T2 - Protein Structure + Folding

Question 1

describe the general structure of an amino acid

Answer 1

• amino acids are monomers that make up polypeptides
• they consist of a central carbon atom (the a-carbon)
• they have an amino group (-NH2)
• they have a carboxyl group (-COOH)
• they have a hydrogen atom
• and they have a distinctive R group (aka the side chain)

there are 20 different amino acids due to the different R groups. The characteristics of an AA are determined by the R groups

Question 2

describe the key features of peptide bonds

how features contribute to proteins structure on other side

Answer 2

• the peptide bonds are formed at the ribosome during protein synthesis (translation)
• removing a molecule of water (OH from carboxyl, H from amine)
• covalent bond between C and N
• (O)C-N(H)
• peptide bonds are planar
• Psi ψ bond (Cα and C)
• Phi φ bond (Cα and N)
• more about Psi and Phi on other side

Question 3

how does features of amino acid/polypeptide contribute to protein structure

Answer 3

• Psi ψ bond (Cα and C)
• Phi φ bond (Cα and N)
• peptide bonds are planar, meaning that all groups (except for R) lie in the same plane
• peptide bonds are rigid (has partial double bond characteristics due to lots of resonance)
• therefore C-N bond is unable to twist about the bond
• peptide bonds always adopt a trans confirmation (carbonyl oxygen and amide hydrogen are on opposite sides of peptide bond)
• R groups are on opposite sides of peptide bond too, otherwise there would be a lot of clash and interaction between groups
• bonds on either side of the peptide bond are free to rotate, which is what determines the 3D structure

Question 4

what are the different levels of protein structure (broad terms)

more details about individual levels on seperate card

Answer 4

• primary is the sequence of amino acids in the polypeptide chain, any changes in this may have a significant affect on the strucutre, and therefore function of protein
• secondary is where α helix or β pleated sheet which is held together by hydrogen bonding
• tertiary is where further folding takes place (to form globular or fibrous proteins)
• quaternary is where several subnits are brought together to form larger protein

Question 5

main features of secondary protein structure

Answer 5

α helix
- can be right/left handed depending on direction of curl
- hydrogen bonding between N-H and C=O stablise the structure
- the distance between two adjacent AAs are about 0.15nm

β pleated sheet
- sheet is composed of adjacent β strands
- structure stablisied by hydrogen bonding between strands
- can be antiparallel, parallel or mixed arrangements between the strands
- the distance between two adjacent AAs are about 0.35nm which is more than twice the distance of that seen in the α helix

Question 6

main features of tertiary protein structure

Answer 6

folding into globular or fibrous structures
globular
- compact structure (very tightly folded structures0
- usually several types of secondary structure ie some α helix and some β pleated sheets

fibrous
- extended conformation (ie less compact)
- single type of repeating secondary structure
- ie collagen which has a triple helix structure for mechanical strength, ie 3 polypeptide chains wound around each other

Question 7

why is protein structure important for protein function

Answer 7

• has different qualities (ie hyrophobic/hydrophilic areas) like membrane proteins that rely on these features
• can have certain areas that are charged
• can have tertiary structure that helps with mechanical strength eg collagen which is triple helix
• can have quaternary or tertiary structure that is very specific for function ie enzyme with complimentary active site or haemoglobin that needs to bind to oxygen, and structure depends on affinity for oxygen

Question 8

basic ideas of protein folding

Answer 8

• folding process is ordered, not random (random would take too long)
• driven by the need to find the most stable conformation
• once the protein adopts a localised, stable conformation, that is held
• ie if stable α helix has formed in polypeptide chain, that is maintained (more stable)
• this means that number of possible confirmations is lowered, so process is more efficient
• all the information needed for folding is contained in the primary sequence, once protein has been denatured it can often refold and become fully functional again
• interactions between amino acids depends on R groups
• protein misfolding can cause disease and the formation of insoluble amyloid fibres

Question 9

basics of classifying amino acids

ie identify the different categories that amino acids can take up

Answer 9

chemical properties
- hydrophobic (and non-polar)
- hydrophilic (and polar)
- acidic (proton donor)
- basic (proton acceptor)

physical properties
- aliphatic (only carbons and hydrogens)
- aromatic (contains aromatic rings)