Chapter 3- Protein Structure and Function
- Proteome: entire protein complement of an organism
3.1 Hierarchial Structure of Proteins
- A protein chain folds into a shape stabilized by noncovalent interactions between regions of the
- Function is derived from 3D structure and structure is derived by amino acid sequence.
- Linear arrangement of amino acids.
- Linked by peptide bonds.
- Backbone exhibits directionality.
- Size of a protein or polypeptide is reported as its mass in daltons or molecular weight (MW).
- Spatial arrangements resulting from the folding of localized parts of a polypeptide chain.
- In the absence of stabilizing noncovalent interactions, a polypeptide assumed a random coil
- Alpha helices and beta sheets are the major internal supportive elements in proteins.
The α Helix
- The carbonyl oxygen atom of each peptide bond is hydrogen-bonded to the amide hydrogen
atom of the amino acid four residues toward the C-terminus.
- Confers a directionality on the helix
- The arrangement holds the backbone in a rodlike cylinder from which the side chains point
The β Sheet
- Consists of laterally packed B strands
- Hydrogen bonding between backbone atoms in adjacent B strands, within either the same
polypeptide chaon or between different polypeptide chains, forms a B sheet.
- Have a directionality defined by the orientation of the peptide bond.
- Composed of 3 or 4 residues, turns are located on the surface of a protein, forming sharp bends
that redirect the polypeptide backbone back toward the interior.
- They are stabilized by a hydrogen bond between their end residues.
- Glycine and proline are commonly present in turns. - A polypeptide may also contain larger bends, or loops.
- Overall conformation of a polypeptide chain.
- Stabilized by hydrophobic interactions between the nonpolar side chains, hydrogen bonds
between polar side chains, and peptide bonds.
- Tertiary structure is not rigidly fixed.
- The simplest way to represent 3D structure is to trace the course of the backbone atoms with a
- Particular combinations of secondary structures.
- Build up the tertiary structure of a protein.
- The helix-loop-helix is a Ca2+ binding motif – oxygen atoms in the invariant residues bind a
Ca2+ ion through ionic bonds.
- The zinc finger motif- an a helix and two B strands with an antiparallel orientation, form a
fingerlike bundle help together by a zinc ion.
- Coiled coil- each polypeptide chain contains a-helical segments in which the hydrophobic
residues are in a regular pattern- a repeated heptad sequence.
- The overall helical structure is amphipathic.
Structural and Functional Domains
- EGF, epidermal growth factor is a domain.
- It Is a small soluble peptide hormone that binds to cels in the embryo and in skin and connective
tissue in adults causing them to divide.
Members of protein families have a common evolutionary ancestor
- 3D structures of myoglobin and the α, β subunits of hemoglobin are similar.
- Many identical or chemically similar residues are found in identical positions throughout primary
structures of both proteins.
- Proteins that have a common ancestor are called homologs.
- Can trace their lineage by comparing their sequences.
3.2 Folding, Modification and Degradation of proteins
- Assembly of amino acids is dictated by Mrna.
- The cell has error-checking processes
- Misfolded proteins are degraded Information for folding is encoded in the sequence
- All molecules adopt a native state conformation (most stable form)
- In vitro protein folding is a self-directed process.
Folding of proteins in vitro is promoted by chaperones
- Cells require a faster, more efficient mechanism for folding proteins into their correct shapes.
- Two general families of chaperones:
o Molecular chaperones: bind and stabilize unfolded or partly folded proteins, thereby
preventing these proteins from aggregating and being degraded.
Consist of Hsp70 in cytosol, BiP in ER and DnaK in bacteria.
When bound to ATP Hsp70-like proteins assume an open form in which an
exposed hydrophobic pocket transiently binds to exposed hydrophobic regions
of the unfolded target protein.
Hydrolysis of the bound ATP causes molecular chaperones to assume a closed
form in which a target protein can undergo folding.
o Chaperonins: directly facilitate the folding of protein.
Formed fron two rings of oligomers.
Eukaryotic chaperonin- TriC
Bacterial, mitochondrial, chloroplast chaperonin- GroEL
In bacteria, a partly folded or misfolded polypeptide is inseted into the cavity of
GroEL, where it binds to the inner wall and folded into its native conformation
In an ATP- dependent step, GroEL undergoes a conformational change
and releases the folded protein, a process assisted by a co-chaperonin,
GroES , which caps the ends of GroEL.
Many proteins undergo chemical modification of amino acid residues
- Acetylation: the attachment of these hydrophobic tails which function to anchor proteins to the
lipid bilayer, constitutes one way that cells localize certain proteins to membranes.
Peptide segments sometimes removed after synthesis
- After synthesis, some proteins undergo irreversible changes that do not entail changes in
individual amino acid residues.
o Sometimes called processing - Most common form is enzymatic cleavage of a backbone peptide bond by proteases.
- Proteolytic cleavage is a common mechanism for activating enzymes.
- Protein self-splicing takes place in bacteria and some eukaryotes.
o An internal segment of a polypeptide is removed and the ends of the polypeptide are
- The excised peptide appears to eliminate itself from the protein by a mechanism similar to that
used in the processing of some RNA molecules.
Ubiquitin marks cytosolic proteins for degradation in proteasomes
- The activity of a cellular protein depends on the amount present, which reflects the balance
between its rate of synthesis and rate of degradation in the cell.
- Eukaryotic cells have several intracellulalar proteolytic pathways for degrading misfolded or
denatured proteins, normal proteins whose concentration must be decreased and extracellular
proteins taken up by the cell.
o One major pathway is degradation by enzymes within lysosomes
Directed primarily toward extracellular proteins taken up by the cell and aged or
defective organelles of the cell.
o There are also cytosolic mechanisms for degrading proteins.
o Chemical modification of ubiquitin, followed by degradation of the ubiquitin-tagged
protein by a specialized proteolytic machine
Ubiquitination is a 3 step process
1. Activation of ubiquitin-activating enzyme (E1) by the addition of a ubiquitin molecule-
2. Transfer of this ubiquitin molecule to a cysteine residue in ubiquitin-conjugating enzyme(E2)
3. Formation of a peptide bond between the ubiquitin molecule bound to E2 and a lysine
residue in the target protein, a reaction catalyzed by ubiquitin ligase. (E3)
- This process is repeated many times, with each subsequent ubiquitin molecule being added to
the preceding one.
- The resulting polyubiquitin chain is recognized by a proteasome which cleaves in an ATP
dependent process that yields short peptides and intact ubiquitin molecules.
- Cellular proteins degraded by the ubiquitin-mediated pathway fall into one of the two general
o Native cytosolic proteins whose life spans are tightly controlled
o Proteins that become misfolded in the course of their synthesis in the ER
- Both contain sequences recognized by the ubiquinating enzyme complex.
- Cyclins are cytosolic proteins whose amount are tightly controlled throughout the cell cycle.
- The misfolding of proteins in the ER exposes hydrophobic sequences. These are transported to
the cytosol where ubiquitinating enzymes recognize the exposed hydrophobic sequences.
Digestive proteases degrade dietary proteins - The major extracellular pathway for protein degradation is the system of digestive proteases
that breaks down ingested proteins into peptides and amino acids in the intestinal tract.
- Three classes of proteases:
o Endoproteases: attack selected peptide bonds within a chain. Ex: pepsin
o Exopeptidases: sequentially remove residues from the N-terminus or C-terminus of a
o Peptidases: split oligopeptides containing as many as about 20 amino acids into di and
tripeptides and individual amino acids.
Alternatively folded pr