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My Packs: (UWO) (BIOCHEM 2280) > (OLD) (Dr. Choy) (Unit A) Topic 3: Protein Structure and Analysis > Flashcards

(OLD) (Dr. Choy) (Unit A) Topic 3: Protein Structure and Analysis Flashcards

1
Q

Proteins are…

A

Linear polymers of amino acids

**

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2
Q

Define:

Dipeptide

A

Peptide chain with two amino acids

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3
Q

Define:

Tripeptide

A

Peptide chain with 3 amino acids

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4
Q

Define:

Oligopeptide

A

Peptide chain with 3-20 amino acids

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5
Q

Define:

Polypeptide

A

Peptide chain with many residues

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6
Q

Define:

Protein

A

1 or more polypeptide chains

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7
Q

True or False:

Peptide bonds exhibits resonance

A

True

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8
Q

What results from a peptide bond’s resonance?

A

40% double bond causes planar structure (cannot rotate around bond)

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9
Q

What bonds are rotateable in a peptide chain? What are they known as?

A
  1. N-Cα, known as Φ rotation angle
  2. Cα-C, known as Ψ rotation angle
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10
Q

List:

Levels of Protein Structure

A
  1. Primary
  2. Secondary
  3. Tertiary
  4. Quarternary
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11
Q

Define:

Primary protein structure

A

Amino acid sequence of protein (residues)

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12
Q

Define:

Secondary protein structures

A

Spatial arrangement of polypeptide backbone

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13
Q

Define:

Tertiary protein structure

A

3-D structure of entire polypeptide, including side chain(s) (only 1 subunit)

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14
Q

Define:

Quaternary protein structure

A

Spatial arrangement of polypeptide chains in protein with multiple subunits

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15
Q

What are the two major types of secondary structures?

A
  1. α-helices
  2. β-sheets
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16
Q

True or False:

Some part of proteins do not have secondary structures

A

True

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17
Q

What are secondary structures stabilized by?

A

Usually stabilized by H-bonds
* Between backbone N-H and C=O groups

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18
Q

What are hydrogen bonds? When are they the strongest?

A
  1. Hydrogen interaction with electronegative atoms
  2. When in a straight line
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19
Q

A hydrogen bond is —- the strength of a covalent bond in an aqueous solution

A

1/20

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20
Q

Describe:

α-helices

A
  • ~3.6 residues per turn
  • 5.4 angstroms rise along axis per turn
  • C=O forms H-bond with N-H group 4 residues down the strand
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21
Q

Why are there not many prolines or glycines in α-helices?

A
  1. Proline causes kinks to appear in helices
  2. Glycine destabilizes the helix (has many conformations, not favourable for helix)
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22
Q

What forms β-sheets?

A

Hydrogen bonds betwen neighbouring strands

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23
Q

What are the two types of β-sheets?

A
  1. Antiparallel sheets (N to C beside C to N)
  2. Parallel sheets (N to C beside N to C)
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24
Q

What bonds form β-sheets?

A

Hydrogen bonds between the carboxyl and amide groups

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25
Q

State:

Classes of Protein Structures

A
  1. All-α protein
  2. All-β protein
  3. α/β protein
  4. Intrinsically disordered protein
26
Q

What does an “intrinsically disordered protein” mean?

A

Means that the protein has no significant amount of secondary structure

27
Q

Tertiary structures involve the spatial arrangement of…

A
  • Chain’s regular - Irregular secondary structures
  • Conformations of side chains
28
Q

What is the 3D structure of a protein stabilized by?

A

Interactions between side chains and backbone atoms

29
Q

True or False:

Interactions in tertiary structures can be between resides distant in the sequence

A

True

30
Q

List:

Intermolecular interactions by strength (strongest to weakest)

(in aqueous solution)

A
  1. Covalent
  2. Ionic
  3. Hydrogen
  4. Van der Waals force
31
Q

What types of van der Waals forces are there?

A
  1. Between permanent dipoles
  2. Dipole induced dipole interactions
  3. London Dispersion Forces
32
Q

What other interactions are possible in tertiary structure?

A
  1. Ionic interactions (between charged amino acids)
  2. Disulfide bonds
33
Q

Describe:

Disulfide bonds

A

Strong bonds, formed between chains
* Specifically between cysteine molecules
* Stabilizes protein
* Broken by strong reducing agent
* Only occurs in oxidizing environment

34
Q

What types of representations of proteins are there?

A
  1. Backbone model
  2. Ribbon model
  3. Wire model
  4. Space filling model
  5. Electrostatic potential map
35
Q

What are quaternary structures stabilized by?

