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Module 102: Molecular cell biology > Proteins > Flashcards

Flashcards in Proteins Deck (17)
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Primary structure of a protein.

Composed of a chain of amino acids maintained by peptide bonds.

C-terminus is the start of the chain.

N-terminus is the end of the chain.


Secondary structure of a protein

Composed of the primary folding of the polypeptide chain into an alpha helix or beta pleated sheet.

Maintained by hydrogen bonds.


Alpha helix

- Composed of a polypeptide chain coiled into a helical structure

- Hydrogen bonds are formed between amine and carboxyl group 4 amino acids down.

- This causes an outward turn every 3.6 amino acids and the sidechains to face outward.


Beta pleated sheet

- Polypeptide chain laterally packed into beta strands.

- Hydrogen bonds are formed between the amine and carboxyl group of neighboring amino acids.

- Causes the side chains of the amino acids to be above and below the beta sheets.

- The sheets can run anti-parallel or parallel.


Non-essential vs essential amino acids

Non essential: amino acids that are made in the body or obtained from breaking down other amino acids.

Essential amino acids:
Amino acids that are not made in the body and so can only be obtained from food.


Protein domain

Globular unit of a protein from the same polypeptide chain.

Each domain is separated by an inner chain of the same polypeptide chain.

Each domain has a specific DNA sequence that performs a certain function even though it is from the same polypeptide.


Signaling sequence in proteins

A sequence of 15-60 amino acids located in the polypeptide chain that signals for where the protein should go after synthesis.


Creutzfelat-Jakob disease

(Also known as mad cow disease)

- Neurodegenerative disease caused by mis-folding of prion proteins in the brain.

- This causes subacute spongiform encephalopathy


How does CFTR mutation affect protein structure?

The deletion of phenylamine at amino acid 508 causes an impaired Cl- transporter.


Structures found in the protein that is not an alpha helix of beta pleated sheet.


- Barrel: Where the first and last part of the strand closes

- Random coils.


R-group interactions

- In an aqueous environment:
Hydrophilic parts of the protein are external and exposed to the environment.

Hydrophobic side chains are internal, does not interact.

- Interactions included:
Hydrogen bonds
Van der Waal forces
Electrostatic attractions
Covalent bonds, Disulphide bonds


Assisted folding of proteins

- Certain proteins assist the folding of proteins are molecular chaperones:

Do so without altering the protein shape

Prevents protein aggregation and repairs incorrectly folded proteins.

Heat shocking proteins: Stabilises protein folding in response to elevated temperatures


Quaternary structure of a protein

R-group interactions between more than one polypeptide chains to form sub-units.


Disulphide bonds

Covalent bond formed between Sulphur atoms attached to a polypeptide.
Found in cysteine.

This is an oxidation reaction:
Causes proteins with this bond to be located extracellular as the cytosol has reducing conditions.


Folding funnel

Idea that proteins will always fold into the configuration that gives then the lowest free energy.

Proteins will fold until entropy is very low, which allows a stable molecule so that the bonds do not move.


How can protein activity be regulated.

Controlling the amount present:
Controlling the synthesis
Controlling secretion

Controlling the activity of the protein:
Post-translational modification
Further interactions with other molecules: i.e cofactors



Protein complex that degrades protein that is in excess or that has folded incorrectly.

Causes proteolysis, which breaks down the peptide bonds in proteins.