Proteins and Amino Acids Flashcards

1
Q

What are proteins?

A

Proteins are biopolymers composed of amino acids joined together by amide bonds.

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2
Q

What are the difference between peptides and proteins?

A

Peptides are less than 50 amino acids in a chain whereas proteins contain an amino acid chain longer than 50 amino acids.

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3
Q

What are some of the functions of proteins?

A

They act as catalysts
Help give the cell structure
Regulate flow of information and what is allowed to enter the cell
Generate electrical impulses
Help immune response, antibodies are essentially proteins

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4
Q

What is the general structure of amino acids?

A

A carbon attached to an amine group, R group (coming out of the page, carboxylate group and hydrogen.

In solution as an amino acid contains an acidic and basic functional group it acts as a zwitterion (acidic group is deprotonated therefore negative charge, basic group protonated therefore positive charge).

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5
Q

How are the different amino acids distinguished?

A

Three nucleotide bases (A, C, U and G) code for 1 amino acid. In total you can code for 64 amino acids however there are only 20 amino acids and therefore they is significant redundancy in the genetic code.
The 20 amino acids are distinguishable from each other by the side chain (R).

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6
Q

How are peptide bonds stabilized?

A

Peptide bonds are amide bonds and through resonance delocalisation the lone pair of electrons on the sp2 hybridised nitrogen are in conjugation with the pi orbitals of the sp2 hybridised carbon-oxygen double bond.

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7
Q

How are peptide chains able to coil and fold?

A

Whilst rotation cannot occur around the peptide bonds (due to conjugation), there is the potential for rotation around C-N bonds (not conjugated) and C-C bonds which enables the peptide chain to fold and to rotate.

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8
Q

What is protein conformation?

A

Protein conformation is the spatial arrangement of atoms in its structure.
Protein conformation directly affects its function so if the conformation of a protein changes (e.g the atom arrangement alters) the protein becomes denatured and can no longer perform its function.

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9
Q

What is the primary structure of a protein?

A

It is simply the sequence of amino acids in a polypeptide change.

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10
Q

How do secondary protein structures form?

A

Due to the peptide bond being able to rotate and fold in on itself, the amino acid chain can coil round.
The peptide bonds are polar so hydrogen bonds can form between other peptide bonds further down the chain. This gives the structures of a helix and beta sheets.

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11
Q

How are alpha helices further stabilized?

A

Each peptide bond forms two hydrogen bonds with peptides four ahead and four behind. The helix is further stabilized by complimentary side chain interactions (if one side chain is positively charged and one is negatively charged).

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12
Q

Describe the structure of beta sheets.

A

Long strands of the amino acids chains which forms interactions (hydrogen bonds) with chains above and below the sheets.
All the side chains are hydrophobic so there are hydrophobic binding interactions between side chains.

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13
Q

How are tertiary and quaternary structures formed?

A

Interactions with amino acid side chains.

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14
Q

What are some of the types of side chain interactions?

A

Electrostatic interactions (opposite charges)
Disulfide bonds
Hydrophobic interactions
Hydrogen bonds

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15
Q

What is the pharmaceutical relevance of knowing the 3D conformation of proteins?

A

It is the first step in drug design; gain an insight into its function, solubility, dissolution, melting point etc

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16
Q

Describe the structure of insulin

A

Two short peptide chain (less than 50 amino acids) held together by two cysteine-cysteine disulfide bonds as well as another disulfide bond within one of the chains stabilising the structure.

17
Q

How is the strength of electrostatic interactions determined?

A

The strength of electrostatic interaction is inversely proportional to distance, so the further away the ions the weaker the interaction.
However the compared to other interactions the rate of decrease with distance is not as significant.

18
Q

Explain how hydrogen bonds are formed?

A

Formed between an electron deficient hydrogen (hydrogen bond donor) and an electron rich heteroatom- oxygen or nitrogen (hydrogen bond acceptor).

19
Q

What is pi-pi stacking?

A

It is attractive non-covalent interactions between layered aromatic rings.
It is very common in drug target interactions as drug molecules often contain aromatic rings.

20
Q

Which interactions occur in hydrophobic regions of a drug?

A

Van der Waals forces - areas of high and low electron densities form temporary dipoles so dipole-dipole interactions occur.
Hydrophobic interactions- water molecules interact with each other and form an ordered layer near hydrophobic regions of a drug.