biochem unit 2

why is collagen unusual and not suitable for alpha helix or beta sheets

• fits only a triple helix because the middle is glycine

• hydrogen bonds stabilize

hypro and pro make up what percent of collagen residues

30%

what angle constraints are the structures of collagen helices

phi= -60 psi =-4.137 bars 120

interchain bonds H-bonds involving Hyp do what on the helix

stabilize

fibrils are strengthened by ___

intrachain lysine-lysine and interchain by hydroxyprridinium crosslinks

fibroin and b-keratin are composed of

-gly-ala/ser-gly-ala/ser

in fibrous proteins residues of a b sheet extend how

above and below the plane of the sheet

• putting all glycine on one side and all Ala and see on other side

• glycine interacts with glycine on the adjacent sheet

the surfaces of proteins are ____ to the molecules they bind to

complementary

the surface of a globular protein includes ____

water molecules - solvation layer

polar backbone and side chain group on the surface of globular proteins

make H bonds with the solvent

polypeptide chains containing more than 200 residue

usually fold into two or more globular clusters called domains which give these proteins bio multimodal appearance

why are proteins only marginally stable

flexibility and motion

what is the kd for two subunits

10^-8 and 10^-16 - this means the interaction is strong

entropy is gained in protein subunits by

burying hydrophobic groups 

• however there is entropy loss by association 

quaternary structures are maintained by

• stability; reduction of surface to volume ratio

• genetic economy:;less dna to code for a monomer that assembles as a hetromultimer

• brings catalytic sites together

  • the monomer may not constitute a complete enzyme active site

• cooperatively: regulation of catalytic activity by means of subunit interaction

i

heterologous

interfaces formed by different surfaces on the two subunits

many proteins form tetramers by means of

2 sets of isologous interactions

the tetramer of transthyretin is formed by

isologous interactions between two large beta sheets of 2 dimers

disulfide bonds can occur between

two molecules (intersubunit) and within the same subunit (intrasubunit)

rank interactions from strongest to weakest in protein folding

hydrophobic interactions > ionic interactions > H-bonds> Van der Waals

what drives protein folding

hydrophobic interactions

ionic interactions usually occur in

on protein surface

where are hydrogen bonds formed on proteins

wherever possible

van der Waals interactions in proteins

ubiquitous

which noncovalent interactions stabilize the higher levels of protein structures 

• electrostatic interaction between a positively charged glutamate carboxyl group

what factors influence the folding process in proteins

• certain regions along the chain may act as nucleation points

• protein chain tries to reach the most stable conformation

• chaperones may help

• side chains of amino acids interact for structure

  • hydrophobic, h bonds,oxidation, electrostatic

ribonuclease can be unfolded by

treatment with urea and MCE (mercaptoethanol)

-mce reduces disulfide bonds

classic experiment that proved that sequent determined structure 

• the experiment showed that ribonuclease function and structure could be restored under appropriate conditions

proteins composed of less than 250 amino acids often have a
_____ structure

simple globular

larger globular proteins have ___ distinct structural features

2+ (domains and modules)

domains are 

compact folded protein structures that are usually stable by themselves in aqueous solutions 

in some proteins the domain sequence is interrupted by

a sequence belonging to another domain of the protein

malonyl CoA ACP transaclase

metabolic enzyme containing two subunits

• large subdomain consists of a beta sheet surrounded by 12 alpha helixes

• small subdomain consists of 4 stranded antiparallel beta sheets and two alpha helices

multi domain proteins are 

• the sum of the functional properties and behaviors of their constituent domains

• evolved from the fusion of genes that once coded for separate proteins 

• a sampling of proteins that consist of mosaics of individual protein modules

% of domains in proteins have been duplicated in other proteins

90%

many proteins contain _____ of the same domain

multiple copies

ribbon structures of several protein modules used in construction of complex multimodule proteins

some proteins share similar structural features but ______

carry out different functions

proteins with different structures can ______

carry out similar functions

the cellular environment is suited to 

maintain weak forces that preserve protein function + structure

what can denature a protein

heat, chemical treatment

denaturization is

the process by which proteins lose their structure and functionality due to external stressors.

