lec10-11 Flashcards
What atoms form hydrogen bonds in an alpha-helix? and what level of structure
The carbonyl oxygen (C=O) of one amino acid hydrogen bonds with the amide hydrogen (N-H) of the amino acid four residues earlier.
secondary
Which amino acids are less likely to be found in an alpha-helix and why?
Proline: No N-H for hydrogen bonding, rigid structure breaks helix.
Glycine: Too flexible, destabilizes the helix.
How do you determine if an alpha-helix is right-handed or left-handed?
Use the right-hand rule: curl your right hand’s fingers in the direction of the helix turn. If your thumb points to the C-terminus, it’s a right-handed helix (which is the most common form).
–thumb points in c direction cuz c is starting poitn and it progesses on n side
What is the structure of hemoglobin?
Globular protein, consisting of alpha-helices that allow for efficient oxygen binding and release.
What is the structural composition of ferritin?
4-helix bundle, forming a spherical structure for iron storage. (alpha-helices)
“ferrous sulfate Holds iron Hostage”-h for helix
What is the structure of a leucine zipper?
2 separate proteins that dimerize, each protein containing two alpha-helices (forming a dimer).
What are superhelical structures in proteins, and how do they form?
Superhelical structures occur when alpha-helices or beta-strands twist around each other, creating a stronger, coiled structure. Examples include keratin, fibrin, and tropomyosin, where multiple helices or strands intertwine to provide stability and function.
keratin
is alpha helix (super helix)
Two helices wind around one
another to form a super-helix (tertiary)
is alpha helix right or left handed
right.
eg) collagen is non alpha helical its left handed helical
What defines a superhelical protein
Superhelical proteins have multiple helices that wrap around each other to form a stable superhelix. This structure is stabilized by interactions like hydrophobic forces and hydrogen bonds. Examples: keratin, collagen, myosin. Not all proteins with multiple helices form superhelices; some helices are simply part of a larger structure without coiling together.
eg)ferratin, keratin
What is the structure of collagen, and what are its key features?
Collagen is made up of three left-handed helical polypeptide chains that form a right-handed superhelix, not an alpha helix. The collagen triple helix is composed of repeating amino acids: glycine, proline, and 4-hydroxyproline. The structure is stabilized by hydrogen bonds and is extremely strong. Every 3rd residue is glycine, found at the center of the superhelix, allowing the chains to pack tightly. The repeating peptide unit is Gly-Pro-4-Hyp.
porin
Type and Location: Porin is a transmembrane protein found in the outer membrane of bacteria.
Structure: It has a β-barrel structure, formed by multiple antiparallel beta-strands arranged in a cylindrical shape.
Lipid Bilayer Interaction: The outer surface of the β-barrel is lined with hydrophobic side chains that interact with the hydrophobic lipid bilayer of the membrane.
Inner Channel: The inner surface of the β-barrel is lined with hydrophilic amino acids, creating a selective channel that allows the passage of small molecules (e.g., ions, nutrients) while excluding larger molecules
beta-sandwich
-2 beta-sheets are stacked upon eachother
-side chains project into the middle and they have to complement eachother (often hydrophobic)
eg)fibroin (GAGAGA cuz they have small side chains)
What are loops in protein structure?
Flexible, irregular regions connecting secondary structure elements (alpha helices, beta strands, beta sheets).
No regular or repeating structure.
Connect alpha helices with beta strands, alpha helices with other alpha helices, or beta strands with other beta strands.
Allow the protein chain to change direction.
Contribute to protein shape and function.
In beta sheets, parallel strands are often joined by loops, which may contain alpha helices or beta strands.
Looser than beta turns, often containing more than 3-4 amino acids
What are the two types of beta turns?
helps protein fold into glubular shapes by allowing tight turns and compact packing
Type I Beta Turn
Most common.
Peptide bond between residues 2 and 3 in a trans conformation.
Type II Beta Turn
Peptide bond between residues 2 and 3 in a cis conformation.
Often has glycine at position 3 due to its flexibility.
Both types help in sharply turning the polypeptide and stabilizing beta sheet structures.
_______ and ______ residues are often found
at the boundaries of a-helices and in turns
proline and glycine. these are found less frquently in alpha-helices
eg of coiled coil alpha helix (seen in 4 examples)
keratin (Also has disulfide bonds)
mysosin
tropomyosin
fibrin
eg of 2 seperate alpha-helix proteins (dimer)
leucine zipper
zippER dimER dime is two digits so its two seperate proteins
ferritin
4 helix bundle
of alpha helices
keratin
alpha helical coiled coils (2 helices)
collagen
not an alpha helix
triple left handed helices
gly-pro-4hyp
porin
beta-sheet
hydrophylic inner and hydrophobic outer
transmembrane protein
fibroin
beta-sandwich
gagagagaga
interdigitate (interlock r groups)
silkworms
antibody structure
disulfide bonds
beta sheets
