3 Proteins (DIY)

• Structure of amino acid

  • STRUCTURE: a central alpha-carbon (GREY) covalently bonded to:
  • A hydrogen atom (RED)
  • An amino group (-NH2) (BLUE)
  • A carboxyl group (-COOH) (GREEN)
  • A variable R group - determines the physical and chemical property (YELLOW)

  
• R-group properties

  1. Electrically Neutral

  • Non-polar, hydrophobic (do not form H-bonds with water)
  • Polar, hydrophilic (forms H-bonds with water)

  1. Electrically charged (all hydrophilic)

  • Negatively-charged: acidic amino acids (due to carboxyl group which dissociates to form -COOH at cellular pH)
  • Positively-charged: basic amino acids (due to amino group which accepts H+ to form NH3+
• Zwitterions (STRUCTURE)

  • Ionised amino acids in solution that carry both positive and negative charges (due to solubility in water)
  • Non-ionised amino group (-NH2) receives an H+ ion to become positively-charged -NH3+
  • Carboxyl group (-COOH) dissociates, releasing an H+ ion to become negatively-charged (-COO-)
• Zwitterions (FUNCTIONS)

  • acts as buffers due to amphoteric nature (protonated amino group and deprotonated carboxyl group acts as acids and bases)
  • Acid added: COO- of zwitterion accepts a H+ to become COOH
  • H+ removed from solution → no change in pH but amino acid becomes positively charged
  • Alkali added: NH3+ of zwitterion loses a H+ to become NH2
  • Neutralises the OH- in the solution, preventing change in pH of solution but amino acid becomes negatively charged
• Temperature effect on protein

  • As temperature increases, proteins containing more disulfide bonds are more stable to heat denaturation (Tertiary Structure)
  • Else, protein becomes denatured and loses its specific 3D conformation due to high temperatures increasing the intramolecular vibrations which break the bonds in the protein
• pH value effect on protein

  • As pH increases/ decreases from the optimum pH level, charged of acidic/ basic R groups may be altered and affect the stability of ionic bonds within a protein (secondary, tertiary and quaternary structures)
  • Protein will lose its specific 3D conformation due to the changes in ionic bonds holding together the polypeptide chain regions
• Peptide Bond

  • FORMATION: joined through a condensation reaction that links the carboxyl group (-COOH) of 1 amino acid to the amino acid group (-NH2) of another
  • Eliminates 1 water molecule
  • BREAKAGE: through a hydrolysis reaction that requires a water molecule per reaction
• Polypeptide

  • FORMATION: by amino acid monomers during the process of translation (regular repeating polypeptide backbone with variable regions by different R-groups)
  • Has directionality (N [amino end] T U C [carboxyl end])

  
• Organisation: PRIMARY structure

  • SINGLE polypeptide chain: number, sequence and type
  • Specified by nucleotide sequences in genes
  • Sequence of amino acids (with variable R groups) determines the type and location of chemical interactions
  • Protein folds into a specific 3D conformation where there are complementary surfaces and clefts that fit only with specific molecules
  • R-groups dictate the orientation, strength and duration of proteins (Dictate its amino acid sequence)
  • Conformation of determined, which results in FUNCTION
• Organisation: SECONDARY structure

  •  SINGLE polypeptide chain: spatial arrangement (regular coiling: alpha-helix, or pleating: beta-pleated sheets)
  • Maintained by H-bonds at regular intervals (formed between C=O and -NH groups of the polypeptide backbone)
  • Oxygen and Nitrogen are electronegative
  • Hydrogen of -NH or -OH group is electropositive
  • Collectively able to support the conformation of a polypeptide chain (strong)
• SECONDARY structure: alpha-helix

  • ALPHA-HELIX
  • SINGLE polypeptide chain wound into a regularly coiled helical structure
  • All C=O and -NH groups along polypeptide backbone are involved in H-bond formation every 4th peptide bond (considerable stability)
  • Lone pair of electrons on the O-atom of a C=O group forms a hydrogen bond with the hydrogen atom of the -NH group 4 amino acids away in a single polypeptide chain
  • 3.6 amino acid residues per turn of the helix structure
• SECONDARY structure: beta-pleated sheets

  • BETA-PLEATED SHEETS
  • SINGLE polypeptide chain has 2 or more regions that lie side by side being linked by H-bonds
  • H-bond formed between C=O group of one region and the -NH group of an adjacent region of the polypeptide backbone of a SINGLE chain
  • Regions can run parallel or antiparallel in a flat-folded sheet
• Organisation: TERTIARY structure

  • SINGLE polypeptide chain: further folding and bending (usually forming a compact, globular/ spherical molecule)
  • Allows residues that are far apart on the polypeptide chain to be brought closer together → determines the specific 3D conformation
  • Contains intramolecular interactions: hydrogen bonds, ionic bonds, hydrophobic interactions and disulfide bonds
• INTRAMOLECULAR interactions (1: Hydrogen Bonds)

  • Formed between polar R groups of amino acids
• INTRAMOLECULAR interactions (2: Ionic Bonds)

  • Formed between oppositely-charged R groups of amino acids at the ends of a polypeptide chain
  • Acidic (negatively-charged): COO-
  • Basic (positively-charged): NH3+
  • Charge in pH of surrounding medium might alter such charges and affect the stability of ionic bonds within a protein
• INTRAMOLECULAR interactions (3: Hydrophobic interactions)

