Protein Structure pt 1

linear sequence of a.a. is referred to as a protein’s - structure

primary

>40 a.a are -

<40 a.a. are -

proteins

peptides

40 a.a. is the minimum length that a polypeptide can fold into a protein with a - or -

2D, 3D structure

polypeptides rarely exceed - a.a.

1000

- reaction between a.a. reflects what is happening in vitro

in vivo, a ribozyme is required

condensation

resonance between the carbonyl double bond and peptide bond gives the peptide bond -

this resonance makes peptide bond - and C-N atoms are not able to - freely

~40% double bond character

rigid, rotate

in majority of proteins, peptide groups are in - configuration

trans

rotations occur about the Φ and the Ψ

phi and psi

Φ bond refers to the - bond

Ψ bond refers to the - bond

C represents a - around which peptide groups rotate

C-N

C-CO

pivot

Φ and Ψ angles that place atoms of adjacent or nearby peptide groups too close to each other aren’t permitted, this is called - and it defined by the - radii of neighbouring atoms

large R groups will impose even greater - on permissible bond rotations

steric hindrance, VDW

restrictions

permissible phi and psi bond rotations for each amino acid can be calculated and represented in a - plot

blue areas show typical limits for all amino acids except - and -

Ramachandran

glycine, proline

glycine is much less constrained because the R group is a -

rotations about the phi and psi bond are much less likely to - with carbonyl O or amino H

small H

collide

proline is much more constrained because its cyclic side chain is - back to its amino acid group in the pp chain

repeating proline residues form the -

covalently bonded

left-handed helix

secondary structure of proteins refers to the local spatial arrangement of the - without contribution from, but still constrained by, the -

polypeptide backbone, side chains

tertiary structure of proteins refers to the unique - of the entire polypeptide, mainly due to the arrangement of its -

3D structure

side chains

quaternary structure of proteins refers to proteins composed of - that have a specific - of subunits

2 or more polypeptide chains

spatial arrangement

H bonds between - and - groups in the polypeptide backbone and between - a.a. residues

amino, carbonyl, polar

ionic bonds between charged groups in - and - a.a. residues

acidic, basic

disulfide bonds between - groups in cysteine a.a. residues

thiol/sulfhydryl

VDW bonds between - groups in - a.a. residues

hydrophobic, nonpolar

the only helical structure that allows both intra-helical H-bonding and permissible Ramachandran phi and psi angles is the - helix

carbonyl O of residue ‘n’ is H-bonded to amino ‘H’ of the ‘-’ distal residue

creates a regular right-handed rotation around helical axis with - a.a. residues per turn

R groups are pointed -, avoiding interference

right-handed alpha

n+4

3.6

outwards

adjacent beta strands of the same polypeptide chain from a kinky linear alignment, which allows optimal H-bonds to form with permissible - and - bond rotations

H-bonding occurs between - strands, creating beta sheets of 2-22 strands with a highly - structure

phi, psi

adjacent, rigid

optimal H bonds between beta strands are -

polypeptide backbone forms - to accommodate optimal H-bonding between strands and results in beta sheets with a pleated edge

R groups in the same beta strand - project to - sides of the sheet

R groups on adjacent beta strands project in the - direction

straight

kinks

alternately, opposite

same

what type of beta strand is this

anti-parallel

what type of beta strand is this

parallel

in anti-parallel beta sheets, adjacent beta strands line up so that H bonds are - and -

in parallel beta sheets, beta strands are not lined up perfectly, so H bonds are not -, which likely explains the - (less/more) stable structure compared to anti-parallel beta sheets

short, stable

straight, less

reverse turns or beta bends involve - (how many?) successive a.a. residues in a type I or II arrangement

residue 2 is often -

residue 3 is often - in type II to deal with steric hindrance

4

proline

glycine

fibrous proteins are - and are usually higher order - structures formed from regular repeating - structures

globular proteins are functional and are usually unique - structures formed by combinations of common - structures plus - structures

structural, quaternary, secondary

tertiary/quaternary, secondary, irregular or unique

collagen is most - vertebrate protein

involved in --bearing components of - tissues, such as bone, teeth, cartilage, tendon and the matrices of skin and blood vessels

abundant

stress, connective

collagen fibre contains 3-polypeptide chains, derived from many different genes

typical collagen chain has ~1000 residues in repeating triplets of -, X is often - and Y is often -

proline residues cannot participate in a classic -, so instead, individual collagen chains form a very - with 3 residues/turn

- (how many) left-handed helices wind around each other, forming a - to form a -, collagen fiber

every third residue of an individual left-handed helix passes through the - of the triple helix, which is why glycine is - in the collagen sequence, only glycine can fit

- between all three chains holds triple helix together

Gly-X-Y, proline, Hyp

right-handed alpha-helical structure, tight left-handed helix

3, right-handed rope-like twist, triple helix

centre, invariant

H bonds

beta bulges are strands of beta sheet containing an - that is not - to its neighbouring strand

extra residue, H bonded

helix caps are ends of alpha helical strands often contain - or -, whose R groups can bend back to - with 1 of 4 terminal residues

Asn, Gln, H bond

what is this

beta-alpha-beta motif

what is this

beta hairpin

what is this

alpha alpha motif

two successive antiparallel alpha helices packed against each other

what is this

greek key, a beta hairpin is folded over to form a 4 stranded antiparallel beta sheet