Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry > Proteins L2 AND L3 > Flashcards

Proteins L2 AND L3 Flashcards

1
Q

What did Anfinsen’s experiment demonstrate about protein folding?

A

Anfinsen’s experiment showed that proteins lose their function when they lose their 3-D structure but can be refolded and regain their function in vitro, indicating that the information for proper folding is within the amino acid sequence.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How do hydrophobic interactions contribute to protein folding?

A

Hydrophobic interactions between hydrophobic amino acid side chains are the main driving force in overall protein folding, as they help to bury nonpolar residues away from the aqueous solvent.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What determines the positioning of an α-helix in a protein structure?

A

The arrangement of amino acids with hydrophobic or hydrophilic side chains in an α-helix affects its positioning in the protein structure.

Hydrophobic residues lead to the helix being packed inside the protein, while amphipathic helices are on the surface, and hydrophilic helices are completely exposed to the aqueous solvent.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Define an amphipathic α-helix.

A

An amphipathic α-helix is a helix in which the amino acid residues have a combination of hydrophobic and hydrophilic side chains, causing one side of the helix to face the interior of the protein (hydrophobic) and the other side to face the aqueous solvent (hydrophilic).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How do hydrophobic regions in β-sheets determine their packing in a protein structure?

A

In β-sheets, alternating hydrophobic and hydrophilic amino acid residues can create one hydrophobic side facing the protein’s interior and the hydrophilic side facing the aqueous solvent.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Define an amphipathic β-sheet.

A

An amphipathic β-sheet is a sheet-like pleated structure in which alternating hydrophobic and hydrophilic amino acid residues create one hydrophobic side facing the protein’s interior and the hydrophilic side facing the aqueous solvent.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How do motifs and secondary structures contribute to the tertiary structure of a protein?

A

Secondary structures, motifs, and domains fold together to form the tertiary structure of a protein, with hydrophobic or nonpolar residues sandwiched between hydrophilic or polar layers to minimize exposure to the aqueous solvent.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Describe the thermodynamic effects of protein folding on polar and nonpolar amino acids and water molecules.

A

Protein folding results in changes in enthalpy (ΔH) and entropy (-TΔS).

The enthalpy changes are due to interactions with water molecules and hydrophobic amino acids.

The entropy changes are driven by the reorganization of water molecules, favoring the folded state due to reduced water ordering around nonpolar residues.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Explain the concept of the energy landscape funnel in protein folding.

A

The energy landscape funnel illustrates how a polypeptide chain can start from various conformations and move down the energy surface toward the lowest energy native state.

It can involve intermediates and transition states, with the possibility of stable misfolded states.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Why do some proteins require assistance in folding, and what are heat shock proteins?

A

Larger and more complex proteins may require assistance in folding due to the need for establishing specific interactions between N-terminal and C-terminal parts.

Heat shock proteins bind to exposed hydrophobic regions in unfolded or partially folded proteins, protecting them from aggregation. These proteins can assist in ATP-dependent folding.

Heat shock proteins are so named because they are induced by cellular stress, such as heat.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What Directs Protein Folding?

Anfinsen’s Experiment: 4 CONCLUSIONS

A
  1. Unfolded proteins are inactive THEREFORE
    Structure –>Activity.
  2. Correct disulphide bond formation occurs after folding.
  3. All the information for a protein to fold correctly is
    contained in the amino acid sequence.
  4. Disulphide bonds stabilise folded proteins.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

ANFINSEN’S EXPERIMENT (6) EXPLANATIONS SLIDE 4

A
  1. RNase A native molecule (active)
  2. Oxidation with O2 at pH 8 (renaturing conditions)
  3. Reduction with HOCH2CH2SH (denaturing conditions)
  4. Reduced denatured molecule (INACTICE)
  5. Oxidation (denaturing conditions followed by renaturing conditions)
  6. 1 of 104 possible random disulphide bond combinations that form (ALL BUT ONE FORM INACTIVE)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What Directs Protein Folding

A

The different types of BOND, or INTERACTION make different CONTRIBUTIONS to protein folding.

They have different STRENGTHS, different DIRECTIONAL PROPERTIES , and different ROLES in the
PROCESS OF FOLDING.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Thermodynamics Definitions:

A

Classical Thermodynamics: the alteration of in the content of energy and its
distribution that take place when a system passes from an initial, defined state into a
terminal state at equilibrium.

Thermodynamics can describe processes at all temperatures and pressures.

For most of Biochemistry we can assume constant temperature and pressure, which simplifies things

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Folding Initial state to Terminal state..

A

Initial state: Unfolded protein in solution

folding

Terminal state: Folded protein in solution
at equilibrium

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

ΔX – the change in X:

A

– Changes in temperature, ΔX, is defined as:

e.g. ΔT = Tfinal – Tinitial

– Can be applied to both chemical and physical changes.
* Chemical changes –> chemical reactions.

