test 2: protein structure Flashcards
covalent bonds are present in what protein structure level
primary
what bonds do secondary protein structure have
covalent and hydrogen bonds
what bonds are more prevalent in tertiary and quaternary protein structuer
hydrophobic effect
what is significant about covalent bonds in protein strucutre
- shows in amino acid sequence
- location of s-s bonds
H bonds
- interaction of amino acids close to each other
- form specific patterns
hydrophobic effect level
- 3d structure of polypeptide
quat - arrangement of multiple folded molecules
what % of DB character does a peptide bond have
40
what are the characteristics of a peptide bond
- planar
- no rotation around peptide bond
- cis/ trans isomerism
what isoermism are peptide bonds
- nearly 90% are trans
- 10% are cis
why is trans configuration better than cis
steric hinderance and interactions
in peptide bond where can rotation occur
around the alpha carbon but there is no rotation at all
what does a ramachandran plot show
- sterically allowed alpha and beta angles for a polypeptide chain
- limited amount of allowed configurations
2nd protein structure is found where
- local segments of biopolymers
- proteins and nucleic acids (DNA/ RNA)
- local conformations
what is an example of a secondary protein structure
- alpha helix
- beta strnad
- beta bend
- collagen triple helix
- loops and turns
what bonding is present in secondary
- H bonding between backbone amide NH of one AAand the carbonyl of another
who proposed the alpha helix
linus pauling
what bonds are present in alpha helix
- h bonds between n and n+4 residue
where do R groups poin on alpha helix
outward, perpendicular to the axis
what are some characteristics of alpha helix structure
- h bonds are parallel
- pitch = 5.4 angstrom
- 3.6 residue/ turn
1.5 Rise/AA - right hand
-charged AA - dipole polarity
how is alpha helix dipole polarity
- all c=O grpups point toward C and give dipole with + N, (-) C termini