proteins

• everything in a living cell is either

  • a protein or
  • made by a protein or
  • put there by a protein
• • DNA codes for proteins
  • a gene is a stretch of DNA that codes for proteins
  • sole purpose of genetic code or the cells DNA is to contain code for making proteins
  • DNA is NOT protein
• proteins contain 5 elements (CHONS):

  • carbon
  • hydrogen
  • oxygen
  • nitrogen
  • sulfur
• monomers of proteins = amino acids (aas)

  • there are 20 aas within proteins in nature
  • proteins of all living cells are made of teh same 20 aas
  • a very large variety of dif. protein chains (aa sequences) exist: e.g. a protein containing 10 aas could have 20X20X20X20X20X20X20X20X20X20 possivle variations
  • in comparison the number of dif. types of lipids and carbs is very limited e.g. starch or glycogen have the same repeating unit: alpha glucose
• proteins are specific to species:

  • sequence of aas in proteins (e.g. haemoglobin) will be dif. for dif. species
  • the more similar the aa sequence of teh proteins, the closer the 2 species are in evolutionary history, this info. can help build an evolutionary tree and is the basis of phylogeny
• ROLES OF PROTEINS

  • enzymes: catalyse reactions which enable metabolism
  • membrane protein: transmembrane proteins such as carrier proteins or ion channels allow transport of substances into and out of cells and organelles
  • antibodies: recognise foreign antigens and allow the immune system to attack and destroy these
  • filamentous: found in muscle tissue as well as the cytoskeleton. allow movement within tissues and cells
  • buffers: soluble proteins in the blood which help stabilise the pH of blood
• ROLES OF PROTEINS (part 2)

  • fibrous: protein found in structural tissue such as hair, skin, nails, tendons, bones. allow for strength and where required flexibility. include collagen elastin and keratin
  • transport: e.g. haemoglobin. carry molecules e.g. oxygen, around the body
  • regulatory: allow for control of gene expression
  • hormones and receptors: cell signalling involves hormones (some of which are proteins e.g. insulin) and cell surface receptor proteins (often glycoproteins)
  • storage for growth: proteins found in seeds, milk and eggs
• Monomers:

  • amino acids
  • there are 20 aas which make up the strcuture of proteins
  • plants and some microorganisms can synthsesise all 20aas
  • animals can only synthesise some aas: non essentual amino acids
  • must obtain others from diet: essential amino acids
  • all aas have this structure:

  A) R

  B) OH

  C) =O

  D) N

  
• when free in solution they become a zwitterion and form this structure:

  A) o-

  B) H+

  
• there are 5 features:

  • only R group (side chain) is different for different aas
  • there are 20 R groups in nature
  • R groups give each aa its charecteristic property
• POLYMERS

  • aa + aa ----condensation reaction----> di-peptide ( by the formation of a peptide bond)

  A) N-H

  B) C=O

  
• a polypeptide = a sequence of aas joined by peptide bonds

  a polypeptide with 5 aas will have 4 peptide bonds

  
• protein structure:

  • proteins have 4 levels of structure:
  • primary structure:
  • determined by genetic code on the DNA/gene or the base sequence of the DNA
  • may be 100s of aas long - very diverse
  • each protein has a specific aa sequence
  • secondary structure:
  • initial local folding of pp chain
  • 2 regular shapes (alpha helices and beta pleated sheets) from between parts of pp chain which are close
  • these regular shapes form due to h bonds between amine groups (slightly electropositive) and the carboxyl group (slightly electronegative) of the peptide bonds of dif. neighbouring aas
• secondary structure

  A) carboxyl

  B) amine

  
• the 2 regular periodic folds of the polypeptide chain in secondary structure:

  • alpha-helix
  • beta pleated sheet

  
• tertiary structure:

  • further folding of pp chain to give 3d strcuture of the polypeptide
  • the alpha helices and beta sheets of 2 structure are brought together by:
  • (further H bonds between peptide bonds but not in regular patterns as for 2 structure)
  • bonds formed between side chains/R groups of dif. aas
  • R groups are important for 3D folding of protein chain and form the following types of bonds depending on the nature of the R group involved
• bonds involved in the tertiary structure of proteins:

