Download Understanding Proteins: Structure, Function, and Composition and more Study notes Biology in PDF only on Docsity! Proteins
They are a relatively homogeneous class of molecules. All are the same type of
linear polymer built of various combinations of the same 20 amino acids
differing only in the sequence.
Their functional diversity lies in the three-dimensional structures that these
linear polymers can make by simply being linked in different sequences.
What do proteins do? Pretty much everything *Store and transport a variety of molecules *Guide flow of electrons in processes such as photosynthesis *Transmit information between specific cells within an organ *Control passage of molecules across membranes of compartmentalized cells and organelles *Function in immune system to defend against intruders (antibodies) *Control gene expression by binding to specific sequences of nucleic acids to turn them on/off *Structural stability within cells including hair, nails, tendons, and bones of animals In proteins, the amino acid is linked together by PEPTIDE BONDS
H
Amino acid 1 Amino acid +
o,
sk
ri bond
Each amino acid in a polypeptide chain is referred to as a residue Usually between 50 to 3000 linked together to form a polypeptide chain > 50 – protein <50 – polypeptide This polymeric, linear linkage—Primary sequence structure The sequence of amino acids in a protein/polypeptide chain generally identifies a protein unambiguously. Asymmetric center Peptide bond: appears to have ~40% double bond character which makes it strong Rotation about this bond is restricted and pretty planar Shorter bonds are stronger and have less movement. Trans‐ Conformer The peptide backbone is not very reactive chemically. The only groups usually ionized are the terminal α ‐amino and carboxyl groups, which normally have pKa values of about 7.4 to 3.9, respectively depending on the nature of the terminal amino acid residue. A proton is added or lost to internal peptide bonds only at extremes of pH. The apparent pK value of the amide NH for deprotonation is between 15 and 18 and is in the region of ‐8 to ‐12 for protonation. The oxygen atom of the carbonyl group is protonated more readily, with an apparent pK of about ‐1. These properties facilitate the exchange of hydrogen isotopes between the backbone and aqueous solvents, which is important to the study of protein fluctuations in solution. The amide proton has the ability to exchange with the solution to create a constant exchange process. Glycine It has no αC asymmetry Glycine is a very flexible residue because there is no steric hindrance. This allows glycine to be dynamic . It is very common in loops. Aliphatics Hydrophobic‐ They hate water but love each other They also like other non‐polar atoms. They are referred to as STICKY. They help stabilize the folded conformations of proteins. Acidic residues Even though they look similar, the are not close functionally due to the extra –CH2 on Glutamine. The –COO group clearly likes positive charges which makes these good for metal ion binding. Proteins do whatever necessary to dispel charge such as binding to metals. Amide Residues Neither is too reactive Have polar ends and are H‐bond acceptors and donors e.g. If an Asn and Gly are next to each other, a kink could possibly form due to deamidation (side chain and backbone react)…why Gly? Basic Residues Interact with DNA (nucleic acids) Normally ionized but if not , the side chain becomes very reactive and a potent nucleophile Good H‐bond donor Tend to be hydrophobic within chain and very non‐hydrophobic at end of chain Has a very long side chain which likes to interact with water in solution because end is polar Searches for negative species, mostly on surface of proteins Molar absorptivity, €
40,000 |-
20,000
10,000
5,000
2,000
1,000
500
200
100
50
20
Tt TdAeae i 2 Cet TO T TTT T
240 260
Wavelength (nm)
280
300
320
The aromatic residues are
responsible for ultraviolet and
fluorescence properties of
proteins, also known as
chromophores. The spectral
properties of the side chains
are very sensitive to local
environmental changes and are
useful probes of structures.
Sulfur containing residues
BES
TaN "COOH
H
methionine
Non-polar and unreactive.
The sulfur can not be
protonated.
Acts as a nucleophile a little.
cysteine
Very reactive
The —CH2 can ionize at mild
alkaline conditions.
Disulfide bonds can form between two cysteine residues in
deprotonating conditions. The cysteines will lose their H’s when
in a pH above 7. To break the bond, decrease pH below 7.
cysteine
