Protein shape

primary structure

• linear sequence of amino acids residues

• determined by mRNA code

• in combination with protein’s environment determines secondary, tertiary, quaternary

is the amino acid sequence of every protein identical to the genetically encoded primary sequence?

yes

secondary structure

• folding and twisting of peptide backbone

• held together by weak H-bonds between C=O and N-H groups in backbone

• R-groups stick out from backbone

  • two well-known secondary structures: alpha helices and beta sheets

alpha helix

• rigid cylindrical structure

• forms when H-bonding occurs between a C=O and N-H groups that are 4 amino acids apart on polypeptide backbone

• coiling happens in a clockwise direction down the length of chain

beta sheet

• flat sheet like structure

• form when H bonding occurs between C=O and N-H groups on adjacent polypeptide chains

what do rigid proline residues do for protein backbone?

it inserts a kink in and disrupts secondary structures

tertiary structure; its held together by?

• 3D arrangement of secondary structures

• mostly held together by noncovalent attractions between:

  • R-groups

  • between R-groups and the surrounding environment (ie aqueous or hydrophobic lipid bilayer interior)

unstructured loops (aka random coils)

link secondary structures together

what do covalent disulfide bonds do for cysteine residues

they cross-link parts of the polypeptide backbone

3D folding of proteins into results in structures that assume the —

lowest possible energy state

protein stability depends on —

the free energy change between the folded and unfolded states; deltaG = Gfolded - Gunfolded

proteins become more stable as Gunfolded — Gfolded

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chaperonins

molecular chaperones that many proteins require that provide an isolated chemical environment in which they can fold

steps of chaperonin bondings

prions

• a disease of protein folding

• prion proteins can adopt an alternative folded state

• abnormally folded protein causes a normally folded protein to adopt the abnormal conformation

protein domains

• a region of the protein that folds independently of other regions

• protein can have single/multiple domains

• domain often represents a functional region of the protein

function of catalytic domain

inhibits host cell protein synthesis

function of receptor binding domain

attaches to cell surface

function of hydrophobic domain

inserts into membranes

motifs

similar domain which occur in many related proteins ex. DNA-binding motif

quaternary structure

• arrangement of multiple tertiary structures

• held together by weak bonds and some disulphide bonds

homomers

identical subunit polypeptidesd

heteromers

different subunit polypeptides

proteolytic cleavage

removes amino acids from the original translated sequence

protein kinases

a class of enzymes that catalyzes reactions

protein phosphatases

catalyzes phosphate removal; reverses phosphorylation

many changes in protein structure and activity are driven by —

phosphorylation

each phosphate group adds — to the protein

two negative charges

the added phosphate group may create a — — — that allows other proteins to bind to the phosphorylated protein

new recognition site

many changes in protein structure and activity are driven by phosphorylation because:

• each phosphate group adds two negative charges to the protein

• Can drive major structural changes, activity changes, or changes in protein solubility

• Added phosphate group may create a new recognition site that allows other proteins to bind to the phosphorylated protein

You are studying a protein that is turned on by phosphorylation at a specific serine residue. What do you expect would happen if the serine is mutated to aspartic acid?

the protein will always be turned on

ubiquitin

• small cytosolic protein (76 amino acids)

• covalently attached to proteins (reversible)

• serves as tag that can either mark proteins for degradation or direct proteins to specific locations in the cell

• (strand: degradation; singular: translocation)

all proteins bind to other molecules, those molecules are called - of the protein in question

ligands

a protein’s physical interaction with other molecules determines —

its biological properties

because ligand binding is generally achieved by noncovalent bonds it is —

reversible

ligand binding is generally achieved by — bonds

noncovalent

why must protein binding be strong enough to withstand the jolting of molecular motions

molecules are in constant motion, bumping into one another

binding strength is achieved through

• 3D complementarity of binding

  • formation of several noncovalent bonds (strength in numbers)

ligand binding sites are — dimensional

3

amino acids that contribute to binding a liganf are often far apart on — but come together when —

a proteins primary sequence; protein folds

lower dissociation rates =

lower Kd values and stronger binding

Kon and Koff are rates of the — and — rxns that create/breakdown protein ligand complex

forward (association); backward (dissociation)

association Ka measures the strength of binding such that

Ka = Kon/Koff

relationship of dissociation constant to association constant

Kd=1/Ka

having multiple modification/interaction sites allows proteins to act as —

molecular integrators