peptide bonds and secondary structure

how is the peptide bond formed

from the joining of two or more amino acids through condensation

what is the directionality of a peptide bond

from the N- terminus to the C- terminus

at what level does the joining of amino acids happen

at the level of ribosomes

why are amino acids in a polypeptide known as residues

a water molecule is removed in the condensation reaction that joins two amino acids together so the leftover part is called a residue

why are amino acid residues arranged in an antiparallel way

due to sterics, the amino acid side chain takes up the space around the amino acid

define protein

a polypeptide or complex of polypeptides that has attained a stable three dimensional structure and is biologically active

how many amino acids make up a peptide

10 or less

what prevents two groups approaching each other

steric hindrance - they can only approach each other to what is allowed by their van der waals radii

what configuration do adjacent amino acids adopt and why

trans - the amide group must remain in a planar orientation relative to the carboxyl group

what gives rise to psi and phi angles around the alpha carbon

amino acids can rotate around covalent bonds to the alpha carbon as well as rotational freedom of the side chains

what else is needed to stabalise regular folded proteins

non covalent bonding such as hydrogen bonds

what are the two main factors that affect confirmation

the chirality of amino acids and the planarity of the peptide bond

what is the chirality required

L amino acids

why is the peptide bond planar

it is due to the partial dipole of the C-N linkage between two residues formed due to resonance

what bond refers to the phi angle

rotation around the N-Ca bond

which bond is the psi angle

rotation around the Ca-C bond

how can the allowed combinations of phi and psi angles be visualised and what is this used for

in a ramachandran plot which is used when determining a protein structure

how does a ramachandran plot work and what is the exception

alpha helices and beta sheets take up specific regions - glycine is the exception because it is the most flexible

where is glycine found

in regions where greater flexibility is requires or where long extended helices are needed

proline

rigid structure and is often referred to as a helix breaker

why is the polypeptide backbone hydrophilic and what must be done and how to have a hydrophobic core

it is hydrophilic due to -NH and -C=O groups, this needs to be neutralised and it is done through alpha helices and beta sheets

how can beta sheets be arranged

either parallel or antiparallel

how is an amino acid defined

a curved structure with a constand pitch

how many amino acyl residues are in a 360 degree turn

3.6

what distance does the coil traverse and what is the pitch

it traverses a distance of 1.5 andstoms and the pitch is 5,4

what type is bonding is required to neutralise the partial charges of the carbonyl and amide groups

hydrogen bonding

what is the average length of an alpha helix and how many turns and what is the bitch

10 residues with 3 turns which is 15 angstroms in length

what results because of the hydrogen bonds

the dipoles of each peptide bond are aligned so there is a net dipole with the N terminus being positive and C terminus being negative

why is the charge in alpha helices useful

this is found in the binding site of many ligands such as ATP

what can be said about the side chains in alpha helices and what is found as the end

they project outwards with proline found at the end

what is the most common use for alpha helices

they are used to anchor proteins to the membrane

what helices are called amphipathic

the number of hydrophobic residues a protein has

how many turns in a beta sheet and what is the pitch

2 residues with a pitch of 3.5 angstroms

where do the NH and C0 groups form covalent bonds and why

with adjacent beta strands- they are too far apart to do that with each other

why are beta sheets rigid

the psi bond is fully extended with no planar rotation

what can beta strands combine to give

mixed beta sheets with both parallel and antiparallel sheets - there is strong bias against this formation

what is the other major use of beta sheets

membrane proteins which form barrels which can form channels

where do loops occur and why

at the surface of a protein so that the backbone carbonyl and amide groups form H bonds with water

what are loops rich in

polar and charged side chains

what are loops used for

to connect alpha helices and beta sheets

why else are loops found at the protein surface

so they can form binding sites

what are loops that connect two adjacent beta strands called and what do they involve

hairpin loops that involve 4 amino acid residues in a 180 degree tuen

describe b type 1 turns

the first and fourth amino acids residues hydrogen bond which allows the chain to turn quickly

describe b type 2 bonds

glycine is the second residue which allows a tight turning arrangement

describe gamma turns

they involve 3 residues in a 180 degree turn and proline is always the second residue