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Secondary structure Repeating patterns created by folds Two most common α- helix β-pleated 1940s -proposed by Linus Pauling and Robert Corey Hydrogen bond between the backbone –C=O and N-H- Distinguishes a secondary structure and a tertary structure
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CHAPTER 14 NOTESSections 14.9, 14.10, 14.11, and 14.12
Hannah Nowell and Jenny Sulouff
Secondary Structure of a Protein14.9
Random coilWheat
α helix
Secondary structure Repeating patterns created by folds Two most common
α- helix β-pleated 1940s -proposed by Linus Pauling and
Robert Corey Hydrogen bond between the
backbone –C=O and N-H- Distinguishes a secondary structure and
a tertary structure
Secondary Structure (con.) A R group can replace the hydrogen
bonding On side chains
Hydrogen bond between the backbone –C=O and N-H- Distinguishes a secondary structure and
a tertiary structure A R group can replace the hydrogen
bonding On side chains
Random Coil
Does not show any signs of a repeating pattern
Main structure of a protein Most proteins are not mainly α- helix or
β-pleated The remainder is a random coil
Especially common in globular proteins Mostly soluble in water Mainly only used for nonstructural
purposes
α-helix
Resembles a right-handed spring A helix
The twists are kept by intramolecular hydrogen bonds Between the backbone –C=O and H-N-
Hydrogen bond between the –C=O and H-N-
Maintain the helical shape -C=O point down H-N-point up All amino acid side chains point away from
the helix
β- pleated sheet
The alignment of the protein chains are maintained by intermolecular or intramolecular hydrogen bonds
When peptide chains run parallel N- terminal ends are on one side
Or when they are antiparallel Neighboring N-terminal ends are
alternating sides Can occur when a hairpin structure is
formed when a polypeptide makes a U-turn Pleated sheet is antiparallel
β- pleated sheet (con.) Microcrystals are deposited in the
fiber axis, during the formation of β-pleated sheets
Can occur when a hairpin structure is formed when a polypeptide makes a U-turn Pleated sheet is antiparallel
Microcrystals are deposited in the fiber axis, during the formation of β-pleated sheets Microcrystals are found in Spider silk and
silkworm silk Allow the silk to be super strength and
toughness Unmatched by synthetics
Fibrous protein
β-pleated sheets
Keratin Hair Fingernails Horns Wool
Fibroin Silk
Extended Helix
Made of collagen Repeated units The third amino acid is a glycine
Shortest of all the amino acid chains Protein of connective tissues; bones,
skin, tendons, etc. Gives protein strength and elasticity 30% of the body’s protein
Tertiary Structure of a Protein14.10
Tertiary Structures
3D arrangement of the atoms in a protein
Refers to the conformation or shape that is different for every protein molecule
Interactions between the amino acids side chains
There are five ways to stabilize a tertiary structure; covalent bonds, hydrogen bonding, salt bridges, hydrophobic interactions, metal ion coordination
Covalent bonds and hydrogen bonding
Covalent bonds Most commonly used Disulfide bond Formation of a disulfide bond allows
covalent linkage, which binds the two chains together
Hydrogen bonding Between polar chains
On side chains between side chains and a peptide
backbone
Salt bridges
Salt bridges Also called electrostatic attractions Between a acidic amino acid (-COO-) and
a basic amino acid (-NH3+)
It is a simple ion-ion attraction
Hydrophobic Interactions
Hydrophobic Interactions Aqueous solution Polar groups turn outward, towards
aqueous solvent; Non-polar turn inward, away from water molecules
Series of Hydrophobic interactions occur The hydrophobic bond is weaker then the
hydrogen bonding and salt bridges Acts over large areas Can stabilize a loop and other tertiary
structures
Metal ion coordination
Same charge side chains linked by a metal ion Ex:
Two glutamic acid side chains are attracted to magnesium ion Forms a bridge
Human body needs selected trace minerals for components of proteins
Chaperones
Biologically active conformation is caused by a protein that helps other proteins
Helps stabilize polypeptide chains prevents folds that would cause
biologically inactive molecules
Quaternary Structure of a Protein14.11
Quaternary structure
Spatial relationship along with the interactions of subunits in a protein that consists of multiple polypeptide chains
Determines how subunit are organized
One of the four levels of protein structures
Hydrogen bonds hold and pack the subunits together Along with salt bridges and hydrophobic
interactions hold and pack them together
Hemoglobin
Made of four chains, chains are called globin
Two identical α-chains which consist of 141 amino acid residues
Two identical β-chains which consist of 146 residues
Chains containing non-amino acids are called conjugated proteins The non-amino acid part is called a
prosthetic group
Collagen
High organization of subunits Triple helix is called tropocallagen
Found in only fetal or young connective tissues
As it ages it organizes into fibrils cross link Insoluble
Cross linking consist to covalent bonds Link together in two lysine residues Ex. Of tertiary structures
Integral membrane proteins Traverse completely or partially into
a membrane bilayer 1/3rd of all proteins The outer surface is nonpolar
Interacts with lipid bilayer Two quaternary structures
6-10 α-helices that cross the membrane Β-barrels consisting of 8, 12, 16, or 18 β-
sheets that are antiparallel
How Proteins are Denatured14.12
What is Denaturation?
• Any type of chemical or physical agent that can destroy the structure of a protein– The structure becomes a random shape
protein– The agents do not break the peptide
bonds so the sequence of amino acids remain the same.
• Only effects a secondary, tertiary, or quaternary structures not a primary structure– Denaturing a primary structure would
cause a change in the arrangement of amino acids
Protein Denaturation
Denaturing Agent Affected RegionsHeat H bondsDetergents Hydrophobic regionsAcids, bases Salt bridges, H bondsSalts Salt bridgesReducing agents and Heavy metals
Disulfide bonds
Alcohol Hydration layers
Reversible Denaturation
If the change in the protein is only minor than denaturizing can be reversed. By chaperones
Not all denaturation can be reversed. Ex.
A hard boiled egg can not be un boiled.