BSC360: Protein Structure and Function

negativley charged polar amino acid

hydrophilic

negativley charged polar amino acid

hydrophilic

Aspartic Acid

Negatively charged polar amino acid

hydrophilic

Glutamic Acid

positively charged polar amino acid

hydrophilic

Arginie

positively charged polar amino acids

amphipathic

lysine

positively charged polar amino acid

hydrophilic

histidine

uncharged polar amino acids

hydrophilic

Asparagine

uncharged polar amino acids

hydrophilic

glutamine

uncharged polar amino acid

hydrophilic

serine

uncharged polar amino acid

hydrophilic

threonine

uncharged polar amino acid

amphipathic

tyrosine

nonpolar amino acids

hydrophobic

alanine

non polar amino acid

hydrophobic

glycine

nonpolar amino acids

hydrophobic

valine

nonpolar amino acid

hydrophobic

leucine

nonpolar amino acid

hydrophobic

isoleucine

nonpolar amino acid

hydrophobic

proline

nonpolar amino acid

hydrophobic

phenylalanine

nonpolar amino acid

amphipathic

methionine

non polar amino acid

amphipathic

tryptophan

polar amino acids

hydrophobic

cysteine

amino acids

building blocks of polypeptides that have an amino group (H2N) and a carboxyl group, with a unique side chain group

primary structure

initial linear sequence of amino acids liked with peptideds bonds

can contain 30-2,000 amino acids

forms via condensation reaction

grows from N terminus to C terminus (Amino acid adds to the carboxyl group of another aa acid)

polypeptide

chain of amino acids

aqueous

as primary structure transitions to secondary in this type of environment, non polar side chains cluster together to avoid water and polar side chains Hydrogen bonds on the outside, creating a hydrophobic core

cysteine

amino acid that cross links its peptide chain by a disulfide bond *r group) and creates speical strucutes in proteins

serine, threonine, tyrosine

amino acid that OH side chain group can be phosphorylates and makes the aa negatively charged

effects conformation

secondary structure

structure with local folding

long polypeptide chains are very flexible structures and can fold in different ways

amino acid sequence dictates the noncovalent interactions(how the protein folds)

stabilized by hydrogen bonds between amino and carboxyl group

alpha helix

helical secondary structure formed by twisting around itself

→ each turn is 3.6 aa

→ r groups located outside helix

→ hydrogn bonding between carbyoxl group and amino hydrogen

beta sheet

secondary sheet sturcutred from different segments of polypeptides

→ can be formed within the same polypeptide or between different ones

→ backbones arragned PARRALLEL to each other in either the same direction or different (anti-parrallel, parrallel_)

→R groups project ABOVE or BELOW the plane giving a crinkle structure

parrallel bonds held together by hydrogen bonds

anti parrallel

neighboring segements in a beta sheet run in opposite directions

(C terminus to the left, then right)

parallel

neighboring segments in a beta sheet run in the same direction

golgi appartus

site of modification of proteins and lipids made in the endoplasmic reticulum and sorts them for transport to other sites

cytosol

unstructured aqueous phase of the cytoplams exluding organelles, membranes, and insolubal cytoskeletal components

cytoplasm

the contents of a cell exlcusing the plasma membrane and nucleus , but inclduing other subcellular structures

mitochondria

organelle that carries out oxidative phsophorlation and produces most of the ATP in eukaroytic cells

nucleus

contains the DNA of a eukaryotic cell, site of transcirption

chloroplast

contains chlrophyll and serves as the site for photosyntehsis

endoplasmic reticulum

site of protein synthesis and folding, and lipid biogenesis

two types roguth (with ribosomes) and smooth (no ribosomes)

20

# of unique amino acids

4

number of unique nucleotides

nucleotides

monomer of nucleic acids that are linked by phosphodiester bonds

amino acids

monomers of polypeptides held together by peptide bonds

lipids

hydrophobic macromolecule made up of fatty acids and glycerol

fatty acids

carboxylic acid witha long hydrocarbon chain

→ monomer of lipid

→ satured: no C-C double bonds

Unsatured- has C-C double bonds casuing kinks inchain

triaclyglycerols

type of lipid

a glycerol molecules and three fatty acids tails

store larges amount of energy

→ consdiered fats

→ can be saturated or unsatured

hydrogen bonds, ionic bonds, van der waals force, hydrophobic interactions

types of noncovalent bonds

number of unique types of monomers^ actual number of monomers in a polymer

complexity of macromolecules formula

tetirary structure

overrall conformation and three dimensional arragment of all amino acids

→ stablized by noncovalent bonds

→ Folds in the the lowest energy form: most stable conformation

contain protein domains

protein domains

region of proteins folded to a stable strucutre with a specific function

ex: kinase domains have 4 sites: 2 for regulation and another for catayltic activity