  • Physical changes –> phase change, protein folding
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

First law of thermodynamics:

A

‘the total energy (U) of an isolated system is constant, though within
that system it may change its form’.

It can never be created or
destroyed.

  • If the energy of the system changes, it must be transferred to another
    system:

ΔU = q + w
q = heat and w = work

Heat is transfer of energy due to a temperature difference

Work is motion against and opposing force (e.g. pressure causing a change in
volume)

ΔU = q + w

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q
  • Enthalpy (H) is a more convenient parameter
A

the quantity of heat absorbed by a system when it undergoes a change of state without performing any work except that associated with its change in volume.

During this change of state:

  • If heat is released into the surroundings, the system has a decrease in
    enthalpy (ΔH < 0), and the process is exothermic
  • If heat is absorbed from the surroundings, the system has an increase in
    enthalpy (ΔH > 0), and the process is endothermic
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

release of heat is not enough to make a process happen
spontaneously

A

release of heat is not enough to make a process happen
spontaneously

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Standard enthalpy change:
- Standard states
- Standard enthalpy of reaction

A

Standard states:
* Pressure of 105 Pa.
* Concentration of 1 M.

– Standard enthalpy of reaction:

  • Value of ΔH for a reaction occurring under standard conditions (ΔrHθ; kJ
    or kJ mol–1).
  • Involves the actual numbers of moles specified by the coefficients of the
    equation.
20
Q

thermochemical equation

A
  • Always gives the physical states of the reactants and products.

– Its value of ΔrHθ is only true when coefficients of reactants and products are numerically equal to the number of moles of the
corresponding substances.

21
Q

Hess’s law:

A

The overall enthalpy change for any process is constant, regardless of how the reaction is carried out

22
Q

What is entropy?

A

Just because a reaction or process produces heat, this does not mean that it
will happen spontaneously.

Just because a process requires the input of
heat does not mean that it cannot happen spontaneously. There is another factor: entropy

  • Entropy and probability:
    – Spontaneous processes tend to proceed from states of low probability to
    states of higher probability.

– Spontaneous processes tend to disperse energy.

23
Q

Entropy is often described as “amount of disorder”

A

– E.g. When all other things are equal, reactions that increase the number of particles in the system tend to have a positive entropy
change

24
Q

Entropy (S) describes

A

the number of equivalent ways that energy can be
distributed in the system.

Like Enthalpy, Entropy is a state function:
ΔrS = Sproducts – Sreactants

The units of ΔrS are
J mol-1 K-1

Any event that is accompanied by an increase in the entropy of the system has a tendency to occur spontaneously

25
Q

Thermodynamics – Gibbs Energy

A

Whenever a spontaneous event takes place in our universe, the total entropy
of the universe increases (ΔStotal > 0).

– Entropy change of the universe:
ΔStotal =ΔSsystem +ΔSsurroundings

26
Q

So, for a process to be spontaneous:

A

ΔH system -T ΔS system < 0

27
Q

It is now possible to formally define Gibbs energy (G):

A

G = H–TS

– For constant p and T:
ΔG = ΔH -TΔS

– A process is spontaneous when ΔG< 0 at constant p and T.

28
Q

The free energy of a system (G) has two components:

A

Enthalpy (H) – the heat content of a system

Entropy (S) – the disorder of a system

Such that G = H – TS
Where T is the absolute temperature (K)

For a reaction there is a change in free energy given by:
DG = Gproducts – Greactants = (Hproducts – Hreactants) – T(Sproducts – Sreactants)

DG = DH - TmentropyS - a reaction will proceed spontaneously if Gibs energy is negative.

For bond breakage DH is positive; and for bond formation it is negative
In going from a state with more disorder to one with less disorder DS is negative, hence
-T entropyS is positive.

29
Q

Thermodynamics – Protein Folding

A

When unfolded, in aqueous solution, a protein is interacting with surrounding water molecules and ions, via hydrogen bonds, van der Waals interactions, and ionic bonds.

30
Q

When folded, bonds to water are broken and intramolecular bonds are formed: 4

A
  • Hydrogen bond energy: ~20 kJmol-1 and directional (orientation of atoms matters)
  • Ionic bond energy: ~80 kJmol-1 and not directional (but decreases with distance)
  • Van der Waals interactions: very weak, but can sum up to a large favourable energy
  • Disulfide bond: ~250 kJmol-1 but only form after folding. The contribution to maintain
    stable structure.
31
Q

Interactions Between Amino Acids In Proteins: van der Waals Interactions

A

hydrogen bonding and ionic interactions.

The other interactions that occur in proteins between amino acid residues are van der Waals interactions that are weak dipole interactions.

