L2 - structure of proteins

• 7 categories of protein:

  -enzymes

  -structural proteins

  -signal proteins

  -contractile proteins

  -storage proteins

  -defence proteins

  -transport proteins
• Enzymes: control biological reactions (eg. catalase)
• Structural proteins: form part of the body of organisms (eg. collagen)
• Signal proteins (hormones): carry messages around the body (eg. insulin)
• Contractile proteins: involved in movement (eg. actin)
• Storage proteins (eg. albumin)
• Defense proteins (eg. antibodies)
• Transport proteins (eg. haemoglobin)
• Proteins are polymers made of monomers called amino acids
• Amino acids:

  -there are 20 naturally occurring amino acids

  -all of these have the same basic structure
• Amino acids consist of an amine group (2 hydrogens and 1 nitrogen), an R group or side chain, and a carboxylate acid group (2 oxygens, 1 carbon and 1 hydrogen)

  
• General amino acid properties:

  -colourless

  -crystalline solids

  -generally water soluble

  -insoluble in organic (carbon based) solvents (eg. fuels like alcohol)

  -act as buffers by resisting changes in pH (help maintain a stable pH in solutions)
• In general, acids will donate H+ ions and bases will accept H+ ions. Amino acids make good pH buffers as the carboxylic group is acidic so it donates H+ ions and the amine group is basic so it accepts H+ ions
• Amino acids are differentiated by the side chain or R group. R groups can be:

  -small or large

  -positively or negatively charged

  -hydrophobic (water fearing so do not dissolve in water). These usually contain carbon or hydrogen

  -hydrophilic (water loving so do dissolve in water). These usually contain oxygen or nitrogen
• How plants obtain amino acids:

  -can manufacture their own amino acids if they can obtain nitrate from the soil

  -nitrates are converted to R groups and bonded to organic groups made from the products of photosynthesis
• How animals obtain amino acids:

  -can manufacture ‘non essential’ amino acids

  -must get ‘essential’ (about 8 to 10) amino acids from our diet (mainly meat) as we cannot directly take in nitrates

  -the protein we eat gets digested into amino acids

  -we can build up the proteins we need from these monomers
• Removing amino acids:

  -animals cannot store excess amino acids

  -the amine group makes them toxic if too many are present

  -the liver removes the amine group (called deamination)

  -the removed amine group is converted into urea

  -urea is removed via urine
• Dipeptide formation:

  -amino acids join together by forming a bond between the amine group of one and the carboxylic group of the other

  -this requires removing part of each amino acid to form a new product
• Making a dipeptide is an anabolic (joining) reaction called a condensation reaction

  -this produces a molecule of water

  -the covalent bond formed between the amino acids is called a peptide bond
• Creating proteins:

  -amino acids join together to make a chain (this allows proteins to form)

  -two amino acids joined is called a dipeptide

  -more that two amino acids joined is a polypeptide
• Breaking a polypeptide bond is a catabolic (breaking) reaction called a hydrolysis “water breaking” reaction
• Polypeptide formation

  
• There are four different levels of protein structure:

  -primary

  -secondary

  -tertiary

  -quaternary
• Primary protein structure: the number and order of different amino acids in a polypeptide chain
• Primary structure:

  -always one end with a free amine group (N terminus) and one end with a free carboxyl group (C terminus)

  -the type of protein produced all depends on which amino acids are bonded together and in what order
• Secondary protein structure:

  -when the polypeptide chain twists and coils to form different shapes

  -weak hydrogen bonds form between amino acids in different parts of the chain

  -two shapes that form are alpha helix and beta pleated sheet
• Alpha helix:

  -has 36 amino acids per 10 turns of the coil

  -hydrogen bonds form between the amine group of one amino acid and the carboxyl group of one four places along the chain
• Beta pleated sheet:

  -the polypeptide chain can also fold to lie parallel joined by hydrogen bonds, to form beta pleated sheets

  -again hydrogen bonds form between the amine group of one amino acid and the carboxyl group of the one parallel to it
• Tertiary protein structure:

  -the polypeptide chain can fold up again to form a more complex 3D shape

  -the shape is held in place by bonds forming between the R groups of different amino acids
• Four types of bonds that can occur in a tertiary structure:

  -hydrophobic interactions (weakest)

  -hydrogen bonds

  -ionic bonds

  -disulfide bonds (strongest)
• Hydrophobic interactions:

  -in the water based environment where they are assembled, hydrophobic amino acids will be most stable if they are held together with water excluded

  -hydrophilic amino acids tend to be found on the outside folds, with hydrophobic amino acids on the inside

  -this slight attraction between hydrophobic R groups is very weak
• Hydrogen bonds:

  -where slightly positively charged R groups are attracted to slightly negatively charged R groups (dipoles)

  -the hydrogen bond is not very strong and is easily broken by high temperatures or changes in pH
• Ionic bonds:

  -R groups carry a positive or negative charge

  -where oppositely charged R groups are found close to each other they form ionic bonds

  -this is much stronger than a hydrogen bond but can be broken by pH changes
• Disulfide bonds:

  -form between the R groups of the amino acid cysteine that contains sulfur

  -where two cysteines are close to each other a disulfide bridge forms

  -are strong covalent bonds but can be broken by reducing agents (eg. DDT)
• Quaternary protein structure:

  -proteins that contain more than one polypeptide chain have a quaternary structure

  -almost all working proteins are composed of more than one polypeptide chain
• Haemoglobin consists of four chains arranged in a tetrahedral (pyramid) structure
• Antibodies comprise four chains arranged in a Y-shape
• The enzyme ATP synthase is composed of 22 chains forming a rotating motor
• Collagen consists of three chains in a triple helix structure
• Actin consist of hundreds of globular chains arranged in a long double helix