Cell bio Ch. 4

Enzymes

help with chemical reactions inside of the cell

structural proteins

make up shape of the cell

transport proteins

help things get across the cell membrane

motor proteins

help cell move (like muscle cells contracting)

storage proteins

store amino acids for the cell to use by breaking down the protein and using the amino acids

signal proteins

send signals to other cells or intracellular signals

receptor proteins

receive signals from signal proteins

transcription regulator

prevents or allows transcription and gene expression

special purpose proteins

highly variable, things like GFP that don’t fit into other categories

amino acid sequence

the types and orders of amino acids

What determines the shape and structure of proteins?

its amino acid sequence

Which types of amino acids are ok in water?

polar

What helps proteins fold into a conformation of lowest energy?

noncovalent interactions; these interactions are favorable and lowest energy is most stable

What stabilizes the structure of a protein?

the additive effect of all these weak noncovalent interactions

How do hydrogen binds within a protein help stabilize its folded shape?

• large numbers of hydrogen bonds form between adjacent regions of a folded polypeptide chain

• backbone to backbone: hydrogen bond between atoms of 2 peptide bonds

• backbone to side chain: hydrogen bond between atoms of a peptide bond and an amino acid side chain

• side chain to side chain: hydrogen bond between atoms of 2 amino acid side chains

What helps proteins fold into compact conformations?

• hydrophobic forces

• polar side chains can form hydrogen bonds to water

• nonpolar side chains are packed into the interior of the protein away from water to create the compact shape

Primary structure of a protein

amino acid sequence

What is the alpha helix?

• one of the secondary structures of a protein

• polypeptide chains fold into a repeating alpha helix

• this folding is driven by the backbone; NH is hydrogen bonded to the backbone C=O located 4 amino acids away

What is a coiled coil?

• 2 alpha helices intertwine together because the alpha helix has a hydrophobic amino acid every 4 away so the helices wrap around eachother to minimize exposure of hydrophobic amino acid side chains to aqueous environment.

What is a beta sheet?

• another secondary structure

• formed by hydrogen-bonding between peptide bonds in adjacent strands

Chaperone proteins

• guide the protein during folding to make sure it folds correctly

isolation chambers

• type of chaperone proteins

• newly made partially folded proteins go inside the chamber isolated from binding to anything else, gets correctly folded, and released again when the cap dissociates.

Protein domains

different domains have different functions, like DNA domains, ATP domains, etc

Quaternary structure

only applicable if the protein is made of multiple polypeptide chains

Intrinsically disordered sequences

• protein domains are usually connected by these unstructured flexible lengths of disordered sequences

• some proteins are almost entirely disordered

functions of intrinsically disordered sequences

binding to other proteins or molecules and sometimes controlling them, tethering different domains within a protein, or acting as scaffold proteins tethering interacting proteins