Protein Structure 2

Question 1

What determines the charge on the protein?

Answer 1

The pH and the number and type of each amino acid residues with ionisable sidechains

Question 2

What is the pH inside lysosomes and why?

Answer 2

pH is 4.5/5

to activate the enzymes

Question 3

Van der Waal interactions
What range is its effect?
Is it weak or strong?
How is it broken?

Answer 3

Very short range effect
Weak electrostatic forces
Broken by heat and denaturing agents

Question 4

What energy is the best for protein folding?

Answer 4

Lowest energy minimum

Question 5

What are protein domains?

Answer 5

Areas of protein that fold independently

these often perform a specific function

Question 6

Is amorphous aggregation is non specific ?

Answer 6

It is non specific

Question 7

Why is Amyloid proteins cause illness?

Answer 7

They can form multiple disordered proteins spontaneously

Question 8

What 5 things can disrupt protein structure

Answer 8

Ionic Strength
pH
heat ( 20-40C)
denaturing agent 
UV / oxidative / radiation damage

Question 9

Can proteins be modified after they are made?

Answer 9

yes

Question 10

Interactions can be what?

Answer 10

Interactions can be transient or stable

Question 11

Name an example of how a protein can be modified

Answer 11

Can have prosthetic groups

proteins compete for binding sites

Question 12

What percentage of proteins have a form that differs from their genetic sequence?

Answer 12

44%

Question 13

What is a proteoform?

Answer 13

proteoform is used to denote all the molecular forms in which the protein product of a single gene can be found

Question 14

When do reactions of sidechains that drive the addition of chemical groups?

Answer 14

It occurs post translation

Question 15

Name 7 modifications that can occur to a protein

Answer 15

Phosphates
Lipids
Acetylation
Methylation
Proteins
Glycans/carbs
Proteolytic maturation

Question 16

Which three amino acids commonly phosphate

Answer 16

S T Y

Question 17

What is phosphorylation important in?

Answer 17

Important in downstream cellular signal

Question 18

What enzyme phosphorylates?

Answer 18

Kinase

Question 19

What enzyme dephosphorylates?

Answer 19

Phoslase

Question 20

Describe glycosylation

Answer 20

Addition of complex carbohydrate groups

N-linked to Asn or O-linked to Ser/ Thr

Question 21

What is palmitoylation?

Answer 21

Long lipid groups help anchor proteins in membrane

Modification on cysteine, glycine, lysine

Question 22

Which amino acids side chain can be used to make isopeptide bonds?

Answer 22

The lysine side chain can be used to make isopeptide bonds with the carboxyl
terminus of ubiquitin

Question 23

What are Zymogens?

Answer 23

Precursors of enzymes that are activated in a proteolytic cascade after release as granules into the duodenum

Question 24

Name 3 examples of groups that can be conjugated that are non protein

Answer 24

Heam
Lipid
Mental ion
Nucleic Acid

Question 25

What is the meaning of homomeric and hetromeric?

Answer 25

``` Homomeric= all the same units Heteromeric= differing units ```

Question 26

What do oligomeric interactions of the proteins require? | What are these driven by?

Answer 26

Complementary interfaces , often dormains or motifs | Driven by hydrophobic packing or electrostatic/ polar interactions

Question 27

Interactions between protein can be | t_____ or s_____

Answer 27

Transient or Stable

Question 28

What is PKR?

Answer 28

PKR= kinase that is activated when double stranded RNA is present in the cell

Question 29

What is often a sign of a viral infection in the cell?

Answer 29

Double stranded RNA

Question 30

How does PKR help stop a viral infection

Answer 30

Double stranded RNA binds to the PKR which causes a conformational change and dimerisation so the kinase becomes activated Activated PKR then phosphylates the substrate and switches off general translation hence inhibits the viruses replication

Question 31

Which protein acts in blood to decrease the circulation of elastase?

Answer 31

Alpha-1-antirypsin