Biology 2430 Lecture Notes

Chapter 14 : Translation

Outline Protein structure Translation A codon is translated into an amino acid by a tRNA with complementary sequence Ribosomes are protein factories Protein folding extremely complex Protein Function and Malfunction

Protein structure

• Proteins are polymers composed of monomers called amino acids. Each amino acid is composed of a chiral carbon bound to 4 different groups (Fig 14.1):

1. hydrogen 2. amino group 3. carboxyl group 4. R-group (only variant group). There are 20 amino acids. Each amino acid differs in their R-group (Fig 14.2 ). Amino acids linked by peptide bonds (Fig 14.3) Polypeptide chains have directionality (amino end and carboxyl end).

• Proteins are organized at 4 structural levels (Fig 14.4)

1. primary structure (amino acid sequence); determines other structural levels 2. secondary structure (e.g. a-helix, b-sheet); results through H-bond interactions among components of polypeptide backbone. 3. tertiary structure ; overall folding of polypeptide; driven by hydrophobic effect and stabilized by interaction of R-groups (ionic interactions, H-bonds, disulphide bridges, van der Waals). 4. quaternary structure: polypeptides (identical or not) coming together through weak interactions to form functional protein (e.g. hemoglobin). Not all proteins have a quaternary structure.

• Shape is all-important to a protein. Specific shapes give rise to different functions.
  
• Many proteins are enzymes which recognize specific substrates at active site.

Translation

• Sequence of nucleotides in DNA of a gene is transcribed into mRNA. Ribosomes move along mRNA (5' to 3' direction) and read nucleotide sequence of mRNA one codon at a time.
• The genetic code is a triplet code which is nonoverlapping and has no spaces between adjacent codons.

• Each codon stands for a specific amino acid. There are 64 possible codons (triplet code) (Fig 14.5 ).

  Genetic code is:        1. universal (with some exceptions)        2. degenerate        3. unambiguous

A codon is translated into an amino acid by a tRNA with complementary sequence

• basis for specificity between codon and amino acid lies in structure of tRNA.
  structure of tRNA (Fig 3.21):

  
  

• two dimensional shape like cloverleaf: 4 double-helical stems, plus 3 single stranded loops.
  middle loop contains anticodon, which binds with a specific codon in mRNA by complementary base pairing.
  3'-end of tRNA carries an amino acid. Each tRNA specific for a only one amino acid.
  
• amino acids attached to 3'-end of tRNA (Fig 14.10)by enzymes called aminoacyl-tRNA synthetases. Each amino acid has a specific synthetase (Fig 14.9). tRNAs with attached amino acid are said to be charged.

Ribosomes are protein factories

• ribosomes are large molecular assemblies consisting of a large and a small subunit (Fig 3.23).
  
• Each subunit made up of various rRNAs and up to 50 different proteins.

• ribosomes have binding sites for tRNAs, mRNAs and other protein factors necessary for translation (Fig 3.24) .
  
• mRNA binds to small subunit
  
• tRNAs bind to A-site (entry site for aminoacyl-tRNA) and P-site (peptidyl-tRNA carrying growing polypeptide).
  each new amino acid is added by the transfer of the growing chain to the new aminoacyl-tRNA forming a new peptide bond.

  
  

  Action of ribosome during translation divided into 3 steps: initiation, elongation, and termination.
  
  • Initiation (Fig 14.11)
    
    • in bacteria, first amino acid always N-formylmethionine; in eukaryotes it is methionin; initiation codon preceded by Shine-Delgarno sequence in bacteria (pair with 3' end of 16S rRNA of small subunit).
      
    • in eukaryotes, initiation codon positioned in ribosome using 5'cap. Ribosome then scans transcript and translation starts at first ATG encountered.
    Elongation (Fig 14.13)
    
    • assisted by various elongation factors
    • decoding and addition of each amino acid to the nascent polypeptidechain involves a three-step minicycle:
      • 1. codon recognition: an incoming aminoacyl-tRNA binds to codon at A-site
        2. peptide bond formation: peptide bond is formed between new amino acid and growing polypeptide chain (Fig 14.14) .
        
      • 3. Translocation; tRNA that was in P site is released. tRNA in the A site is translocated to the P site. In the process, ribosome advances by one codon.
  • Termination (Fig 14.16)
    
    • stop codons are not recognized by any tRNA. This ultimately leads to disassembly of translation apparatus and polypeptide is released.
• Poplypeptides destined to be integrated into membranes or released by cell have signal peptide at amino terminus. Ribosomes which lach on to mRNA encoding such polypeptides will eventually bind the endoplasmic reticulum (making it rough) where translation of rest of polypeptide can proceed directly into cell membrane or lumen (Fig 14.17).

Protein folding extremely complex

• The number of possible ways in which a polypeptide can fold is almost unlimited, and yet a given polypeptide sequence almost always folds in same way. The final conformation is that which is most energetically favored (i.e. most stable).
  
• Most protein folding is aided by molecular chaperones. This process is remains relatively mysterious.
  
• Prediction of protein 3-D structure using primary sequence alone represents the Holy Grail of biotechnology. Need very powerful computers, accurate and detailed knowlege of the forces governing protein folding, and sophisticated software. State of the art is already pretty good and making fast progress.

Protein Function and Malfunction

• Many diseases result from mutations to genes encoding proteins with essential functions. These mutations can either lead to total absence of protein in cell, or alter its function, or lead to increased or decreased levels in the cytoplasm. (Fig 14.5 ).Basis of dominance/recessive relationship between alleles.
• Protein function is very diverse. Suffice it to say that proteins are involved in almost all aspects of cellular and organismal function.

End of chapter questions: 1-4, 6, 7, 8, 10, 12, 13, 15, 17, 20, 21, 25, 27, 30.

Useful links:

• Translation animation
• Gene expression animation