Amino Acids And Proteins Flashcards
What’s a hydrogen bond?
Electromagnetic attraction that occurs between a H atom and an electronegative atom (N,F or O)
Positives of being hydrophobic
Can pass through lipid bilayers
Good for anhydrous storage
Characteristics of the peptide bond
No rotation due to double bond characteristics
Planar
Carbonyl oxygen and amide hydrogen in trans orientation
Stronger than most other bonds
What is the pI?
The pH at which the protein has no net overall charge
How do pI and pH interact
pH>pI then protein is deprotonated, loses H+ therefore becomes more negative
pH<pI then protein is pronated, gains H+ therefore becomes more positive
What is the primary structure of a protein ?
The unique sequence of amino acids in a protein
Bonds involved I primary structure…
Covalent bonds
What is the secondary structure of proteins?
Local spatial arrangement of polypeptide backbone
Bonds in secondary structure…
Hydrogen bonds
Features of an a-helix
Right handed
3.6 AAs per turn
0.54 nm pitch
All amide hydrogens point up and all carbonyl oxygens down
What are helix formers?
Small hydrophobic residues such as ala and leu
What helix breakers?
Pro = as rotation around N-C (centre C)bond is impossible Gly = tiny R groups support other conformations
Features of a B sheet
Fully extended conformation
0.35 nm between adjacent AAs
R groups alternate between opposite sides of the chain
Why are bonds in parallel sheets weaker than anti parallel ?
In parallel bonds are at angles so weaker, while in parallel they are straight
Bonds in tertiary and quarternary structures?
Hydrogen bonds Van der waals Hydrophobic interactions Covalent bonds Ionic interactions
What does tertiary structure do?
Produce an overall 3D structure
Involves folding of secondary structure which can bring AAs further away in primary structure closer together
What is quarternary structure?
Interactions between and arrangement of different polypeptides chains within the same protein
Differences between globular and fibrous proteins
Globular have roles of catalyst, regulation and have a compact shape, fibrous involved in support, protection, shape and have many long starbdsc
Globular have several types of secondary and fibrous single type of secondary structure
Globular are usually soluble and fibrous insoluble
Globular have complex tertiary structure and fibrous have little or no tertiary structure.
How are amyloid fibrils formed?
From proteins that contain B-sheets as part of their normal structure. In disease states fibrils form because Bsheets from 1 protein molecule associate with the same region on another molecule. This continues resulting in formation of large insoluble aggregates –> fibrils
How do aromatic compounds stop the formation of amyloid fibrils?
Aromatic AAs are important I’m stabilising interaction of Bsheets between adjacent proteins. Therefore aromatic compounds have been found to interfere with amyloid fibril formation by blocking the interaction of aromatic side chains.
