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Biochemistry - Mid > CH3 | Protein Structure > Flashcards

CH3 | Protein Structure Flashcards

1
Q

What is the fundamental relationship between a protein’s structure and its function?

A

A protein’s structure determines how it works.

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2
Q

How is a functional protein physically characterized in its native conformation?

A

A functional protein is one or more polypeptides twisted, folded, and coiled into a unique 3D structure.

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3
Q

What is the origin of a protein’s specific activity?

A

The specific activities of proteins result from their intricate three-dimensional architecture.

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4
Q

Provide 4 examples of differently-structured proteins.

A

Hemoglobin, antibody, enzymes, and polymerase are differently structured.

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5
Q

What is a protein’s native conformation?

A

It is the unique 3D structure a protein takes, which determines how it will work.

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6
Q

What are the two key abilities that determine a protein’s function?

A

A protein’s function depends on its ability to (1) recognize and (2) bind to another molecule.

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7
Q

Complete the sentence: “A protein’s function is determined by how it _______ and ______ to other molecules.”

A

A protein’s function is determined by how it recognizes and binds to other molecules.

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8
Q

True or false: protein function is only determined by recognition.

A

False, recognition and binding are required. (True or false to test more careful understanding).

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9
Q

Describe the four levels of protein structure, including their names, a brief description of each.

A

Primary Structure: The linear sequence of amino acids. (Visual: List of amino acids like “Pro, Ala, Asp…”)

Secondary Structure: Regular, repeating local structures like the alpha-helix. (Visual: Alpha-helix depicted as a coil).

Tertiary Structure: The overall 3D shape of a single polypeptide chain. (Visual: Complex folded polypeptide chain).

Quaternary Structure: The arrangement of multiple polypeptide subunits into a functional protein complex. (Visual: Multiple subunits assembled together).

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10
Q

What defines the primary structure of a protein?

A

The unique sequence of amino acids linked by peptide bonds.

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11
Q

What determines a protein’s primary structure?

A

Inherited genetic information determines it.

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12
Q

How does the primary structure relate to the protein’s overall function?

A

The primary structure dictates how the protein folds into its 3D structure, which in turn determines its function.

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13
Q

What is an analogy for the primary structure of a protein?

A

The order of letters in a long word.

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14
Q

What is secondary protein structure?

A

Particularly stable arrangements of amino acid residues that form recurring structural patterns (like coils and folds).

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15
Q

What type of bond stabilizes secondary structures, and where does it occur?

A

Hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone.

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16
Q

Name the most common secondary structures found in proteins.

A

Alpha-helix, beta-pleated sheet, beta-turns, and loops.

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17
Q

If the Φ and ψ angles are known for all amino acid residues in a polypeptide segment, what can be completely determined?

A

The secondary structure of that polypeptide segment.

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18
Q

What is a technique used for assessing common secondary structures and monitoring protein folding?

A

Circular dichroism spectroscopy.

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19
Q

What are the two main categories of secondary structures in proteins?

A

Repetitive structures and non-repetitive structures.

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20
Q

What proportion of an average globular protein is organized into repetitive structures? What are two examples?

A

Approximately one-half. Examples: alpha-helix and/or beta-sheet.

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21
Q

Are non-repetitive structures considered “random”? Why or why not?

A

No, they are not “random.” They simply have a less regular structure than repetitive structures.

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22
Q

What is a common example of a non-repetitive secondary structure?

A

Loop or coil conformation.

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23
Q

What does the term “random coil” actually refer to?

A

The disordered structure obtained when proteins are denatured.

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24
Q

What type of secondary structure is an alpha-helix?

A

A form of repetitive secondary structure.

