Midterm 2

Question 1

Define secondary structure of a protein

Answer 1

Linear chains of amino acids fold locally to give secondary structure(local structural conformations) that are dependent on hydrogen bonding

Question 2

What are the two types of secondary structure called?

Answer 2

• alpha Helix

- Bata Sheet

Question 3

What is the alpha-helix? Explain the shape, the way the structure is stabilized and the orientation of side chains

Answer 3

Is a secondary structure that has coiled strands. The side chains of the aa’s extend to the outside of the helical circle and on an angle. Hydrogen bonds form between the oxygen of the C=O of each peptide bond in the strand and the hydrogen of the N-H group of the peptide bond four amino acids below it in the helix. The hydrogen bonds stabilize the alpha helix.

Question 4

What is a beta sheet? Explain the shape, the way the structure is stabilized and the orientation of side chains

Answer 4

Secondary structure where the polypeptide backbone is fully extended rather than coiled. It is stabilized by hydrogen bonds between carbonyl oxygens and amino hydrogens. The hydrogen bonding is between strands rather than within strands like the alpha helix and can either be parallel or anti parallel

Question 5

What is the difference between parallel and antiparallel hydrogen bonds of beta sheets?

Answer 5

Antiparallel: h bonds are very straight and strong
-strands are going in opposite directions

Parallel: H bonds are much weaker and more crooked
-strands are going in the same direction

Question 6

What is s B-Turn

Answer 6

Allows protein to chain directions

Question 7

What are proteins

Answer 7

Chain of amino acids joined together by peptide bonds

Can vary greatly in the number of amino acids

Question 8

What is the primary structure of proteins

Answer 8

The sequence or order of amino acids in the chain

-this info is stored in the gene encoding the protein(DNA)

Question 9

What are supersecondary structures? Give example

Answer 9

A supersecondary structure is a compact three-dimensional protein structure of several adjacent elements of a secondary structure
Ex. Beta barrel
A beta barrel is a large beta-sheet that twists and coils to form a closed structure

Question 10

What is the tertiary structure of a protein? What are its features ?

Answer 10

Is the unique 3D conformation that a protein attains in its native(biologically active) state

• many fold so that amino acids that are distant from each other P.S., are close on proximity in 3D space when folded
• have globular proteins

Question 11

What are globular proteins ?

Answer 11

Compact and efficiently packed with hydrophobic side chains on the interior and hydrophilic ones exposed on the surface
-feature of tertiary structure

Question 12

What is a domain in the context of a globular protein?

Answer 12

Large globular proteins often contain compact units called domains.
-fold spontaneously on their own

Question 13

What’s a modular protein?

Answer 13

Many eukaryote proteins are modular meaning that they contain numerous duplicates or imperfect copies of domains linked together
-often each domain is encoded on a separate exon

Question 14

What state is favoured in a protein? Folded or unfolded?

Answer 14

The folded state is favoured but it is still possible to unfold
-delta G is negative

Question 15

What is the hydrophobic effect?

Answer 15

• works in opposite direction from conformational entropy
• hydrophobic side chains are folded into the interior of the protein, the ordered water cages around them break, giving a positive delta S (more disorder)
• favours folding

Question 16

What are the two thermodynamic parameters of entropy contributions that effect protein folding
-do they favour folding or unfolding?

Answer 16

1. Conformational folding
   - favours unfolding
2. Hydrophobic effect
   - favours folding

Question 17

What are the two thermodynamic parameters of enthalpy contributions that effect protein folding
-do they favour folding or unfolding?

Answer 17

1. Interactions from ion interactions, hydrogen bond formation& van der waals interactions
   * these are favourable interactions(neg. delta H)
2. Hydrogen bonds forming within backbone and breaking with water
   * can be unfavourable or neutral

Question 18

Why are reactions coupled? And how is it done?

Answer 18

Because many reactions in living systems have positive delta G° values (thermodynamically unflavoured) but this can be overcome by “coupling” the reaction to one that has a negative delta G°
-it’s the sum of the delta G° ‘s of the two couples reactions that determines whether the reaction can occur

Question 19

What is the phosphoryl group transfer potential?

Answer 19

The tendency for ATP to undergo hydrolysis (with its large negative delta G°)

Question 20

Why is the transfer of a phosphate group so exergonic(accompanied by the release of energy)?

Answer 20

• at physiological pH, the ATP carries 4 neg. charges. hydrolysis of ATP reduces the electrostatic repulsion by moving some of the charges away
• products of hydrolysis are resonance stabilized(electrons spread out over more space)
• products are more easily solvated than ATP(decreases repulsive forces)
• increase in disorder/entropy (2 molecules made from 1)

Question 21

What is the Isoelectric Point?

Answer 21

Where polyprotic acids are characterized by a pH in which the net charge is zero

Question 22

What are the important properties of a peptide bond?

Answer 22

• made of carbonyl group and amino group
• bond is planar
• the carbonyl oxygen and amino hydrogen are in trans