Special Topics: Protein Structure and Function Flashcards
What is the central Dogma
DNA (genes) >RNA > Amino Acids > Polypeptide (proteins)
How many proteins in a bacteria cell?
~2 million
How many proteins in a human cell
~1-3 billion
What is a protein/polypeptide?
A chain/polymer of amino acids linked by peptide bonds (Polypeptide)
What is a peptide?
Short polypeptides (approx. less than 50 aa)
What is a dipeptides, tripeptides, or tetrapeptides?
Very short peptides (2,3,4 amino acids in length)
What is a residue?
Individual amino acids in a polypeptide/protein
What are proteins made of?
amino acids
What is the term given to the the central carbon of an amino acid
Alpha carbon
What are the parts of an amino acid
They have an amino, carboxyl group, central alpha carbon and a side chain
They can also have an ionised form
How is a peptide bond formed?
Amino group targets carbonyl group fo the second amino acid, it releases water and they join together in a condensation/dehydration reaction
What are the main properties of a peptide bond
Rigid (cannot rotate), O-C-N-H of the Peptide bonds are coplanar
Where can rotation occur in amino acids?
Rotation can occur at the single bonds between the α-carbon and is neighbouring atoms
What is the more stable R-group orientation in an amino acid?
Trans (side chains alternate)
What is the least stable R-group orientation in an amino acid?
Cis (due to repulsion of side chains)
What direction are proteins drawn?
from N (amino) terminus to the C (carboxyl) terminus
What determines the behaviour of a amino acid in a protein?
Its side chain (hydrophobic, polar, hydrophilic, nonpolar, positive and negative charged)
What is the shape of a protein important for?
Its function
Where does the shape of an active site in a protein/enzyme come from?
This shape is driven by the chemical properties and sequences of the amino acids in the protein
What proteins have an active site?
Enzymes to allow substrates to bind
How do enzymes interact with substrates?
A substrate binds to an active site can cause conformational changes which provide a function or strengthen the interaction
What are the two types of models for proteins?
Induced fit (has conformational change) and “lock and key” model
What is the induced fit model?
The model of the enzyme that shows the substrate binding to the active site and the active site altering slightly
What is the lock and key model?
The model of the enzyme that shows the substrate fitting perfectly into the active site
What is the primary structure of a protein
The unique sequence of amino acids of a protein
How can we know what the primary structure of a protein is?
Looking at the DNA sequence of genes
What is a secondary structure
Localised folding of the polypeptide driven by hydrogen bonding interactions within the polypeptide backbone
What is NOT involved in secondary structures
R groups
What are the two types of secondary structures?
β sheet (aka β pleated sheet) and the α helix
What are the large aromatic residues favoured in β strands
tyrosine, phenylalanine, tryptophan
What are the β-branched amino acids favoured in β strands
threonine, valine, isoleucine
What are the residues favoured in α helices?
Methionine, alanine, leucine, glutamate, and lysine
What residues are NOT favoured in α helices?
Proline and glycine
Can we predict the secondary structure of a protein from its DNA sequence?
Yes (due to favoured residues)
How can β sheets be arranged?
They can be parallel (both strands going from N Terminus to C) or going in opposite directions
What causes β sheets to be formed
H bonding between a backbone Amine (N-H) group on one strand, and a backbone Carbonyl (C=O) group on another strand
What direction are α helices
right handed
Number of amino acids in one turn of the helix
3.6
Pitch of an alpha helix
5.4 Å (Angstroms)(0.54 nm)
What causes α helices to form?
Driven by H bonding between a backbone Amine (N-H) group a backbone Carbonyl (C=O) group 3 or 4 residues earlier.
Which type of secondary structure is tightly packed?
α helices
Which type of secondary structure has side chains protruding outwards?
α helices
What is the tertiary structure of a protein?
The three dimensional shape of a protein
What causes a tertiary structure?
the chemistry of the side chains (R groups) and interactions between them
What is the general type of bond in a tertiary structure?
Non covalent
What is an ionic bond in a tertiary structure?
Opposite charged R groups attract. Like charges can repel
What is a hydrophobic bond in a tertiary structure?
Hydrophobic R groups of non-polar amino acids cluster in the interior of the protein
What is a hydrophilic bond in a tertiary structure?
Hydrophilic R groups lie on the outside surface of the protein to interact with water
How do hydrophobic R groups work in membrane spanning proteins
Hydrophobic R groups may be outside interacting with the lipid tails
What is a disulfide bond in a tertiary structure?
Thiol (S-H) groups are oxidized removing the H and forming a covalent linkage between the two Sulphur atoms.
What is the amino acid capable of forming a disulphide bond?
