Proteins

• Basic structural units or ___ of proteins called ___ ___

  20 of them used in the bio synthesis of proteins in cells


  monomers, amino acids
• Proteins consist of 5 elements

  Carbon, hydrogen, oxygen, nitrogen, (sulphur in some proteins)
• Amino acid consists of an ___ atom that is ___ bonded to 4 groups

  1. ___ atom
  2. an ___ group (-NH)
  3. a ___ group(-COOH)
  4. a ___ _ group (side chain)

  a-carbon, covalently

  hydrogen

  amino

  carboxyl

  variable R
• Draw general structure of amino acid molecule

  a-carbon in the centre

  
• 20 ___ acids differ only in their ___ groups

  ___ and ___ properties of the __ groups determine the uniqueness of each amino acid

  amino, R

  physical, chemical, R
• Electrically ___ amino acids have

  non-polar, ___ R groups

  or

  polar, ___ R groups

  neutral

  hydrophobic

  hydrophilic
• Electrically ___ amino acids

  1. ___ amino acids have negatively-charged R groups due to presence of ___ group which ___ to form COO- at ___ pH
  2. ___ amino acids have positively-charged R groups due to presence of ___ group which accepts H+ to form ___


  charged

  acidic, carboxyl, dissociates, cellular

  basic, amino, NH3+
• Electrically charged amino acids are ___ and able to form ___ with water


  hydrophilic, interactions
• ___ are amino acids that carry both ___ and ___ charges


  zwitterions, positive, negative
• How do zwitterions form?

  Amino acids are generally ___ in water and become ionized)

  (same as the charged amino acids)

  un-ionised ___ group receives ___ ion, is ___ and becomes ___ charged (NH3+)

  ___ group dissociates and released a ___ ion, is ___ and becomes ___ charged (COO-)

  amino, H+, protonated, positively

  carboxyl, H+, deprotonated, negatively
• Amino acids as ___ in biochemical reactions (changes in pH)

  buffers
• In ___ form, the protonated ___ group and the deprotonated ___ group acts as an ___ and ___ respectively

  Amino acids are considered to be ___, and can ___ against small changes in pH in their environment


  zwitterion, amino, carboxyl, acid, base

  amphoteric, buffer
• Ion when solution becomes low pH: (added ___) ___ of zwitterion accepts ___ and becomes ___

  ___ is removed from solution, maintaining the pH of the solution

  amino acid is now ___-charged

  H+, COO-, H+, COOH

  H+, positively (added H+)
• Ion when solution becomes high pH (added ___): ___ of zwitterion loses a ___ and becomes a ___

  the H+ from NH3+ ___ the OH- and prevents change in the pH of solution

  amino acids is now ___ charged


  OH-, NH3+, H+, NH2,

  neutralises

  negatively
• Amino acid monomers are joined via ___ reactions which ___ the ___ group (-COOH) of one amino acids to the ___ group (-NH2) of another, with the ___ of one ___ molecule ( formation of ___ bonds)

  Amino acid monomer is now known as a ___

  condensation, link, carboxyl, amino, elimination, water

  peptide bonds formed

  residue
• Breaking of the peptide bond: ___, requires 1 ___ molecule

  hydrolysis, water
• More than 2 amino acids can be joined together, forming __peptides, ___peptides, ___peptides (___ to 10), and ___peptides (>10 amino acids)


  di, tri, oligo, poly
• Polypeptides are amino acids joined together to form ___ polymers

  Components:

  regular,___ part, main chain: polypeptide ___

  ___, variable R-groups


  linear

  repeating, chain

  distinct
• Polypeptide chain has ___, 2 different ends

  directionality
• 2 different ends of the polypeptide chain:

  Amino ___: has a ___ amino group at the ___ of the polypeptide chain

  ___ terminus: has a ___ carboxyl group at the ___ of the polypeptide chain

  terminus, free, start

  carboxyl, free, end
• Amino terminus is also known as the _-terminus,

  carboxyl terminus is also known as the _-terminus


  N

  C
• The polypeptide ___ into a ___ with a ___ three-___ shape/ ___


  folds, protein, specific, dimensional, conformation
• 4 levels of organisation in the structure of proteins:

  P___

  S___

  T___

  Q___

  primary, secondary, tertiary, quaternary
• Primary structure refers to the n__, s__, and t__ of amino acids in a ___ polypeptide chain.

