Proteins and Amino acids Pt 2 Flashcards
Proteins are covalently linked amino acids formed according to the genetic code
What is the name of this covalent bond
Peptide bond
The peptide bond forms between which two groups
Amine and carboxyl group
In a polypeptide, how are the different R groups ortientated in the adjacent amino acids
One R group will point upwards, and the next will point downwards, and the next upwards and so on….
A polypeptide will have an intrinsic positve and negative end
Why?
Carboxylate ion on one end will be negative
Amide on the other end will be positive
Explain how there is resonance hybridisation of the peptide bond
Delocalisation of electron density between carbon-oxygen bond and carbon-nitrogen bond
Results in electrostatic interactions and peptide bond being polar
Explain how there is resonance hybridisation of the peptide bond
Delocalisation of electron density between carbon-oxygen bond and carbon-nitrogen bond
Results in electrostatic interactions and peptide bond being polar
The only freedom of movement for amino acids in the polypeptide backdone is rotation about two bond
What are they?
What can limit this rotation?
C-C (ψ)
N-C (ϕ)
The rotation allowed for these bonds for each amino acid depends on the steric potential for steric clash between the amino acid R group and the main backbone
Proline kinks the peptide backbone
What is the benefit of this
It makes the protein with proline more readable by other proteins
Proteins fold into a conformation of the …..
lowest energy
What aids in the folding of a protein
a chaperon molecule
Urea is a denaturing agent
What happens when urea is added to a purified protein then removed again
A single, isolated protein can have the forces abolished by the denaturing agent urea, unfolding the protein
If the urea is removed, the protein snaps back into the original folded conformation
Hence the amino acid sequence is all information required to fold a protein
What bonds are crucial in secondary structure
hydrogen bonds
How were chaperone first discovered
- The phages proteins fold by hijacking the bactieral cells’ chaperones
- In bacterial cells that were resistant to phages, it was noticed that they lacked chaperones
What is protein structure heirarchy
- Primary structure: sequence of amino acids
- Secondary structure: using hydrogen bonding
- Tertairy structure: using hydrophobic interactions
- Quaternary: multiple tertiary structures coming together
What are the 3 componets of Secondary structure
α-helix: 31% of structures
β-chain/sheet: 28% of structures
turns: 30% of structures
Describe the α-helix structure
- most common
- energetically favourable due to peptide backbone interactions (not R group) using hydrogen bonds (carbonyl and 4th amino group)
- right handed
the hydrogen-bond dipoles of the α-helix all point in the same way, making the helix itself a
mega dipole
α-helix amino acid composition depends on the position of the helix in the protein
Why?
Hydrophillic amino acids would likley be arranged on the outside, while hydrophobic ones would be on the inside
Describe the β-helix
- β-strands rely on associations with other β-strands for stability
- 3x β-strands for β-sheets, stuck together with hydrogen bonds (can be parallel of antiparallel not using R group)
- major protein of silk and fibroin
What is a protein turn
- the bits that join helices and strands together
- They are defined as not hydrogen bonding within the main body of the secondary structure
- often as few as 3-5 amino acids residues linking
- Can allow DNA binding to occur
What is the super-secondary protein structure
A secondary structure which is starting to move towards a tertiary structure by forming bundles
e.g α-helix coiled coil - which puts hydrophillic amino acids on the outside and hydrophobic on the inside
How does the super-secondary structure of β-stranded sheet work
- a small beta sheet lies across DNA major groove
- the β-strand are hydrogen bonded to one other by peptide backbone interactions
- leaves R group free to interact with DNA backbone and bases
the fundemental unit of a protein’s overall tertiary structure is a
domain
a protein may comprose one or serveral domains, each with different roles
What is a domian
are autonomously folding parts of the protein
(each domain of the polypeptide chain, had the ability to fold on its own, without the rest of the chain)
the same domain will have the same function in different proteins
What is a motif
Exists within a domain
a sequence of amino acids within the primary sequence of a protein that have the same specific function
conserved across diverse range of organisms
An example of a motif is the Walker A box
what is its’ function ?
In helicase enzymes, the RecA domain binds to ATP via this motif which contains the Lysine residue (positive charge)
What is a structural motif compared to a sequence motif
These are distinguished from sequence motifs in that although they are folded into the same secondary structure they can not often be spotted in amino acid sequences (due to many different structural motifs producing the same shape)
example: helix-turn motif
What is a homodimer
it is a quaternary structure with 2 of the same proteins bonded together
(e.g. restriction enzymes are homodimers are they cut DNA in two different places)
helicase, which is used in DNA replication to unwind DNA is what type of complex
hexameric
6 different protein acting together
UvrD is a type of helicase
How does it bind to DNA
in UvrD there are 4 helix-turn-helixes that make contact with DNA
This is done soley through hydrogen bonding
Many protein complexs will contain metal ion
What types of amino acids are bound to them
Negative ones
