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Biochemistry > Globular Proteins > Flashcards

Globular Proteins Flashcards

1
Q

Tertiary Protein Structure

A
  • The globular three-dimensional structure (conformation) of a polypeptide that results from the folding, aggregation or interactions of the various regions of secondary structure in a polypeptide as it assumes its biologically active shape
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2
Q

Four Main Chemical Interactions that Help Stabilize Tertiary Structure

A
  1. Hydrophobic interactions
  2. Electrostatic (ionic) interactions.
  3. Hydrogen bonds.
  4. Covalent bonds (think disulfides).
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3
Q

Three ways to represent the 3D structure of the small, single chain protein ubiquitin

A
  1. Cartoon
  2. Stick model and close up
  3. Solvent accessible surface model
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4
Q

Larger proteins often contain two or more distinct _______ of compact folded structure

A
  • “domains”
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5
Q

What is protein tertiary structure characterized by?

A
  • the content of helix and sheet secondary structures as well as defined turns that link these secondary structures
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6
Q

Irregularly structured regions

A
  • random coil

- not all parts of globular protein structure can be categorized as helix, sheet or turn

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7
Q

Unstructured proteins

A
  • some proteins are partially or completely unstructured
  • unstructured proteins are referred to as intrinsically unstructured proteins (IUPs) or natively unfolded proteins
  • often these proteins are involved in searching out binding partners
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8
Q

First common principle with a dominant motif

A
  • alpha helices like myoglobin
  • beta sheets like neuraminidase
  • equal amounts of both like TIM
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9
Q

Second common motif

A
  • many proteins are made up of more than one domain
  • domain is a compact locally folded region of tertiary structure about 150-250 AA
  • Different domains perform different functions
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10
Q

third common principle

A
  • domains may themselves be composed of repeating secondary structure motifs.
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11
Q

Common features of folded globular proteins

A
  • have a nonpolar (hydrophobic) interior and a more hydrophilic exterior
  • B sheets are usually twisted or wrapped into barrel structures
  • the polypeptide chain can turn corners
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12
Q

How does protein folding occur

A
  • a non random process
  • occurs in a stepwise manner with free energy decreasing at each step
  • steps are not always the same or in the same order
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13
Q

When does formation of secondary structure occur?

A
  • alpha helices and B sheets formation is an early process
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14
Q

Folding of larger polypeptides involves _____ intermediates

A
  • “stable”

- molten globules

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15
Q

What is the purpose of hydrophobic interactions

A
  • exclude water molecules while directing and sequestering hydrophobic residues towards the interior of the folding protein
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16
Q

What does solvent exclusion, van der waals forces and H bonding help to do?

A
  • align secondary structures
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17
Q

The molten globule

A
  • a compact, partially folded intermediate state that has native-like secondary structure and backbone folding topology, but lacks defined tertiary structure interactions of the native state
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18
Q

Energy Landscape Model

A
  • aka folding funnel explains how conformational restriction can be achieved during folding.
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19
Q

What does the depth and width of the funnel correspond to

A
  • The depth of the funnel corresponds to free energy, and the width of the funnel corresponds to the number of conformational states at a given value of free energy.
  • as the funnel becomes narrower the number of conformations accessible to the protein decreases as a protein molecule follows a downhill trajectory toward the folded conformation (aka state of lowest free energy).
20
Q

What ”mishaps” can occur at local energy Minima.

A
  • Also evidence for off-pathway states aka a key element is incorrectly folded
  • those states correspond to local free energy minima in the funnel and may temporarily or permanently trap the protein
  • most common folding errors is the cis-trans isomerization
21
Q

Molecular chaperones

A
  • discovered in relation to heat shock stress in higher plants and Drosophilia
  • an accessory protein that binds to and stabilizes a non-native protein against aggregation and/or helps it achieve folding to its native state, but not part of the final functional structure of the correctly folded protein
  • given the name heat shock proteins, or hsp’s
22
Q

heat shock proteins

A
  • conferred thermo-tolerance to organisms subjected to non-lethal high temperature stress (form of cellular quality control).
  • can promote refolding of proteins resulting from stress conditions
  • if refolding is not possible, then they promote protein degradation
  • Specific hsp’s are named on the basis of their molecular weights
  • Hsp’s can have many subunits.
  • are preventing irreversible denaturation of cellular proteins, once temp is restored any temp sensitive proteins can be refolded so the viability of the cell is preserved through the action of molecular chaperones.
23
Q

What is the function of chaperones

A
  • promote proper folding of proteins and thereby prevent the formation of aggregated states associated with disease
  • we know misfolding or aggregation of proteins is associated with several widespread diseases.
24
Q

Why are chaperones needed?

A
  1. The intracellular environment is very crowded which can cause problems
  2. They play a critical role in protecting cellular proteins during times of stress
  3. Provide critical mechanism for cells to survive mutations that might render a protein less stable and/or more susceptible to misfolding.
25
Q

Hsp 70s

A
  • Function individually.
  • Bind to hydrophobic regions of nascent polypeptides during early stages of folding.
  • Binding prevents unwanted hydrophobic interactions.
  • Some reactivate denatured proteins.
26
Q

Hsp 60s

A
  • Oligomerize to form complexes.
  • Receive unfolded polypeptides from hsp70.
  • Assist in final folding of polypeptide.
27
Q

Release of polypeptides from hsp70 & hsp60 requires ____.

