BIOFOUND 2.2 Biological Molecules pt 2

because they form numerous non-covalent bonds

why are proteins able to fold?

hundreds or thousands of weak bonds!

how many bonds are used to hold a protein in its folded shape?

hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern

how do non-covalent bonds contribute to the protein structure in the secondary structure stage?

forms a 3D folding pattern of protein due to side chain interactions

how do non-covalent bonds contribute to the protein structure in the tertiary structure stage?

affects the way proteins interact with each other

how do non-covalent bonds contribute to the protein structure in the quaternary structure stage?

electrostatic interactions

the first type of non-covalent bond: an attraction between positive and negative charges, if a positively charged amino acid is near a negatively charged one they can attract each other

hydrogen bonds

the second type of non-covalent bond: a weak electrical attractions between two polar covalent bonds, a hydrogen atom that is partially positively charged will be attracted to an atom in a different part of the protein that is partially negatively charged

hydrophobic effect

the third type of non-covalent bond: where nonpolar molecules cluster together to avoid water. In proteins, nonpolar amino acid side chains pack inside the folded structure, while polar or charged side chains remain on the outside.

van der waals attraction

the fourth type of non-covalent bonds: a weak electrical attraction between two non-polar covalent bonds, these occur when non-polar side chains are shoved really close together in a proteins 3D chat

because of the patterns that are formed by the non-covalent bonds

why do proteins have a unique 3D shape and structure?

conformation

the proteins 3D shapee

in order to function properly

why is a protein required to have a 3D shape?

the function of the protein is changed

how do changes to the proteins shape effect the protein?

binding

a proteins ability to function that requires them to attach to other atoms and molecules

ligand

the molecule or atom that a protein bonds to

binding site

the specific place on a protein where it binds to another atom or molecule

must be able to form non-covalent bonds with it

what must a protein be able to do in order to form a bond with any atom or molecule?

they can only be formed by having very close contact between proteins and ligands

what can non-covalent bonds be formed by?

the 3D shape of the protein must very closely match the 3D shape of its ligand

how does a protein and its ligand become close in contact?

by protein folding

how is a binding site formed in a protein?

the binding site is ideal for the formation of non-covalent bonds with its ligand

how does protein folding allow it to bind to a ligand?

catabolite activator protein, it activates genes that increase the metabolism of glucose and other sugars in bacterial cells

what does CAP stand for and what is its purpose?

receptors

proteins that are able to transmit as a signals when they bind to other molecules

weak and temporary

non-covalent bond characteristics

denaturation

when proteins lose their 3D shape

if chemical conditions cause their non-covalent bonds to weaken and break

how can protein folding be reversed?

by acid and heat

how is denaturation caused?