cell and molecular lecture 3: protein structure and function

proteins come in all shapes and sizes, why?

- different amino acid sequences

- different 3D structure

- different chemical properties

- different functions

- form = function

- sequence -> structure -> function

how do proteins function?

- binding: interacting specifically with other molecules

- catalysis: accelerating chemical reactions

- channels + pores: controlling movement across membranes

- regulation, structure, signaling

amino acids

- protein monomers

- 20 different amino acids, aka residues

- each amino acid has central carbon atom bonded to 4 different chemical groups: amino group (-NH2), carboxyl group (-COOH), hydrogen atom (H), and a variable group (side chain/R group, determines chemical properties of each amino acid)

important amino acids

- serine, tyrosine, threonine, all have hydroxyl (OH) group

peptide bond

- forms between the amino group of one amino acid and the carboxyl group of another amino acid

directionality of polypeptides

- protein polymer: polypeptide

- N-terminus: free amino group

- C-terminus: free carboxyl group

primary structure

- the linear sequence of amino acids in a polypeptide

- sequence matters

secondary structure

- the local folding of the polypeptide backbone stabilized by hydrogen bonds

- contain α helix and β sheet

α helix

- hydrogen bonds form within a region of the polypeptide backbone

β sheet

- hydrogen bonds form between neighboring segments of the polypeptide backbone

tertiary structure

- the overall 3D shape of a single polypeptide

- driven by interactions among amino acid side chains: hydrophobic interactions, hydrogen bonds, ionic interactions, van der Waals interactions, disulfide bonds (amino acid: cystine)

quaternary structure

- aka multimeric proteins

- the organization of two or more polypeptide chains into a functional protein

- ex: hemoglobin: 4 polypeptide subunits

- hemagglutinin (HA): one polypeptide -> tertiary, multiple polypeptides -> quaternary

supramolecular complezes

- assemble multiple proteins, often with other macromolecules, into large functional machines

- their individual activities carry out complex cellular processes

molecular chaperones

- bind and stabilize unfolded or partially folded proteins

- newly synthesized proteins must fold into the correct 3D structure to function properly

chaperonins

- provide protected chambers in which proteins can fold

protein misfolding

- misfolded proteins can associate into aggregates or plaques inside or outside cells

- these aggregates are often resistance to degradation and can disrupt cellular function

sequence -> structure -> function

- sequence: the amino acid sequence influences how a protein folds

- structure: folding produces a specific 3D structure

- function: structure determines how a protein interacts with other molecules

- proper folding is essential for protein function!