(OLD) (Dr. Choy) (Unit A) Topic 3: Protein Structure and Analysis Flashcards
1
Q
Proteins are…
A
Linear polymers of amino acids
**
2
Q
Define:
Dipeptide
A
Peptide chain with two amino acids
3
Q
Define:
Tripeptide
A
Peptide chain with 3 amino acids
4
Q
Define:
Oligopeptide
A
Peptide chain with 3-20 amino acids
5
Q
Define:
Polypeptide
A
Peptide chain with many residues
6
Q
Define:
Protein
A
1 or more polypeptide chains
7
Q
True or False:
Peptide bonds exhibits resonance
A
True
8
Q
What results from a peptide bond’s resonance?
A
40% double bond causes planar structure (cannot rotate around bond)
9
Q
What bonds are rotateable in a peptide chain? What are they known as?
A
- N-Cα, known as Φ rotation angle
- Cα-C, known as Ψ rotation angle
10
Q
List:
Levels of Protein Structure
A
- Primary
- Secondary
- Tertiary
- Quarternary
11
Q
Define:
Primary protein structure
A
Amino acid sequence of protein (residues)
12
Q
Define:
Secondary protein structures
A
Spatial arrangement of polypeptide backbone
13
Q
Define:
Tertiary protein structure
A
3-D structure of entire polypeptide, including side chain(s) (only 1 subunit)
14
Q
Define:
Quaternary protein structure
A
Spatial arrangement of polypeptide chains in protein with multiple subunits
15
Q
What are the two major types of secondary structures?
A
- α-helices
- β-sheets
16
Q
True or False:
Some part of proteins do not have secondary structures
A
True
17
Q
What are secondary structures stabilized by?
A
Usually stabilized by H-bonds
* Between backbone N-H and C=O groups
18
Q
What are hydrogen bonds? When are they the strongest?
A
- Hydrogen interaction with electronegative atoms
- When in a straight line
19
Q
A hydrogen bond is —- the strength of a covalent bond in an aqueous solution
A
1/20
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
21
Q
Why are there not many prolines or glycines in α-helices?
A
- Proline causes kinks to appear in helices
- Glycine destabilizes the helix (has many conformations, not favourable for helix)
22
Q
What forms β-sheets?
A
Hydrogen bonds betwen neighbouring strands
23
Q
What are the two types of β-sheets?
A
- Antiparallel sheets (N to C beside C to N)
- Parallel sheets (N to C beside N to C)
24
Q
What bonds form β-sheets?
A
Hydrogen bonds between the carboxyl and amide groups
25
# State:
Classes of Protein Structures
1. All-α protein
2. All-β protein
3. α/β protein
4. Intrinsically disordered protein
26
What does an "intrinsically disordered protein" mean?
Means that the protein has no significant amount of secondary structure
27
Tertiary structures involve the spatial arrangement of...
* Chain's regular - Irregular secondary structures
* Conformations of side chains
28
What is the 3D structure of a protein stabilized by?
Interactions between side chains and backbone atoms
29
# True or False:
Interactions in tertiary structures can be between resides distant in the sequence
True
30
# List:
Intermolecular interactions by strength (strongest to weakest)
| (in aqueous solution)
1. Covalent
2. Ionic
3. Hydrogen
4. Van der Waals force
31
What types of van der Waals forces are there?
1. Between permanent dipoles
2. Dipole induced dipole interactions
3. London Dispersion Forces
32
What other interactions are possible in tertiary structure?
1. Ionic interactions (between charged amino acids)
2. Disulfide bonds
33
# Describe:
Disulfide bonds
Strong bonds, formed between chains
* Specifically between cysteine molecules
* Stabilizes protein
* Broken by strong reducing agent
* Only occurs in oxidizing environment
34
What types of representations of proteins are there?
1. Backbone model
2. Ribbon model
3. Wire model
4. Space filling model
5. Electrostatic potential map
35
What are quaternary structures stabilized by?
* Hydrogen bonds
* Ionic bonds
* Van der Waals interations
* Disulfide bonds
* Others
36
What type of hydrogen bonds can occur in quaternary structures?
1. Backbone to backbone
2. Backbone to sidechain
3. Sidechain to sidechain
37
Why are quaternary structures important?
Have strong implications in protein function (ex. hemoglobin)
38
# Define:
Hydrophobic effect
When proteins fold:
* Hydrophobic side chains mainly fold into core
* Polar and charged side chains are on the outside
39
Why must the hydrophobic effect occur?
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
# Describe:
Entropy changes in protein folding
1. Entropy of water increases
2. Entropy of protein decreases
41
What are the function of chaperone proteins?
Helps proteins to form properly
42
What type of chaperone proteins are there?
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
What forms of protein denaturation are there?
1. Chemical denaturation
2. Thermal denaturation
44
# Define:
Chemical denaturation
* Add chaotropic agents (eg. urea)
* Increases solubility of nonpolar substance in water
* Can refold protein by removing chemical
45
# Define:
Thermal Denaturation
* Proteins unfold by applying heat
E.x. Albumin in eggs
* Proteins unfold (linearized)
* Forms random bonds
* Forms disulfide bonds
* IRREVERSIBLE
46
What are protein domains?
Distinct region of protein
* Can fold independently from each other
* Provide structure/function (or both)
* Only TERTIARY (one subunit)
47
Why is protein purification necessary?
Purify protein samples to study a specific protein function
* Get rid of impurities, inhibitors etc.
48
What are the 3 types of chromatography?
1. Size Exclusion Chromatography
2. Ion Exchange Chromatography
3. Affinity Chromatography
49
# Describe:
Size Exclusion Chromatography
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
Does shape of protein affect the speed in size exclusion chromatography?
Yes
51
# Describe:
Ion Exchange Chromatography
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
Can ion exchange chromatography be done with negatively charged beads?
Yes, it would be called cation exchange column (collecting positively charged proteins)
53
# Define:
Isoelectric point
The point (pH) where the charge of the protein is 0
54
What would happen if:
1. pH > pI
2. pH < pI
1. The protein's overall charge is negative
2. The protein's overall charge is positive
55
# Describe:
Affinity Chromatography
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
# Define:
SDS-PAGE
Analytical technique
* SDS = Sodium dodecyl sulfate
* PAGE = Polyacrylamide Gel Electrophoresis
57
What is sodium dodecyl sulfate in SDS-PAGE?
* Ionic detergent
* Binds to hydrophobic groups
* Helps solubilize them
* Average 1 SDS binds to 2 proteins
* Results in overall positive charge complex
58
What does SDS-PAGE show?
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
What is mass spectroscopy used for?
Used to characterize proteins in mixtures
* Isolate proteins via isolation
* Fragmentation
* Mass analysis
60
What information does mass spectroscopy provide?
* Sequence
* Abundance
* Various modifications in protein
61
What does X-Ray Crystallography tell us? What are its limitations?
Shows us 3D structures of the protein
* Protein must be able to crystallize
* Needs to be done with pure samples
62
What is NMR? What is its benefits?
Nuclear Magnetic Resonance
* Shows 3D structures of small proteins
* Shows ensemble of structures
* Good for small proteins
* No need for crystallization
