • Sedimentation 80S 40S 60S coefficient
  • Mass (kDa) 4220 1400 2820
  • Major RNAs 18S (1874 b) 28S (4718 b)
  • Minor RNAs 5.8S (160 b) 5S (120 b)
  • RNA mass 2520 700 1820
  • RNA proportion 60% 50% 65%
  • Proteins 33 49
  • Protein mass 1700 700 1000
  • Protein 40% 50% 35%
mechanics of protein synthesis
Mechanics of Protein Synthesis
  • All protein synthesis involves three phases: initiation, elongation, termination
  • Initiation involves binding of mRNA and initiator aminoacyl-tRNA to a small subunit, followed by binding of a large subunit
  • Elongation: synthesis of all peptide bonds - with tRNAs bound to acceptor (A) and peptidyl (P) sites.
  • Termination occurs when "stop codon" reached

Basic steps in protein syn-thesis

Two binding sites

Transfer of a polypeptide to the amino group of amino acid carried by the tRNA in the A site

Aminoacyl tRNA is at the A site; polypeptidyl-tRNA is at the P site

One codon translocation; tRNA expulsion

prokaryotic initiation
Prokaryotic Initiation
  • The initiator tRNA is one with a formylated methionine: f-Met-tRNAfMet
  • It is only used for initiation, and regular Met-tRNAmMet is used instead for Met addition
  • N-formyl methionine is first aa of all E.coli proteins, but this is cleaved in about half
  • A formyl transferase adds the formyl group

Structure of N-formyl-methionyl-tRNA[Met]

Differences with other tRNAs

more initiation
More Initiation
  • Correct registration of mRNA on ribosome requires alignment of a pyrimidine-rich sequence on 3'-end of 16S RNA with a purine-rich part of 5'-end of mRNA
  • The purine-rich segment - the ribosome-binding site - is known as the Shine-Dalgarno sequence
  • Initiation factor proteins, GTP, N-formyl-Met- tRNAfMet, mRNA and 30S ribosome form the 30S initiation complex
events of initiation
Events of Initiation
  • 30S subunit with IF-1 and IF-3 binds mRNA, IF-2, GTP and f-Met-tRNAfMet
  • IF-2 delivers the initiator tRNA in a GTP-dependent process
  • Loss of the initiation factors leads to binding of 50S subunit
  • The "acceptor site" is now poised to accept an incoming aminoacyl-tRNA

Peptide chain initiation

30S subunit (IF-3:IF-1) binds mRNA

IF-2 delivers the initiator f-Met-tRNA to the P site

IF-2 dissociates from 30S subunit

GTP hydrolysis is accompanied by IFs release and binding of the 50S subunit


A structure of non-hydrolyzable analog of GTP

Allowed separation of GTP binding from GTP hydrolysis

the elongation cycle
The Elongation Cycle
  • The elongation factors are vital to cell function, so they are present in significant quantities (EF-Tu is 5% of total protein in E. coli )
  • EF-Tu binds aminoacyl-tRNA and GTP
  • Aminoacyl-tRNA binds to A site of ribosome as a complex with 2EF-Tu and 2GTP
  • GTP is then hydrolyzed and EF-Tu:GDP complexes dissociate
  • EF-T recycles EF-Tu by exchanging GTP for GDP
elongation factors
Elongation factors

Factor Mass Molecules/Cell Function

  • EF-Tu 43 kDa 70,000 Binds tRNA-GTP
  • EF-Ts 74 kDa 10,000 Displaces GDP from EF-Tu
  • EF-G 77 kDa 20,000 Binds GTP, promotes translocation of ribosome

Reaction of the tRNA-linked peptidyl chain with the a-amino group of an adjacent aminoacyl-tRNA -

no energy is required for activation

peptidyl transferase
Peptidyl Transferase
  • This is the central reaction of protein synthesis
  • 23S rRNA is the peptidyl transferase!
  • The "reaction center" of 23S rRNA - the catalytic bases are among the most highly conserved in all of biology.
  • Translocation of peptidyl-tRNA from the A site to the P site follows

Ribosome is a ribozyme (catalytic rRNA)

Catalytic center is located in the 50S particle

The peptidyl transferase center of 23S rRNA


Ribosome is ribozyme

Puglisi JD, Blanchard SC, Green R, Nat Struct Biol 2000 Oct;7(10):855 Approaching translation at atomic resolution.

Atomic resolution structures of 50S and 30S ribosomal particles have recently been solved by X-ray diffraction

In the 50S structure, the active site for peptide bond formation was localized and found to consist of RNA. The ribosome is thus a ribozyme

In the 30S structure, tRNA binding sites were located

The 30S subunit particle has three globular domains, and relative movements of these domains may be required for translocation of the ribosome during protein synthesis


Ribosome structure

Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF.

Science 2001 Mar 29

Crystal Structure of the Ribosome at 5.5 A Resolution.

We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound mRNA and tRNAs at 5.5 A resolution. All of the 16S, 23S and 5S rRNA chains, the A-, P- and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 A movements associated with tRNA translocation with intersubunit movement.

the role of gtp hydrolysis
The Role of GTP Hydrolysis
  • Two GTPs are hydrolyzed for each amino acid incorporated into peptide.
  • Hydrolysis drives essential conformation changes
  • Total of four high-energy phosphate bonds are expended per amino acid residue added - three GTP here and two in amino acid activation via aminoacyl-tRNA synthesis
peptide chain termination
Peptide Chain Termination
  • Proteins known as "release factors" recognize the stop codon at the A site
  • Presence of release factors with a nonsense codon at A site transforms the peptidyl transferase into a hydrolase, which cleaves the peptidyl chain from the tRNA carrier