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BB10003 Biochemistry > Proteins > Flashcards

Proteins Flashcards

1
Q

Analysis of Genomes BACTERIUM

A

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

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2
Q

Analysis of Genomes YEAST

A

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

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3
Q

Analysis of Genomes HUMANS

A

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

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4
Q

What is C value?

A
  • quantity of DNA in the haploid nucleus

- related to genome size

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5
Q

Why is E. coli a good model?

A

physiology
genetics
metabolism

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6
Q

What did human genome discover?

A
  • only have twice as many genes as a fruit fly

- share lots of genes with a banana

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7
Q

How is the proteome more complex than the genome?

A
  • alternative splicing of pre-mRNA
  • 25,000 genes can generate up to 100,000 proteins
  • post-translational modification: proteolytic cleavage glycosylation, phosphorylation etc
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8
Q

What does the Neuraminidase protein do?

A

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

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9
Q

Glucose dehydrogenase features

A
  • from thermoplasma acidophilum
  • 4 polypeptide chains
  • each chain has 352 amino acids
  • subunit Mr - 40000
  • Functional Protein Mr - 160k
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10
Q

The function of a protein depends on its …

A

3-D structure

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11
Q

Neuraminadase – inhibitor =

A

tamniflu

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12
Q

What do the diff levels of protein structures determine?

A

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

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13
Q

Hydrophobic amino acids -

A
  • 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.
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14
Q

Charged amino acids

A
  • aspartic acid and glutamic acid both -ve

- lysine and arginine both +ve

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15
Q

Polar amino acids

A
  • serine
  • threonine
  • tyrosine
  • histidine
  • cysteine
  • tryptophan
  • aspharagine
  • glutamine
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16
Q

Tyrosine –

A

very good absorber of UV

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17
Q

Histidine –

A

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

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18
Q

Phenylalanine – UV ABSORPTION

A

worst

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19
Q

Amino acids are chiral meaning they have a

A

L and D isomer

20
Q

3 types of classifications of proteins

A
  • operational classification
  • fisher convention
  • cahn-ingold-prelog system
21
Q

Teratogenic means… (eg in thalidomide)

A

causing abnormalities of physiological development

- L/S thalidomide

22
Q

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

A

(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

23
Q

Both threonine and isoleucine have a second …

A

asymmetric carbon center at carbon position 3 along their chains

24
Q

Features of a dipeptide

A
  • peptide bond between carboxyl and amino group
  • amino terminus
  • carboxy terminus
  • two side chains
25
Q

Synthesis occurs in

A

N —–> C

26
Q

What shape is a peptide bond?

A
  • planar
27
Q

Never see glycine in…

A

beta sheet or alpha helix as too flexible

28
Q

Secondary structure elements consist of

A

Alpha helix, beta sheet and loop

29
Q

Regular polypeptide structures

A
  • 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

30
Q

α-helix: 3.613

PERFECT A HELIX

A
  • 3.6 residues per turn (13 main chain atoms)

- dipole moment

31
Q

Every peptide bond has a…

A

dipole moment

32
Q

Alpha helix dipole movement

A

C terminus delta neg at n delta positive charged

33
Q

What PHI angles on a Ram Plot

A
  • zero never

- 180 good

34
Q

In a parallel beta sheet…

A
  • 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
35
Q

β-sheet has no

A

dipole moment

36
Q

Is a beta helices rare or common?

A

RARE

  • bind to water at a certain distance so they don’t form crystal
  • antifreeze
37
Q

What is a beta turn?

A
  • also call loops beta turns

- they connect alpha helix and beta sheet

38
Q

Tertiary structure

A

Segments of secondary structure (here α-helix)

Linked by less regular segments turns (loops)

Results in a compact, globular structure

39
Q

Non-covalent interactions in polypeptides

A 
hydrogen bond
ionic interaction (salt bridge)
hydrophobic interaction
van der Waals interaction
40
Q

Role of a disulphide bond

A
  • stabilise the conformation of a protein

- covalent bond between cysteine side chains

41
Q

Insulin feautures

A
  • 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)
42
Q

Protein purification - methods

A

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

43
Q

separation influenced by:

In ION EXCHANGE

A
  • Choice of beads (+ve or –ve charge)
    • pH of protein-containing solution
    • Ionic strength of solution
44
Q

pKa value of COO- group on amino acid

A

2.2

45
Q

pKa value of NH2 on amino acid group

A

9.5

BB10003 Biochemistry (5 decks)

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