A
  • Hydrogen bonds
  • Ionic bonds
  • Van der Waals interations
  • Disulfide bonds
  • Others
36
Q

What type of hydrogen bonds can occur in quaternary structures?

A
  1. Backbone to backbone
  2. Backbone to sidechain
  3. Sidechain to sidechain
37
Q

Why are quaternary structures important?

A

Have strong implications in protein function (ex. hemoglobin)

38
Q

Define:

Hydrophobic effect

A

When proteins fold:
* Hydrophobic side chains mainly fold into core
* Polar and charged side chains are on the outside

39
Q

Why must the hydrophobic effect occur?

A
  1. Water forms extensive Hydrogen bonds and have high level of freedom
  2. Hydrophobic groups in solution decreases bonds between water and decreases entropy (unfavourable)
40
Q

Describe:

Entropy changes in protein folding

A
  1. Entropy of water increases
  2. Entropy of protein decreases
41
Q

What are the function of chaperone proteins?

A

Helps proteins to form properly

42
Q

What type of chaperone proteins are there?

A
  1. Directly binding ones that can guide protein into correct conformation
  2. Chamber-like with a cap, allows protein to properly fold inside the chaperone protein
43
Q

What forms of protein denaturation are there?

A
  1. Chemical denaturation
  2. Thermal denaturation
44
Q

Define:

Chemical denaturation

A
  • Add chaotropic agents (eg. urea)
  • Increases solubility of nonpolar substance in water
  • Can refold protein by removing chemical
45
Q

Define:

Thermal Denaturation

A
  • Proteins unfold by applying heat

E.x. Albumin in eggs
* Proteins unfold (linearized)
* Forms random bonds
* Forms disulfide bonds
* IRREVERSIBLE

46
Q

What are protein domains?

A

Distinct region of protein
* Can fold independently from each other
* Provide structure/function (or both)
* Only TERTIARY (one subunit)

47
Q

Why is protein purification necessary?

A

Purify protein samples to study a specific protein function
* Get rid of impurities, inhibitors etc.

48
Q

What are the 3 types of chromatography?

A
  1. Size Exclusion Chromatography
  2. Ion Exchange Chromatography
  3. Affinity Chromatography
49
Q

Describe:

Size Exclusion Chromatography

A

Uses porous gel beads (has a gel matrix inside)
* Smaller proteins go into bead (slower to go through)
* Larger proteins go around bead (faster to go through)

50
Q

Does shape of protein affect the speed in size exclusion chromatography?

A

Yes

51
Q

Describe:

Ion Exchange Chromatography

A

Uses charged beads (positive charged ones in anion exchange columns)
* Negatively charged proteins bind to beads
* Uncharged and positively charged proteins go through
* Increase salt concentration to get remainder “stuck” proteins to detach

52
Q

Can ion exchange chromatography be done with negatively charged beads?

A

Yes, it would be called cation exchange column (collecting positively charged proteins)

53
Q

Define:

Isoelectric point

A

The point (pH) where the charge of the protein is 0

54
Q

What would happen if:
1. pH > pI
2. pH < pI

A
  1. The protein’s overall charge is negative
  2. The protein’s overall charge is positive
55
Q

Describe:

Affinity Chromatography

A

Uses beads containing a ligand that can only bind to a specific protein
* Those proteins will get stuck with the ligand
* The other proteins are washed down with the buffer

56
Q

Define:

SDS-PAGE

A

Analytical technique
* SDS = Sodium dodecyl sulfate
* PAGE = Polyacrylamide Gel Electrophoresis

57
Q

What is sodium dodecyl sulfate in SDS-PAGE?

A
  • Ionic detergent
  • Binds to hydrophobic groups
  • Helps solubilize them
  • Average 1 SDS binds to 2 proteins
  • Results in overall positive charge complex
58
Q

What does SDS-PAGE show?

A

An gel apparatus with negative charge at the bottom and positive charge at the top
* Smaller proteins move down to the negative end faster
* Larger proteins get stuck in the gel and move slow

59
Q

What is mass spectroscopy used for?

A

Used to characterize proteins in mixtures
* Isolate proteins via isolation
* Fragmentation
* Mass analysis

60
Q

What information does mass spectroscopy provide?

A
  • Sequence
  • Abundance
  • Various modifications in protein
61
Q

What does X-Ray Crystallography tell us? What are its limitations?

A

Shows us 3D structures of the protein
* Protein must be able to crystallize
* Needs to be done with pure samples

62
Q

What is NMR? What is its benefits?

A

Nuclear Magnetic Resonance
* Shows 3D structures of small proteins
* Shows ensemble of structures
* Good for small proteins
* No need for crystallization

My Packs: (UWO) (BIOCHEM 2280) (23 decks)

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