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Proteinstructures
PROTEINS -> the shape of a protein is specified by its amino acid sequence, many of them held
together by peptide bonds -> aka polypeptides, polypeptide chains
Covalent peptide bond -> forms when the carbon atom of the carboxyl group of one amino
acid, shares electrons with the nitrogen atom from the amino group of the second
amino acid. These bonds allow for free rotation, so polypeptides are very flexible
Polypeptide backbone -> formed from a repeating sequence of the core atoms found in every
amino acid. Has side chains that are not involved in forming peptide bonds, generally
referred to as R.
Polypeptide chains have a N-terminus (carrying the amino group) and a C-terminus (carrying the
carboxyl group).
Folding polypeptides -> by weak noncovalent bonds from the side chains or the backbone,
but with many together are strong enough. (Hydrogen bonds, electrostatic
attractions, Van der Waals attractions, and hydrophobic force that tends to cluster in
the interior of the folded protein//polar (hydrophilic) bonds are on the exterior to
possibly form bonds with water and other molecules, or when inside bonded with
hydrogen bonds.)
Conformation -> final folded structure, a protein generally folds into a shape in which its free
energy (G) is minimized. Folding process = energetically favourable, releases heat and
increases disorder in the universe.
Denaturation/renaturation -> synthetically unfolding/naturally refolding of protein -> way to fold
info is contained in amino acid sequence.
Chaperone proteins -> assist protein folding. Some bind to partly folded chains and help
them fold in the most energetically favourable way, others create an ‘isolation
chamber’ to make them fold without risking binding to other molecules.
The confirmation of each protein is unique, but some regular folding patterns can be detected. A-
Helix and B-sheets are common folding patterns. Result from hydrogen bonds that
form between N-H and C=O groups in the polypeptide backbone. Amino acid side
chains are not involved, so the form can be generated by many different amino acid
sequences.
A-Helix -> N-H of every peptide bond is hydrogen bonded to the C=O of a neighbouring peptide
bond four amino acids away in the same chain. Right-handed and left-handed twists
are possible (follow from bottom to top to know which side it turns)
Many membrane-bound proteins cross the lipid bilayer as an a-helix because the hydrophobic parts
of the backbone can stick outside and the hydrophilic parts to the inside. Not a
channel through the membrane, but often found in proteins that are embedded in
cell membranes, like transport proteins and receptors.
Coiled-coil -> structure of multiple a-helices twisted around one another, forms when most
nonpolar(hydrophobic) side chains along one side, so they can twist around one
, another with the hydrophobic side facing inward to minimize contact with the
aqueous cytosol.
B-sheet -> several segments (strands) of an individual polypeptide chain are held together by
hydrogen-bonding between peptide bonds in adjacent strands, they lay side by side.
Can form a parallel B sheet or antiparallel B sheet. The side chains project
alternately abide and below the plane of the sheet, giving two sides different
properties. In drawing the arrow points at the c-terminus.
Amyloid structures -> B-sheets are stacked together in long rows with their amino acid side
chains interdigitates like the teeth of a zipper. When proteins fold incorrectly,
amyloid structures can damage cells or even whole tissues (can cause
neurodegenerative diseases like Alzheimer’s, Huntington’s, Mad cow etc).
Prion -> Misfolded protein. Prion form of a protein can convert the properly folded
version of the protein in an infected brain into the abnormal conformation -> form
aggregates that can spread rapidly from cell to cell, eventually causing death. Are
infectious.
Proteins have several levels of interdependent organization:
Primary structure -> amino acid sequence
Secondary structure -> a-helices and B-sheets
Tertiary structure -> Full, three-dimensional conformation formed by an entire
polypeptide chain.
Quaternary structure -> interacting polypeptides. if the protein consists as a complex of more
than one polypeptide chain.
Protein domain -> any segment of a polypeptide chain that can fold independently into
a compact, stable structure. The modular unit from which many larger proteins are
constructed. Different domains of a protein are often associated with different
functions (small domain that binds to DNA and a big domain that binds to AMP).
Small protein molecules contain only a single domain. Larger proteins can contain many domains
connected by relatively short, unstructured lengths of polypeptide chain. These
intrinsically disordered sequences can continually bend and flex.
Many protein formations are possible, but only few used by cells -> most biological functions depend
on proteins with stable, well-defined three-dimensional conformations. Also,
proteins must be ‘’well behaved’’ and not engage in unwanted associations with
other proteins in the cell.
Stable conformation -> proteins are built so precisely that a change in even a few
atoms in one amino acid can sometimes disrupt the structure of a protein and
thereby eliminate its function.
Protein families -> useful proteins can slightly chance their conformation (in evolution)
to enable new functions. The amino acid sequence and a three-dimensional
conformation closely resemble family members.
