(8+9) Protein Structure and Binding

Proteins are the of the cells

work horses

About _ of the weight of dry matter of cells is made of proteins

half

Draw a simple protein made of two amino acids with R for functional groups. Label alpha carbons.

Amino acids are linked together via _ bonds in a protein

peptide

Which bond is rather inflexible in amino acids/proteins?

the double bond between the oxygen and carboxyl carbon

N-terminus/amino-terminus

end of a amino acid chain where there is an amino (NH2) group

C-terminus

end of a amino acid chain where there is a carboxyl group

You read a protein from the ___-terminus to the ____ terminus

N/amino; C

Amino acids are usually added to the ____ terminus when extending the chain

C

The typical cells has - different proteins

20-20,000

The average protein is around amino acids long. Proteins this long have possible configurations. Why is there less than this amount of proteins found in cells?

300; 10^390; Proteins must be stable enough to not fall apart but flexible enough to be able to do work

Globular

arrangement of protein in which it takes on a spherical shape

Fibrous

arrangement of protein in which it takes on a long fiber-shape

Primary structure

arrangement of amino acids read of the N-terminus to the C-terminus. Held together only by covalent bonds (no weak bonds involved)

Secondary structure

occurs when a protein begins to fold and form beta sheets and alpha helices. Has both covalent (peptide) and hydrogen bonds. R-groups uninvolved.

Beta sheet (draw one)

common hydrophobic structure in a peptide chain.

Alpha helix (draw one)

common hydrophobic structure in a peptide chain

Tertiary structure

basic 3D structure of the protein. Final structure of a single polypeptide. Only one N-terminus and 1 C-terminus. Held together by peptide bonds, hydrogen bonding, and weak bonds between R groups or occasionally disulfide bridges. Protein may be separated into domains.

A tertiary protein may have how many N-termini? C-termini?

1;1

Monomer

a protein with one C-terminus and one N terminus with a tertiary structure

Disulfide bridge

covalent tertiary structure interaction in which the sulfur between two cysteine amino acids of a peptide form a covalent bond. Creates more structural stability

Disulfide bridges are typically found in what types of proteins

proteins that are to be exported out of the cell

When does secondary and tertiary structure form?

as the protein is being synthesized

Domain of a protein

represents a structural entity that is usually no more than 150 amino acids in length. Domains are separated “hinges points”.

Domains allow proteins to have more and _

flexibility and surface area

T/F monomers may have multiple domains and domains may have multiple monomers

False

Quaternary structure

higher order protein structure in which multiple proteins interact to form into a single unit. Stabilized by hydrophilic interactions.

Dimer

quaternary complex formed from 2 peptides interacting together

Heterodimer

dimer formed from 2 different proteins

Homodimer

dimer formed from 2 of the same protein

T/F quaternary protein structure is usually very energy intensive to make

false, polymer creation usually takes no energy at all

Polymer

quaternary complex formed from more than one peptides interacting together

t/f there is a 5’ and 3’ end of a protein

false

Residues

another word for amino acids

amino acids which are largely (hydrophobic or hydrophilic) mainly maintain the structure of the protein while the (hydrophobic or hydrophilic) _ amino acids maintain protein function

internal;hydrophobic;external;hydrophilic

Ligand

generic term for any structure that will bind to a protein

Binding site

general term for a site at which a ligand binds

Usually less than ___ amino acids are involved in a binding site

6

Usually a ligand interacts with a protein via a _

weak bond

Cofactor

other molecules that binds to a protein to make it work more effectively at binding ligands