Chapter 4

Question 1

What are the 7 psychological roles of proteins?

Answer 1

1. Enzymes
2. Storage and transport
3. Physical cell support and shape
4. Mechanical movement
5. Deciding cell information
6. Hormones and/or hormone receptors
7. Other specialized functions

Question 2

Roughly how many proteins do humans have?

Answer 2

~25 000 unique proteins

Question 3

What is the smallest and largest proteins in length?

What’s the formula for finding the number of amino acids in a formula?

Answer 3

Insulin- 51 amino acids
Titin- 34 350 amino acids

An approximation by dividing the proteins molecular weight by 110

Question 4

What are the most important forces stabilizing the specific structures of proteins?

Answer 4

Non-covalent forces

Question 5

What does a protein conformation with a low free energy mean?

Answer 5

Means it has a bigger number of weak interactions

Question 6

How is the stability of a protein determined?

Answer 6

It is the difference in the free energies of the folded and unfolded states

Folded proteins occupy a low energy state

Question 7

What is denaturation?

Answer 7

Disruption of native conformation with loss of activity
(Reversible process)
Renaturation
Fast process (sigmoidal curve)

Question 8

What is the primary structure, secondary structure, tertiary structure and quaternary structure summed up?

Answer 8

Primary structure- linear sequence of amino acids
Secondary structure- localized interactions within a polypeptide
Tertiary structure- final folding pattern of a single polypeptide
Quaternary structure- folding patter with multiple polypeptides

Question 9

How is the primary structure of proteins written out?

Answer 9

The one letter code of amino acids

Ex: NCCNCC

Question 10

What are the two types of secondary structure?

Answer 10

α-helicies- loops (like handwritten l)

β-sheets- rolled over each other (like a drifty mountain road)

Question 11

What are the two things the folding pattern must do to represent a viable form of secondary structure?

Answer 11

1. Optimize the hydrogen bonding potential of main chain carbonyl and anode groups (anything that can must form hydrogen bond)
2. Represent a favoured conformation of the polypeptide chain

Question 12

What are the hydrogen bond donors and acceptors on a polypeptide main chain?

Answer 12

O-C acceptor
N-H donor

The carbon of oxygen and the hydrogen of nitrogen are in opposite sides of each other
(Therefor the side chain of amino acids will rotate sides of the main polypeptide chain)

Question 13

What is native conformation?

Answer 13

The biologically active form of a protein

Question 14

Can there be rotation around the C-N bond in polypeptides?

Answer 14

No it is restricted due to partial double bond nature of the peptide bond

Question 15

What does cis and trans mean?

Answer 15

Cis- the carbon of oxygen and the hydrogen of nitrogen are on the same side so the side chains would be on the same side
Trans- the carbon of oxygen and the hydrogen of nitrogen are on opposite sides so the side chains rotate sides every connection

Question 16

What is a α-carbon?

What are he two types of bonds?

Answer 16

Means a carbon held within the main chain by single bonds (means freedom of rotation)

Phi (Φ) Cα-N
Psi (Ψ) Cα-C
Both can range from -180 to 180 rotation but interference prevents it

Question 17

What is a ramachadran plot?

Answer 17

Illustrates all possible combinations of phi and psi and highlights combinations that are observed in actual proteins

Areas that are white are known as the disallowed region

Question 18

What is a α-helix? (Direction, etc)

Answer 18

Right handed helix (right hand fingers curl around thumb direction) 🔄

3.6 residues per turn (residues separates by 3-4 positions in primary structure are close in helical structure)

Each C=O (residue n) forms hydrogen bond with snide hydrogen of residue n+4 (bends around)
Diagram on α-helix slide

Question 19

What are the rules/trends with the helicies of proline and glycine?

Answer 19

Proline- because of its rigidity it is a helix breaker and is not usually found in α-helicies
Glycine- because of its flexibility it is uncommon in α-helicies

Question 20

What is the helix dipole?

Answer 20

A small electrical dipole that exists in each peptide bond that is communicated through the helix by hydrogen bonding
An uneven distribution of charge that results in the helix having a net dipole (N terminus has partial positive charge while C terminus has partial negative charge)

Question 21

What are β-sheets?

Answer 21

They involve multiple β strands arranged side by side
The strands can be parallel (strands run in same direction) or anti-parallel (strands run in opposite direction)
Anti parallel are more stable (better geometry of hydrogen bonding)

Look at diagram on parallel and anti parallel slide

Question 22

What does amphipathic β sheets mean?

Answer 22

Alternate polar, non polar, polar, non polar, etc

The side chains are in trans alternating above and below the polypeptide chain

Question 23

What ultimately determines tertiary structure?

Answer 23

The amino acids sequence creates the final folding pattern which results in unique functions

Question 24

What are quaternary structures composed of?

Answer 24

Multiple subunits in which each subunit is a separate polypeptide chain (can be multiple units of the same polypeptide or different ones)

Question 25

What are the biological advantages associated with quaternary structure?

Answer 25

• may help stabilize subunits and prolong life of protein

- helps facilitate unique and dynamic combos of structure function

Question 26

What is keratin?

Answer 26

Principle component of hair that contains a pseudo-seven repeat
(Diagram on keratin slide)
Keratin forms right handed amphipathic α-helicies (results in hydrophobic strip running across length

Question 27

What is the quaternary structure of keratin?

Answer 27

Hydrophobic surfaces and each two helicies interact and form a coiled coil where right handed helicies wrap around each other in a left handed fashion
(Very strong because of this)
Disulfide bonds like individual units

Question 28

What is collagen?

Answer 28

Major part of vertebrates that are multiple repeats of Gly-X-Y which forms left handed helix ↩️ of 3 residues per turn
The quaternary structure has left handed helicies wrapping in a right- handed fashion

Question 29

What diseases related to collagen and lack of vitamin C?

Answer 29

Scurvy

Question 30

Why is silk so strong and flexible?

Answer 30

It has fully extended polypeptide chains for strength, has an association of strands by hydrogen bonding, and has an association of sheets by van der waals and hydrophobic interactions

Question 31

What are disease specific prion vaccines?

Answer 31

Diseases caused when a protein unfolds and new regions are exposed for antibody binding
Also called disease-specific epitopes (DSEs)