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Proteins Flashcards

1
Q

What are proteins?

A

Complex molecules that perform the majority of work in cells and organisms.

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2
Q

List some diverse roles of proteins.

A
  • Structure of cells
  • Replication
  • Enzymes
  • Transport
  • Catalysis
  • Signaling
  • Combating infection
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3
Q

What is the relationship between protein sequence, structure, and function?

A

Sequence gives rise to structure, and structure gives rise to function.

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4
Q

How many common amino acids are there?

A

20

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5
Q

What is a polypeptide chain?

A

A string of amino acids linked together.

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6
Q

Describe the four levels of protein structure.

A
  • Primary: amino acid sequence
  • Secondary: local arrangements like alpha helices
  • Tertiary: overall 3D arrangement of a single polypeptide
  • Quaternary: arrangement of multiple polypeptides
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7
Q

What is the primary structure of a protein?

A

The sequence of amino acids.

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8
Q

What is a secondary structure of a protein? Give an example.

A

Localized arrangements of atoms in 3D space that creates some kind of repeating structure. An example is an alpha helix.

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9
Q

What is the tertiary structure of a protein?

A

The overall arrangement of all amino acids in 3D space.

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10
Q

What is the quaternary structure of a protein?

A

The arrangement of multiple polypeptide subunits.

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11
Q

What are the key features of amino acids?

A
  • Capacity to polymerize
  • Useful acid-base properties
  • Diverse physiochemical properties
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12
Q

Describe the basic structure of an amino acid.

A

A central carbon (C alpha) with an amino terminus (N terminus), a carboxyl terminus (C terminus), and a side chain (R group).

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13
Q

What is a zwitterion?

A

An amino acid in its protonated form, with a positive charge on the amino group and a negative charge on the carboxyl group.

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14
Q

What are the general categories of amino acid side chains?

A
  • Non-polar
  • Aromatic
  • Negatively charged
  • Positively charged
  • Polar
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15
Q

What is a peptide bond?

A

The bond that forms between two amino acids via a condensation reaction.

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16
Q

What is the result of a peptide bond?

A

The carboxyl terminus of one amino acid and the amino terminus of the other come together in a condensation reaction, releasing a molecule of water and forming a rigid structure called a peptide bond.

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17
Q
A
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18
Q

What is the confirmation of a protein?

A

The final functional form or forms a protein adopts. Often referred to as the native confirmation.

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19
Q

What are the main weak interactions that drive protein folding?

A

Hydrogen bonds, ionic interactions, and the hydrophobic effect. Van der Waals interactions also contribute.

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20
Q

What is the role of hydrogen bonds in protein structure?

A

They are super important in stabilizing protein structure, arising between a covalently bound hydrogen (donor) and a lone pair of electrons in another atom (acceptor).

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21
Q

What is the hydrophobic effect and how does it contribute to protein folding?

A

It’s the phenomenon where hydrophobic amino acids are buried inside the protein, increasing entropy as water doesn’t need to form an ordered array around them. This drives protein folding.

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22
Q

Where are hydrophobic amino acids typically located in a protein in an aqueous environment?

A

Largely buried inside the protein, in the interior.

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23
Q

What are the common types of secondary structure in proteins?

A

Alpha helix, beta sheet (composed of beta strands), and beta turns.

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24
Q

How is the alpha helix stabilized?

A

Maximized internal hydrogen bonding between the carbonyl group of one amino acid and the amino group of an amino acid four residues down the chain (I and I+4).

