Cell Biology Chapter 4

primary

this level of structure in a protein is its amino acid sequence

secondary

this level of structure in a protein is determined by local folding structures including alpha helices and beta sheets

tertiary

this level of structure in a protein is the 3D structure of the entire polypeptide, usually contains independently folding domains

quaternary

this level of protein stucture is from multiple polypeptides folding together

polypeptide

what is the polymer of amino acids

no

can peptide bonds rotate

amino (N)

what terminus does peptide synthesis begin at

carboxyl (C)

what terminus does peptide synthesis ends at

polypeptide backbone

what is able to bend within a polypeptide and is very flexible, giving rise to countless different protein shapes

lowest energy

when a protein is in its most stable conformation, what will its energy level be at

electrostatic attractions, van der waals attractions, hydrogen bonds

what non-covalent bonds are responsible for stabilizing protein folding

hydrophobic core

this part of a protein forms in an aqueous environment from the nonpolar side chains being packed into the center of the peptide

• the polar side chains are exposed to the environment and form hydrogen bonds with water

hydrogen bonds from polypeptide backbone

what type of bond is responsible for the secondary structure of a protein and where do they come from

chaperone

this protein is responsible for ensuring a protein folds into its correct conformation

• can prevent aggregation of proteins

  • cannot force a protein into any structure other than its native state

amorphous aggregate

this can form when there is a high concentration of unfolded proteins, typically very hydrophobic, that clump together instead of folding individually into their natural state

cysteine

disulfide bonds form between what amino acid side chains

• catalyzed by ER enzymes

conservative

this type of mutation results in a different amino acid with similar properties

• maintains chemical properties and size

nonconservative

this type of mutations swaps in a significantly different amino acid which can alter chemical properties and/or size of a protein

binding site

region of protein that interacts with specific molecule (ligan)

ligand

the specific molecule bound by a particular protein, each binding site binds only 1 or a few of these

structural protein

this type of protein supports and/or strengthens cells and tissues and facilitates movement of vesicles, organelles, membranes, and cells

• fibrous or globular

hydrolase

general term for enzymes that catalyze hydrolytic reactions

• ex: proteases, nucleases, lipases

protease

hydrolyze peptide bonds in polypeptides, can completely degrade polypeptides or cleave only at specific sites

ATPase

this enzyme hydrolyzes ATP, usually as part of additional functions

• motor proteins, membrane transport proteins, kinases

kinase

transfers phosphate groups between molecules, usually from ATP

phosphatase

an enzyme that removes a phosphate group from a molecule hydrolytically, releasing inorganic phosphate (Pi)

phosphorylase

this enzyme catalyzes the addition of an inorganic phosphate (Pi) to a molecule

align substrates, alter substrates shape, alter electron distribution, form temporary covalent bonds

what are 4 ways in which an enzyme can catalyze a reaction

lysozyme

an enzyme, specifically a hydrolase that is secreted as part of innate immunity

• works to hydrolyze covalent bonds in polysaccharides of bacterial cell walls

• the spontaneous hydrolysis of a polysaccharide is extremely slow

  • does this by 1. strains substrate into transition state and 2. alters electron distribution

Km

what value tells the binding affinity of an enzyme to a substrate

• low ___ = high affinity

• substrate concentration that yields half Vmax

Vmax

this is the maximum possible rate an enzyme can convert substrate to produce in non-limiting substrate conditions

Km

in a low substrate environment, the rate of a reaction catalyzed by an enzyme is determined by the ___

Vmax

in a high substrate environment, the rate of a reaction catalyzed by an enzyme is determined by the ___

competitive inhibitor

this type of inhibitor directly interfers in substrate binding

• results in a higher Km and an unchanged Vmax (the actual rate isn’t affected when a substrate binds (Vmax), the issue is getting a substrate to bind (Km))

statin

what type of drug is an example of a competitive inhibitor used to reduce cholesterol synthesis

ATP hydrolysis

what process is linked to a conformational change in motor proteins to make movement irreversible

• linking energetically favorable reactions via ATP is very common through a cell

biomolecular condensates

the subcompartments formed in a cell without the use of membranes

• the phase separation and clumping together of molecules due to shared characteristics ex: hydrophobicity

  • ex: nucleolus

scaffold protein

this type of protein exists to bring together other proteins so they can form their desired protein complex

rhodopsin

light receptor protein in rod of cell eye

• requires retinal to absorb light and change chape

• example of small organic molecules being required for some proteins to help them function