Cystine
Strength of bonds in tertiary structures from strongest to weakest
Disulphide > Ionic > hydrogen > Van der Waals
What is a cofactor?
Non-protein helpers that may be bound to the protein
Examples of cofactors
Metal ions (Mg, Mn, Zn, Fe, Ca), organic molecules (heme), or vitamins
How and why do proteins use cofactors
Some proteins (particularly enzymes) can coordinate a cofactor or “prosthetic groups” within the protein using the R groups. This may be essential for the function and/or structure of the protein
What is a quaternary structure?
Arrangement of two or more polypeptide chains. Because some proteins are composed of more than one polypeptide chain so they need to fold the multiple protein subunits
What is a homooligomer
Quaternary structure is constructed from a single type of subunit
What is a heterooligomer
Quaternary structure is constructed from different types of subunits
What drives quaternary structures?
Ionic interactions, hydrogen bonding, hydrophobic interactions
Are quaternary structures dynamic?
Yes
What are the types of proteins?
Globular, fibrous, membrane
Are globular or fibrous proteins soluble in water?
Globular
What are the functions of globular proteins?
enzymes, transport, immune
How are globular proteins arranged?
Irregular sequence and secondary structure
How much quaternary structure do globular proteins have?
Moderate or none
Are globular proteins stable?
They are not very stable
Examples of globular proteins
Enzymes, hemogloblin, antibodies
What are the functions of fibrous proteins?
structural
How are fibrous proteins arranged?
often repetitive primary and secondary structures
How much quaternary structure do fibrous proteins have?
High level
Are fibrous proteins stable?
Very stable (e.g. heat, pH)
Examples of fibrous proteins
Keratin, Actin, collagen, silk
What are membrane proteins?
proteins that traverse through a lipid bilayer (membrane)
What is contained in a transmembrane region?
single α-helix or α-helical bundle (R groups out and hydrophobic)
What do mitochondria and Gram negative bacteria contain in their membranes?
β-barrel ™ proteins
What type of amino acids are most present in membrane proteins?
non-polar (hydrophobic) amino acids
Where do non-polar side chains face in membrane proteins
Non-polar (hydrophobic) side chains face out toward the membrane
Where do polar side chains face in membrane proteins
Polar (hydrophilic) side chains face inwards
What does Abbe’s diffraction limit mean?
Abbe’s diffraction limit means we cannot see anything smaller than a mitochondrion on a microscope so we cannot see proteins
What is Abbe’s diffraction limit?
0.2 micrometres
What is Levinthal’s paradox
It is mathematically impossible for protein folding to occur by randomly trying every conformation until the lowest-energy one is found
What are the factors that contribute to successful protein folding
environment, temporality, chaperone proteins, enzymes
What are example of a correct environment needed for protein folding?
solute, salt concentration, pH, temperature, macromolecular crowding (how much is being crowded in)
What is temporality in protein folding?
Timing: co-translational folding as the polypeptide is coming of the ribosome (i.e. N folds before C term)
What do chaperones do in protein folding?
other proteins which bind to and prevent misfolding of parts of the protein
What do enzymes do in protein folding?
Enzymes form disulfide bonds
Which way of studying protein structure is the best
X Ray crystallography
What is resolution?
is the distance corresponding to the smallest observable feature: if two objects are closer than this
distance, they appear as one combined blob rather than two separate objects
What are the four types of protein structure models
Backbone Model
Ribbon Model
Wire Model
Space filling model
How does X-ray crystallography/diffraction occur?
You crystallise a pure protein and use the short wavelength of X-Rays and the basic principles of diffraction in a crystal lattice to deduce the atomic structure of a protein (using Bragg’s law and some complex math)
What is the most common type of method used to determine protein structure?
X-ray crystallography/diffraction
Which type of protein structure determining method has the best resolution?
X-ray crystallography/diffraction
Advantages of X-ray crystallography
Molecule size unimportant, very high resolution
Disadvantages of X-ray crystallography
crystallisation is slow and doesn’t always work, must be soluble
Disadvantages of NMR
molecules must be <30kDa, must be tagged with heavy C/N, must be soluble
How does Single Particle Cryogenic Electron Microscopy
work?
Freeze suspension of particles in thin layer of virtuous ice
Advantages of cryo-electron microscopy
relatively fast, high resolution, Can gain insights in to protein dynamics/movements
Tease out multiple conformations in one sample, can look at big protein complexes and membrane proteins which would never crystallise
Disadvantages of cryo-electron microscopy
molecules must be >100kDa, must be soluble
What method of protein structure determination was used for COVID-19?
Single Particle Cryogenic Electron Microscopy