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25
How do the R groups project in an alpha helix?
They project outwards around the helix.
26
How are beta sheets formed?
By hydrogen bonding between two or more beta strands.
27
How do the R groups project in a beta sheet?
They project above and below the plane of the sheet, alternating.
28
What are the two types of beta sheets?
Parallel and antiparallel. Antiparallel sheets are stronger due to linear hydrogen bonds.
29
What is the function of a beta turn?
To connect two antiparallel beta strands, allowing the polypeptide chain to change direction.
30
What amino acids are commonly found in type 1 and type 2 beta turns?
Type 1: Proline at position 2. Type 2: Glycine at position 3.
31
What is a ribbon representation in protein visualization?
A common method where secondary structures are represented as ribbons, with alpha helices shown as helices and beta sheets as flattened sheets with arrowheads.
32
What does a surface contour representation help visualize?
It helps appreciate the surface accessible regions of a protein rather than just looking through gaps.
33
How are side chains represented in ribbon structures?
They can be included to highlight particular areas and show interactions with the protein structure.
34
What is a space-filling model?
A representation that shows the actual position of atoms in a protein, often used by structural biologists.
35
Define tertiary structure in proteins.
The native conformation that gives rise to a protein's functional form.
36
What type of bond is a disulfide bond?
A covalent crosslink formed by the reaction of two cysteine amino acids.
37
What is the difference between intra- and interchain disulfide bonds?
Intra-chain bonds occur within a polypeptide chain, while interchain bonds form between two separate polypeptides.
38
True or False: Disulfide bonds are permanent and cannot be broken.
False. They can be broken depending on the reducing or oxidizing environment.
39
What are the two common classes of tertiary structure?
* Fibrous * Globular
40
What is a fibrous protein?
A structural protein that usually has a long repeating secondary structure, like keratin or collagen.
41
What characterizes globular proteins?
They are compact, often spherical, with hydrophobic amino acids buried within the molecule.
42
What is a quaternary structure?
A protein structure formed by two or more separate polypeptide chains, known as subunits.
43
Define homodimer and heterodimer.
A homodimer has two identical subunits; a heterodimer has two different subunits.
44
What is a motif in protein structures?
Recognizable folding patterns that link two or more secondary structures.
45
What distinguishes domains from motifs in protein structures?
Domains are independently stable parts of a protein with separate roles, while motifs are patterns formed by secondary structures.
46
What is an example of a domain in proteins?
The calcium binding domain of troponin C.
47
Fill in the blank: A protein's primary structure refers to its _______.
sequence of amino acids
48
Fill in the blank: A beta-alpha-beta loop is an example of a _______.
motif
49
What is the role of cysteine in forming disulfide bonds?
Cysteine has a reactive thiol group that can link two cysteines together.
50
What is the significance of hydrophobic amino acids in fibrous proteins?
They tend to be buried within the protein structure, contributing to its insolubility in water.
51
True or False: Hemoglobin is an example of a quaternary protein structure.
True. It consists of four polypeptide subunits.
52
What happens if a protein doesn't fold correctly?
It loses its function and may become unfolded or degraded, leading to potential aggregates inside the cell ## Footnote Aggregates can lead to neurological diseases like Parkinson's and Alzheimer's.
53
What are amyloid fibers?
Discrete, insoluble protein aggregates that can form in the brain, affecting neurological function ## Footnote They often consist of rod-like structures with beta strands running anti-parallel.
54
What is the initial step in the life of a protein?
Synthesis of a polypeptide from the ribosome in translation.
55
What role do chaperones play in protein folding?
They help proteins fold into their native form and can assist in disaggregating misfolded proteins.
56
What is the outcome of protein degradation?
Proteins are broken down into peptides, which may be recycled for use in other proteins.
57
What did Christian Anfinsen study?
The relationship between the native conformation of RNase A and its functionality.
58
What does urea do to proteins?
It is a strong denaturing agent that disrupts hydrogen bonding and hydrophobic interactions.
59
What is the effect of mercaptoethanol on proteins?
It is a strong reducing agent that breaks disulfide bonds.
60
Fill in the blank: The correct disulfide bonds are necessary for the folded structure and function of a protein because _______.
they ensure proper three-dimensional conformation.
61
True or False: The amino acid sequence alone is sufficient for a protein to fold into its native conformation.
True.
62
What are some interactions that influence protein folding?
Covalent disulfide bonds, hydrogen bonding, electrostatic interactions, van der Waals forces, and hydrophobic effects.
63
What is the thermodynamic principle driving protein folding?
A combination of decreasing enthalpy and increasing entropy.
64
Describe the hydrophobic effect in protein folding.
Hydrophobic amino acids tend to aggregate to minimize their exposure to water, increasing overall entropy.
65
How do lipids demonstrate the principle of the hydrophobic effect?
They form micelles where hydrophobic tails are sequestered inward, reducing the ordered state of water around them.
66
What is the significance of the protein folding funnel model?
It represents the energy landscape a polypeptide explores while folding, transitioning from high energy and high entropy to low energy and low entropy.
67
What is the role of heat shock proteins?
They protect proteins from misfolding and assist in the refolding process.
68
What happens to the entropy of a protein during folding?
The entropy of the protein decreases as it becomes more ordered.
69
What are the two opposing entropy concepts discussed in protein folding?
The entropy of the protein decreases while the entropy of the surrounding water increases.
70
What is the process called when a cell degrades its own components to remove aggregates?
Autophagy.
71
List the types of protein aggregates mentioned.
* Amorphous aggregates * Oligomers * Amyloid fibrils
72
What does the term 'native conformation' refer to?
The specific three-dimensional structure that a protein must achieve to function properly.
73
What does the term 'misfolded protein' refer to?
A protein that has not attained its correct three-dimensional structure, leading to loss of function.
74
What are the three main categories of proteins discussed?
Globular proteins, fibrous proteins, and membrane proteins.
75
What is the typical structure of globular proteins?
They are compact, spherical, and have hydrophobic amino acids buried within.
76
Give two examples of globular proteins.
Myoglobin and haemoglobin.
77
What type of protein structure does myoglobin represent?
Tertiary structure.
78
What type of protein structure does haemoglobin represent?
Quaternary structure.
79
Why are most enzymes considered globular proteins?
Because they have cavities for substrate binding and catalytic activity.
80
What distinguishes fibrous proteins from globular proteins?
Fibrous proteins have long, extended secondary structures and are often insoluble in water.
81
What structural feature strengthens keratin?
Disulfide bonds between polypeptide chains.
82
Where is collagen commonly found?
They span lipid bilayers with hydrophobic amino acids inside the membrane and polar ones outside.
83

BMS1011 (2 decks)

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