Proteins

Question 0

Aromatic amino acids

Answer 0

Tyrosine, tryptophan, phenylalanine

Question 1

Aliphatic amino acids

Answer 1

Glycine, alanine, valine, lucine, isolucine

Question 2

Sulfur containing amino acids

Answer 2

Cysteine, methionine

Question 3

Cyclic amino acids

Answer 3

Proline

Question 4

Basic amino acids

Answer 4

Histidine, lysine, arginine

Question 5

Hydroxy amino acids

Answer 5

Serine, threonine

Question 6

Amide amino acids

Answer 6

Asparginine, glutamine

Question 7

Acidic amino acids

Answer 7

Aspartic acid, glutamic acid

Question 8

Hydrophilic amino acids

Answer 8

Cysteine, serine, threonine, histidine, lysine, aspartic acid

Question 9

Isoelectric point

Answer 9

pH at which molecules have no net charge

Question 10

Why is ionization NB

Answer 10

Closure pka of drug to tissue the more effective it is. Eg. Alkalinise tissue when giving anaesthetic.

Question 11

Chiral molecule

Answer 11

Lacks internal plane of symmetry

Non superimposable mirror image

Question 12

D, L enantiomers indicate..

Answer 12

Different optical activities. (Ability to rotate a plane of polarised light)

Question 13

Protein assembly involves what reactions?

Answer 13

Dehydration synthesis and polymerization of aas.

Question 14

Principles of Ramachandran plot

Answer 14

1. Bond length and angles must be similar to aas
2. Peptide bonds are planar
3. No overlaps
4. Stabilisation - steric a permit H-bonds

Question 15

Protein interaction promoted by:

Answer 15

Chaperones
Membrane proteins
Cystolic/extra cellular elements

Question 16

Class

Answer 16

2ndry structure composition

Question 17

Motif

Answer 17

Small specific combinations of secondary structure elements

Question 18

Fold/ architecture

Answer 18

Shape/ orientation of secondary structure

Question 19

Domain

Answer 19

Functional property of fold

Question 20

Recognition motif for glycosylation

Answer 20

Asn-xaa- ser/thr

Question 21

The role of glycosylation in protein folding

Answer 21

Glucose trimmed. Protein interacts with calnexin. Glucosidase cleaves glucose. If still misfolded, glucosyl transferase adds protein. REPEAT. when folded correctly, exit ER.

Question 22

Process of glycosylation

Answer 22

Precursor oligosaccharide formed on dolichol lipid.

Transferred to growing protein on recognition motif.

Question 23

Functions of glucosidation

Answer 23

1. Stabilize proteins against proteolysis.
2. Modulation of immune response.
3. Provide sorting signals.
4. Contributes to events in development.

Question 24

What do motor proteins do?

Answer 24

Move chromosomes Move organelles Move enzymes along DNA

Question 25

Phosphorylation of ... Regulates protein synthesis

Answer 25

Eukaryote initiation factor 2

Question 26

Process of ubiquitin conjugation

Answer 26

High energy thiol ester formed between ubiquitin C-terminal Gly and Cys on E1. Ub transferred to Cys of E2. Peptide bond forms between Ub Gly and e-amino group of lysine on target protein.

Question 27

... recognized for Ub degradation

Answer 27

Lys 48 linked chain

Question 28

Define an enzyme

Answer 28

Substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change.

Question 29

Factors that effect the rate of enzyme reactions

Answer 29

Enzyme concentration Ligand concentrations Physical conditions (pH, temp, ionic strength)

Question 30

Assumptions of Michaelis-Menten kinetics

Answer 30

Formation of enzyme substrate complex Assumes ES is in rapid equilibrium with free enzyme K-1 is faster than k2.

Question 31

What is Km under assumed conditions?

Answer 31

The measure of binding affinity between E and S

Question 32

What does Vmax mean?

Answer 32

The maximum reaction rate for a given range of substrate with a fixed amount of enzyme.

Question 33

What is Kcat?

Answer 33

''Turnover number'' the number of substrate molecules turned into product per molecule of enzyme in a unit time (when enzyme is totally saturated with substrate.

Question 34

How are enzymes controlled?

Answer 34

Transcription Compartmentalisation Enzyme regulation Kinetic regulation

Question 35

Competitive inhibitors..

Answer 35

Bind active site. | Increases Km.

Question 36

Non-competitive inhibitors..

Answer 36

Bind allosteric site. | Lowers Vmax

Question 37

Major players in protein folding.

Answer 37

``` Chaperones/ chaperonins ATP Peptide binding proteins Disulfide isomerase Peptidyl Prolyl cis/trans isomerase ```

Question 38

Features of improperly folded proteins

Answer 38

Aggregate Non-functional Resource drain Target for degradation

Question 39

Two units of chaperone complex

Answer 39

GroEL and GroES

Question 40

What does a folio some consist of ?

Answer 40

DnaJ (Hsp40) and DnaK (Hsp70)

Question 41

What does calnexin do?

Answer 41

Keen misfolded protein in ER.

Question 42

CATH

Answer 42

Class Architecture Topology Homologous superfamily

Question 43

Models to determine protein structure

Answer 43

Repositories - protein data bank, molecular modelling database Resolution - X-ray crystallography, NMR spectroscopy, EM Databases - CATH, SCOP Prediction - Ab-initio, theoretical modeling, conformation space search. Energy minimalisation. Threading.

Question 44

Write down enzyme equations

Answer 44

...

Question 45

Process of protein structure

Answer 45

- assembly - folding - packing - interaction

Question 46

Why are proteins modified?

Answer 46

- regulation of activity - protein-protein interaction - sub cellular localization - aging

Question 47

Functions of glycosylation

Answer 47

- stabilize proteins against proteolysis - modulation of immune response - provide sorting signals - differentiation in development