Proteins Flashcards
4 functional types of protein
structural proteins, enzymes, transporters and regulatory proteins
Amino acid definition
Zwitterionic monomers with a carboxyl and amino group and R group that undergo condensation reactions to form polypeptides.
What charge do amino acids have at pH 7?
0
5 functional types of amino acid side groups
Acidic, basic, hydrophobic, hydrophilic and structural
Basic amino acids
Arginine, lysine, histidine
Acidic amino acids
aspartate and glutamate
Hydrophobic amino acids
valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan and tyrosine
Which hydrophobic amino acid is the odd one out and why?
Tyrosine, as it is uncharged but still hydrophobic
Hydrophilic amino acids
cysteine, asparagine, glutamine, serine and threonine
Structural amino acid + what happens
Proline, produces kinks in chains due to its distinctive cyclic structure
Type of bond between two amino acids
Peptide bond
Properties of the peptide bond
Electrons are shared along the CO-NH system, resulting in partial charges on the oxygen and hydrogen.
The sharing of electrons means no rotation around the peptide bond, creating a rigid planar structure called the amide plane.
C-N bond has characteristics of a double bond, decreasing the length of time required for the proteins to fold.
What rotation occurs within amino acids?
Between C alpha - C and C alpha- N bonds , represented by phi and psi angles, which give proteins their 3D shape and flexibility
Why does stereoisomerism take place?
alpha carbon is chiral, as there are 4 groups attached, thus two isomers exist.
What isomer are human proteins made from?
L-type amino acids
What isomers do bacteria use + drug development?
D- type, thus when creating antibiotics, proteins are produced that mimic D-isomers to target bacteria
Significance of peptide bond in secondary structure
Carboxyl oxygen and amino hydrogen have partial charges, enabling them to hydrogen bond, producing a helix.
Levels of organisation of protein structure
Primary, secondary, tertiary and quaternary
Primary structure definition
The order and number of amino acids
Secondary structure definition
Three dimensional form of local segments of protein, containing hydrogen bonds.
Two main types of secondary structure
Alpha helix and beta pleated sheet
Alpha helix structure
Single polypeptide chain that twists around itself to form a rigid cylinder. Hydrogen bonds, running parallel to the helical axis, form every fourth peptide bond, linking the C=O and N-H. Helix twists every 3.6 amino acids.
Are alpha helices left or right hand and why?
Right hand, due to the L-type amino acids
Do R groups affect the alpha helix structure + why?
No, as the side chains project outwards
What are termed helix breakers + why?
Proline amino acids, as they do not have a primary amine group, thus cannot hydrogen bond as effectively.
What other intermolecular force is present in secondary protein structures?
Van der Waals
What are Van Der Waals and what is their function?
Weak attractive forces of attraction formed due to the instantaneous dipoles that arise as a result of the random movement of electrons in the protein. Are stronger over a shorter distance, which is the case in alpha helices.
Alpha helix advantages
Structural stability and optimised H bonding. Atoms touching so strong van der Waals, little steric clashing as side chains are outside the helix. Rigid, useful as transmembrane receptors.
Beta pleated sheet structure
Several beta strands, with 5-10 residues each align into sheets so that adjacent strands form hydrogen bonds.
How are steric clashes minimised in a beta pleated sheet?
R groups are found above and below the beta plane
Two types of beta pleated sheet
parallel and antiparallel
Difference between parallel and antiparallel beta pleated sheets
Parallel has the polypeptides running in the same direction, forming weaker hydrogen bonds at an angle, and greater distance, due to the incomplete sharing of the oxygen electron pair. Anti-parallel has the chains running in opposite directions, forming strong perfectly aligned hydrogen bonds.
Beta pleated sheet eventual structures
Globular proteins
What is a loop/turn?
Polypeptide chain makes a 180 degree change in direction- a dihedral angle
What forms a loop?
Carbon atoms of two residues are close, separated by 1-5 peptide bonds, forming an inter main chain hydrogen bond which causes a turn.
Example of a loop
Beta hairpin, two antiparallel strands linked by a loop
What amino acids often involved + why?
Glycine and proline, as they often produce a dihedral angle
Tertiary structure definition
Organisation of the secondary structure into a defined 3D shape, with interaction between R groups
Interactions in tertiary structures
Van der Waals, disulfide bridges, hydrophobic interaction, ionic bonds and hydrogen bonds
Explain ionic bonds
Charge-charge or charge-dipole. Longer distance interactions.
Explain hydrophobic interactions
Polar, hydrophobic side chains tend to be forced together when in water and hydrophilic ones face the water to produce a more stable molecule. Present in globular proteins and transmembrane proteins.
Explain disulfide bridges
Covalent bonds that form between two cysteine amino acids, stabilising the protein.
Examples of domains and functions
Beta domain- barrels and saddles, such as immunoglobulin
Alpha domains- helix-loop-helix structures
ABC membrane domain- alpha helical, such as the CFTR transmembrane protein.
What is a domain?
unit of organisation where the motifs appear to be structurally stable. Part of a protein that can fold independently from the rest of the protein into a compact and stable structure, often associated with different functions.
What is the quaternary structure?
Interactions between many polypeptide chains and/or prosthetic groups to form a complex 3D structure- a complete functional protein unit.
Oligomeric protein definition
A protein complex made of two or more subunits
Two types of oligomeric protein
Homo-oligomeric and hetero-oligomeric
Homo-oligomeric definition
protein formed of the same subunits- dimers, trimers etc.
Hetero-oligermeric definition
Protein formed of different subunits- e.g Haemoglobin formed of two alpha globin and two beta globin subunits
Myoglobin versus haemoglobin
Myoglobin consists of eight alpha helices connected by loops- single polypeptide chain with one haem group. Haemoglobin formed of 4 polypeptide chains each with a ham group
Post translational modifications examples
disulfide bonding, cross linking and peptidolysis
Crosslinking explained
covalent bond formed between adjacent amino acids in the same protein, or in different proteins forming a sub unit
Peptidolysis explained
enzymic removal of part of a protein after synthesis. Often unassembled protein units or misfolded proteins removed
Non-peptide attachments examples
Glycosylation, phosphorylation, adenylation and farnesylation
Glycosylation explained. 3 amino acids involved
Addition of oligosaccarides to form glycoproteins. Attach to NH on asparagine and OH on serine and threonine
Adenylation explained. 3 amino acids involved
addition of AMP group to protein, often to tyrosine, threonine or serine
Phosphorylation explained. 3 amino acids involved
Addition of phosphate via kinases. Threonine, serine and tyrosine
Farnesylation explained. Amino acid involved
Farnesyl (hydrocarbon) anchor which inserts into plasma membrane. Added to cysteine.
functions of post translational modifications
regulation, targeting, inducing turnover, improve structure
two different types of domains
structural and functional
