Biochemistry - Chapter 4: Levels of Protein Structure

protein structure: parts 1 and 2

native conformations

3D shapes of proteins with biological activity

levels of protein structure

1) primary

2) secondary

3) tertiary

4) quaternary

primary structure (1^o)

order in which amino acids are covalently linked together

secondary structure (2^o)

ordered 3D arrangement of the backbone atoms in a polypeptide chain

tertiary structure (3^o)

3D arrangement of all atoms in a protein, including those in side chains and prosthetic groups

prosthetic groups

non-peptide compounds that mostly attach to proteins and assist them in different ways

configuration of prosthetic groups

usually trans to each other, but sometimes cis

quaternary structure (4^o)

arrangement of subunits with respect to one another in more than one polypeptide chain

primary structure is always written from ___________

amino terminal to carboxyl terminal, from left to right

components of a polypeptide chain

constant backbone and variable side chains

benefit of trans configuration in peptide bonds

minimizing steric clashes between neighboring R groups

peptide bonds in cis configuration

those involving the imino nitrogen of proline

residue

each amino acid in a protein

what the amino acid sequence helps determine

the 3D conformation of a protein

what the conformation of a protein determines

its properties

hemoglobin S (HbS)

sickle cell hemoglobin

sickle cell hemoglobin is caused by _________

substitution of valine instead of glutamate at position 6 of β chains

CFTR protein

cystic fibrosis transmembrane conductance regulator

CFTR protein function

a channel across the membrane of cells that produce mucus

delta 508

most common mutation in CFTR protein, deleting one amino acid at position 508

effect of delta 508

resulting abnormal cell membrane channel prevents the normal transport of chloride ions and water into and out of cells, causing abnormally thick, sticky mucus production in the cells that line the passageways of the lungs and other organs, obstructing airways

planar configuration of peptide bonds restricts ____________

rotation around the bond

card and swivel analogy

peptide chains (cards) linked at opposite corners by swivels

secondary structure and angles

secondary structure can be described by the two angles at which the two bonds coming from an α-carbon can rotate

phi (Φ)

angle between the α-carbon and amino nitrogen

psi (ψ)

angle between the α-carbon and carboxyl carbon

when two amide planes are parallel, both angles are assigned the value of _______

180^o

secondary structure

3D structure formed by hydrogen bonds between peptide NH and CO groups of amino acids near one another in the primary structure

prominent examples of secondary structure

α-helix and β-sheets

α-helix

stabilized by hydrogen bonds that are parallel to the helix axis within the backbone of a single polypeptide chain

features of an α-helix

• clockwise or right-handed coil

• 3.6 amino acid residues for each turn of the helix

• linear distance between corresponding points on successive turns (pitch = 5.4 Angstroms)

  • 1.5 Angstroms per amino acid residue

1 Angstrom =

10^-10 m

features of hydrogen bonds in β-sheets

• occur between peptide chains as interchain or intrachain

• perpendicular to the direction of the protein chain

• give rise to the zigzag structure

parallel β-sheets occur when _______________

the adjacent chains run in the same direction as one another

antiparallel β-sheets occur when _____________

adjacent chains run in opposite directions of each other

position of the R groups of β-sheets

alternate between being above and below the plane

β-strand structure

• fully extended polypeptide

• 3.5 Angstroms between amino acid residues

antiparallel β-pleated sheets

hydrogen bonds between strands are more straight

parallel β-pleated sheets

hydrogen bonds between strands are more diagonal

antiparallel β-pleated sheet arrangement

hydrogen bonds are perpendicular to the direction of the polypeptide

benefits of antiparallel orientation

allows for maximum hydrogen bonding because the oxygen, hydrogen, and nitrogen atoms are in a straight line

supersecondary structures result from ___________

combination of α- and β-strands

βαβ unit

the most common supersecondary structure in which two parallel strands of β-sheets are connected by a stretch of α-helix

reverse turn

type of non-regular secondary structure that changes the direction of a polypeptide chain

reverse turn with proline

addition of proline puts a kink in the chain that sets up the reverse turn

benefit of R-group in glycine being H in a reverse turn

H is a small atom, allowing glycine to fit inside the reverse turn

fibroin

protein of silk produced by insects and spiders; composed almost entirely of β-sheets

fibroin structure

layers of antiparallel beta sheets rich in alanine and glycine residues with small side chains interdigitated, allowing close packing of sheets

noncovalent interactions tertiary structures depend on

1) hydrogen bonding

2) hydrophobic interaction

3) electrostatic attraction

4) complexing several side chains to a single metal ion

hydrogen bonds in tertiary structures occur between _________

polar side chains of amino acids

hydrophobic interactions in tertiary structures occur between ____________

nonpolar side chains

electrostatic attraction in tertiary structures occur between ____________

side chains of opposite charge

covalent interactions tertiary structures depend on

disulfide bonds between side chains of cysteines

function of disulfide bonds in tertiary structures

restrict folding patterns available to polypeptide chains

disulfide bonds are absent in ______ and ______ but present in ______ and ______

myoglobin, hemoglobin; chymotrypsin, trypsin

in some proteins, polypeptide chains can be cross-linked by ______________ through oxidation and reduction mechanisms

