T3 Flashcards
Describe the four levels of protein structure and the two ways of visualizing protein structures.
Primary structure: linear sequence of the amino acids of a peptide or protein. By convention, the primary structure of a protein is read and written from theamino-terminal (N) to the carboxyl-terminal (C) end. Each amino acid is connected to the next by a peptide bond.
- Secondary structure: local arrangement of the chain in space. Several common secondary structures have been identified in proteins, such as alpha helix and beta
sheet. They are mainly held by hydrogen bonds.
- Tertiary structure: refers to the three-dimensional structure of an entire polypeptide chain. The linear chains fold into specific three-dimensional conformations, which are
determined by the sequence of amino acids. Covalent disulfide bonds can be introduced between cysteine residues placed in close proximity in 3D space – this
provides rigidity.
- Quaternary structure: is the three-dimensional arrangement of the subunits in a multisubunit protein. Quaternary structure in proteins is the most intricate degree of organization still considered a single molecule. To be considered to have quaternary
structure, a protein must have two or more peptide chains forming subunits. The subunits can be different or identical, and in most cases they are arranged symmetrically.
- The two possible ways to visualize protein structures are the space filling model and the ribbon diagram. In the first one, the models are constructed by drawing
each atom as a Van der Waals sphere with the atom’s nucleus at the center of the sphere. These are useful because they show how much space an atom (or molecule)
occupies. On the other hand, ribbon diagrams are 3D schematic representations of protein structure and are one of the most common methods used.
The two methods to determine protein structures and who discovered them
a) X-ray diffraction of crystals: was obtained by Max Perutz and John Kendrew in 1950 using crystals of whale myoglobin. They received the Nobel Prize in Chemistry 1962. The three components in an X-ray crystallographic
analysis are a protein crystal, a source of x-rays, and a detector. X-ray crystallography is used to investigate molecular structures through the growth of solid crystals of the molecules.
b) Cryo-Electron Microscopy (Cryo-STEM): was discovered by Jacques Debouchet, Joachim Frank and Richard Henderson, and for their discovery they also received the Nobel Prize in Chemistry 2017. The technique involves
flash-freezing solutions of proteins or other biomolecules and then bombarding them with electrons to produce microscope images of individual molecules. These are used to reconstruct the 3D structure of the molecule.
Why are peptide bonds rigid and exist in trans conformation with exception of X-proline bonds?
Peptide bonds are rigid because they have a partial double bond character and therefore cannot rotate, unlike the rest of simple bonds. In most cases, the peptide bonds in proteins are trans due to the steric clashes that occur between groups attached to the alpha carbon atoms in cis form, which hinder formation of this configuration.
However, proline is the only amino-acid which can be found in cis conformation because of the smaller energy difference of proline (it has two carbons bound to the N) between cis and trans states compared to other amino-acid residues (which have a H and a C atom bonded to the peptide N). In other words, X-proline peptide bonds may exist in cis conformation because they are more stable than in trans due to steric clashes of amino acid side chains in both isomers. During protein folding it is catalyzed by prolyl cis-trans isomerases.
Describe the alpha helix of proteins
The alpha helix is a coiled structure stabilized by intrachain hydrogen bonds It’s a right-handed helix with a length of 1.5 nm/10 amino acids and width of 1.2 nm.
The helix is composed of 3.6 amino acid residues per turn
Describe the coiled coil superhelix of fibrous proteins
Coiled coils (hélice superenrollada) are α-helical structures in which helices are wound around each other to form superhelical bundles. They contain around 3.5
residues per turn (heptad repeats) and can have length of 100 nm.
They usually consist of two or three helices in parallel or antiparallel orientation (but structures with seven and more helices have been determined). They are usually oligomers either of the same (homo) or of different chains (hetero), but can also be formed by consecutive helices from the same polypeptide chain, which in that case almost always have an antiparallel orientation.
Why are most proteins in continuous turnover and how does this occur?
Most proteins are in continuous turnover for several reasons: irreversible denaturation, chemical damage (oxidation, radiation, chemical modification) and the need to stop regulatory proteins when they are not useful. The resulting supply of amino acids is important in cells. The two steps of protein degradation are:
1) Tagging of the selected protein by ubiquitination, consisting of formation of isopeptide bonds of a small (76 amino acids) conserved protein known as ubiquitin,
whose carboxyl terminus reacts with the amino groups at the side chain of lysins. These isopeptide bonds are generated by ubiquitin ligases, which are very important
cell regulators.
2) Degradation by the proteasome, a protein complex bigger than ribosomes. Theubiquitinated proteins are recognized
by the two regulatory subunits flanking a central catalytic core containing the proteases. The regulatory parts utilize ATP to pump ubiquitinated proteins inside the catalytic part. The regulatory subunits hydrolyze and release the ubiquitin for reutilization at the cytoplasm.