A
  • ATP
28
Q

Structure of chaperonin

A
  • A complex of numerous hsp60 subunits arranged in three overlapping domains with a central core throughout (double-ringed complexes = chaperonin).
29
Q

Hsp70 structure

A
  • One large polypeptide (blue) with two domains plus one small peptide (pink) deeply embedded in one domain.
30
Q

GroEl is an example of _____ and GroES is a ______

A
  • Hsp

- chaperone

31
Q

Amyloid Fibrils

A
  • Highly ordered amyloids form from non-native folding intermediates or disordered aggregate states
  • characterized by highly organized arrays of Beta sheet structure, the fibrils are formed from a right handed helix of four protofibrils
  • the cross-Beta structure is characteristic of amyloids.
32
Q

Prions as an agent

A
  • Infectious agents that cause disease by inducing amyloid formation on contact
33
Q

Alzheimer’s Disease

A
  • Associated with insoluble fibrous aggregates of B-amyloid protein (plaques) in brain neurons involved in memory & cognition.
  • its the amorphous aggregate precursors
  • Amyloid protein is derived from the proteolytic cleavage of “amyloid precursor protein” (a transmembrane protein with unknown function).
  • A mutation in “APP” causes aggregation / precipitation of APP so that normal process for removal of protein becomes defective.
34
Q

How does prion-related protein (PrP) cause disease

A
  • Under not well defined conditions PrPc(nonpathological form) can change conformation to become PrPSC which is disordered and can form amyloids and disrupt the nervous system
35
Q

Prions Characteristics

A
  • “Proteinaceous Infectious Particles”.
  • Cause the irreversible change in folding patterns of pre-prions.
  • can solely transmit diseases
  • Pre-prions are natural proteins in brain & spinal cord neurons.
  • Prions are chemically resistant.
  • All prions are untreatable and fatal
36
Q

Most human misfolding diseases are associated with

A
  • the formation of highly ordered protein aggregates called amyloid plaques
  • these are proteins that misfold to form amyloid structures which are called amyloidogenic.
37
Q

Mad Cow Disease

A
  • medically known as Bovine Spongiform Encephalitis
  • A “prion”- mediated degeneration of brain & spinal cord neurons resulting in a “spongy” appearance of brain tissue and associated “Mad Cow” symptoms.
  • Of Great concern because of a very similar disease in humans called Creutzfeldt-Jakob disease.
38
Q

Functional Advantages of Quaternary Structure

A
  • Synthesis and folding of separate subunits may be more efficient than that of a single very long polypeptide chain.
  • Replacement of smaller worn-out or damaged subunits can be more effectively managed (especially supra-molecular complexes).
  • Interactions between subunits can afford unique regulatory properties to multi-subunit proteins (especially enzymes – i.e. “allosteric regulation”).
39
Q

Structure and Function of Myoglobin vs Hemoglobin

A
  • Very similar polypeptide tertiary structures.
  • Same heme “prosthetic group”.
  • Very similar functions (oxygen transport).
  • Myoglobin is a monomer
  • Hemoglobin is a tetramer.
  • Different physiological locations, affinities for O2, kinetics of binding & dissociation of O2.
40
Q

Myoglobin

A
  • a monomeric heme protein that binds and releases O2 in tissues (O2 storage)
  • Found in skeletal & cardiac muscles
  • Especially prevalent in diving mammals that stay submerged for long periods.
  • Two histidine residues facilitate O2 binding.
  • Folded polypeptide with 8 regions of a-helix (A – H) forms a hydrophobic crevice that encloses the heme group
41
Q

Hemoglobin

A
  • a tetrameric heme protein that transports O2 from lungs or gills to peripheral tissues and returns CO2 to gills or to lungs for exhalation
  • Found in red blood cells.
  • Binding of first O2 changes conformation and enhances subsequent O2 binding (“cooperative binding”).
  • Comprised of four subunits (2 a-chains & 2 B-chains, designated as a2B2).
  • arranged as two identical dimers
42
Q

Sickle Cell disease

A
  • Abnormal erythrocytes block circulation in capillaries and lyse due to their fragility, causing anemia. Heterozygotes with half mutant and half normal Hb are asymptomatic except when oxygen-stressed
43
Q

G-actin structure

A
  • ATP binding by globular actin leads to polymerization and the formation of filamentous actin
44
Q

Myosin S1

A
  • a proteolytic fragment of myosin 2 which functions in muscle contraction and cell motility
45
Q

How does a muscle contract?

A
  • the thin filaments (actin) moves toward one another surrounding the thick filament (myosin)
46
Q

Muscle contraction steps

A
  1. ATP binds to the myosin head
    - actin-binding site on myosin releases from actin
  2. Actin binding site closes followed by ATP hydrolysis
    - Myosin head “cocks”
  3. weak binding of myosin to actin
  4. Pi release results in strong binding of myosin head to actin
  5. Muscle contraction, power stroke as myosin head retracts
  6. ADP is released
47
Q

What are motor proteins?

A
  • Myosins are a superfamily of actin motor proteins that convert chemical energy in the form of ATP to mechanical energy, thus generating force and movement. The first identified myosin, myosin II, is responsible for generating muscle contraction.

Biochemistry (15 decks)

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