,Binding site -> any region on a protein’s surface that interacts with another
molecule through sets of noncovalent bonds.
Subunit -> each polypeptide chain in a protein with a quaternary structure. May contain
one or more domain.
In the simplest case, two identical, folded polypeptide chains form a symmetrical complex of two
protein subunits (called a dimer) that is held together by interactions between two
identical binding sites. Can also be formed by multiple copies of the same
polypeptide chain, and nonidentical binding sites. Many proteins contain multiple
subunits, and they can be very large. Watch again movie 4.5
Dimer -> two identical, folded polypeptide chains that form a symmetrical complex of two
protein subunits.
Proteins can form even larger assemblies than those discussed so far. A chain of identical protein
molecules can be formed if the binding site of two of the same type of protein
molecules is complementary. Bound to neighbour in identical way -> often a helix
that can be extended indefinitely in either direction.
Many large structures, such as viruses and ribosomes, are built from a mixture of one or more types
of protein plus RNA or DNA molecules. All information needed for assembly of the
complicated structure is contained in the macromolecules themselves -> self-
organizing.
Globular proteins -> Polypeptide chain folds up into a compact shaped like a ball with an
irregular surface. Like enzymes. Quaternary structure with an overall rounded shape.
Fibrous proteins -> relatively simple, elongated three-dimensional structure (coiled-coil).
Especially abundant outside the cell where they form gel-like extracellular matrix,
that helps cells to form tissues.
Collagen and elastin are fibrous proteins in the extracellular matrix. Extracellular proteins are often
stabilized by covalent cross-linkages, these linkages can either tie together two
amino acids in the same polypeptide chain or join many polypeptide chains in a large
protein complex. Most common:
Disulphide bonds aka S-S bonds -> most common covalent cross-linkages. Do not change
proteins conformation, but act as a ‘’atomic staple’’ to reinforce the protein’s most
favoured conformation. Generally, don’t form in cytosol. Both between molecules
and inside one molecule.
For proteins, form and function are inextricably linked. The activity of proteins depends on their
ability to bind specifically to other molecules, allowing them to act as catalysts,
structural supports, tiny motors, etc.
All proteins bind to other molecules with great specificity: each protein molecule can bind just one or
a few molecules. Sometimes tight, sometimes weak, and short lived.
Ligand -> any substance that that is bound by a protein – whether it is an ion, a small organic
molecule, or a macromolecule. Binding through weak non-covalent bonds (hydrogen,
van der Waals, electrostatic, hydrophobic forces), so many are needed. Should fit the
, protein molecule like a glove. The affinity of the molecules binding together will
determine how long they will stay bound.
Organic molecules -> Contain a carbon skeleton (carbons bonded to other carbons), Have
only covalent bonds, typically are quite large. Contain only carbon, hydrogen, oxygen,
sulphur, nitrogen, and phosphorus.
Inorganic molecules -> Do not usually have carbon, can contain many different elements,
often contain charged ions (ionic bonds), like salts, metals, and minerals
Binding site -> region of a protein that associates with a ligand. The atoms in the interior of
the protein have no direct contact with the ligand, but they provide an essential
framework that gives the surface its contours and chemical properties.
Antibodies-> immunoglobulin proteins produces by the immune system in response to
foreign molecules. Each antibody binds to a particular target molecule extremely
tightly, either inactivating the target directly or marking it for destruction. Y-shaped
molecules with two identical antigen-binding sites, each complementary to a small
part of the antigen.
Antigen -> target molecule recognized by the antibody. Because there are potentially
billions of different antigens we might encounter, humans must be able to produce
billions of different antibodies – one of which will be specific for almost any antigen
imaginable.
Hypervariable loops (in variable domain)-> amino acid sequence in the loops on y-arms
(consisting of variable domain and constant domain) of antibodies can vary greatly
without altering the basic structure of antibody, which allows for an enormous
diversity of antigen-binding sites by changing length and amino acid sequence of the
loops.
For many proteins, binding to another molecule is their main function. There are also proteins for
which ligand binding is a necessary first step in their function, this is the case for
enzymes.
Enzymes -> remarkable and important molecules responsible for nearly all the chemical
transformations that occurs in cells. Bind to one or more ligands (substrates) and
convert them into chemically modified products, doing this repeatedly without
themselves being changed. Act as a catalyst, that creates and maintains all cell
components, making life possible.
Substrates -> ligands that enzymes bind to.
Each type of enzyme is highly specific. Often work in sets, with the products of one enzyme becoming
the substrate for the next -> resulting in an elaborate network of metabolic
pathways.
Vmax -> rate of enzymes with overflow of substrate so working as much as they can. An
enzyme’s performance depends on how rapidly it can process its substrate.
Km, Michaelis Constant -> to determine the concentration of substrate at which an enzyme
works at half it’s maximum speed.
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