Proteins Flashcards
Analysis of Genomes BACTERIUM
Total DNA bp - 4.6x10 6
Total no. of chromosomes - 1
Number of genes - 4400
Analysis of Genomes YEAST
Total DNA bp - 1.2x10 7
Total no. of chromosomes - 16
Number of genes - 6200
Analysis of Genomes HUMANS
Total DNA bp - 3.2x10 9
Total no. of chromosomes - 46
Number of genes - 20-25000
What is C value?
- quantity of DNA in the haploid nucleus
- related to genome size
Why is E. coli a good model?
physiology
genetics
metabolism
What did human genome discover?
- only have twice as many genes as a fruit fly
- share lots of genes with a banana
How is the proteome more complex than the genome?
- alternative splicing of pre-mRNA
- 25,000 genes can generate up to 100,000 proteins
- post-translational modification: proteolytic cleavage glycosylation, phosphorylation etc
What does the Neuraminidase protein do?
Cleaves sialic acid from the surface of cell in order to release virus
Glucose dehydrogenase features
- from thermoplasma acidophilum
- 4 polypeptide chains
- each chain has 352 amino acids
- subunit Mr - 40000
- Functional Protein Mr - 160k
The function of a protein depends on its …
3-D structure
Neuraminadase – inhibitor =
tamniflu
What do the diff levels of protein structures determine?
Primary – sequence of amino acids
Secondary strutures – beta sheets, alpha helix
Teritary structure – arrangement of alpha helix,
Quaternary – Folding
Hydrophobic amino acids -
- 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.
Charged amino acids
- aspartic acid and glutamic acid both -ve
- lysine and arginine both +ve
Polar amino acids
- serine
- threonine
- tyrosine
- histidine
- cysteine
- tryptophan
- aspharagine
- glutamine
Tyrosine –
very good absorber of UV
Histidine –
used for purifying protein or clone or express and purify; histamine tag – metal ion bolts used to find those proteins.
Phenylalanine – UV ABSORPTION
worst
Amino acids are chiral meaning they have a
L and D isomer
3 types of classifications of proteins
- operational classification
- fisher convention
- cahn-ingold-prelog system
Teratogenic means… (eg in thalidomide)
causing abnormalities of physiological development
- L/S thalidomide
All naturally-occurring amino acids have the what configuration???
(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
Both threonine and isoleucine have a second …
asymmetric carbon center at carbon position 3 along their chains
Features of a dipeptide
- peptide bond between carboxyl and amino group
- amino terminus
- carboxy terminus
- two side chains
Synthesis occurs in
N —–> C
What shape is a peptide bond?
- planar
Never see glycine in…
beta sheet or alpha helix as too flexible
Secondary structure elements consist of
Alpha helix, beta sheet and loop
Regular polypeptide structures
- 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
α-helix: 3.613
PERFECT A HELIX
- 3.6 residues per turn (13 main chain atoms)
- dipole moment
Every peptide bond has a…
dipole moment
Alpha helix dipole movement
C terminus delta neg at n delta positive charged
What PHI angles on a Ram Plot
- zero never
- 180 good
In a parallel beta sheet…
- 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
β-sheet has no
dipole moment
Is a beta helices rare or common?
RARE
- bind to water at a certain distance so they don’t form crystal
- antifreeze
What is a beta turn?
- also call loops beta turns
- they connect alpha helix and beta sheet
Tertiary structure
Segments of secondary structure (here α-helix)
Linked by less regular segments turns (loops)
Results in a compact, globular structure
Non-covalent interactions in polypeptides
hydrogen bond ionic interaction (salt bridge) hydrophobic interaction van der Waals interaction
Role of a disulphide bond
- stabilise the conformation of a protein
- covalent bond between cysteine side chains
Insulin feautures
- 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)
Protein purification - methods
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
separation influenced by:
In ION EXCHANGE
- Choice of beads (+ve or –ve charge)
- pH of protein-containing solution
- Ionic strength of solution
pKa value of COO- group on amino acid
2.2
pKa value of NH2 on amino acid group
9.5
