L8: Protein Structure

what shape is an amino acid

tetrahedral

how do R groups differ

their chemical and physical properties

how are amino acids classified

interaction w/H2O (hydrophobic/hydrophilic), acidic or basic, polar or nonpolar

where are hydrophobic amino acids

inside protein

what do the R-groups of hydrophobic amino acids consist of

hydrocarbons (H—C)

what type of bonds are in hydrophobic amino acids

non-polar covalent with very little charge

what type of R-group makes up hydrophilic amino acids

polar with 1+ oxygen

types of hydrophilic amino acids

basic, acidic, polar

positively charged hydrophilic amino acid

basic

negatively charged hydrophilic amino acid

acidic

when basic and acidic amino acids interact with each other, what forms

ionic bond

special amino acids

glycine, proline, cysteine

glycine

contributes to flexibility of protein structure

proline

contributes to rigidity

cysteine

uses sulfydral group (—SH) to form a very stable covalent disulfide bond

how is a peptide bond formed

carboxyl group of one AA reacts w amino group of another AA resulting in a release of H20

what is the C=O group in a peptide bond known as

carbonyl group

what is the N-H group in a peptide bond known as

amide group

carboxyl end

C-terminus

amino end

N-terminus

polymer of amino acids connected by peptide bonds

polypeptide

primary amino acid

sequence of amino acids

what protein structures do all proteins undergo

primary

how is a primary structure listed

N-terminus to C-terminus

secondary structure

interactions between stretches of nearby amino acids; stabilized by hydrogen bonds

what are the types of secondary structures

alpha-helix & beta-sheet

alpha-helix

hydrogen bonds between carbonyl group and amide group is 4 amino acids away

beta-sheet

polypeptide folds back and forth on itself to form a pleated sheet that is stabilized by hydrogen bonds between carbonyl groups in one chain and amide groups in other chain; less rigid

tertiary structure

3D shape of protein; determines protein structure and function; interactions with R-groups

what structure do most proteins stop at

tertiary

types of tertiary structures

ball and stick, ribbon, space-filling

ball and stick

atoms in an amino acid chain

ribbon

alpha helices and beta sheets

space-filling

shape and contour of folded protein

what structure determines the secondary and tertiary structures of a protein

primary structure

what structure determines protein’s function

tertiary structure

denaturation

when proteins are unfolded by chemicals or heat and lose their function

renaturation

when optimal conditions are returned and protein refolds and regains function

what structure is unaffected by denaturation

primary; because it is already unfolded

quaternary structure

tertiary structures combine to form a single protein; influences protein structure

chaperone proteins

provide proteins with a protective environment for slow-folding proteins to fold

which amino acids primarily need chaperone proteins

hydrophobic