Engineering Proteins

EP2 Building Proteins

Insulin the protein

  • Human insulin consists of two short chains of amino acid residues
  • Amino acid residues are the parts of the original amino acids that join to form the protein insulin
  • All the proteins in the living world are made from just 20 α-amino acids
  • Eight of these amino acids cannot be synthesised by the human body
  • They are taken from food and are called essential amino acids
  • The other twelve can be synthesised from carbohydrate and other amino acids
  • Amino acids are assembled to make a collection of proteins
  • Each of us has our own individual collection of proteins

 

Assignment 1

a  List four amino acids in each case which you think have

          i            non-polar side chains

 

Glycine (Gly), Alanine (Ala),Valine (Val), Phenylalanine (Phe)

I chose these ones because they are hydrocarbons.  They don’t have any polar hydroxyl groups.  I don’t really know about the polarity of nitrogen and sulphur bonds though L.

 

        ii            polar side chains

 

Serine (Ser), Threonine (Thr), Tyrosine (Tyr), Aspartic Acid (Asp)

These ones all have OH groups so that must make them polar.

 

      iii            ionisable groups on their side chain.

 

All carboxylic acids are ionisable (to H+).  So Aspartic acid (Asp) and Glutamic Acid (Glu) must be ionisable.  I don’t know if Proline (Pro) contains a carboxylic acid, because it only says –COOH.  Might be one.  I can’t think of a reason for any others to be ionisable but I don’t know very much about the other groups.  Maybe –NH is, which would make Arginine (Arg) ionisable.

 

b  Look at the structures of leucine and isoleucine.  Explain why isoleucine is so named.

 

Isoleucine is a structural isomer of leucine.  Much like 2,2,4-trimethylpentane is called iso-octane because it is an isomer of octane, isoleucine must be so named because it is an isomer of leucine.

           

c  List one amino acid in each case in which the R group contains

          i            a primary alcohol group             Serine (Ser)

        ii            a secondary alcohol group        Threonine (Thr)

      iii            a phenol group                         Tyrosine (Tyr)

       iv            a carboxylic acid group             Glutamic acid (Glu)

Making Peptides

·        Amino acids combine to form a protein

·        The carboxylic acid group on one amino acid joins the amino group on the next amino acid

·        Since and H and an OH are lost in the joining, water is formed

·        This process is called condensation

·        The –CONH- (secondary amide) group linking the amino acid residues in the protein formed is called a peptide link

·        Two amino acids joined by a peptide link are called a dipeptide

 


This reaction is the condensation of two amino acids into a dipeptide

 

This dipeptide is called Gly Ala since it consists of Glycine and Alanine

Assignment 2                                 

a  Draw the structure of the dipeptide Ala Gly.

 

 

b  In the tripeptide Ser Gly Ala, which amino acid has an unreacted

          i            NH2 group?       Ser (Serine)

        ii            COOH group?   Ala (Alanine)

 

Optical isomers

·        Amino acids have a three-dimensional structure

·        All except glycine, that’s 19 amino acids, can exist as either of two isomeric forms

·        These isomers are known a D or L optical isomers

·        D stands for dextro- since it turns a plane of polarised light to the right

·        L stands for levo- since it turns a plane of polarised light to the left

·        Two optical isomers which are the mirror images of each other are called enantiomers, meaning opposite molecules in Greek.

·        Chemical Ideas 3.6 is about optical isomerism.  3.3 is about shapes of molecules and 3.5 is about geometric isomerism.

How cells make proteins

    • Cells need three things to synthesise a protein:
    • Instructions which give the primary structure of the protein
    • Supplies of the amino acids needed to make the protein
    • A way of making amino and carboxylic acid groups react together

 

    • Messenger RNA, called mRNA, provides the order of the protein
    • Transfer RNA, called tRNA, select & separate the amino acids needed
    • The cell has a different tRNA for each amino acid
    • The cell also has a set of enzymes which recognise the specific tRNA and amino acid.  They catalyse the formation of an ester bond between the –COOH of the amino acid and the –OH of the tRNA.
    • The tRNA-amino acid complex can then diffuse to where it is needed

 

RNA structure

  • RNA is a chain made of ribose sugar molecules and phosphate groups
  • The backbone of RNA is ribose-phosphate-ribose-phosphate-etc
  • One of four bases is attached to each ribose unit
  • The bases are uracil, cytosine, adenine and guanine: U, C, A, G.

