Protein Tertiary Structure

Tertiary structure refers to the ___________ of the secondary structural elements in the polypeptide chain

spatial arrangement

What happens to the short range secondary structures in the folded tertiary structure

they are brought together

Noncovalent interactions occur between amino acid _______ in tertiary proteins

side chains

what is the major stabilizing force in tertiary proteins

hydrophobic effect

what kind of bond occurs between two nearby cys residues?

disulfide bonds

iron and zinc are _______ that help stabilize tertiary proteins

metal ions

What are the two major classes of tertiary protein structure? What do they each do?

Fibrous proteins for structural function

Globular proteins for chemical function

Globular proteins fold into defined structures called

domain

When describing protein structure, what questions do you ask?

How many amino acids?

How many domain?

What is the major secondary structure?

What type of motif does it contain?

What is a protein domain?

A compact, independently folded region of tertiary structure

The size of a domain

from as few as 25-30 to several hundreds of amino acids

A domain frequently possesses some ________? Give examples

defined function.

DNA recognition

oligomerization

cofactor binding

four types of major secondary structure

predominately alpha helix

predominately beta strand

alpha/beta

alpha+beta

What are motifs?

super-secondary structures in close proximity

motif are associated with ________?

particular functions

What are the most common motifs and what do they do?

alpha alpha corners and beta alpha beta loops. Provide two layers of secondary structure

What is a helix bundle and what does it do?

Contains 4 or more alpha helices

Provides hydrophobic pockets or hydrophilic channels

What is a beta barrel and what does it do?

Contains multiple twisted beta strands forming a beta sheet in a barrel structure

Provides channel for polar molecules

What is a greek key fold and give an example

Consists of 4 or more beta strands linked together to form a beta sheet structure

Bacterial copper binding protein

What is a Rossman fold and where is it found? Give an example

Complex protein fold in which there are alternating alpha helices and beta strands

Found in proteins that bind nucleotides

bacterial lactate dehydronase

What is a TIM barrel and where is it found? Give an example

Consists of alternating alpha helix/beta strand barrel

Found in a large number of metabolic enzymes

triose phosphate isomerase