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25
What stabilizes an alpha-helix, and between which groups does this occur?
Stabilized by hydrogen bonds between peptide bond carbonyl oxygen and amide hydrogen (Intra-chain H-bonds)
26
How are the R side chains positioned in an alpha-helix?
The R side chains extend outward from the helix axis.
27
Can polar but uncharged amino acids participate in the hydrogen bonding in alpha-helices?
Yes, they can.
28
How many amino acid residues are there per turn of an alpha-helix? What does this imply about their spatial arrangement?
3.6 amino acid residues per turn. This means that residues 3 or 4 positions apart in the sequence are brought close together in space.
29
What is a defining characteristic of beta-sheets in terms of peptide bond components?
All the peptide bond components are involved in hydrogen bonding.
30
What is the difference between the hydrogen bonds in beta-sheets compared to alpha-helices?
Beta-sheets have inter-chain hydrogen bonds (between different strands), whereas alpha-helices have intra-chain hydrogen bonds (within the same chain).
31
Can uncharged but polar amino acids participate in the hydrogen bonding in beta-sheets?
Yes, they can.
32
Why are beta-sheets called "pleated"?
Because their surface appears to have a folded or pleated shape.
33
What are beta-sheets composed of?
Two or more peptide chains called beta-strands.
34
What are the two ways in which polypeptides of beta-sheets can be arranged?
Parallel and antiparallel.
35
How are the N- and C-termini arranged in a parallel beta-sheet?
All N-termini are together, and all C-termini are together (N --> C, N --> C).
36
How are the N- and C-termini arranged in an antiparallel beta-sheet?
N-termini are adjacent to C-termini (N --> C, C <-- N).
37
What is a protein motif or fold?
A recognizable folding pattern involving two or more elements of secondary structure and their connections.
38
What is a simple motif, and what is an example?
Two secondary structure elements folded against each other, representing a small part of a protein. Example: Beta-alpha-Beta loop.
39
What is a complex motif, and what is an example?
More than two elements of secondary structure. Example: Beta-barrel.
40
What does tertiary structure represent in a protein?
The overall three-dimensional structure of a single polypeptide chain (its native conformation).
41
What determines the tertiary structure of a protein?
Interactions among various side chains (R groups) in the polypeptide.
42
Name the four types of interactions that stabilize tertiary structures in globular proteins.
1) Disulfide bonds, 2) Hydrophobic interactions, 3) Hydrogen bonds, 4) Ionic bonds.
43
Which interaction stabilizing the tertiary structure is covalent, and between which amino acid residues does it occur?
Disulfide bonds are covalent and form between the SH groups of two cysteine residues.
44
Are hydrophobic, hydrogen, and ionic bonds considered covalent or non-covalent interactions in the context of protein structure?
Non-covalent.
45
What are protein domains?
The fundamental functional and three-dimensional structural units of a polypeptide.
46
What are three key characteristics of protein domains?
Each domain has a (1) distinct structure and (2) function independent of other domains. (3) It is self-stabilizing and folds independently.
47
How does tertiary structure relate to domains?
Tertiary structure refers to the folding of the individual domain and the final arrangement of domains in the polypeptide.
48
Do polypeptides with a large number of amino acid residues tend to have domains? If so, how many?
Yes, they often fold into two or more domains, sometimes with different functions.
49
What does the quaternary structure of a protein represent?
The arrangement of multiple protein subunits into a functional complex.
50
When does a protein have a quaternary structure?
Only when it consists of multiple polypeptide chains (subunits).
51
What type of interactions hold subunits together in a quaternary structure?
Non-covalent interactions (hydrogen bonds, ionic bonds, and hydrophobic interactions).
52
What happens to a protein's structure during denaturation?
It unfolds and loses its 3-D (native) conformation and disorganization.
53
What is the functional state of a denatured protein?
Biologically inactive (non-functional).
54
Which protein structural levels are affected by denaturation?
Secondary, tertiary, and quaternary structures.
55
Does denaturation break peptide bonds?
No, it does not involve hydrolysis of peptide bonds.
56
What is the schematic cause of protein denaturation?
Extreme environments (like temperature, pH) disrupt protein shape and function
57
How does protein denaturation affect the primary structure of a protein?
It does not affect the primary structure because it is stabilized by covalent (peptide) bonds.
58
What is the effect of protein digestion on the primary structure?
It breaks down the primary structure by damaging the peptide bonds.
59
What are the agents that can cause protein digestion?