  • maintained by ___ bonds between ___ amino acid r__ ( already a part of the polypeptide chain)
  • specified by ___ sequences in ___


  number, sequence, type, single

  peptide, adjacent, residues

  nucleotide, genes
• The number of different combinations of a polypeptide with n residues are _^n (number of types of proteins is 20)

  the sequence of amino acids of the polypeptide determines the ___ and ___ of the chemical ___, thus the pattern of ___ of the polypeptide to form a ___

  20

  type, location, interactions, folding, protein
• Polypeptides fold into specific 3D conformation, ___ clefts and surfaces that can fit with ___ molecules

  different R groups at these sites can enable protein to form interactions with other molecules, controlling ___ ___, ___ and ___ of these interactions.

  e.g. enzyme-substrate, ligand-receptor

  complementary, specific

  precise orientation, strength, duration
• A proteins function is determined by its ___ which is dictated by its ___ ___ sequence in the ___ structure

  conformation, amino acid sequence, primary
• the secondary structure refers to the ___ ___ formed by the regular c__ or p__ of a ___ polypeptide chain

  • maintained by ___ bonds at regular ___, formed between the _=_ and -__ groups of the polypeptide backbone
  • R-groups are/ are not involved in the formation of bonds in the secondary structure


  spatial arrangement, coiling, pleating

  hydrogen, intervals, C=O, -NH

  are not involved
• The hydrogen bond in the secondary structure:

  • O__ and N__ are electro___, while H__ is electro___
  • electro___ and electro___ atoms form ___ bonds
  • individually hydrogen bonds are ___, but ___ hey are strong and able to ___ the conformation of the polypeptide chain

  oxygen, nitrogen, electronegative (delta-), hydrogen, electropositive (delta+)

  electropositive and electronegative, hydrogen

  weak, collectively, support
• a-helix (alpha helix)

  • made of a ___ polypeptide chain ___ into a regularly ___ ___ structure
  • stabilised by ___ bonds between the _=_ and -__ groups _ residues apart
  • ___ chain spirally coiled with each helix turn containing _ amino acids

  single, wound, coiled helical

  hydrogen, C=O, -NH, 4

  3.6
• • ___ pair of electrons from oxygen atom bond with hydrogen atom _ amino acids away in a single polypeptide chain
  • ___ C=O and -NH groups (in a polypeptide backbone) are involved in ___ bond formation: ___ stability in the secondary structure
  • _.6 amino acids per turn of a-helix

  lone, 4

  all, hydrogen, considerable

  3.6
• example of protein with a-helix structure (hair, nails, wool)

  keratin
• name the 2 different structures that can be found in the secondary structure

  A)

  B)

  
• B-pleated (beta pleated) sheet:

  • formed when _ or more ___ of a single polypeptide chain lying ___ by ___ are linked by ___ bonds
  • hydrogen bond formed between _=_ of one segment and -__ of ___ segment

  2, segments, side by side, hydrogen

  C=O, -NH, adjacent
• segments of polypeptide chain may run ___ (same direction) or ___ (different direction), resulting in the formation of ___ ___ sheets in an B- pleated sheet

  parallel, anti-parallel, flat folded
• example of a protein with B-pleated structure: (silk)

  fibroin
• Secondary structure includes the ___ and the ___ structure

  a-helix

  B-pleated
• Tertiary structure: formed by ___ folding and ___ of the ___ polypeptide chain, forming a ___, ___/ spherical molecule, give rise to ___ 3D conformation of protein

  furthur, bending, single, compact, globular, specific
• Due to furthur folding and bending, residues that are ___ ___ as well as those which are ___ can be brought ___ together

  far apart, adjacent, closer
• Tertiary structure maintained by _ types of ___molecular interactions formed between the _ groups of the amino acid residues

  • h___ bonds
  • i___ bonds
  • ___ interactions
  • d___ bonds

  4, intramolecular, R-groups

  hydrogen

  ionic

  hydrophobic

  disulfide