Proteins Flashcards
What is a polypeptide?
A linear sequence of amino acids covalently joined together by peptide bonds.
What is a cofactor?
- Non-protein component that aids protein function.
- Can be organic or inorganic in nature.
- Prosthetic group: organic cofactor is tightly bound to a protein.
What are the different structural levels of proteins?
- Primary structure: The specific number and sequence of amino acids in a polypeptide.
- Secondary structure: The folding or coiling of a polypeptide due to hydrogen bonding (e.g. of secondary structures: alpha-helix & beta-pleated sheet).
- Tertiary structure: The three-dimensional shape of a protein due to bonds and interactions (e.g. hydrogen bond, ionic bond, disulphide bond and hydrophobic interaction) between amino acid R-groups.
- Quaternary structure: the three-dimensional shape of a complex that is formed by two or more polypeptides coming together via bonds and interactions (e.g. hydrogen bond, ionic bond, disulphide bond and hydrophobic interaction) between amino acid R-groups.
Define the term amphoteric.
A compound with both acidic and basic properties in aqueous solution.
Define a buffer.
Substance that can reisist changes in pH in a solution when small amounts of an acid or alkali is added to it.
What is a domain in proteins?
A domain is defined as a discrete, locally folded unit of tertiary structure that usually has a specific function.
State the differences in structures and properties of fibrous and globular proteins.
(Hint: 5)
Fibrous proteins:
1. Long fibres making up its structure of fibrous proteins
2. Fibrous proteins are insoluble in water.
3. The polypeptide chains of fibrous proteins usually have repetitive sequence of amino acids.
4. Fibrous proteins usually provide structural support to cells.
5. The length of two polypeptides chains of the same protein may vary.
Globular proteins:
1. Polypeptide chains are folded into globular shape.
2. Globular proteins can be soluble in water.
3. The polypeptide chains do not consist of repetitive amino acid sequences, hence there is a large variety of amino acids in a globular protein.
4. Globular proteins perform a variety of functions, such as enzymatic function (amylase) and transport function (haemoglobin) etc.
5. The length of two polypeptide chains of the same protein will always be identical.
Relate haemoglobin’s structural features to it’s function.
(Hint: 6)
S: Haemoglobin is a globular protein and therefore has a compact structure.
F: Its compact structure allows many haemoglobin molecules to be packed into a red blood cell to maximise the oxygen-carrying capacity of each red blood Each haemoglobin molecule has 4 subunits (2 α chains and 2 β chains), each with a haem prosthetic group attached.
S: Each haemoglobin molecule has 4 subunits (2 α chains and 2 β chains), each with a haem prosthetic group attached. A haem group contains a porphyrin ring bound to an iron (II) ion (Fe2+). The Fe2+ ion of a haem group in each subunit binds one molecule of oxygen.
F: Each haem prosthetic group is capable of binding to one oxygen molecule, thus each haemoglobin molecule can transport four molecules of oxygen.
S: The four subunits (two alpha-chains and two beta-chains) of a haemoglobin molecule are held together by R group interactions, such as hydrophobic interactions and ionic bonds, allowing the binding of oxygen to the haem group of subunit. The tertiary structure of each polypeptide chain in haemoglobin can change to increase the affinity of each subunits to oxygen. Hence, haemoglobin molecule changes from a weak oxygen binding form to a strong oxygen binding form.
F: This phenomenon is known as cooperative binding, for the effective loading and unloading of oxygen from the haemoglobin molecules.
S: The haem group lies in a hydrophobic cleft of each haemoglobin subunit, lined with amino acid residues with hydrophobic R groups.
F: Haem groups can be held in the clefts of haemoglobin subunits via hydrophobic interactions.
S: The haem group is orientated such that its Fe2+ on one face is complexed to an amino acid residue, leaving the other face accessible to bind oxygen.
F: This allows oxygen to efficiently bind to the haem groups within haemoglobin and allows haemoglobin to transport oxygen.
