FOB 3 proteins

• peptides


  small <70 aa's or <50. dipeptide, tri and oligo etc. the molecule pre-protein that lacks a stable tertiary/quaternary structure
• residues

  aminoacids after having lost water to form a protein / peptide
• protein


  usually larg >70 aa or >50. peptides in a stable confirmation
• protein fucntions

  enzymes/biological catalysts (pyrophospatase), transport proteins (haemoglobin), nutrient and storage proteins (ovalbumin), contractile or motile proteins (muscle actin), structural proteins (collagen), defence proteins (antibodies), receptor proteins (G-proteins), signalling proteins (anti-diruetic hormone)
• peptide bonds

  condensation reaction forms an amine bond. the hydrogen on amine group undertakes a nucleophilic attack on the carboxylic acid group forming a new covalent bond between the nitrogen of amine and the carbon of carboxylic acid. reversible. amine group on the left N terminus, and carboxylic acid group on the right C terminus where new residues are added. rigid bonds, only alpha carbon can rotate on either side rather than the peptide bonds. carboxylic acid is protonated and amine is deprotonated in drawing
• formation rate of peptide bond

  does not happen at an appreciable rate in nature because high activation energy is required. the carboxyl group of the amino acid must be activated by aminoacylation. this allows the a-amino group of the next aa to undertake a nucleophilic attack. amino acid is covalently attached to the ribose of transfer rna which activates carboxyl group. trna bring aa's together and nucleophilic attack occurs
• drawing a protein


  show the reaction of formation with water going in and out (and the correct number of molecules). label n and c terminus (amino and carboxyl terminus). label peptide bonds (amide linkage), indicate r groups and their classes
• ionisation and polarity


  ionisable properties of amino acids are lost when they react to form a peptide. polar properties are gained. positive charge on the hydrogen end of the amine link and negative charge on the oxygen end of the link. the n and c terminus are still ionisable. polar and or ionisable properties of r groups
• protein size and function

  size can indicate function. small peptide hormones, oxytocin, more likely to be signaling because it is too small to be structural. larger peptides cannot act as a signalling molecule as they are too large and overwhelm receptors. over 200 residues, is is structural, globular, enzyme? - determined by r groups.
• calculating protein size

  MW of aa's: 138 g/mol , (weighted average as smaller are more common) 128 g/mol, (- water as it is lost in peptide formation) 110 g/mol. APPROXIMATION
• protein structure and function

  number of residues, r groups on aas, number of aa chains (quaternary structure), diversity of aa in chains (are chains different), formation of conjugated protein. cofactors: lipids (lipoprotein), carbohydrates (glycoprotein), haem (hemoprotein), metals (metalloproteins)
• 4 levels of protein structure

  1 - aa sequence - doesn't indicate function. 2 - local spatial arrangement of polypeptide backbone, driven by peptide linkages and hydrogen bonds between them (alpha helix, beta pleated sheet). 3- the overall three-dimensional structure of all atoms in a protein, driven by r group interactions. 4 - interactions between different polypeptide chains to form a final active molecule, not all proteins have
• configuration


  amino acid sequence, hard to break as held together by strong covalent bonds
• conformation


  arrangement of a chain in 3D space. can be easily changed, held together by weaker bonds usually. bonds in conformation - hydrogen bonds, hydrophobic interactions, ionic interactions, di-sulfide bonds (covalent but less numerous than peptide bonds)
• Proteins with similar functions across organisms

  Have similar primary structures
• Amino acids present in the primary structure

  • Proteins have different configurations based on the order of these amino acids
• Primary structure

  Refers to the specific sequence of amino acids in a protein
• Primary structure

  • Specific regions of a protein's amino acid sequence will be highly conserved (homogenous) between species and between common family members
  • Other regions will be highly heterogenous
  • Conserved regions are critical to the structure and function of a protein
  • A single aa change can cause loss of function
  • Can use aa sequence to predict the function, location and modifications of proteins
• Proteins with different functions

