Proteins

Question 1

What are proteins?

Answer 1

Proteins are a major class of functioning molecules w/in cells. They can be catalysts that mediate biochemical reactions) or structural components (i.e. membranes, cell wall)
-They are ultimately polypeptides made of amino acids joined by peptide bonds

Question 2

Features of proteins

Answer 2

• have a Amino acid end (NH2) and a carboxyl end (COOH)
• synthesised from amino end to caroxyl end (A comes before C)
• Has a peptide backbone w/ side groups/chains branching off
  
  • the interaction between side chains is what determins the structure of the protein & therefore determines activity

Question 3

Bonds within proteins (4)

Answer 3

• Bonding can occur between a.a. that are quite far from each other
• Disulphide bonds (b/w sulphur) are one of strongest
• Hydrogen bonds can also occur (same type that holds bases together)
• Ionic Bonds
• Van der Waals (hydrophobic interactions) - found in globular proteins where inside is hydrophobic and external is hydrophilic

Question 4

Protein structures

• types
• role of chaperones

Answer 4

• Helic and beta-sheets are common structureal motifs in proteins
• Protein structures are complex and very diverse
  
  • Function determines structure
  • If folding left unregulated, there’d be many 3D conformations made - most being inactive
    - CHAPERONES therefore regulate folding - ensure only correct a.a. folding occurs

Question 5

Process of folding

-consequences of incorrect folding (3)

Answer 5

Ribosome -> primary polypeptide -> correct folding
-> incorrect folding

Consequences of incorrect folding;

• wastes energy
• incorrect product
• inhibits metabolic reactions (as can bind to other proteins & stick to them)

Question 6

Electrophoresis of Proteins

• Why difficult?
• How we overcome these difficulties

Answer 6

• Nucleic acids are easy (as have negative charges), proteins are harder to do as can have positive or negative charge & they have a huge diversity in shape
• Able to overcome this problem by coating proteins w/ detergent called SDs - gives a negative charge to protein
  
  • no. of SDs that bind to a protein depends on the size of the protein (therefore charge depends on the size)

-Proteins can then move in inverse relation to size (smaller fragments move faster than larger)

Question 7

Electrophoresis of Proteins

• Gel properties, type
• probing

Answer 7

• Polycrylamide used as gel matrix (only forms gel in anaerobic conditions - is put b/w 2 glass plates)
• Gel stained w/ a general protein stain
• Blot gel onto membrane & probe w/ antibodies against a specific protein - antibodies are labelled (radioactively or w/ flourescence) = WESTERN BLOT
  
  • antibody binds to specific protein
  • band density = protein expression

n.b. genes may be transcribed but not necessarily made

Question 8

2D gel electrophoresis of proteins

• What is it
• Uses

Answer 8

• run proteins along pH gradient as each protein has isoeletric point (particular point where it is least soluble and may precipiate out of solution) on pH scale
• separates by size and pH (moves down gel due to size, moves across gel due to pH)

Useful in investigating processes such as cancer development in cells (is how we find genes for cloning - i.e. such as breast cancer genes)