Chapter 4

Question 1

What is Kinesin?

Answer 1

motor protein, transports cellular cargo like organelles

Question 2

What determines the function of a protein?

Answer 2

it’s shape

Question 3

What is a primary structure? (1’)

Answer 3

linear sequence of amino acids

Question 4

What holds together a primary structure?

Answer 4

peptide bonds hold together the linear AA’s

Question 5

What is a secondary structure? (2’)

Answer 5

They are alpha helixes and beta strands

Question 6

What holds together a secondary structure?

Answer 6

H-Bonds in the backbone of AA’s

Question 7

What is a tertiary structure? (3’)

Answer 7

it is a 3D structure of a polypeptide

Question 8

Other characteristics of the tertiary structure?

Answer 8

• 1 protein and 1 polypeptide
• H-bonds, Hydrophobic bonds, Van Der Waals, and polar/ non-polar bonds hold this together
• all of secondary elements come together

Question 9

What is a Quaternary Structure? (4’)

Answer 9

It is the same as a tertiary structure but it has 2 or more polypeptides

Question 10

What is the shape of an alpha helix?

Answer 10

It is helix/ spiral shaped

Question 11

what is the shape of a beta-strand?

Answer 11

Shaped like an arrow

Question 12

What type of bond does protein folding depend on?

Answer 12

weak non-covalent bonds

Question 13

Where are the hydrophobic bonds on the folded protein?

Answer 13

Inside

Question 14

Where are the non-hydrophobic bonds? (hydrophilic)

Answer 14

Outside

Question 15

What is a homodimer?

Answer 15

The same peptide twice

Question 16

What is responsible for denaturing (unfolding) proteins?

Answer 16

• Urea
• Change in PH or Heat
• Noncovalent bonds break first

Question 17

What happens when the urea is removed?

Answer 17

The protein refolds into it’s original conformation

Question 18

What is the native state of a protein?

Answer 18

full biological activity

Question 19

What do chaperones do?

Answer 19

chaperones help proteins fold in the cell

Question 20

What happens if chaperones are absent?

Answer 20

Proteins won’t have biological activity (which could lead to disease)

Question 21

What would happen to a protein without chaperones?

Answer 21

They would fold incorrectly

Question 22

One example of a disease caused by misfolded proteins

Answer 22

Mad Cow Disease (Bovine SPongiform encephalopathy) which is an infectious neurodegenerative disease

Question 23

What causes Alzheimer’s Disease

Answer 23

plaques in brain amyloid beta protein aggregation

Question 24

Where do H-bonds occur in an alpha helix?

Answer 24

They make up the back-bone and occur every 4 amino acids

Question 25

What proteins have the propensity to form an alpha helix?

Answer 25

M.A.L.E.K

Question 26

What makes up the backbone of the beta-sheet?

Answer 26

H-bonds

Question 27

What are the two types of beta sheets?

Answer 27

Parallel and Antiparallel

Question 28

What proteins have the propensity to form beta sheets?

Answer 28

W.I.F.T.Y.V.

Question 29

What are Amphipathic Motifs?

Answer 29

They are coils comprised of Hydrophobic and Hydrophilic components

Question 30

Where are Amphipathics Motifs found?

Answer 30

proteins are commonly found within the lipid bilayer

Question 31

What is a protein domain?

Answer 31

any segment of a polypeptide that can fold independently

Question 32

Factors for Binding site compatibility

Answer 32

-Size -Shape -Specific Interactions

Question 33

What do Enzymes do?

Answer 33

catalyze reactions

Question 34

How do Enzymes catalyze reactions?

Answer 34

- Orients two substrate molecules - Rearrange charges in substrate - changes shape of substrate

Question 35

What is a Ligand?

Answer 35

Any substance bound by a protein

Question 36

What is another way to describe drugs (medicine)?

Answer 36

They are Ligands

Question 37

What causes Chronic myelogenous leukemia?

Answer 37

reciprocal translocation of chromosomes 9 and 22 (this speeds up cell division and prevents DNA repair)

Question 38

What is Linade and what does it do?

Answer 38

It is a Phosphorphorylate, it turns on mechanisms

Question 39

Why are some patients immune to the effects of Gleevec?

Answer 39

Random mutations in the BCR-Abl protein

Question 40

What is Nilotinib?

Answer 40

It is a second-generation CML drug, created by binding the Gleevec structure to the Abl Kinase domain.

Question 41

What does the positive track look like?

Answer 41

A makes B, then B makes C. A -> B -> C

Question 42

What does Negative feedback look like?

Answer 42

A makes B which makes X, when too much of X is created, the Feedback Inhibitor stops X from being produced.

Question 43

What is Allosteric Regulation?

Answer 43

The regulatory molecule binds to sites other than the active site (induces conformational change)

Question 44

What is the role of ADP in Allosteric Regulation?

Answer 44

It is needed so the sugar can bind effectively to the Alosteric site.

Question 45

What does Protein Kinase do during phosphorylation?

Answer 45

Adds a phosphate group and it turns protein on

Question 46

What does protein Phosphatase do during Phosphorylation?

Answer 46

It removes the phosphate and turns protein off.

Question 47

DO eukaryotes have a five prime cap?

Answer 47

yes

Question 48

do prokaryotes have a five prime cap?

Answer 48

no they have an RBS