Lecture 2

Question 1

What structure do proteins of the leucine-rich receptor class adopt?

Answer 1

A curved structure

Question 2

What is a protein secondary structure solely due to?

Answer 2

Backbone hydrogen bonding

Question 3

Describe alpha amino acids.

Answer 3

only one carbon atom separates the amino group from the carboxylic acid group (attached to the same carbon).

Question 4

Are amino acids chiral?

Answer 4

Yes

Question 5

What are the free ends of the linear chain of a protein chain denoted as?

Answer 5

Amino terminus (N-terminus) - where free amino group is located, and carboxy terminus (C-terminus) - where the free carboxylic acid group is located

Question 6

What makes a residue?

Answer 6

when a free amino acid is incorporated into a protein chain

Question 7

What gives each protein its unique structural and functional properties?

Answer 7

Side chains

Question 8

What is the backbone of the protein made up of?

Answer 8

Atoms that form the peptide bonds, N-terminus, C-terminus

Question 9

What does Ca represent?

Answer 9

Alpha carbons of the two amino acid residues linked by the peptide bond

Question 10

What are the consequences of the peptide bond’s partial double bond character? (3)

Answer 10

No free rotation about the peptide bond (w), Two alpha carbons (Ca) are usually trans to each other, and The six backbone atoms about each peptide bond (C, O, N, H) are coplanar

Question 11

Why do peptide bonds usually have trans geometry?

Answer 11

For stability of the molecule

Question 12

Can rotation occur anywhere besides the peptide bond?

Answer 12

Rotation can occur at psi and phi, but may be sterically hindered

Question 13

What would make up a forbidden psi and phi combination?

Answer 13

Steric crowding between main-chain atoms - tripeptide

Question 14

What is an allowed psi and phi combination?

Answer 14

Dipeptide - two amino acid residues linked by a peptide bond - Hold one bond angle fixed, Rotate the other bond through a given angle.

Question 15

How are permitted combinations determined?

Answer 15

Computational tools or modelling kits

Question 16

What is the Ramachandran plot?

Answer 16

A map of all theoretically possible combinations of psi and phi angles

Question 17

What makes up hydrogen bond length?

Answer 17

The distance between the electronegative donor and acceptor atoms

Question 18

Are covalent bonds stronger than hydrogen bonds?

Answer 18

Yes, 10 to 100 times stronger

Question 19

What results in attraction vs. repulsion

Answer 19

attraction if opposite charge, repulsion if they have the same charge

Question 20

What was determined before the first protein was?

Answer 20

men predicted the existence of secondary structures: repeat structural patterns formed due to repeat hydrogen bonding patterns in the protein main chain.

Question 21

Primary structure

Answer 21

amino acid sequence of the chain - Linear sequence of amino acid residues in the protein chain

Question 22

Secondary structure

Answer 22

arises from backbone H-bonding in the chain

Question 23

Tertiary structure

Answer 23

folding of the secondary structures, involving side chains

Question 24

Quaternary structure

Answer 24

Arises with multichain proteins.

Question 25

What is the formula for where H-bonds are formed?

Answer 25

n + 4

Question 26

What is the helix translation?

Answer 26

the distance moved along the helix per residue

Question 27

What is the pitch of the helix?

Answer 27

Length per turn

Question 28

Where are H-bonds on an alpha helix?

Answer 28

co-linear with the chain direction

Question 29

Where are H-bonds on beta sheets?

Answer 29

at nearly right angles to the direction of the chain, and are between at least two strands

Question 30

What is the difference between the resulting structure in parallel strands & antiparallel strands?

Answer 30

Parallel strands tend to give flatter extended sheets, Antiparallel strands have a slight twist and can form barrel-like structures

Question 31

On the basis of mass, which is most abundant in a living bacterial cell?

Answer 31

Water

Question 32

Covalent bonds are formed by the sharing of electrons. In the cell, how are covalent bonds broken?

Answer 32

by enzyme catalysis that is specific for a protein and its substrate

Question 33

How do protein, nucleic acid, and polysaccharide molecules polymerize (grow in length)?

Answer 33

Condensation reactions