Chapter 4-Three Dimensional Structure of Proteins

3

protein molecules adopt a _______ dimensional configuration. each structure is able to fulfill a specific function

native fold

what is the structure of a protein called ?

entropy cost

there is an _______ _________ to folding the protein into one specific native fold

hydrophobic effect

___________ is the release of water molecules from the structured solvation layer around the molecules as protein folds incresses net entropy

hydrogen bonds

_________ ________ is the interaction of N-H and C=O of the peptide bond leads to local regular structures such as alpha helices and beta sheets

london dispersion

__________ ____________ is a medium range attraction between all atoms and contributes significantly to the interior of the protein

electrostatic interactions

__________ _____________ are long-range interactions between permanently charged groups. creates salt bridges

primary, secondary, tertiary, quaternary

what are the 4 levels of protein structure?

primary amino acid

what is shown?

properties of peptide bond

what is the structure of the primary structure dictated by?

rigid, planar

the peptide bond in a primary structure is __________ and nearly __________

rotation around peptide bond

what is not permitted due to the resonance structure of primary structure?

around bonds connected to alpha carbon

what rotation is permitted in primary structure?

amide nitrogen bond

what bond goes with the phi angle?

carbonyl carbon bond

what bond goes with the psi angle?

180 degrees

in a fully extended polypeptide both y and f are __________

planes

the polypeptide is made up of a series of __________ linked at alpha carbons

antiparallel

is antiparallel beta plated sheets stronger or parallel?

steric crowding

some f and y combinations are very unfavorable because of _______ _________ of backbone atoms

favorable H-bonding interactions

some f and y combinations are more favorable because of a chance to form what along the backbone?

ramachandran plot

what is shown?

distribution of f and y dihedral angles that are found in a protein

what does a ramachandron plot show?

ramachandran plot

_________________ shows common secondary structure elements and reveals regions with unusual backbone structure

secondary amino acid

what is shown?

alpha helix and beta pleated sheet

what are the two arrangements for secondary structures?

hydrogen bonds between nearby residues

what are alpha helixes stabled by?

hydrogen bonds between adjacent segments that may not be nearby

what are beta pleated sheets stabilized by?

random coli

irregular arrangement of the polypeptide chain is called the __________ _______

n, n+4

helical backbone is held together by hydrogen bonds between the backbone amides of an ______ and ___________ amino acids

right

the alpha helix is a _______- handed helix with 3.6 residues per turn

4-5 A

what is the inner diameter of the helix (no side chains)?

10-12 A

what is the outer diameter of the helix (with side chains)?

Alanine and Leucine

what are the two strong helix formers?

Proline and Gylcine

what are the two helix breakers?

rotation around N-Ca bond is impossible, too rigid

why is proline a helix breaker?

too flexible, it supports other conformations

why is glycine a helix breaker?

attractive or repulsive interactions

what two things with side chains can affect the formation of amino acids in an alpha helix?

peptide

__________ bond has a strong dipole moment in a helix

negative

C-O (carbonyl)= ______________

positive

N-H (amide)= ____________

large macroscopic diploe moment

what is enhanced by unpaired amides and carbonyls near the ends of the helix?

beta pleated sheet

what is shown?

pleated sheet like

the planarity of the peptide bond and tetrahedral geometry of the alpha carbon creates a ______________ like structure

hydrogen bonds

what is the sheet like structure held together by?

parallel beta sheet

what is shown?

same

H bonded strands run in the _______ direction in parallel sheets

antiparallel beta sheet

what is shown?

opposite

H bonded structures run in the ___________ directions for antiparallel beta sheets

b turns

___________ occurs frequently whenever the b sheets change direction

180 degree

what degree turn do beta sheets accomplish over 4 amino acids?

proline and glycine because proline is rigid while glycine is flexible

what two amino acids are common in beta turns and why?

trans configuration

most peptide bonds not involving proline are in the _______ ___________ (greater than 99.95%)

cis

for peptide bonds involving proline, about 6 percent are in the ________ configuration. most of the 6 percent involve beta turns

circular dichroism analysis

what can be used to determine secondary structure?

molar absorption difference of left and right circularly polarized light

what does circular dichroism measure?

chromophores in the chiral environment

____________ produces characteristics signals in circular dichroism analysis

conformation

CD signals form peptide bonds depend on the chain ____________ for circular dichroism

CD analysis

_____________ can be used to identify motives in secondary structures of proteins

tertiary structure

what is shown?

native fold

what is the tertiary structure also called?

numerous weak interactions between amino acid side chains

what is a primary tertiary structure stabilized by?

fibrous and globular

what are two major classes of protein tertiary structures?

disulfide bond

what is the only type of strong bond with tertiary structures that maintains its structure?

disulfide bond

what is the only covalent bond that you can find in tertiary structures?

peptide bonds

what bonds do you find in primary structures? (1)

hydrogen bonding between hydrogens and oxygens

what bonds do you find in secondary structures?

hydrogen bonds between different r groups, disulfide bonds, 3 nonpolar covalent bonds

what bonds do you find in tertiary structures? (3)

keratin, collagen, silk fibroin

what are three examples of tertiary structure proteins?

right handed alpha helix

what is the secondary structure of keratin?

left handed alpha helix

what is the secondary structure of collagen?

glycine and proline

what is a collagen chain rich in? (2)

collagen fibril

what do many collagen triple helices assemble into to form?

vitamin C

collagen fibrils will be brittle if they lack what?

cross links, covalent bonds

strands of collagen fibrils are based on ________ ______ and determined by modified amino acids. Modified amino acids create what type of bonds?

anti parallel beta pleated sheets

what is the secondary structure of fibroin?

left handed double helix

what is the quaternary structure of keratin?

right handed triple helix

what is the quaternary structure of collagen?

no

does fibroin have a quaternary structure?

fibroin

__________ is the main protein in silk from moths an spiders

alanine and glycine

what small side chains allows for the close packing of beta pleated sheets? (2)

hydrogen bonding within sheets, London dispersion interactions between sheets

what is silk fibroin stabilized from? (2)

flexible, resistant

silk fibroin is very __________ and _________

proteins that are folded into a compacted spherical shape. this enables them to carry our biological functions

what are globular proteins?

specific arrangements of several secondary structure elements

what are motifs/ folds?

alpha helix and beta pleated sheets

what are two examples of motifs in proteins?

motifs

globular proteins are composed of different ________ folded together

motifs

a beta barallel and a beta alpha beta loop is an example of what?

lysine, arginine, glucose, proline

what are 4 amino acids that intrinsically disordered proteins use whose higher concentration forces less defined structure?

more than 1 polypeptide chain

what forms a quaternary structure?

disulfide

__________ bonds are important for antibodies

x- ray crystallography, and biomolecular NMR

what are the two tests to run on quaternary structures?

figuring out 3 dimensional shape of protein

what is x-ray crystallography and biomolecular NMR used for?

for x-ray crystallography you need to crystalize the protein first but for biomolecular NMR you do not

what is the major difference between x-ray crystallography and biomolecular NMR?

flexible

biomolecular NMR can show what regions of the protein are more __________/ Ridgid

lowest

proteins always fold into the native fold because it always has the _________ energy

protein that helps another protein to fold

what is a molecular chaperone?

denaturation

loss of structural integrity with accompanying loss of activity is called ___________

heat/cold, ph extremes, organic solvents, chaotropic agents

what are 4 things that can denature a protien?

secondary, tertiary, quaternary, primary

what structures does denaturation destroy? (3) what does it leave you with?

hydrolysis

what activity would break down primary-quaternary?