32
Q

van der Waals interactions: 3

A
  1. interactions between permanent dipoles
  2. dipole-induced dipole interactions
  3. london dispersion forces
33
Q

Properties of Amino Acid Side Chains and Their Arrangement

Determine Properties of a-Helices and How They Pack in Protein Structures

A
  1. Amphipathic a-helix
  2. Hydrophobic a-helix
  3. Hydrophilic a-helix
34
Q
  1. Amphipathic a-helix
A

Amphipathic a-helix
in flavodoxin.

Amphipathic ahelix, with mainly HYDROPHOBIC residues on one side, facing inwards to the centre of the protein and mainly HYDROPHILIC residues
on the other, facing the aqueous solvent

35
Q
  1. Hydrophobic a-helix
A

Hydrophobic a-helices
in dimeric citrate
synthase.

HYDROPHOBIC a-helix,
with mainly
HYDROPHOBIC residues,
where the helix is buried in the hydrophobic interior
of the protein.

36
Q

Hydrophilic a-helix

A

Hydrophilic a-helix in
calmodulin.

Hydrophilic a-helix,
with mainly
HYDROPHILIC residues,
where the helix is completely accessible to the aqueous solvent

37
Q

Properties of Amino Acid Side Chains and Their Arrangement

Determine Properties of b-Sheets and How They Pack in Protein Structures

A
  1. Hydrophobic b-Sheet
  2. Hydrophilic b-Sheet
  3. Amphipathic b-Sheet
38
Q

Hydrophobic Layers in Protein Folding

A

To bury the hydrophobic
residues within the protein structure, alternate layers of hydrophobic and hydrophilic residues are often sandwiched together in the tertiary structure.

39
Q

Protein in a vacuum

A
  • No solvent contributions
  • triangle H chain favourable (increased H-bonding, Van der Waals & electrostatic interactions) - major factor
    • T triangle Schain unfavourable (decreased entropy)
  • triangle G total favourable
40
Q

Nonpolar amino acid side chains in aqueous solvent (5)

A
  • DHchain unfavourable (decreased electrostatic
    interactions)
    • T DSchain unfavourable (decreased entropy)
  • DHsolvent favourable (increased water-water interactions)
  • -T DSsolvent favourable (entropy of water increased) -major factor
  • DGtotalfavourable
41
Q

Polar amino acid side chains in aqueous solvent =4

A
  • DHchain unfavourable (decreased interactions with water)
    • T DSchain unfavourable (decreased entropy)
  • DHsolvent favourable (increased water-water interactions)
  • -T DSsolvent favourable (entropy of water increased)
  • DGtotal neutral
42
Q

The Problem of Protein Folding 4

A

A protein is synthesised as a linear polymer of amino acids.

  • A functional protein has a well-defined and specific 3-dimensional structure.
  • The structure of a protein is determined by the sequence of amino acids in its polypeptide chain.
  • A protein folds because the folded polypeptide chain, plus water solvent, have
    a lower free energy than the unfolded chain, plus water solvent.
43
Q

How does a protein fold from being a relatively disordered linear polymer of
amino acids to a highly ordered, structured, functional molecule?

A

One possibility is that the polypeptide chain samples all possible conformations in random way until it finds the native, lowest free energy state.

The Leventhal paradox - consider a protein of 100 amino acids, assume that
there are only 2 conformational possibilities per amino acid, therefore for the protein there are 2^100 = 1.27 x 10^30 possibilities.

If it takes only 10-^13s to test
each conformational possibility it will take 1.27 x 1017s to test them all i.e.
4,000,000,000 YEARS!!!!!!

Protein folding must follow some kind of defined pathway(s)

44
Q

Folding Energy Landscape Funnels

A

Multidimensional energy landscape models of folding show how there are potentially many possible folding pathways

Schematic diagram of a folding energy landscape.

Denatured molecules at the top of the funnel might fold to the native state by a myriad of different routes, some of which involve
transient intermediates (local energy minima) whereas others involve significant kinetic traps (misfolded states).

45
Q

Protein Folding in the Cell:

Schematic diagram of protein folding in the cytosol of eukaryotes and prokaryotes.

A

(a) Unassisted folding.

(b) Folding assisted by heat shock proteins

(c) Folding assisted by both heat shock proteins and GroEL/GroES (in
prokaryotes).

46
Q

Heat shock proteins (Hsps) are also known as
chaperones. 2

A
  • Expression of Hsps is upregulated in cells briefly exposed to high temperatures (~42°C).
  • Hsps can allow mis-folded proteins a chance to fold correctly.
47
Q

GroES-GroEL - Anfinsen Cage

A

The GroES-GroEL structure is a macromolecular complex of proteins.

The GroEL structure is hollow and barrel-shaped and provides the chambers in which unfolded and partially folded proteins can fold in an ATP-dependent process, protected from the rest of the proteins in the cell when the GroES lid is in place.

Biochemistry (14 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions