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BIOCHEMISTRY > WEEK 4 > Flashcards

WEEK 4 Flashcards

1
Q

What is the bond formed between two amino acid molecules and how is it formed?

A

Peptide bond

A condensation reaction between a hydroxyl group from the alpha-carboxyl group of one amino acid and a hydrogen atom from the alpha-amino group of another

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2
Q

What is the reverse of a condensation reaction?

A

Hydrolysis/Hydrolytic cleavage

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3
Q

On the basis of shape, which groups can proteins be divided into?

A

Fibrous proteins & Globular proteins

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4
Q

What are the four structures of proteins?

A

Primary structure
Secondary structure
Tertiary structure
Quaternary structure

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5
Q

Proteins with significant similarity in primary structure and/or with similar tertiary structure and function are said to be in the same ________________________

A

Protein family

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6
Q

What is a ‘Superfamily’?

A

When two or more families that have little similarity in amino acid sequence but make use of the same major structural motif have functional similarities

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7
Q

Why must the three-dimensional structure of a protein meet certain requirements?

A

To enable the protein to function in the cell or extracellular medium of the body

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8
Q

What are the requirements of the three-dimensional structure?

A
  • Creation of a binding site specific for just one molecule or a group of molecules with similar structural properties
  • Exhibit degrees of flexibility and rigidity
  • External surface that is appropriate for its environment
  • Conformation must be stable (no precipitating in the cell/refolding into a form that cannot fulfilled its function)
  • Structure that can be degraded when damaged or no longer needed in the cell
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9
Q

What does flexibility and mobility in structure enable the protein to do?

A

Fold as it is synthesised and adapt as it binds to other proteins and small molecules

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10
Q

Define ‘Primary structure of a protein’

A

The sequence of amino acids linked together to form a polypeptide chain

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11
Q

Define ‘Secondary structure of a protein’

A

The shape taken up by the polypeptide chain within a protein molecule as the result of the formation of hydrogen bonds between amino acids

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12
Q

What are the two forms of secondary structure of proteins?

A

a-helix and b-pleated sheet

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13
Q

What is an a-helix and how is it formed?

A

a-helix is a polypeptide chain that forms regular helical coils

The a-helix coils are stabilised by hydrogen bonds between carbonyl oxygen of first amino acid and amide of fourth amino acid

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14
Q

Keratin is an example of what secondary structure of protein?

A

a-helix

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15
Q

What is the composition of the b-pleated sheet and how is it formed?

A

B-pleated sheet consists of a number of adjacent polypeptide chains which can run in the same direction (parallel) or in opposite direction (anti-parallel)

The sheet is established by hydrogen bonds between CO group of one polypeptide chain and the NH group of adjacent polypeptide chains

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16
Q

Fibroin (silk) is an example of which secondary structure protein?

A

B-pleated sheet

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17
Q

What is a ‘motif’ or ‘fold’?

A

A recognisable folding pattern involving two or more elements of secondary structure and the connection(s) between them

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18
Q

What is distinguishable about a ‘motif’?

A
  • can be very simple
  • may represent only a small part of a protein
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19
Q

How are globular proteins constructed?

A

By combining secondary structural elements including a-helices, b-sheets and coils producing specific geometric patterns or motifs

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20
Q

Where can the helix-loop-helix motif be found?

A

In a number of proteins that function as transcription factors

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21
Q

What is the difference between a-helices and b-pleated sheets & bends, loops and turns?

A

a-helices and b-pleated sheets are patterns of regular structure with a repeating element of the ordered formation of hydrogen bonds

bends, loops and turns are non-regular secondary structures that do not have a repeating element of hydrogen bond formation

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22
Q

What is the tertiary structure of proteins?

A

When the secondary structure polypeptide chain is further folded, super-folded and twisted about itself forming many sizes

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23
Q

Which structure is common in globular proteins?

A

Tertiary structure

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24
Q

What is a ‘domain’?

A

A fundamental functional and three-dimensional structural unit of polypeptides and is part of a polypeptide chain that is independently stable or could undergo movements as a single entity with respect to the entire protein

25
Q

Folding of the peptide chain within a domain usually occurs ___________________ of folding in other domains

A

independently

26
Q

Different domains have distinct _____________, such as the binding of small molecules or interaction with other proteins

A

functions

27
Q

How many domains do small proteins usually have?

A

One

28
Q

Where do hydrophobic interactions normally occur in amino acids?

A

between non-polar side chains of amino acids

29
Q

What is the importance of hydrophobic interactions in amino acids?

A

They constitute the major stabilising forces for tertiary structure forming a compact three-dimensional structure

30
Q

Where are hydrogen bonds usually formed in amino acids?

A

Hydrogen bonds are normally formed by their polar side chains

31
Q

Where can ionic/electrostatic interactions be found in amino acids?

A

Interaction occurs between charged polar side chains of amino acids such as basic and acidic amino acids

32
Q

Where do van der Waals forces occur in amino acids?

A

occur between non-polar side chains

33
Q

Which bonds can be found in amino acids?

A

Hydrogen bonds
Ionic/electrostatic interactions
Van der Waals forces
Disulphide bonds

34
Q

Where can disulphide bonds be found within amino acids?