  • Formed between non-polar, hydrophobic R groups (tend to interact and cluster at the core of a protein to avoid water)
  • Polypeptide folds in such a way so hydrophobic R groups points towards the centre of the roughly spherical molecule, shielding from the aqueous environment
  • Hydrophilic R groups face outwards into the aqueous environment → protein is soluble
• INTRAMOLECULAR interactions (4: Disulfide bonds)

  • Formed between 2 cysteine amino acid residues by oxidation of sulfydryl (-SH) groups
  • Strong covalent bond → STRONGEST interaction that contributes to the stability of the protein
  • As number of disulfide bonds increases, the stability of a protein to heat denaturation increases
• Organisation: Quaternary Structure

  • MULTIPLE polypeptide chains: association into 1 functional protein molecule
  • Not necessary to contain 2nd and 3rd structures
  • Each polypeptide is referred to as a subunit and are held together by intermolecular bonds between R groups (similar to Tertiary Structure)
• Haemoglobin (STRUCTURE)

  • Metabolic role: Transport
  • Transports oxygen in the blood and is found in Red Blood Cells
  • STRUCTURE:
  • GLOBULAR protein
  • Quaternary structure consisting of 4 polypeptides (2 alpha-globin subunits + 2 beta-globin subunits)
  • Polypeptide chain: globin
  • Prosthetic (non-protein) component: haem group
  • Consists of a porphyrin ring and an Fe+ iron (II) ion that can bind reversibly to oxygen
  • 1 haemoglobin : 4 oxygen molecules
• Haemaglobin (PROPERTIES - 1)

  • Soluble in water
  • In each subunit, most of its polar/ charged, hydrophilic amino acid R-groups are on the external surface
  • Can interact with aqueous environment and form H-bonds
  • Most of its non-polar hydrophobic R-groups of amino acids are oriented towards the interior, shielded away from the aqueous environment
• Haemoglobin


  • Subunits formation allows for movement relative to each other
  • Held together by ionic bonds, hydrophobic interactions and hydrogen bonds
  • No disulfide bonds
• Planar heme


  Binding of 1 O2 molecule to 1 haemoglobin subunit increases affinity for oxygen
• Domed heme


  Unloading of 1 subunit’s O2 molecule decreases affinity for oxygen
• Cooperative binding

  1. Initial ‘hesitant’ loading of the 1st O2

  2. Rapid loading of other 3 O2
• Subunits formation allows for a change in information that influences each subunit’s affinity for oxygen
• Haemoglobin is held together by ionic bonds, hydrophobic interactions and hydrogen bonds with no disulfide bonds
• Loading of the 1st O2 results in the rapid loading of the other 3 O2
• Collagen (STRUCTURES)

  • Structural role
  • Overall function: essential component of connective tissue in tendons, bonds, skins and teeth (most abundant fibrous protein in the human body)
  • STRUCTURE:
  • Quaternary structure consisting of 3 helical polypeptides (forming one collagen molecule: tropocollagen)
  • Each loose helix contains about 1000 amino acids
  • Amino acid sequences is usually a repeating tripeptide unit: glycine X-Y (X: proline, Y: hydroxyproline)
• Collagen (PROPERTIES)

  • High tensile strength in collagen
  • Tight triple helix as every 3rd amino acid in each polypeptide chain is glycine (smallest amino acid)
  • Can fit into the tight spaces in the centre
  •  Insoluble in water
  • Hydrogen bonds are unable to form between adjacent polypeptide chains where the amino acid residues in different helices are already extensively involved in intermolecular hydrogen bonding so interaction with water is limited
  • Rigidity of the molecule
  • Bulky and relatively inflexible proline and hydroxyproline (within glycine)
• Collagen (ORGANISATION)

  • Collagen fibrils → cross-linking of adjacent tropocollagen molecules
  • Greatly increases tensile strength
  • Covalent cross-linking (covalent bonds between lysine residues)
  • Collagen Fibres → Fibrils coming together to form bundles
  • Even more increased tensile strength of collagen
  • Banded appearance (Staggered arrangement of tropocollagen molecules)
• Explain why collagen is described as a fibrous protein

  1. It has a primary structure of repeating tripeptide sequence of glycine-X-Y, where X and Y are usually proline and hydroxyproline respectively, and this results in an ordered helical secondary structure.
  2. Adjacent tropocollagen form covalent crosslinks with each other to form a collagen fibril, which come together to form long fibres.
  3. Insoluble in water due to its large size, relatively weak ability to form hydrogen bonds with water due to extensive intermolecular hydrogen bonding in tropocollagen.
•  Describe the main features of collagen that contribute to its tensile strength

  1. Numerous hydrogen bonds are formed between 3 polypeptide chains to form a tropocollagen molecule.
  2. Covalent cross-links form between adjacent tropocollagen molecules to form collagen fibrils.
  3. Collagen fibrils lie in parallel bundles to form collagen fibres
  4. Staggered arrangement of tropocollagen molecules minimises points of weaknesses along the length of fibre.
• Suggest how the mutation could have increased affinity for human cells

  1. Mutation changes sequence of amino acids / primary structure and this causes change in type and location of R groups which in turn changes the location and type of bonds formed in the tertiary structure
  2. 3D conformation of tertiary structure altered leading to a larger binding site that is more complementary in conformation to the receptors of the target cells