High temperature with strong acid (e.g., 100°C and 1M HCl) or proteolytic enzymes (proteases).
60
What are the products of protein digestion?
Amino acids (the constituent monomers of proteins).
61
What is the main difference between protein denaturation and protein digestion?
Denaturation affects only the secondary, tertiary and quaternary structures, leaving the primary structure intact, while digestion breaks down all structures including the primary structure (peptide bonds).
62
What are the most common observations of protein denaturation?
Protein precipitation or coagulation.
63
Why does denaturation often lead to precipitation or coagulation?
Because denaturation usually reduces a protein's solubility.
64
What is renaturation?
The inverse process of denaturation, where a denatured protein regains its native structure and biological activity.
65
How common is renaturation?
It is rare (unlikely to happen).
66
How can denaturation be observed in common food examples?
In the production of yogurt (proteins in milk denature and coagulate) and the solidification of boiled eggs (egg white proteins denature and coagulate).
67
What are denaturing agents?
Factors (physical or chemical) that damage the bonds stabilizing the tertiary structure of proteins, leading to denaturation.
68
List the common physical and chemical denaturing agents.
Physical: Heat, mechanical disruption (agitation), radiation. Chemical: Extreme pH, alcohol, heavy metals (e.g., lead, mercury), reducing agents, neutral salts, organic solvents.
69
How do proteins reach their stable structure?
Through several stages (a stepwise process).
70
What is the first step in protein folding?
Formation of a secondary structure.
71
What is the second step in protein folding?
Formation of domains.
72
What is the final step in protein folding?
Formation of the final protein monomer.
73
Do all proteins fold spontaneously in the cell?
No, many proteins require chaperones for proper folding.
74
What are chaperones?
Proteins that assist in the proper folding of other proteins.
75
What are the main mechanisms of action of chaperones?
Interact with partially folded or improperly folded polypeptides. Facilitate correct folding pathways. Provide microenvironments in which folding can occur.
76
How widely distributed are chaperones in nature?
Chaperones are found in organisms ranging from bacteria to humans.
77
What are the two major families of chaperones?
Heat shock protein 70 (Hsp70) and chaperonins.
78
Give examples of diseases associated with protein misfolding.
Alzheimer's, Parkinson's, and mad cow disease.
79
What are amyloids and prions?
Examples of pathogenic neurotoxic proteins formed by the misfolding of normal proteins.
80
What are the two main consequences of protein misfolding, as shown in the diagram?
Gain of toxic activity. Loss of biological function.
81
What is the general process that leads from misfolded proteins to cellular damage (as per the diagram)?
Misfolding leads to aggregation of proteins, which in turn causes neurodegeneration.
82
In Alzheimer's disease, what is the main misfolded protein involved?
Amyloid-beta (Aβ).
83
What gene is associated with Parkinson's disease and what is the involved protein?
The α-synuclein gene, leading to misfolding of the α-synuclein protein.
84
What type of protein is implicated in prion diseases?
Prion protein (PrP).
85
What are the key characteristics of prions?
Misfolded, infectious, and self-propagating proteins.
86
What does it mean for a prion to be "infectious"?
It can transmit its misfolded shape to other normal proteins, effectively "infecting" them.
87
What is the name of the misfolded prion protein that causes disease?
PrPSc.
88
What are the diseases caused by PrPSc collectively called?
Transmissible Spongiform Encephalopathies (TSEs).
89
Give examples of TSEs and the species they affect.
Creutzfeldt-Jakob disease (humans) Bovine Spongiform Encephalopathy (Mad Cow Disease) (cattle) Scrapie (sheep)
90
What is the cellular nature of PrPC?
It is a normal, cellular, endogenous protein.
91
How does PrPSc differ from PrPC in terms of its state?
PrPSc is a misfolded protein.
92
What is the infectious nature of PrPC vs. PrPSc?
PrPC is non-infectious, while PrPSc is infectious.
93
What is the secondary structure of PrPC vs PrPSc?
PrPC has an alpha-helical structure; PrPSc has a beta-sheet structure.
94
What is the normal function of PrPC?
Facilitates cell-cell communication.
95
What is the function of PrPSc in disease?
Acts as a template to convert more PrPC into PrPSc, leading to aggregation (fiber growth) and disease.
96
In the prion replication cycle, what does an infectious PrPSc molecule initially interact with?
A normal PrPC molecule.
97
What is the effect of PrPSc interacting with PrPC?
It mediates the transformation of PrPC into PrPSc.
98
After the initial conversion, what do the two PrPSc molecules do?
They segregate and transform more PrPC molecules into abnormal PrPSc molecules.

Biochemistry - Mid (7 decks)

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