L9 - Protein Structure

Question 1

What are proteogenic amino acids?

Answer 1

The 20 naturally occuring a/a found in proteins
- alpha a/a
- all are chiral (except glycine)

Question 2

How do a/a form peptides and proteins?

Answer 2

Polymerise, linking with peptide (amide) bonds by condensation reaction

Question 3

How are peptides and proteins synthesised?

Answer 3

N-terminus (amino group) to the C-terminus (a-carboxylate group)

Question 4

What does the backbone of proteins consist of?

Answer 4

-N-Ca-C-N-Ca-C-

Constant across a/a and form a continuous chain

Question 5

What is the primary structure of a protein hekd together by?

Answer 5

Covalent bonds

Question 6

Which properties are determined by protein primary structure?

Answer 6

• molecular mass = yk what atoms are there
• protein shape = determines the shape the seq. folds
• overall electric charge = yk what +ve/-ve charges are present
• hydrophibicity = yk what a/a will be on the inside based on the environment they’re put in
• surface charge = yk what a/a are on the outside

Question 7

What is the peptide bond like?

Answer 7

Planar (flat)

Question 8

What does the eq between the 2 isomers of the peptide bond result in?

Answer 8

• partial double bond characteristic = planar bond
• stable bond and modified reactivity of the ketone and amine
• trans isomer most energetically favourable

Question 9

Who were set out to calculate all H-bonded structures that could be formed from a single polypeptide chain?

Answer 9

Linus Pauling
Robert Corey
Herman Branson

Question 10

What do a-helices involve?

Answer 10

Non covalent interactions between residues close together in primary sequence

Question 11

What is some extra info about a-helices?

Answer 11

• they are right handed
• each turn has 3.6 a/a
• the pitch of the helix is 5.4 Å

Question 12

What are the helices stabilised by?

Answer 12

Hydrogen bonds between the backbone amine (NH) and the bacbone carbonyl (CO) of another a/a 4 residues earlier

Question 13

What is a H bond?

Answer 13

Non-covalent interaction in which the H covalently attached to one electroneg atoms is shared with another electroneg atom that possesses a lone pair of electrons

Question 14

What were LRH close about with their structure?

Answer 14

Their calculated structures aren’t quite what we see in protein structures

Question 15

What were LRH correct on?

Answer 15

That parallel and anti-parallel structures are formed

Question 16

What do B-sheets involve?

Answer 16

Non-covalent interactions between residues which may be far apart in primary sequence

Question 17

What are the polypeptide chains like in B-sheets?

Answer 17

• extended
• run parallel or anti-parallel (more common)

Question 18

What are B-sheets stabalised by?

Answer 18

The backbone of hydrogen bonds between CO and HN in another

Question 19

What are a-helices and B-sheets commonly connected by in proteins?

Answer 19

Loops or regions of irregular structures

Question 20

What is the secondary structure of proteins hekd together by?

Answer 20

Non-covalent interactions

Question 21

What elements of secondary structure found as? And how are they formed?

Answer 21

• regular structure found in proteins
• formed by non-covalent interactions between backbone atoms

Question 22

What is the secondary structure mostly independent of?

Answer 22

Only involves bacbone atoms
- independent of the detailed primary structure of the protein

Question 23

What does the tertiary structure encompass?

Answer 23

All non-covalent a/a interactions between a/a of a single polypeptide chain (not included in the definition of the 2nd structure

Question 24

What interactions are part of the tertiary structure?

Answer 24

Interactions between:
- protein sidechains
- protein sidechains and the backbone

Involves interactions between residues which are far apart in terns of primary sequence

Question 25

What is the quaternary structure?

Answer 25

Interactions holding multiple polypeptde chains together into one protein

Question 26

What are the polypeptide chains called in quaternary structure? How are they held together?

Answer 26

Subunits: 2 dimers, 3 trimers, 4 tetramers

Held together by the same non covalent interactions as tertiary stucture

Question 27

What are the 3D structure of proteins stabilised by?

Answer 27

Large numbers of weak non-covalent interactions

Question 28

What is secondary structure stabilised by?

Answer 28

Hydrogen bonds

Question 29

What are the tertiary and quaternary stabilised by?

Answer 29

• hydrogen interactions
• hydrogen bonds
• salt bridges (pairs acidic and basic a/a close together in structure, +ve/-ve charges)
• vdw interactions (permanent or transient delta+/delta- charges)
• disulphide bridges (covalent bond S-S bond between 2 cysteines close in space)