  Have different configurations
• protein folding

  alpha carbons can rotate on either side (Ca - C and N - Ca) while peptide bonds are rigid. these rotation angles are phi (o| N-C) and psi (trident C-C) these bonds can rotate 360 degrees (+180 or -180) but many angles are prohibited by steric interference. angles that work are 180 for both, (no phi 0 psi 180 and no 0,0)
• a-helix


  right-handed helix, from the left moving right. hydrogen bonds with oxygen from every fourth plate. r groups stick outside to avoid steric hindrance. 3.6 residues per turn with a distance of 5.4 angstroms in height gained per turn or 0.54 nm (the distance of a single c-h bond).
• draw general alpha helix

  3.6 resides per turn, 5.4 angstrom per turn, hydrogen bond between oxygen and hydrogen 4 plates away. c and n terminus, r goups are facing outward.
• disrupting a helix

  consecutive similarly charged r groups will repel and cause distortion. bul groups consecutive or closely associated. proline causes a kink due to its rigid ring. glycine is too flexible with only a hydrogen as the r group.
• beta pleated sheets


  held by hydrogen bonds between peptide groups. parallel (chains are parallel, shorter repeat period, steeper plate rise and fall, hydrogen bond at an angle therefore longer and weaker) or anti-parallel (chains are not parallel, longer repeat period, hydrogen bonds are straight and closer therefore stronger). sharp turn at the end of the chain (type 1 (contains prolene) and type 2 (contains glycine)) residue 1 and 4 hold turn together while residues 2 and 3 create the turn.
• teriary structrue


  involves interactions between r-groups (hydrogen bonds between polar side chains, dispersion forces, electrostatic interactions (attraction and repulsion) from charged groups, hydrophobic interactions (the most common force) and covalent cross-links as disulphide bonds. forms fibrous (commonly structural) and globular proteins (commonly functional such as enzymes)
• disulphide bridges


  when the r groups of two cystines come together they let off a hydrogen each and covalendly bond to each other. primary occur in secreted extracellular proteins
• loss of teritary structure

  small environmental changes can change conformation. denaturation (unfolded state) - loss of function. caused by adding energy (heat, pH which changes charge, organic solvents whichinduce the rearrangement of non-covalent bond and disrupts hydrophobic interactions). structure can be reformed if the denaturing condition is removed
• protein types

  globular (form globular shapes are functional like haemoglobin) and fibrous (form long strands or sheets which provide structure like collagen)
• keratin


  hair, feathers, nail, wool. 2 - alpha helix , 3 - simple. 4- twist a helix around eahother twisting to the left forming a two-chain coiled coil formed by hydrographic r group interactions. they are linked together to form protofilaments and then protofibrils. contains many cysteine residues so considerable disulfide linkages between chains. number of cysteine residues holding the coiled coils together determines rigidity
• myoglobin

  (oxygen storage found in tissue). myoglobin is a single polypeptide chain of 153 aa, formed by 8 a helixes and has a compact structure with a single haem molecule in the protein pocket lined with hydrophobic aas. oxygen can reversibly bind to the haem group when iron is in it oxidised state. Releases oxygen when oxygen is depleted. Has a high affinity for O2 even at a low partial pressure of oxygen. 
• Strongest interactions

  Between a1b1 and a2b2
• Four O2 molecules can be bound per haem molecule
• Cooperatively binding

  The binding of the next two molecules of O2 becomes more favourable
• Chains with a haem group

  • Alpha chains
  • Beta sheets
• Binding of the first O2 molecule

  Causes a conformational change in the shape of the other chains (taut T state to R relaxed state)
• Partial pressure

  Pushes haemoglobin into r or t state
• Haemoglobin

  Oxygen transporter
• Conformational change in the shape of the other chains


  Makes the binding of the next two molecules of O2 more favourable
• Components of haemoglobin

  • Two alpha chains (141 aa)
  • Two beta sheets (146 aa)
• Haem group

  Can reversibly bind to one O2 molecule