proteins Flashcards
(15 cards)
Describe the structure of an amino acid.
Basic amine group (NH2)/N terminus, acidic carboxyl group (COOH)/C terminus, a hydrogen atom and R group
What are the properties of amino acids?
- Ability to form zwitterions (electrically neutral, dipolar ion)
- Ability to act as a buffer
- Unique properties based on R group — non-polar, polar or charged
What is the primary structure of proteins?
the unique number and linear sequence of amino acids that constitute the polypeptide chain, how a polypeptide chain coils and folds into a specific 3D conformation and how each polypeptide chain will interact with another is dependent on primary structure
Describe the two types of secondary structure and how they are formed.
They are formed by hydrogen bonds between the N-H and C=O groups, which can be between the same chain or between neighbouring chains.
The a-helix is an extended spiral spring, with R groups projecting outside the helix, preventing steric interference.
B-pleated sheets take on an extended zig-zag sheet like conformation that can be parallel or anti parallel. Amino acids usually only have small R groups since bulky R groups will cause steric hindrance.
What is tertiary structure and what bonds maintain it?
Tertiary structure refers to the further bending, twisting and folding of the polypeptide chain with the secondary structures to give an overall specific 3D conformation of a protein. Maintained by HIHI and disulfide (strong covalent) bonds within the same polypeptide chain
What is quarternary structure and what bonds maintain it?
Quaternary structure is the overall protein structure that results from the association of two or more polypeptide chains to form a functional protein. Maintained by HIHI and disulfide bonds
What level of structure is haemoglobin? Describe this level of structure
Quarternary structure — it is a multimeric protein with 2 a-chains and 2 B-chains, ie a tetramer made up of two identical dimers. Held by non-covalent interactions, mainly hydrophobic interactions
Describe the tertiary structure of haemoglobin and relate this to its function.
Hydrophobic amino acids are in interior and hydrophilic molecules are on exterior — soluble and a good transport protein for oxygen
Hydrophobic cleft allows for haem prosthetic group to bind on each polypeptide chain — haemoglobin molecule can bind to 4 molecules of O2.
Describe the role of the haem prosthetic group in haemoglobin in cooperativity
The haem group consists of Fe2+ held in a porphyrin ring. It can combine reversible with O2 and releases O2 to aerobically active muscles. As Fe2+ in the first haemoglobin subunit binds 1 molecule of O2, the F helix is pulled closer to the haem group. This pull creates a strain on the other haemoglobin subunits, such that the previously obscured haem groups of the other subunits are revealed. Hence, the remaining subunits changed their 3D conformation slightly, allowing their respective haem groups to bind O2 more readily, i.e. the remaining subunits’ affinities for O2 molecules increases.
Describe and explain the shape of the oxygen-dissociation curve of haemoglobin.
It is sigmoidal. Oxygen is loaded onto haemoglobin when partial pressure is high and unloaded when it is low. Such subunit cooperativity allows haemoglobin to be an efficient oxygen carrier.
Describe the primary, secondary and tertiary structure of collagen.
The amino acid sequence of a collagen polypeptide consists of a
repeating tripeptide sequence of Glycine – X – Y where X is often proline, Y is often hydroxyproline or hydroxylysine.
Each collagen polypeptide assumes a left-handed helical conformation with about three residues per turn known as the collagen helix. Each of these polypeptide chains is called an a-chain.
Three parallel α-chains wind around each other with a gentle, right-handed, rope-like twist (i.e. right-handed triple-helix) to form the basic structural unit of collagen (tropocollagen).
Explain the reason for order of amino acid residues in the primary structure of tropocollagen.
Every third residue of each polypeptide passes through the centre of the triple-helix, which is so crowded that only the small R group of glycine can fit in. This allows the three helical α-chains to pack tightly together, which provides high tensile strength.
The residues in the X and Y positions are located on the outside of the triple-helix, where there is room for the bulky R groups of proline and other residues.
Proline’s ring structure, stabilises the rigid three-stranded collagen helix.
Explain what contributes to high tensile strength in collagen.
Tropocollagen is held together by an extensive network of hydrogen bonds, between N-H and C=O groups of neighbouring chains and between OH groups of amino acid residues. Many tropocollagen molecules lie side-by-side, linked by covalent cross-links, forming collagen fibrils. They are also arranged in a staggered manner stabilised by hydrophobic interactions. Aggregation or collagen fibrils form a collagen fibre.
What is denaturation?
Denaturation is the loss of the specific 3D conformation of a protein molecule.
How do different factors lead to denaturation?
- Excessive heat increases vibrations of the atoms, leading to disruption of HIHI bonds.
- pH: changes the charges in the acidic and basic R groups, leading to disruption of ionic bonds and hydrogen bonds.
- Organic solvents: Transfer of a protein from an aqueous environment to an organic solvent can disrupt hydrophobic interactions that make up the stable core of globular proteins. The protein turns inside out and the hydrophobic regions changes place with the hydrophilic regions.
- Urea detergents: chemicals disrupt ionic and hydrogen bonds.