disulfide bonds between cysteine residues

conformation of polypeptide backbones constrains ________

the possible arrangement of side chains

structural features of myoglobin

• eight α-helical regions

• no β-pleated sheet regions

• exterior containing mostly polar side chains

• interior containing nonpolar side chains and two histidine residues

myoglobin

single polypeptide chain with one oxygen-binding site

stabilization of α-helical regions in myoglobin occurs by ______________

hydrogen bonding in the polypeptide backbone

features of myoglobin chain

• single polypeptide chain of 153 amino acid residues

• heme prosthetic group in a hydrophobic pocket

heme

iron-containing cyclic compound

subunit

each chain in a quaternary structure

oligomers

molecules made up of a number of smaller subunits

methods by which chains interact with one another noncovalently in quaternary structures

• electrostatic attractions

• hydrogen bonds

• hydrophobic interactions

allosteric

property of multisubunit proteins in which a conformational change in one subunit induces a drastic change in another subunit

tetramer overall structure with two α-chains and two β-chains

α₂β₂

homologous

when the same amino acid residues in the same positions

examples of polypeptide chains that are homologous

α-chain, β-chain, and myoglobin

denatured proteins can only recover their natural shapes when ____________

their primary structures are left intact

conformation of a protein is determined solely by ___________

its amino acid sequence

shape of myoglobin

globular

features of fibrous proteins

• contain polypeptide chains organized approximately parallel along a single axis

• consist of long fibers or large sheets

• tendency to be mechanically strong

• insoluble in water

• play important structural roles in nature

examples of fibrous proteins

keratin and collagen

globular proteins

proteins in which the polypeptide backbone folds on itself to produce a more spherical shape

features of globular proteins

• most of their polar side chains are on the outside

• most of their nonpolar side chains are buried on the inside

• substantial sections of α-helices and β-sheets

• tend to be soluble in aqueous solutions

• have compact structures

collagen

fibrous protein organized in water-insoluble fibers of great strength

collagen fibers (tropocollagen)

consist of three polypeptide chains wrapped around each other in a triple helix

repeating sequence of amino acid residues in collagen

X-Pro-Gly or X-Hyp-Gly

Hyp

hydroxyproline

hydroxyproline

formed in posttranslational modification from proline by a specific hydroxylating enzyme after the amino acids are linked together

three collagen strands

each a helix; held together by hydrogen bonds involving hydroxyproline and hydroxylysine to make a superhelical cable structure

protein folding in fibrous proteins

• overall shape is a long rod

• the backbone of the protein doesn’t fold back on itself

• the only important aspect of tertiary structure that is not specified by secondary structure is the arrangement of atoms in the side chains

info needed for protein folding in globular proteins

• how helical and pleated sheet sections fold back on each other

• positions of side-chain atoms

• positions of any prosthetic groups

folding patterns in tertiary structures often _________________

bring residues that are separated in the primary amino acid sequence into proximity to one another

denaturation

the unraveling of the 3D structure of a macromolecule caused by the breakdown of noncovalent interactions

factors that can cause denaturation

• heat

• large pH changes

• detergents

• urea and guanidine hydrochloride

effect of detergents on hydrophobic interactions

disrupts them

sodium dodecyl sulfate (SDS)

detergent and protein disruptor

effect of urea and guanidine hydrochloride on proteins

disrupts their hydrogen bonding

reduction of covalent disulfide bonds

leads to more unraveling of the 3D structure of a macromolecule

double-headed arrow

denotes when a native conformation can be recovered when denaturing conditions are removed

β-mercaptoethanol’s role in the denaturation of ribonuclease

used to reduce disulfide bridges to two sulfhydryl groups

urea is added to a reaction mixture of β-mercaptoethanol and ribonuclease to ______________

facilitate unfolding and increase the accessibility of the disulfides to the reducing agent

heme group consists of

a metal ion Fe(II) and an organic part protoporphyrin IX

features of the metal ion of heme group

has six coordination sites and forms six metal-ion complexation bonds

• four sites are occupied by the N atoms of the four pyrrole-type rings in porphyrin

• fifth coordination site is occupied by one of the N atoms of the imidazole side chain in histidine residue F8

• O₂ is bound at the sixth coordination site

protoporphyrin IX in a heme group

consists of four five-membered rings that are linked by methine (-CH=) groups; based on pyrrole structure

pyrroles

five-membered rings with the formula C₄H₄NH that can form metal complexes

heme group structure

presence of His E7 _______ affinity of free heme for carbon monoxide by ____

reduces,100x