Protein Structure. Flashcards
How many levels of structure are there to a protein?
There are 4 levels of protein structure.
However, most proteins only use 3 levels of protein structure.
What is the primary structure of a protein?
It is the sequence of amino acids that make up the polypeptide.
How are the amino acids attached to each other within the polypeptide?
By peptide bonds.
What is the secondary structure of a protein.
It is the localised 3D arrangement of a polypeptide within space.
What is the tertiary structure?
It is how the secondary structure can be manipulated to give a certain structure.
What is the tertiary structure also known as?
The native structure.
Why is the tertiary structure also known as the native structure?
Because this is the shape that the protein takes up inside the cell.
What is the quaternary structure of a protein?
It is the shape that is taken up when multiple tertiary structures come together.
Why is the primary structure of proteins so important?
Because, if 1 wrong amino acid is inserted into the primary structure, it can lead to an alteration in the overall protein structure.
What is a point mutation?
When 1 wrong amino acid is inserted into the primary structure.
Sickle cell disease arises from point mutations.
Give an example of the primary structure of a protein?
Val-Arg-Leu.
The primary structure has how many amino groups and how many carboxyl groups?
1 amino group.
1 carboxyl group.
Which amino acid can form disulphide bonds?
Cysteine.
When 2 cysteine molecules form a disulphide bridge, what is the resulting molecule called?
Cystine.
Will disulphide bridges be formed between cysteine molecules within the same polypeptide or can they be formed between cysteine molecules within different polypeptides?
Disulphide bridges can be formed between cysteine molecules on the same polypeptide.
Disulphide bridges can be formed between cysteine molecules on different polypeptides.
When a bond is formed between molecules within the same polypeptide, what is the bond referred to as?
An intramolecular bond.
When a bond is formed between molecules within different polypeptides, what is the bond referred to as?
An intermolecular bond.
Can a protein have both inter and intra molecular bonds?
Yes, insulin is made up of 2 polypeptides and has 3 disulphide bonds.
2 intermolecular and 1 intramolecular.
Are peptide bonds covalent or non-covalent bonds?
They are covalent bonds.
What kind of reaction leads to the formation of a peptide bond?
A dehydration or condensation reaction.
What is the name for 2 amino acids joined by a peptide bond?
A dipeptide.
What is a polypeptide?
A polypeptide is made up of many monomers which are the individual amino acid residues.
If the amino acids valine, glycine and alanine are joined together, what is the name of the molecule?
Valyl-glycyl-leucine.
How do you name amino acids in a dipeptide?
The name of the amino acid at the amino terminus is altered, adding the suffix yl to where the ine was.
E.g. valyl instead of valine.
The carboxyl terminus remains unaltered.
If valine and alanine join together, the molecule will be called valylanaline.
How do you name amino acids in a polypeptide?
The middle amino acids will also adopt the yl suffix,
e.g. valine, alanine and leucine will become valylleucylalanine.
Are peptide bonds strong or weak?
Peptide bonds are very strong.
What is required to break a peptide bond?
Acid and heat.
Can rotation occur around a peptide bond?
No.
Why is there no rotation around the peptide bond?
Because the bond has double bond characteristics.
Why does a peptide bond have double bond characteristics?
Because of a resonance of electrons between the double bond to oxygen and the nitrogen.
Describe the resonance of electrons in a peptide bond?
At any point in time the double bond could be between the carbon and the oxygen.
Or between the carbon and the nitrogen resulting in a positive charge on the N and a negative charge on the O.
Do peptide bonds have a net charge?
No.
But, they do have a partial charge.
Describe the partial charge on a peptide bond?
The partial charge arises due to the slight positive charge on the nitrogen and the slight negative charge on the oxygen.
Can peptide bonds be involved in non covalent interactions.
Yes, thanks to their partial charge.
Which components of a polypeptide are able to rotate?
The R groups and the ketone.
Are the R groups within a polypeptide able to take up a cis or trans position?
They can take up both.
In what conformation do polypeptides prefer to have their R groups?
In the trans conformation.
Why do polypeptides prefer to have their R groups in the trans conformation?
So they can minimise steric hindrance and electrostatic repulsion between R groups.
What are the 3 ways to determine the amino acid composition of an unknown protein?
Acid hydrolysis.
Amino acid sequencing from the amino terminus.
DNA sequencing.
How does the acid hydrolysis method of determining protein structure work?
The unknown polypeptide is subjected to concentrated acid at a heat of 100 degrees C for 24 hours.
This will break the peptide bonds within the polypeptide. and the remaining amino acids can be analysed.
Which amino acids are destroyed by the acid hydrolysis technique?
Glutamine.
Glutamate.
Asparagine.
Aspartate.
Tryptophan.
Do the amino acids that remain after acid hydrolysis carry a charge?
Yes.
They carry a positive charge.
How are the positively charged amino acids separated after acid hydrolysis has occurred?
By cation exchange chromatography.
How does cation exchange chromatography work?
The positive amino acids are placed in an ion exchange column.
The pH is slowly changed allowing amino acids to be released from the ion exchange column.
As amino acids are released, they react with ninhydrin and a colour change occurs which is recorded by a photometer.
The photometer will tell you the amino acid composition.
Will acid hydrolysis tell you the exact order of amino acids within the polypeptide?
No.
It only tells you the amino acid composition, not the order.
How does amino acid sequencing work?
It involves using Edmans reagent under alkaline conditions to label and break off the amino terminus.
This single amino acid can then be analysed and identified.
The 2nd amino acid in the chain will now become the new amino terminus.
What is Edmans reagent also known as?
(Phenylisothiocyanate).
Where does amino acid sequencing take place?
In a sequenator.
Does amino acid sequencing give you the exact amino acid sequence?
Yes.
How many amino acids within a polypeptide does amino acid sequencing work for?
100 or fewer.
How does DNA sequencing of amino acids work?
If you know the DNA sequence, then you can work out the gene that encodes for the polypeptide.
What is the secondary structure of a protein?
The localised 3D shape that segments of the polypeptide takes up within space.
What is the most common type of bond within the secondary structure?
Hydrogen bonds.
How do hydrogen bonds occur?
When a hydrogen has a slight positive charge due to being bound to a more electronegative atom.
The slightly positive hydrogen is capable of forming a weak non-covalent bond with an oxygen atom due to the slight difference in charge.
Are hydrogen bonds covalent or non-covalent?
Non-covalent.