Describe what leucine zippers are and their function
The leucine zipper (ZIP) is a common motif found in many DNA-binding proteins and consists of a periodic repetition of a leucine residue at every seventh position (heptad
repeat) and forms an α-helical conformation, which facilitates dimerisation. They play a central role in the dimerization of bZIP (basic-region leucine zipper) family of
transcription factors and their subsequent binding to the DNA promoter regions of target genes.
How disulfide bridges in proteins are broken and reformed
Disulfide bridges between proteins can be broken by reduction with thiol reagents, either by reduction of the cysteines that form it or by mutation: three cysteines, including the two that form the disulfide bond, are replaced by serines.
Besides, these bonds can also be reformed by the activity of a class of enzymes known as oxidoreductases.
How curls are induced in hair?
Disulfide bonds that give a determined shape to the hair are broken by adding a thiol-containing reagent, which is a reductant, and gentle heating. The hair is curled, and an oxidizing agent is added to re-form disulfide bonds to
stabilize the desired shape. The further apart the sulfur atoms, the more the protein molecules bend, and so the
more your hair curls.
Describe the collagen triple helix by their amino acid sequence
The collagen triple strand helix is only characteristic of collagen, as it isn’t present in any other protein.
It consists of 3 levogyre alpha helices that conform to a triple strand dextrogyre helix.
Each strand is hydrogen bonded to the other two strands and has ≈ 1000 residues, with 3 amino acid residues per turn.
Glycine repeats every 3 amino acid residues in order to fit in the center. Besides, there is a high content of proline and hydroxyproline (pyrrolidine rings of prolines are
on the outside to be hydroxylated).
Thus, the sequence can be summarized as: (Gly-X-Y) * n, where X and Y are different amino acids, frequently proline (Pro) and hydroxyproline (Hyp), respectively.
Describe parallel and antiparallel beta sheets
Parallel beta sheets have two polypeptide strands running in the same direction.
These secondary structures are less stable than antiparallel beta sheets since the hydrogen bonds are not linear.
There are 12 atoms in each hydrogen bonded ring in a parallel beta sheet and all of the N-terminus of polypeptide strands are oriented in the same direction. Antiparallel beta sheets are the second major type of beta sheets of proteins. In this structure, the two polypeptide strands run in the opposite direction and the number of atoms in each hydrogen bonded ring alternates between 14 and 10.
Since hydrogen bonds in an antiparallel beta-sheet are linear, it is more stable than parallel beta sheets and the N-terminal of one strand is adjacent to the C-terminal of the next strand. This arrangement forms the strongest inter-strand stability. Antiparallel β-sheets are native proteins.
What is a beta sheet barrel?
In protein structures, a beta barrel is a beta sheet composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded
to the last strand (hydrogen bond).
Beta-strands in many beta-barrels are arranged in an antiparallel fashion. These β-barrel proteins serve essential functions in cargo transport and signaling and are also vital for membrane biogenesis. They have also been adapted to perform a diverse set of important cellular functions including acting as porins, transporters, enzymes, virulence factors and receptors
What is a reverse turn?
A reverse turn is a region of a polypeptide that forms a hydrogen bond between the oxygen of a carbonyl group and the amino group of a residue three residues ahead
of the first one (ie O(i) to N(i+3)). Reverse turns are very abundant in globular proteins and generally occur at the surface of the molecule. It has been suggested that turn regions act as nucleation centres during protein folding.
Describe the quaternary structure of proteins and put an example
The quaternary structure of a protein is the association of several protein chains or subunits into a closely packed arrangement, each of the subunits has its own primary, secondary, and tertiary structure and the subunits are held together by hydrogen bonds and van der Waals forces between nonpolar side chains.
It is the higher order structure and consists of enormous complexes of many proteins that assemble and disassemble in every reaction cycle: machineries for replication and transcription of DNA, RNA processing, protein synthesis, etc(hydrogen bonds and hydrophobic contacts)
Examples of proteins with quaternary structure include hemoglobin, DNA polymerase, ribosomes, antibodies, and ion channels.
Describe chemical modification of amino acids in proteins
These chemical modifications are commonly referred to as posttranslational modifications (PTMs), as they occur after the protein biosynthesis step.
Some examples of chemical modifications are: phosphorylation (addition of a phosphate group to the side chain hydroxyl group of a serine, threonine, and tyrosine residue), ubiquitination (addition of a small protein, ubiquitin, to the side chain amino group of a lysine residue), glycosylation (addition of a saccharide units), acetylation (addition of acetyl groups to the side chain amino group of a lysine residue), formylation (a formyl group is added to the N terminus of a protein), amidation (an amide group is
added at the protein C terminus), etc.
