Protein structure & Alpha helix / Beta sheet

Primary

Sequence of amino acids linked by peptide bonds

Secondary

Structures formed via H-bonds of the carbonyl and amide groups

Tetiary

Secondary structure folds to form 3-D structure of an intact polypeptide chain

quaternary

More than one polypeptide chain

N, C

Amino Acid sequence is written left to right from ( _____ -terminus to ___-terminus)

PIG TVNDS

Which amino acids are not fully compatible with the alpha helix?

No NH group

Why isn’t Proline not compatible w/ the alpha helix?

too flexible

Why isn’t Glycine not compatible w/ the alpha helix?

branched

Why isn’t Threonine / Valine / Isoleucine not compatible w/ the alpha helix?

val, ile, thr

What are the 3 amino acids that aren’t compatible with the alpha helix due to BRANCHING

Polar groups close to main chain

Why isn’t Asparagine / Aspartate / Serine not compatible w/ the alpha helix?

asn, asp, ser

What are the 3 amino acids that aren’t compatible with the alpha helix due to their POLAR groups

bottom left

Most RIGHT handed helices occur in the ________ quadrant of the Ramachandran Plot

i , i + 4

In an Alpha helix

• A hydrogen bond is formed between the -C=O of residue ____ and -NH of residue ____

-C=O, -NH

In an Alpha helix

• A hydrogen bond is formed between the _______ of residue i and the _____of the residue i + 4

alpha helix

that membrane-embedded portions of proteins are most often ______in structure.

3.6, 0.54

In alpha helices

• a complete turn is _____ residues per turn w/ a pitch of ____ nm

restricted

Alpha helices are HIGHLY ______

polar, surface

the two ends of an alpha-helix are very _____ and are found on the _____ of a protein

right

Nearly all alpha-helix found in proteins are _______ handed

top right

left-handed helices occur in the ______ corner of the Ramachandran Plot

lipid bilayer

The Alpha Helix is often used to cross the _______

NH, C=O

Beta sheet:

• hydrogen bonds formed between the ____ and _____ backbones

weak

Parallel Beta Sheets

• H-bonds are ____ cuz they AREN’T colinear

strong

Antiparallel Beta Sheets

• H-bonds are ____ cuz they ARE colinear

B-hairpin

Antiparallel beta strands joined with a short loop

B.a.B motif

Parallel beta strands joined with a long loop that adopts an alpha helical structure

heptad repeat

Repetitive sequences between two alpha helices with a period of seven residues,

• this residue is a Leucine (L)

Domain

segment of a polypeptide chain that can fold independently into a compact, stable structure

nonpolar

Water-soluble proteins fold into compact structure with a _____ core

Porin

Exception to water soluble proteins where the hydrophobic residues are on the outside and there’s a water-filled hydrophilic channel inside

dimer

quaternary structure that has 2 subunits

B-hairpins

antiparallel beta sheets are linked by _______

B.a.B motifs

parallel beta sheets are linked by ____

hydrophobic, polar

Membrane proteins

• ______ residues on outside, _____ on the inside