S: For each subunit, most of its amino acid residues with hydrophilic R groups (acidic, basic and polar R groups) are on the external surface of its globular structure while amino acids residues with hydrophobic (non-polar) R groups are buried within.
F: This ensures that haemoglobin is soluble in the aqueous medium of red blood cell cytoplasm and can be contained within red blood cells for oxygen transport.
Relate collagen’s structural features to its function.
(Hint: 8)
S: The repetitive amino acid sequence (glycine-X-Y) allows the tropocollagen polypeptide chain to adopt a regular helical structure.
F: The regular helical structure aids in the formation of hydrogen bonds between the polypeptide chains to form tropocollagen, resulting in high tensile strength (resistant to stretching), therefore collagen can provide structural support in connective tissues.
S: Every third amino acid of the tropocollagen polypeptide chain is glycine which has a small R group (hydrogen atom).
F: This allows the three polypeptide chains of a tropocollagen molecule to be wound tightly together and form hydrogen bonds in the triple helix structure, increasing tensile strength of the tropocollagen molecule and allowing tropocollagen to provide structural support in connective tissues.
S: Numerous (inter-chain) hydrogen bonds are formed between the C=O and N-H groups of polypeptide chains when three polypeptide chains wind together to form a tropocollagen molecule.
F: This increases the tensile strength of a tropocollagen molecule (resistant to stretching) and allows it to provide structural support in connective tissues.
S: Many tropocollagen molecules are organised in a parallel staggered arrangement in collagen fibrils.
F: This minimises weak spots running through collagen fibrils.
S: Covalent crosslinks are formed between the C terminal of one tropocollagen molecule and the N terminal of an adjacent tropocollagen molecule.
F: The numerous bonds in bundled tropocollagen molecules increase tensile strength (resistant to stretching) and allowing collagen to provide structural support in connective tissues.
S: Tropocollagen molecules bundle together to form collagen fibrils which then further bundle together to form collagen fibres.
F: This gives collagen fibres high tensile strength (resistant to stretching) and allowing them to provide structural support in connective tissues.
S: Each tropocollagen polypeptide chain has about 1000 amino acid residues and is therefore a large molecule. Three polypeptide chains wind together to form a tropocollagen molecules. Each fibre is made up of a bundle of tropocollagen molecules.
F: Collagen is insoluble in water.
S: There are large number of hydrophobic R-groups (of proline and hydroxyproline residues) on the exterior surface of the tropocollagen triple helices.
F: This ensures that tropocollagen is insoluble in water.
What are G-Protein Linked Receptors (GPLRs)?
GPLRs (also known as G-Protein Coupled Receptors, GPCR) form a large group of proteins that function as cell surface receptors. These receptors on the surface of cells detect the presence of molecules outside of the cell and aid in the activation of intracellular responses.
Relate GPLR’s structural features to its function.
S: The GPLR has seven transmembrane (spans across the membrane phospholipid bilayer) α helices. The exterior surfaces of the helices facing the non-polar fatty acid tails of the phospholipid molecules in the cell surface membrane have many non-polar R groups which interact with the fatty acid tails via hydrophobic interactions.
F: This allows GPLR to be stably embedded in the cell surface membrane to serve as a cell surface receptor.
S: The specific loops between the transmembrane helices of GPLR form binding sites:
- An extracellular ligand-binding site.
- A cytoplasmic/intracellular G-protein binding site.
F: The extracellular ligand-binding site of the GPLR has a complementary shape to the ligand to allow binding of ligand.
The cyctoplasmic/ intracellular G-protein binding site has a complementary shape to the G protein and allows binding of G-protein to the cytoplasmic G-protein binding site of GPLR in the cytoplasm.
What is an allosteric protein?
It is one in which the binding of a ligand to one site affects the binding properties of another site on the same protein. It has other conformations induced by binding of activities or inhibitors.
