biochemistry entry 1 protein structure PUM 2nd year | Quizlet

domain

spatial structural unit of polypeptides

peptide and disulfide bonds, amino acid sequences,

domain may contain

combination of super secondary motifs

the core of a domain may consist of

pro

amino acid with side chain and alpha-amino group forming a rigid structure

resistant to heat and high urea concentration, rigid and linear structure, polar but not charged, isomer forms

name 5 properties of peptide bonds

peptide bonds

amide linkages between alpha-carboxyl groups of two amino acids

exposure to strong acid or base

what is required to nonenzymatically break peptide bonds

from N terminal to C terminal

how are peptide bonds named

Protein

linkage of 50 or more amino acids in unbranched chain through peptide bond

partial double-bond character, rigid and planar, trans config, uncharged but polar

characteristics of peptide bond

primary structure of polypeptide

linear sequence of a amino acids in a protein

4

how many hierarchies of protein structure are there

secondary structure of polypeptide

regular arrangements of amino acids that are located near each other

alpha-helix, beta sheet, beta bend

exmaples of commonly encountered secondary structure in proteins

hydrogen bonds between atoms of peptide backbone

how are secondary structures of proteins stabilized

alpha-helix

most common polypeptide helix

rigid, right handed spiraled structure

structure of alpha helix

tightly packed coiled polypeptide backbone core with side chains of amino acids extending outwards from central axis

structure of alpha helix consists of

keratins, myoglobin

examples of proteins with alpha-helical secondary structure

extensive hydrogen bonding between peptide bond carbonyl oxygens and amide hydrogens

how are alpha- helixes stabilized

up and are parallel

how do hydrogen bonds extend from carbonyl oxygen spiral in alpha-helix

that all but the last and first peptide bond components are linked

hydrogen bond structure in alpha-helix ensures

3,6

how many amino acids are contained in one turn of alpha-helix

amino acids with charged or bulky R groups, or branch at first carbon in R group

amino acids that disrupt alpha helixes

proline, glycine, valine

examples of amino acids that disrupt alpha helixes

surface appears to be folded in pleads

structure of Beta-sheets

two or more laterally aligned peptide chains between carboxyl and amino group of amino acids

structure of Beta-sheets consists of

hydrogen bonds

structure of Beta-sheets is stabilized by

intrachain bond

bond in Beta sheet when peptide chains are far apart on single polypeptide

interchain bond

bond in Beta sheet when peptide chains are in different polypeptide chains

parallel or antiparallel

how cam Beta strands in Beta sheets be aligned to each other

a right handed twist

Beta sheets are not flat they have

in opposite direction

how do R groups of adjacent amino acids on each Beta strand extend

reverse direction of polypeptide chain to form compact globular shape

structure of Beta-bends

surface proteins

where are beta-bends usually found

4 amino acids

beta-bends are generally composed of

Hydrogen bond between first and last residue

how are beta-bends stabilized

motifs

combination of secondary structural elements in globular proteins

the core region

motifs primarily form which region of the protein

supersecondary structure

usally produced by by close packing of side chains from adjacent secondary structural elements

primary structure

determines tertiary structure of protein

folding of domains and their final arrangement

tertiary refers to

compact with high density of atoms in molecule core

tertiary structure of globular proteins in aqueous solutions

Domain

fundamental functional and three dimensional structural unit of polypeptides

1-2

polypeptide chains that are 200 amino acids in length usually consists of how Many domains

domain structure

built from a combination of supersecondary structures (motifs)

independently form other domains in polypeptide chains

folding of peptide chains in domains occurs

amino acid sequence

unique three dimensional structure of polypeptides is determined by

disulfide bonds, hydrogen bonds, hydrophobic interactions, ionic interactions

four types of interactions that cooperate stabilizing tertiary structure of globular proteins

disulfide bond

covalent linkage formed from sulfhydryl groups of two cysteine residues to produce cystine residue

can be separated by many amino acids or on different polypeptides

location of cysteines in disulfide bond

contributes to 3d shape stability and prevents extracellular degradation

function of disulfide bond

disulfid isomerase

breaks and reforms disulfide bonds during folding

nonpolar sidechains tend to be located in interior and polar/charged side chains tend to be on the outside

hydrophbic interactions

hydrophobic interaction

Segregation of R groups that is energetically most favorable

protein solubility

hydrogen binds between polar groups on protein surface and aqueous solvent enhance what

hydrogen bonds

side chains containing oxygen or nitrogen bound hydrogen can for this bond

ionic interactions

reaction of negatively and positively charged groups in side chains

folding of linear polypeptide chains into three dimensional shape of protein

interactions between side chains determine what folding

hydrophobic effect

formation of secondary structures is driven by

denaturation

results in unfolding/disorganisation of secondary and tertiary structure of a protein without peptide bond hydrolysis

heat, urea, organic solvents, strong acids/bases, ions of heavy metals

denaturing agents include

primary structure of polypeptide

information needed for correct protein folding is contained in what

ATP and chaperons

what is needed for protein folding

chaperons

proteins that interact with polypeptide at various stages of folding process

quaternary structure

arrangement of proteins which consist of several polypetidechains

hydrogen, ionic, hydrophobic bonds

subunits in quaternary structures are primarily held together by these bonds

amyloids

spontaneous formation of long fibirliar protein assemblies consisting of beta pleated sheets

alzheimer, parkinson

amyloids are linked to those neurodegenerative diseases