Proteins and Amino acids Pt 2

Question 1

Proteins are covalently linked amino acids formed according to the genetic code
What is the name of this covalent bond

Answer 1

Peptide bond

Question 2

The peptide bond forms between which two groups

Answer 2

Amine and carboxyl group

Question 3

In a polypeptide, how are the different R groups ortientated in the adjacent amino acids

Answer 3

One R group will point upwards, and the next will point downwards, and the next upwards and so on….

Question 4

A polypeptide will have an intrinsic positve and negative end
Why?

Answer 4

Carboxylate ion on one end will be negative
Amide on the other end will be positive

Question 5

Explain how there is resonance hybridisation of the peptide bond

Answer 5

Delocalisation of electron density between carbon-oxygen bond and carbon-nitrogen bond
Results in electrostatic interactions and peptide bond being polar

Question 5

Explain how there is resonance hybridisation of the peptide bond

Answer 5

Delocalisation of electron density between carbon-oxygen bond and carbon-nitrogen bond
Results in electrostatic interactions and peptide bond being polar

Question 6

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?

Answer 6

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

Question 7

Proline kinks the peptide backbone
What is the benefit of this

Answer 7

It makes the protein with proline more readable by other proteins

Question 8

Proteins fold into a conformation of the …..

Answer 8

lowest energy

Question 9

What aids in the folding of a protein

Answer 9

a chaperon molecule

Question 10

Urea is a denaturing agent
What happens when urea is added to a purified protein then removed again

Answer 10

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

Question 11

What bonds are crucial in secondary structure

Answer 11

hydrogen bonds

Question 12

How were chaperone first discovered

Answer 12

• 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

Question 13

What is protein structure heirarchy

Answer 13

• Primary structure: sequence of amino acids
• Secondary structure: using hydrogen bonding
• Tertairy structure: using hydrophobic interactions
• Quaternary: multiple tertiary structures coming together

Question 14

What are the 3 componets of Secondary structure

Answer 14

α-helix: 31% of structures
β-chain/sheet: 28% of structures
turns: 30% of structures

Question 15

Describe the α-helix structure

Answer 15

• most common
• energetically favourable due to peptide backbone interactions (not R group) using hydrogen bonds (carbonyl and 4th amino group)
• right handed

Question 16

the hydrogen-bond dipoles of the α-helix all point in the same way, making the helix itself a

Answer 16

mega dipole

Question 17

α-helix amino acid composition depends on the position of the helix in the protein
Why?

Answer 17

Hydrophillic amino acids would likley be arranged on the outside, while hydrophobic ones would be on the inside

Question 18

Describe the β-helix

Answer 18

• 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

Question 19

What is a protein turn

Answer 19

• 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

Question 20

What is the super-secondary protein structure

Answer 20

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

Question 21

How does the super-secondary structure of β-stranded sheet work

Answer 21

• 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

Question 22

the fundemental unit of a protein’s overall tertiary structure is a

Answer 22

domain
a protein may comprose one or serveral domains, each with different roles

Question 23

What is a domian

Answer 23

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

Question 24

What is a motif

Answer 24

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

Question 25

An example of a motif is the Walker A box
what is its’ function ?

Answer 25

In helicase enzymes, the RecA domain binds to ATP via this motif which contains the Lysine residue (positive charge)

Question 26

What is a structural motif compared to a sequence motif

Answer 26

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

Question 27

What is a homodimer

Answer 27

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)

Question 28

helicase, which is used in DNA replication to unwind DNA is what type of complex

Answer 28

hexameric
6 different protein acting together

Question 29

UvrD is a type of helicase
How does it bind to DNA

Answer 29

in UvrD there are 4 helix-turn-helixes that make contact with DNA
This is done soley through hydrogen bonding

Question 30

Many protein complexs will contain metal ion
What types of amino acids are bound to them

Answer 30

Negative ones