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L02 Protein structure and function

Transcription and translation

DNA acts as a template and is transcribed onto mRNA (AUCG) by RNA polymerase

Protein structure

Proteins are composed of several structures:

Primary structure

This includes the polypeptide chain

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Secondary structure

This involves helices and pleated sheets

Polypeptide chains often fold into a helices and b sheets, which are common folding patterns

Tertiary structure

This is the 3d shape of the protein which requires the lowest amount of energy

Arrangement of amino acids

Improper folding

When proteins fold improperly, they can form aggregates

Quaternary structure

 This involves more than one polypeptide chain

Disulphide bonds

Many proteins molecules are attached to the outside of the plasma membrane or attached to the ECM

Function

The disulphide bonds reinforce the most favoured conformation

Protein diversity

Proteins may be of several different types:

The type of protein will suit its function

Function

Proteins have several functions including:

All proteins will bind to other molecules in some way at their binding site

Regulation of function

Example: Regulation of gene expression

Proteins are only synthesised when and where they are needed, including:

Feedback inhibition

The catalytic activity of enzymes are often regulated by other molecules

Protein modification

Proteins are modified in the endoplasmic reticulum

Adding small molecules can add extra functions to proteins (e.g. Haemoglobin)

Dynamic nature of proteins (protein activation)

The structural arrangement (conformation) of a protein is dynamic

Mechanism

The shift in conformation change is required for function such as enzyme activation, substrate binding

Example: CDK and cyclin

Catalytic protein is cyclin dependent kinase (cdK)

Secretory pathway

This involves:

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Secretory vesicles

If defective or not needed, they can be taken to lysosomes to be degraded

Transport vesicles

Soluble proteins are transported in the cell via a transport vesicle

Molecules transported

Constitutive secretion occurs this way

Transport to ER, mitochondria, peroxisomes

Transport into nucleus

Application: Cystic fibrosis

In cystic fibrosis, the CFTR protein is mutated

  1. 3 mRNA form a codon
  2. This corresponds to an amino acid
  3. The mRNA chain is translated on a ribosome into a protein
  4. As there are 64 possible codes yet 20 amino acid, some of the code is redundant/regulatory
  5. Primary
  6. Secondary
  7. Tertiary
  8. Quaternary (only some proteins)
  9. Amino acids are linked by peptide bonds
  10. Various side chains are exposed
  11. These have properties such as polarity/non-polarity, hydrophobic/philic , + or - charge
  12. These are stabilised by Van der Waals, hydrogen bonds and electrostatic attraction
  13. Alpha helices are stabilised by hydrogen bonds
  14. This is known as the conformation (this may be changed by other molecules binding)
  15. In enzymes, the active site is specific and complimentary to its substrate
  16. Non-polar (hydrophobic) amino acids tend to be inside of the protein
  17. Polar(hydrophilic) amino acids tend to be on the outside of the protein
  18. This can damage cells and tissues (especially if infectious)
  19. This is shown in Alzheimer's and Huntington's
  20. The subunits may be homomers (same) or heretomers (different)
  21. Therefore, to help stabilize them, the polypeptide chains are stabilized by covalent cross-linkages
  22. The most common cross-link is the disulphide bond (S-S bond)
  23. These forms as proteins are exported from cells
  24. The formation is catalysed in the ER by an enzyme which links cysteine side chains together
  25. They do not form in the cell cytosol
  26. This is because there is a high concentration of reducing agents (this converts such bonds back to -SH groups)
  27. Fibrous: Collagen
  28. Globular: Secretory, can be enzymes, haemoglobin. Usually hydrophobic in, and hydrophilic on the outside.
  29. Catalysis: Enzymes
  30. Receptors: Binding ligands(an ion/small molecule/macromolecule which binds to protein)
  31. Switching: Signalling pathways
  32. Structural : Cytoskeletal element, gives cell shape, helps organelles move
  33. Synthesis: Is it present or not?
  34. Localisation : Is it where it needs to be?
  35. Modification: Active/inactive?
  36. Degradation : Is it needed anymore?
  37. Cell differentiation and specialisation
  38. Immune response
  39. In response to signals from other cells
  40. This is done through feedback inhibition
  41. An enzyme acting early in the reaction pathway is inhibited by a later product
  42. Therefore, this reduces the quantity of the later product
  43. Disulphide bonds (reinforce conformation) and glycosylation occurs (adding sugar)
  44. Further modification occurs in the golgi
  45. The conformation can shift to suit the function
  46. This requires phosphorylation (catalysed by protein kinase)
  47. Dephosphorylation is done by protein phosphatase
  48. The phosphate is attached to the protein chain
  49. This inhibits or activates the protein
  50. Therefore, it leads to a conformation change
  51. This is only active when cyclin is present
  52. This allows for a change in conformation
  53. Secretory vesicles
  54. Transport vesicles
  55. Proteins may also be stored in secretory vesicles until an extracellular signal causes them to fuse with the cell membrane
  56. This causes the proteins to be released
  57. The proteins have a sorting signal to direct them to the correct site
  58. They may be taken to organelles where they are required
  59. They can be transported from one compartment to another via transport vesicles
  60. Plasma membrane proteins are transported in this fashion
  61. Proteins are taken to endosomes and lysosomes for degradation
  62. Transport to these organelles from to cytosol is carried out by protein translocation
  63. The molecule will unfold to get through the membrane
  64. Proteins move in via the nuclear pores
  65. The pores are selective gates which actively transport specific macromolecules
  66. This is caused by the deletion of an amino acid
  67. This causes the mutated protein to be incorrectly folded and retained in the ER (degraded, never reaches the membrane)