Ribosomes

  • The cell’s catalyst for protein production is a small particle called a ribosome
  • It contains ribosomal RNA, called rRNA, bound to protein molecules
  • Ribosomes collide with mRNA in the cell’s fluid
  • The ribosome moves along the mRNA like a bead on a chain, reading the code, and catalysing the reactions that form the protein

 

Assignment 3                                 

a  In the formation of RNA, what type of reaction is responsible for the linking of

          i            the ribose and phosphate?        condensation

        ii            the ribose and base?                condensation

b  The skeletal formula of ribose is shown in the illustration of RNA.  Draw a full structural formula for ribose.


 

 

Cracking the code

  • In order to code for 20 different amino acids, a triplet code is needed

 

  • There are four bases, so if a single base coded for one amino acid, only four amino acids would be codable: 41 = 4. If two bases coded for an amino acid, only sixteen amino acids would be codable: 42 = 16.  In actual fact three bases are used, since 43 = 64, and 64 > 20.

 

  • Since there are more possible combinations than there are amino acids, certain amino acids are defined by more than one base triplet

 

  • The bases are uracil, cytosine, adenine and guanine: U, C, A, G.
  • The combinations are called codons
  • Some codons stop the protein chain building

 

Assignment 4                                 

Table 2 shows that for some amino acids only the first two bases of the RNA codon are important.  The identity of the third base does not matter.  Make a list of these amino acids.

 

Amino acids followed by ticks are those for which every codon begins with the same two bases.

 

1)       Alanine (GCx) ü

2)       Arginine (CGx)

3)       Glycine (GGx) ü

4)       Leucine (CUx)

5)       Proline (CCx) ü

6)       Serine (UCx)

7)       Threonine (ACx) ü

8)       Valine (GUx) ü

 

For other amino acids, it is important that all three bases are correct.  Make a list of these amino acids.

 

1)       Arginine (AGA, AGG)

2)       Asparagine (AAU, AAC)

3)       Aspartic acid (GAU, GAC)

4)       Cysteine (UGU, UGC)

5)       Glutamine (CAA, CAG)

6)       Glutamine (GAA, GAG)

7)       Histidine (CAU, CAC)

8)       Isoleucine (AUU, AUC, AUA)

9)       Leucine (UUA, UUG)

10)   Lysine (AAA, AAG)

11)   Methionine (AUG)

12)   Phenylalanine (UUU, UUC)

13)   Serine (AGU, AGC)

14)   Typtophan (UGG)

15)   Tyrosine (UAU, UAC)

 

Codon, and on, and on and on and on

  • tRNA molecules recognise and bind to the codons on mRNA
  • They use so-called anti-codons
  • Base G in the anti-codon specifically recognises base C in the codon (and vice versa)
  • Bases U and A recognise one another in the same way
  • For example, anti-codon CGG binds to codon GCC
  • Anti-codon GUA will bind to codon CAU, a codon for histidine

 

Assignment 5                                 

a  Use the codons from Table 2 to predict the peptides obtained if RNA molecules with the following patterns of bases were used:

          i            AAAAAA...

Lys Lys

 

        ii            CGCGCGCGC...

Arg Ala Arg

 

      iii            UACCUAACU

Tyr Leu Thr

 

b  Predict the anti-codons for these amino acids

           i            Trp       Base pairs: U-A and C-G

Codon = UGG →

Anti-codon =   ACC

 

        ii            Asp.     Codons =               GAU, GAC →

Anti-codons = CUA, CUG