  • ionic bonds (very influenced by pH)
  • hydrophobic interactions of non-polar side chains: occur in: interior of proteins (hydrophobic environment) where it's not in contact with water, parts of membrane proteins in contact with the phospholipid bilayer
  • hydrogen bonds: between polar/hydrophilic R groups easily broken by: increase in temp or change in pH
• bonds involved in tertiary structure of proteins:

  • sulfur bridges: covalent disulphide bonds may occur between 2 sulflur containing aas. only covalent bond formed in folding of pp chain, gives stability to proteins, found in thermophilic bacteria
  • secondary structure is dif. to tertiary in that:
  • it is only formed from hydrogen bonds (which occur between carboxyl and amine groups of nearby peptide bonds), there are no R groups involved in secondary structure
• Quaternary structure:

  • association of 2 or more pp chains to form fully functional protein
  • same bonds that fold the tertiary structure are used to maintain the quaternary structure of the protein
  • many proteins only require 3 structure => dont need to associate into complex to be functional and are made from just one pp chain e.g. many enzymes
• types of proteins with respect to shape and function:

  globular proteins:

  • all proteins e.g. enzymes, hormones, membrane proteins etc. which are soluble (in water) and carry out the cell's metabolic functions
  • folded as globular or spherical molecules
  • exact shape/structure of protein determines its specific function - many irregular shapes
  • can have 3 or 4 structure
• examples (proteins with respect to shape and function): Globular proteins:

  • haemoglobin- globular structure (alpha pp chains), protein part is called globin, non-protein attached is haem with an iron ion in the middle where O binds, binding of O changes shape of haemoglobin, non-protein part is permenantly attached => prosthetic group
• globular proteins examples:

  insulin

  • is a hormone, has quaternary structure

  amylase

  • an enzyme
  • enzymes often have tertiary structure
  • folding determines shape of active site
  • conjugated proteins= globular proteins that have an extra (non-protein) molecule attached

  denaturisation:

  • loss of the exact 3D structure of a protein
  • primary structure remains intact
  • 4, 3 and 2 structures are affected and lost in the order
  • occurs because of:
  • rise in temp above optimum, breaks H bonds
  • change in pH breaks ionic and H bonds
• Fibrous proteins:

  • long chain structural proteins which make up hair, skin, bone, tendons, ligaments
  • also integral to lots of tissues such as alveoli, blood vessels
  • high proportion of hydrophobic and small amino acids, range of aas are small
  • insoluble in water
  • long pp chains
  • very regular shapes
  • strong and stable - dont get denatured as readily as globular proteins
  • all have quaternary structure
  • little tertiary structure
  • many H bonds or covalent cross links between pp give added strength
  • 3 examples - collagen, keratin, elastin
• fibrous proteins:

  collagen:

  • found in: skin, tendons, ligaments, nervous system
  • main aas: glycine
  • structure: 3 pp wound in rope like structure
  • properties: high tensile strength

  keratin:

  • found in: hair, skin, nails
  • main aas: cysteine
  • structure: strong disulphide bonds (disulphide bridges)
  • properties: strong, inflexible, insoluble

  elastin:

  • found in: elastic fibres, walls of blood vessels, alveoli
  • main aas: soluble tropoelastin
  • structure: multiple tropoelastin molecules aggregate via interactions between hydrophobic areas
  • properties: elasticity and strength
• Globular Protein:

  • rounded or spherical
  • role: metabolic or functional (enzymes, hormones)
  • generally soluble in water
  • sequence: irregular amino acid sequence
  • denatured easily by rise in temp or changes in pH

  Fibrous protein:

  • long and narrow
  • role: structural (strength and support)
  • insoluble in water, many hydrophobic residues
  • repetitive amino acid sequence
  • not denatured easily by rise in temp or changes in pH