protein isolation

cells are collected from tissue or cell culture, lysed on a buffer system, sonicated, seared or incubated in mild detergents to disrupt cell membranes

liver tissue to liver extracts

• minced tissue and suspend cells in isotonic buffer,

  • cell suspension

  • sonication, shearing, mold detergents

  • final form cell liver extraction

cell extracts can be separated and purified by

size, binding affinity and electrophoresis

salting out

uses high concentration of salts such as (NH4)2SO4 to make molecules come out of solution

more than one chain in a protein =

multimeric protein

more than one equal polypeptide chain

homomultimer

protein with two or more different chains

heteromultimer

the three structural classes of proteins

• fibrous

• globular

• membrane

proteins are categorized by

shape and solubility 

secondary and higher order protein structures are stabilized by

• hydrogen bonds

• ionic bonds

• van der Waals forces

• hydrophobic effects

configuration rearrangements for proteins

• involves breaking and remaking bonds

structure of proteins depends on

amino acid sequence and weak, noncovalent forms

the number of protein folding patterns is very large but

finite

the structure of globular proteins are

marginally stable

marginal stability facilitates

motion

motion enables

function

hydrogen bonds in protein structures

• can form wherever back bone aide N-H and carbonyl C=O groups or see chains can approach each other

hydrophobic interactions drive

burial of non polar side chains in the protein core

ionic bonds form

between oppositely charged side chains

in isolation ____ of these forces would be enough to fold a typical protein

NONE

all of the bonds in protein folding 

release energy and create favorable entropy 

the unfolded chains many possible shapes when collapsed into a single folded state

reduce disorder - entropy is lost

the overall free energy change of folding and delta g

is only slightly favorable

the peptide backbone in proteins is

rigid and planar

• six atoms of each -CO-NH unit

• stabilized by 80-90 kj mole of resonance energy

conformational flexibility arises only via

rotation about the two flanking bonds

phi vs psi bonds

phi= rotation around alpha carbon-N and psi = rotation around carbon alpha carbon bonds

• these link the alpha carbon to its two amide planes

the most favorable secondary structure phi and psi conformations

phi=-60

psi=180

ramachandran map plotting phi vs psi

ramachandran map plotting reveals psi and phi for high resolution proteins

• only a handful oof populated regions

• a helix region

  • phi = -60 and psi=-50

• beta sheet region

  • phi=-120 psi=140

types of secondary structures stabilized by h bonds

• alpha helices 

• other helices

• beta sheet (strands)

• tight turns (beta turns/beta bends)

in an alpha helix each C=O of residue “I”

H-bonds to N-H, I+4 produces a 3.6 residue turn, rise per turn 5.4 pitch and rise per residue is 1.5

side chains project outward to avoid

steric clash

bond angles in right alpha helix

-60 degrees for phi and -45 degrees for psi

the helix core in alpha helix structures

tightly packed so that the atoms are at or near their van der Waals radii  

what creates a large net dipole moment for the helix

the arrangement of N-H and C=O groups with each having an individual dipole moment

helix capping motifs are 

specific patterns of hydrogen bonding and hydrophobic interactions found at or near the ends of helices in both proteins and peptides 

in a helix the first 4 N-H and last 4 C=O groups

necessarily lack intrahelical hydrogen bonds

• these groups are often capped by alternative hydrogen bond partners

helix capping is a ____ from secondary to super secondary structures

bridge

for two helices connected by a short loop

the hydrophobic interactions spans the C-cap of one helix and the N cap of the other and the intervening non helical segment 

capping _____ conformation

constrains

these are an example of

amphipathic helices

the b pleated sheet is composed of _____ and may be ____ or ____

beta strands, parallel, antiparallel

in beta sheets - the bonds

N-H backbone groups in one strand hydrogen bonds with the C=O groups of aha adjacent strand

strands adopt ____ backbones

zigzag

strands in beta sheets are packed side by side via 

hydrogen bonds 

top vs bottom

top=parallel

bottom= antiparallel

in anti parallel sheets each N-H-O=C pair is nearly

linear

in parallel sheets H bonds are 

somewhat distorted

in b pleated sheets side chains

alternate above and below the sheet so hydrophobic residues may form the sheet core or be solvent exposed in amphipathic sheets

spider web silks are composites of a-helices and b-sheets and the radial strands of webs must be strong and rigid meaning 

higher percentage of beta sheets

circumferential strands must be flexible meaning

higher percent of alpha helixes

beta turns allow for

the peptide chain to reverse direction

in beta turns the carbonyl of one residue is ____ bonded to the amide proton of a residue ____ residues away

H-bonded, three

which amino acids are prevalent in beta turns

proline and glycine

which beta turns are more common

type I more common than type 2