Download What roles do proteins (polypeptides) play? 1. Enzymes (catalysts) 2

What roles do proteins (polypeptides) play?
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Enzymes (catalysts)
Involved in storage and transport (hemoglobin)
Provide support/shape (actin)
Allow for movement (flagella)
Decoder (DNA, gene expression)
Regulators (hormones)
Defense (antibodies)
What is a protein?
• Macromolecule
• Polymer of amino acids
Only 1 way to link the amino acids together: Peptide bond
Sequence of amino acids determine a proteins structure and function
Largest human protein is 34350 amino acids (Titan)
Smallest human protein is debatable…
• 20 standard amino acids
All organisms use these 20 amino acids
These 20 provide enormous possibilities of combinations
For Titan, with 34350 amino acids, there are:
(34350)20 combinations = 5.2 x 1090 possibilities!!
What is an amino acid?
Let’s build an amino acid!
1. C
alpha carbon
2. H
3. Amine (NH3+)
4. Acid (COO-)
5. R group (side chain)
6. Backbone
Chemistry C483
Fall 2009
Prof Jill Paterson
4-1
Amino acid “backbone”
At pH 7.4, the carboxylate group is deprotonated (we will discuss why soon…)
giving a negative charge
At pH 7.4, the amino group is protonated, giving a positive charge
Overall charge of the backbone is 0, [+1 + (-1)] or “zwiterionic”
Amino acid side chains
• 20 different side groups
• Note the stereochemistry (geometry)
• 19 of the 20 are chiral
Steroisomers
• 4 different groups bonded to Cα
• These molecules cannot be superimposed (are mirror images of each other)
• Therefore they are not identical, and are referred to as stereoisomers.
• Using spectrographic instrumentation, the two configurations can be deciphered as
either L or D based on how they rotate light (remember, this is different from assigning
R- and S-).
• Both L- and D- form exist in nature, but only L-forms are used to build proteins (some
exceptions with bacteria)
Chemistry C483
Fall 2009
Prof Jill Paterson
4-2
R v. S
• Assign priority score based on atomic mass (highest being 1)
• Orient the molecule with “4” score pointing away
• Draw line from 1 to 2 to 3.
If Clockwise, the configuration is R
If Counterclockwise, the configuration is S
Chemistry C483
Fall 2009
Prof Jill Paterson
4-3
Nonpolar amino acids
Polar amino acids
Chemistry C483
Fall 2009
Prof Jill Paterson
4-4
Glycine (Gly, G)
• Nonpolar
Aliphatic
• Smallest
• Leads to flexibility in proteins
• Only non-chiral amino acid
(Since R group is H, mirror images are
superimposable and there is a plane of
symmetry)
Alanine (Ala, A)
• Nonpolar, Aliphatic
• Methyl group (β-carbon)
Valine (Val, V)
• Nonpolar, Aliphatic
• Branched, note carbon notations
Leucine (Leu, L)
• Nonpolar, Aliphatic
Isoleucine (Ile, I)
• Nonpolar, Aliphatic
• An additional chiral C (thus 4 conformations
are possible).
Chemistry C483
Fall 2009
• Aliphatic amino acids
Avoid water
Cluster together to keep water out
Involved in hydrophobic interactions
Prof Jill Paterson
4-5
Methionine (Met, M)
• Nonpolar
Highly hydrophobic
• Contains a sulfur group
• Binds to metals
• First of most proteins
Proline
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Nonpolar
Only slightly hydrophobic
Leads to “kinks” in protein
People with naturally curly hair
have a high level of Pro
Phenylalanine (Phe, F)
• Alanine with a phenyl group
• Nonpolar
• Hydrophobic
Tryptophan (Trp, W)
• Nonpolar
• Less hydrophobic than Phe
• Absorbs light at 280 nm
Important for spectrophotometric analysis
of proteins
Serine (Ser, S)
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Polar, uncharged
Slightly hydrophillic
Alcohol
Can form H-bonds
Can be phosphorylated (regulator)
Can have sugar attach
Chemistry C483
Fall 2009
Prof Jill Paterson
4-6
Threonine (Thr, T)
• Polar
• Uncharged
• Slightly hydrophillic
Alcohol
• Can form H-bonds
• Has an additional chiral center, thus 4
conformations
• Can be phosphorylated (regulator)
• Can have sugar attach
Asparagine (Asn, N)
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Uncharged
Polar
Forms H-bonds
Can have sugars attached to form glyco-proteins
Glutamine (Gln, Q)
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Uncharged
Polar
Can form H-bonds
Can have sugars attach
Tyrosine (Tyr, Y)
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Uncharged
Polar
Can form H-bonds
absorbs light at 280 nm
Important for spectrophotometric
analysis of proteins
• Can be phosphorylated
• Is very slightly hydroPHOBIC, even though this is a
polar molecule!
Cysteine (Cys, C)
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Uncharged
Polar
Contains a sulfhydryl group
Can be oxidized to form disulfide bonds
Chemistry C483
Fall 2009
Prof Jill Paterson
4-7
Disulfide bonds
These are covalent bonds which can be broken by a reduction reaction.
Lysine (Lys, K)
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Charged (Positive)
Polar
Can form H-bonds
Basic (we will discuss what this means soon!)
Arginine (Arg, R)
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Charged (positive)
Polar
Can form H-bonds
Basic
Histidine (His, H)
• Charged (sometimes positive)
• Polar
• Can be a proton donor or acceptor, depending on
current pH
• Known for its ability to bind metals
Will we discuss this in detail
during the protein purification
section
Chemistry C483
Fall 2009
Prof Jill Paterson
4-8
Aspartate (Asp, D)
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Charged (negative)
Polar
Can form H-bonds
Acidic
Also known as Aspartic Acid
Glutamate (Glu, E)
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Charged (negative)
Polar
Can form H-bonds
Acidic
Also known as glutamic acid
Other amino acids variants will be known to you
The hydrophobicity of each amino acid
Very hydrophobic
Chemistry C483
Slightly hydrophobic
Fall 2009
Slightly hydrophilic
Prof Jill Paterson
Very hydrophilic
4-9
Where do we find these amino acids in proteins?
• Charged, hydrophilic amino acids are almost always found on the surface of a
protein, interacting with the surrounding water
• Polar residues are usually found on the surface of the protein, but can be buried
• Non-polar, hydrophobic amino acids are usually buried in a protein, but can be
found on the surface
Summary
• The 20 amino acids have been presented
• Each amino acid differs in the side chain, giving each amino acid different chemical
characteristics
__are nonpolar
__ are polar
__of the polar are uncharged
__of the polar are charged
• Each amino acid has a three letter code AND a one letter code
• At physiological pH (7.4), the carboxylic acid of an amino acid is deprotonated
• At physiological pH, the amino group is protonated
• Protonation of the side chains varies, dependent on the chemical group and pH
• Some amino acids are characterized as basic, while others are acid
Chemistry C483
Fall 2009
Prof Jill Paterson
4-10