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BCH210H1 Biochemistry I: Proteins, Lipids and Metabolism > Lecture 9 Studying Protein Structure and Function > Flashcards

Lecture 9 Studying Protein Structure and Function Flashcards

1
Q

What is the purpose of Protein Characterization?

A

the process of determining the structure and function of a protein

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2
Q

how do you characterize a protein?

A

studying the protein’s interactions with its environment, ligands, and other proteins.

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3
Q

What are the different types of spectroscopy used in protein characterization? (6) ICXNCF

A

Infrared (IR) Spectroscopy

Circular Dichroism (CD) Spectroscopy

X-ray Crystallography

Nuclear Magnetic Resonance (NMR)
Spectroscopy

Cryo-Electron Microscopy

Fluorescence Spectroscopy

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4
Q

how does Infrared Spectroscopy work?

A

Uses infrared radiation to study bond vibrations.

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5
Q

what is the frequency of CH bonds like in Infrared Spectroscopy?

A

high frequency

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6
Q

what is the frequency of peptide bonds like in Infrared Spectroscopy?

A

can vary based on hydrogen bonding.

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7
Q

what level of protein structure is Infrared Spectroscopy good for studying?

A

secondary structures

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7
Q

how does Circular Dichroism (CD) Spectroscopy work?

A

Uses polarized light to analyze protein secondary structures.

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8
Q

what is the absorbance peak of Beta sheets in Circular Dichroism?

A

217 nm

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9
Q

what is the absorbance peak of Alpha helices in Circular Dichroism?

A

195 nm

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10
Q

what are the steps of the X-ray Crystallography process?

A

Purify the protein

Form a crystal.

Expose to x-rays.

Analyze diffraction patterns to infer structure.

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11
Q

how does Nuclear Magnetic Resonance (NMR) Spectroscopy work?

A

Studies protein structure by analyzing nuclear spin in a magnetic field.

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12
Q

what setting for proteins is Nuclear Magnetic Resonance most effective?

A

Effective for studying proteins in solution

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13
Q

what protein characterization method is not good for studying proteins in a solution?

A

crystallography

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14
Q

how does monitoring enzyme activity help to study proteins?

A

to understand protein function

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14
Q

what method is used to predict 3D protein structure?

A

AlphaFold

15
Q

how does AlphaFold work?

A

use amino acid sequences to predict a protein’s 3D structure.

16
Q

How does Cryo EM work?

A

Proteins are flash-frozen on a copper grid and subjected to a beam of electrons

The electron diffraction pattern reveals the protein structure

16
Q

what does Cryo-Electron Microscopy do?

A

determine the structure of proteins in solution, especially large proteins and complexes.

17
Q

how does 3D Image Reconstruction work?

A

Multiple images of the protein are taken from different angles, and a 3D structure is reconstructed.

18
Q

what is a Cryo-EM Example involving Proteasome, what is the job of proteasome?

A

Cryo EM helps determine the structure of large protein complexes like proteasomes, which break down proteins for recycling.

19
Q

how is AlphaFold used in terms of Ligands?

A

AlphaFold can predict interactions between proteins and ligands, useful for designing protein-ligand studies.

20
Q

what are the pros of Cryo-EM?

A

No crystallization

realistic image

21
Q

what is a pro of X-ray crystallography?

A

High resolution

22
Q

what is a con of X-ray crystallography?

A

needs crystals

23
Q

what are the pros of NMR spectroscopy?

A

Good for smaller proteins

shows interactions

24
Q

what methods were used to study SARS CoV-2 Spike Protein during COVID-19 and why?

A

Cryo EM and X-ray crystallography were used to determine the structure of the spike protein and its interaction with ACE2.

25
Q

how does Fluorescence Spectroscopy work?

A

A technique to study protein structure using chromophores, which absorb and emit light at different wavelengths.

26
Q

what is the purpose of Green Fluorescent Protein?

A

to visualize proteins inside cells

27
Q

how does Green Fluorescent Protein work?

A

absorbs and emits light.

28
Q

what is the Green Fluorescent Protein?

A

a jellyfish protein

29
Q

how does Tryptophan Fluorescence work?

A

amino acid tryptophan absorbs UV light and emits fluorescence

Its wavelength changes depending on whether it is buried inside or exposed on the protein surface.

BCH210H1 Biochemistry I: Proteins, Lipids and Metabolism (22 decks)

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