A

These are S-S bonds formed between -SH groups of distant cysteine residues

35
Q

What is the quaternary structure of a protein?

A

The quaternary structure of a protein is the association of several protein chains or subunits into a closely packed arrangement

36
Q

Describe the arrangement in quaternary structure of proteins regarding subunits

A

Each constituent peptidechain is called as a monomer or sub unit. The monomers ofprotein can be identical or quite different in primary, secondary or tertiarystructure.

37
Q

What is the difference between primary structure, secondary structure, tertiary structure and quaternary structure?

A

Primary structure = sequence of amino acids
Secondary structure = alpha helices, beta strands
Tertiary structure = fold helices and strands into domains
Quaternary structure = functional assemblies of chains (subunits)

38
Q

What is ‘Protein folding’?

A

A process by which a polypeptide chain folds to become a biologically active protein in its native 3D structure

39
Q

What are the external factors that can influence protein folding?

A
  • Electric and magnetic fields
  • Temperature
  • pH
  • Chemicals
  • Space limitation
  • Molecular crowding
40
Q

What can affect the stability of proteins and cause them to unfold or denature?

A
  • extreme temperatures
  • extreme pH
  • mechanical forces
  • chemical denaturants
41
Q

How does the hydrophobic effect play a significant role in protein folding?

A

The aggregation of non-polar amino acid side chains provides an entropic stabilisation to intermediates and eventually to the final folded structure

42
Q

Folding for many proteins requires ____________

A

Chaperones

43
Q

What are the two major families of chaperones?

A

Hsp70 family & the chaperonins

44
Q

What is the function of the chaperone ‘Hsp70’

A

Hsp70 proteins block the folding of certain proteins that must remain unfolded until they have been translocated across a membrane

45
Q

What are the functions of chaperones?

A
  • protect proteins against heat denaturation
  • help proteins to fold and remain folded under extreme temperatures
  • assist misfiled proteins in unfolding and re-folding correctly
  • Chaperones facilitate correct protein folding by binding to and stabilizing exposed, aggregation-prone hydrophobic regions in nascent and denatured polypeptides, preventing premature folding
46
Q

What is ‘denaturation’?

A

A loss of three-dimensional structure sufficient to cause loss of function

47
Q

What is the effect of organic solvents, urea and detergents on proteins?

A

They act by disrupting the hydrophobic aggregation of non-polar amino acid side chains that produces the stable core of globular protein; this disrupts hydrogen bonds and extremes of pH alter the net charge on a protein, causing electrostatic repulsion and the disruption of some hydrogen bonding.

48
Q

What is ‘Renaturation’?

A

When certain globular proteins that are denatured by heat, extremes of pH or denaturing reagents regain their native structure and their biological activity if they are returned to conditions in which the native conformation is stable

49
Q

What is Renaturation proof of?

A

The tertiary structure of a globular protein is determined by its amino acid sequence

50
Q

What happens to misfolded proteins?

A

They are usually tagged and degraded within the cell

51
Q

What is the name for amyloid deposition diseases that trigger neurodegeneration?

A

Localised amyloidoses

52
Q

What is the mechanism behind Alzheimer disease?

A

Alzheimer disease is associated with extracellular amyloid deposition by neurons involving amyloid-B precursor protein. The dominant component of the amyloid plaque that accumulates in AD is amyloid B (and extracellular peptide containing 40-42 amino acid residues with a B-pleated sheet secondary structure in non branching fibrils).

This peptide when aggregated in a B-pleated sheet confirmation is neurotoxic and leads to cognitive impairment. It is deposited via secretases from the larger amyloid precursor protein (a single transmembrane protein expressed on the cell surface in the brain and other tissues)

53
Q

What is the misfolded protein behind Parkinson’s disease?

A

The misfolded form of the protein a-synuclein aggregates into 574 spherical filamentous masses called Lewy bodies

54
Q

Define ‘Prions’

A

Abnormal, pathogenic agents that are transmissible and are able to induce abnormal folding of specific normal cellular proteins called prion proteins that are most abundant in the brain

55
Q

What is the most known Prion disease in the body?

A

Bovine spongiform encephalopathy (BSE) also known as Mad cow’s disease

56
Q

What are examples of Prions diseases?

A
  • Bovine spongiform encephalopathy (BSE) “Mad cow’s disease”
  • Kuru disease
  • Creutzfeldt-Jakob disease
  • Scrapie (sheep)
  • Chronic wasting disease (deer)
57
Q

Why do prions diseases also get referred to as “spongiform encephalopathies”?

A

The diseased brain frequently becomes ridiculed with holes

58
Q

What are neurological symptoms of progressive neuronal deterioration?

A
  • Weight loss
  • Erratic behaviour
  • Problems with posture
  • Balance
  • Coordination
  • Loss of cognitive function
59
Q

When does illness occur regarding the protein PrP/PrPC?

A

Illness occurs when the protein alters into PrPSc.

The structure of PrPC has two a helices and the structure of PrPSc is amyloidlike beta sheets (VERY DIFFERENT!)

The conversion into PrPSc has a domino effect in which more and more of the brain converts to the disease-causing form

BIOCHEMISTRY (12 decks)

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