Proteins

Question 1

Analysis of Genomes BACTERIUM

Answer 1

Total DNA bp - 4.6x10 6
Total no. of chromosomes - 1
Number of genes - 4400

Question 2

Analysis of Genomes YEAST

Answer 2

Total DNA bp - 1.2x10 7
Total no. of chromosomes - 16
Number of genes - 6200

Question 3

Analysis of Genomes HUMANS

Answer 3

Total DNA bp - 3.2x10 9
Total no. of chromosomes - 46
Number of genes - 20-25000

Question 4

What is C value?

Answer 4

• quantity of DNA in the haploid nucleus

- related to genome size

Question 5

Why is E. coli a good model?

Answer 5

physiology
genetics
metabolism

Question 6

What did human genome discover?

Answer 6

• only have twice as many genes as a fruit fly

- share lots of genes with a banana

Question 7

How is the proteome more complex than the genome?

Answer 7

• alternative splicing of pre-mRNA
• 25,000 genes can generate up to 100,000 proteins
• post-translational modification: proteolytic cleavage glycosylation, phosphorylation etc

Question 8

What does the Neuraminidase protein do?

Answer 8

Cleaves sialic acid from the surface of cell in order to release virus

Question 9

Glucose dehydrogenase features

Answer 9

• from thermoplasma acidophilum
• 4 polypeptide chains
• each chain has 352 amino acids
• subunit Mr - 40000
• Functional Protein Mr - 160k

Question 10

The function of a protein depends on its …

Answer 10

3-D structure

Question 11

Neuraminadase – inhibitor =

Answer 11

tamniflu

Question 12

What do the diff levels of protein structures determine?

Answer 12

Primary – sequence of amino acids
Secondary strutures – beta sheets, alpha helix
Teritary structure – arrangement of alpha helix,
Quaternary – Folding

Question 13

Hydrophobic amino acids -

Answer 13

• Glycine (H side chain gives flexibility)
• alanine
• valine
• leucine
• isoleucine
• Proline (rigid structure)
• phenylalanine (aromatic)
• Methionine
• cysteine as found inside
• all inside the protein structure, they’re oily interior of the protein.

Question 14

Charged amino acids

Answer 14

• aspartic acid and glutamic acid both -ve

- lysine and arginine both +ve

Question 15

Polar amino acids

Answer 15

• serine
• threonine
• tyrosine
• histidine
• cysteine
• tryptophan
• aspharagine
• glutamine

Question 16

Tyrosine –

Answer 16

very good absorber of UV

Question 17

Histidine –

Answer 17

used for purifying protein or clone or express and purify; histamine tag – metal ion bolts used to find those proteins.

Question 18

Phenylalanine – UV ABSORPTION

Answer 18

worst

Question 19

Amino acids are chiral meaning they have a

Answer 19

L and D isomer

Question 20

3 types of classifications of proteins

Answer 20

• operational classification
• fisher convention
• cahn-ingold-prelog system

Question 21

Teratogenic means… (eg in thalidomide)

Answer 21

causing abnormalities of physiological development

- L/S thalidomide

Question 22

All naturally-occurring amino acids have the what configuration???

Answer 22

(S) configuration, except cysteine which is (R): because of its C-S side chain, which unlike all other side chains, has a higher priority than the CO2H group

Question 23

Both threonine and isoleucine have a second …

Answer 23

asymmetric carbon center at carbon position 3 along their chains

Question 24

Features of a dipeptide

Answer 24

• peptide bond between carboxyl and amino group
• amino terminus
• carboxy terminus
• two side chains

Question 25

Synthesis occurs in

Answer 25

N -----> C

Question 26

What shape is a peptide bond?

Answer 26

- planar

Question 27

Never see glycine in...

Answer 27

beta sheet or alpha helix as too flexible

Question 28

Secondary structure elements consist of

Answer 28

Alpha helix, beta sheet and loop

Question 29

Regular polypeptide structures

Answer 29

- α-helix: polypeptide chain adopts a helical (spiral) structure in 3-D - ß-sheet: polypeptide chain adopts a pleated structure (strand) and interacts with adjacent strands - In secondary structure each Cα is in a regular arrangement with respect to its neighbours Secondary structures stabilised by hydrogen bonds

Question 30

α-helix: 3.613 PERFECT A HELIX

Answer 30

- 3.6 residues per turn (13 main chain atoms) | - dipole moment

Question 31

Every peptide bond has a...

Answer 31

dipole moment

Question 32

Alpha helix dipole movement

Answer 32

C terminus delta neg at n delta positive charged

Question 33

What PHI angles on a Ram Plot

Answer 33

- zero never | - 180 good

Question 34

In a parallel beta sheet...

Answer 34

- wonky beta sheets, you cant line up amino groups with carbon groups Wonky interactions H not as stable as they're further apart than in an anti parallel

Question 35

β-sheet has no

Answer 35

dipole moment

Question 36

Is a beta helices rare or common?

Answer 36

RARE - bind to water at a certain distance so they don't form crystal - antifreeze

Question 37

What is a beta turn?

Answer 37

- also call loops beta turns | - they connect alpha helix and beta sheet

Question 38

Tertiary structure

Answer 38

Segments of secondary structure (here α-helix) Linked by less regular segments turns (loops) Results in a compact, globular structure

Question 39

Non-covalent interactions in polypeptides

Answer 39

``` hydrogen bond ionic interaction (salt bridge) hydrophobic interaction van der Waals interaction ```

Question 40

Role of a disulphide bond

Answer 40

- stabilise the conformation of a protein | - covalent bond between cysteine side chains

Question 41

Insulin feautures

Answer 41

- Synthesised as inactive precursor preproinsulin - pre-sequence required for membrane transport - Pre- sequence removed by proteolysis - Proinsulin folds and disulphides form (3) - forms inactive precursor - pro-sequence required for correct folding - Activation involves removal of pro- sequence (4)

Question 42

Protein purification - methods

Answer 42

Column chromatography separations of soluble proteins based on differences in molecular characteristics Gel filtration - separation depends on molecular size Ion exchange - separation depends on molecular charge Affinity chromatography - separation depends on specific binding interaction

Question 43

separation influenced by: In ION EXCHANGE

Answer 43

- Choice of beads (+ve or –ve charge) - pH of protein-containing solution - Ionic strength of solution

Question 44

pKa value of COO- group on amino acid

Answer 44

2.2

Question 45

pKa value of NH2 on amino acid group

Answer 45

9.5