Lecture 5 - Exam 1

Question 1

What does X-ray crystallography do?
What was it used in solving?

Answer 1

Create crystallized structures with ordered molecule and shoot an X ray beam through this, the X rays will be diffracted. Based off diffraction patterns, can determine what molecule you are looking at.
Used in solving the 3-D protein structure

Question 2

Who helped solved the 3-D protein structure?

Answer 2

John Kendrew & Max Perutz
Used Sperm Whale Myoglobin
*Computer modeling too

Question 3

Local amino acid sequences which form stable interactions will serve as…?

Answer 3

Nucleation points in the folding process.

Question 4

What is a fundamental role of proteins?

Answer 4

To act as enzymes.

Question 5

What are enzymes?

Answer 5

Enzymes are catalysts that increase the rate of all chemical reactions in cells. Without enzymes, most biochemical reactions are so slow that they would not occur.

Question 6

What are the fundamental properties of enzymes?

Answer 6

Increase rate of chemical reactions without themselves being consumed or permanently altered.
Increase reaction rates without altering the chemical equilibrium between reactants and products.

Question 7

How is equilibrium determined?

Answer 7

Equilibrium is determined by the final energy states of substrate and product.
The substrate must first be converted to a higher energy state, the transition state.

Question 8

Energy required to reach the transition state =

Answer 8

activation energy.
Enzymes reduce the activation energy.

Question 9

Enzymes must bind their ______ to form _________.

Answer 9

substrates ; enzyme-substrate complex (ES)

Question 10

Where does the substrate bind?
The substrate is converted to ______ while bound.

Answer 10

Active site
The substrate is converted to product while bound to the active site, then released.

Question 11

The enzymes brings the substrates together in proper orientation to _____.

Answer 11

Favor the transition state.

Question 12

Enzymes also accelerate reactions by _________.

Answer 12

Altering the conformation of substrates to approach the transition state.
The stress produced by distortion of the substrate further lowers the transition state by weakening critical bonds in the protein substrate.

Question 13

What is the lock-and-key model?

Answer 13

The substrate fits precisely into the active site.

Question 14

What is induced fit?

Answer 14

Conformation of both enzyme and substrate is modified.

Question 15

Who discovered Chaperons?

Answer 15

F. Ritossa when a lab worker accidentally boosted the incubation temperature of Drosophila.
When examining the chromosomes, Ritossa found a “puffing pattern” that indicated elevated gene transcription of an unknown protein.

Question 16

Defects in protein folding are responsible for?

Answer 16

Protein misfolding diseases.

Question 17

Cystic fibrosis is caused by…?

Answer 17

A mutation that results in a one amino acid deletion that leads to improper folding of protein CFTR. CFTR transports Cl- ions across epithelial cell membranes.
When CFTR is not functional, Cl- ions get trapped in cells and the cell surface doesn’t get hydrated. Secretions which are thin, become thick… coughing up mucus.

Question 18

Alzheimer’s disease, Parkinson’s disease, and type 2 diabetes are associated with…?

Answer 18

Aggregation of misfolded proteins.
The misfolded proteins form fibrous aggregates called amyloids, characterized by B-sheets structures.

Question 19

What does Prion stand for? What are they?

Answer 19

Proteinaceous infectious particle
Prions are misfolded proteins that can self-replicate.
Infection by prions is based on amyloid formation of the protein PrP.

Question 20

[Prions] In mammalian cells, the normal alpha-helical form is…?

Answer 20

PrPC

Question 21

[Prions] In the infectious form, PrP forms a…?

Answer 21

Misfolded amyloid structure, PrPSc.

Question 22

PrPSc can replicate by inducing autocatalytic amyloid formation of endogenous PrPC - a…?

Answer 22

Novel form of propagation that does not require any nucleic acid.

Question 23

What do cell membranes do?

Answer 23

Define the boundary of the cell and cell organelles.
It is a selective barrier to the passage of molecules.

Question 24

Why are steroid molecules able to pass through the cell membrane?

Answer 24

Due to their extreme hydrophobic nature.

Question 25

Phospholipids spontaneously form _____ when…?

Answer 25

Bilayers ; in aqueous solutions.

Question 26

Lipids make up ____% of the mass of the membrane - depending on the membrane.

Answer 26

50
Ex: plasma membranes 50% protein 50% lipid, whereas mitochondrial membranes are 75% protein.

Question 27

Double bonds between carbons affect…?

Answer 27

Physical properties of membranes

Question 28

Unsaturated fatty acids chains have double bonds that result in…? What does this do?

Answer 28

Kinks
This reduces packing and increases membrane fluidity.

Question 29

Membrane fluidity is determined by…?

Answer 29

Temperature and lipid composition.
Think bacon fat versus olive oil at room temperature.

Question 30

What is the structure of a cholesterol?

Answer 30

A sterol ring structure and polar OH head.

Question 31

What does cholesterol help to determine because of its ring structure?

Answer 31

Membrane fluidity

Question 32

Interactions between the hydrocarbon rings of a cholesterol and fatty acid tails makes the membrane more…?

Answer 32

rigid

Question 33

Cholesterol also interferes with interaction between fatty acids, maintaining membrane fluidity at…?

Answer 33

lower temperatures

Question 34

What is the orientation of phospholipids in the cell membrane?
Phospholipids with a negative charge are located where?

Answer 34

Asymmetric
Phospholipids with negative charges are located on the cytosolic face.