Secondary structure

what is Secondary structure

it is the local spatial arrangement of backbone ignoring side chains. Usually B pleated sheets and a helicalase

what bonds are important in α-helices and β-sheets

Hydrogen bonds

in hydrogen bonds which group is Donner and which is acceptor

The group that provides the hydrogen atom is referred to as the hydrogen bond donor (e.g. N-H) ; the group that provides the lone pair is referred to as the hydrogen bond acceptor (e.g. N)

what is stronger covalent or hydrogen bonds?

Covalent

what is the bond dissociation energy for a hydrigen bond?

2-40 KJ/mol

what is bond dissociation energy for a covalent bond?

359 KJ/mol

which is a longer bond hydrogen or covalent bonds?

• hydrogen bonds are longer

Bond length for hydrogen bond

~ 2 Å

bond length for a single covalent bond

~ 1 Å

how does H bonding work in alpha helix

x + 4 rule

a carbonyl group forms a hydrogen bond with an anime group 4 positions down

this patters stabilizes the alpha helix structure

where do teh side chains face in the chain

face outwards so steric interference (when atoms are too close together form repulsion) is avoided with backbone or other side chains

Each residue is related to the next one by a rise of.. and a rotation of…

1.5 Å

100 degree rotation

how many amino acid residues per turn

3.6 amino acid residues per turn

what is the pitch

the vertical distance the helix rises by each turn

• it is the rise between 2 amino acids x the amount of residues per turn

for alpha helix what is the pitch

5.4 Å

what is the screw sence

the direction in which the helicase twists

alpha helicase can be

right handed (twists clockwise N→C, most common)

or

Left handed (twists anticlockwise)

in B -sheets …

neighboring stands H bonds together between C=O and N-H groups

in parallel β-sheet…

stands run in the same direction

NH group of one stand is HB to a C=O of adjacent stand , this C=O is also HB to a amine group 2 residues down the chain

in antiparallel β-sheet

stands run in opposite directions

the C=O groups and NH groups are hydrogen bonded to NH and C=O groups on adjacent stand

what is the distance between 2 adjacent amino acids

3.5 Å

side chains of adjacent amino acids….

point in opposite directions

what can loops and turns do

they connect α-helices and β-sheets and can also cause a change in the polypeptide direction

Loops

• Can vary in length and shape

  • located on the surface of proteins, usually on polar AA

Turns

• when have a loop that is 3-6 AA, a regular hydrogen bond pattern, and specific dihedral angles are called β-turn

β-turn

• or also called reverse turn

• turn 180 dregrees involving 4 amino aicd resiudes

• the C=O at point x is HB to NH group on residue x+3

• this interaction stabilized ppt chain from any abrupt changes in direction

• different classes of β-turns depedning on Psi and Pie angles at x+1 and x+2

• there are TI and TII

φ and ψ angles of the residues at positions x + 1 and x + 2

The x + 2 residue of the type II turn can only be occupied by glycine

which amino acids are most likely to be α-helix former’s

• Alanine

• Glutamic acid

• Methionin

Which amino acids are β-sheet formers

• Isoleucine

• Valine

• Tyrosine

whic amino acids are most likely β-turns

• Asparganine

• Glycine

• Proline

when Proline is involed

60% of bonds are in cis configuration

why does Prolines are rarely found in α-helices and β-sheets

• doensnt really ahve H to take part in HBC

• no rotation aroudn C-N bond so produced destabilizing kink in an α-helix