Lecture 20 - Protein structure Flashcards
To what level is protein synthesis necessary to life
Necessary for protein turnover but not necessary for second to second survival
Peptides/oligopeptides def
20-30 a.a
Polypeptides def
> Peptides
Protein def
Natural polypeptides or complexes of polypeptides with WELL-DEFINED STRUCTURE
Unit of measurement for protein mass
daltons (1 Da = 1 g/mol)
Average weight of an amino acid
110 Da
Average length of a protein/which length it is usually higher than
> 1000 a.a.
largest known polypeptide, length, where it’s found, MW and what to say about his gene
Muscle protein titin, 30 000 a.a, MW = 3 MDa, but not the biggest gene
2 things that determine protein function
1) Overall shape
2) Distribution of amino acids throughout it and their distinctive chemical properties
2 major classes of amino acid side chains
1) Hydrophilic (polar charge distribution) - Can be charged or not
2) Hydrophobic (non polar charge distribution)
Entropy def
Measure of disorder
What is the hydrophobic effect
When hydrophobic molecule is in water, water molecules around it adopt a cage-like organization. When hydrophobic molecules coalesce, less water molecules are necessary to surround them and more are free so entropy is higher.
Oil drop model
Hydrophobic side chains of a protein on its inside
Hydrophilic side chains of a protein on its outside
Why hydrophobic side chains go on the inside in the oil drop model
To not force the cage structure of the water molecules around the hydrophilic side chains on the outside. (Basically, few or no cage structures necessary -> higher entropy)
Possible structures that a protein could adopt based only on the oil drop model and how many it really adopts
Infinite number but will adopt one or a small number of similar structures called conformations
Why protein adopts only one shape
Hierarchy of structural interactions define specific protein shape
What are called the specific local structural interactions in a peptide and what they do
Secondary and Tertiary structures : They define the peptide backbone in space
What would be a primary structure and where does it come from
a.a sequence. Is what is obtained from the ribosome
Secondary structure def
Local folding
Tertiary structure def
Overall conformation of the protein
Quatenary structure def.
Multimeric structure (assembly of independent peptides)
Supramolecular structure def
large-scale assembly (ex. ribosome)
Name 6 functions of proteins. What is function related to
Regulation, Structure (ex. in cell) , Movement, Catalysis, Signaling, Transport. Function related to structure
What is a secondary structure
Interactions within the peptide BACKBONE that can be stable and form regular parts in a protein
2 secondary structures
Alpha helix and Beta sheet
What is a tertiary structure/what defines it
Defined by the way alpha helices and beta sheets interact together
Assembly of alpha helices and beta sheets can form __________ within the tertiary structure
domains
Structure of amino acid
alpha carbon (central one), hydrogen, amino group, carboxyl group
Peptide bond formation and 2 names for the reaction (think about other product of that reaction)
Link between amino group of on a.a and carboxyl group from another a.a. Dehydration/Condensation (you obtain a water molecule)
why do we say that polarity is conserved within a peptide
because always free amino group and free carboxyl group at its ends
N terminus corresponds to the ___ end of the mRNA and C terminus of a peptide corresponds to the _____ end of the mRNA
N - 5’ end
C - 3’ end
2 major peptide chain backbone conformation and their proportion in a polypeptide
alpha-helix and beta-sheet. 60% of length of average polypeptide consists of those
What is the absence of a secondary structure (in some part of a protein) named
random coil
What bond is responsable for secondary structures within a polypeptide (same for the 2)
Bond between oxygen on carbonyl of peptide bond and hydrogen of an amino group
What is peptide bond exactly
N-terminus —- alpha carbon (C alpha) - carbonyl group - N-H group - alpha carbon (C alpha) —— C-terminus Peptide bond between C of carbonyl and N of N-H
alpha helix which groups on the peptide do H bonding
All polar groups of peptide backbone (all N-H and C=O)
alpha helix amount of residues by turn and reason
3.6 residues/turn because H bonds are tilted a little
alpha helix how it is formed and what is an important property of that
O on carbonyl does H-bond with H on N-H that is 4 residues (a.a) further. PERIODICITY
Surface of alpha helix, what its properties depend on
depend on side chains properties
Gross structure and how it is in reality
Straight rod but in fact is a little tilted because of H bonds
Beta sheet how it is formed
H bond formed but between a.a that are further away.
2 conditions for beta sheet to form
Folding will allow it to form and nothing in the way
Where side chains end up on beta sheet
Pointing to the top and to the bottom
Beta sheets can form between independent ________
peptides
Strands within a beta sheet can be _________ or ________
parallel or anti-parallel
Tertiary structure : overall conformation of the polypeptide which refers to the _____________ of its multiple _______ structures
spacial organization of its multiple secondary structures
5 ways of representing a tertiary structure
1) alphaC backbone trace
2) Ball-and-stick model
3) Ribbon diagram
4) Water-accessible surface
5) Hybrid model
C alpha backbone trace characteristics
shows secondary structures based on colour
Ball-and-stick model characteristics
shows every atom so rarely used because too busy
Ribbon diagram characteristics
Most popular. Secondary structures are represented as ribbons but not random coils so allows to identify random coils and secondary structures
Water-accessible surface characteristics
shows surface in 2 colours for positive and negative charge. Important because it’s what is seen by the milieu
Hybrid model characteristics
Enveloppe (surface) + backbone elements)
What is Ras
a small GTPase
3 motifs of protein secondary structure
1) Coiled-coil motif
2) EF hand/helix-loop-helix motif
3) Zinc-finger motif
Coiled-coil motif description
2 alpha helices of same or different protein that coil together because have a repeat of 7 a.a in which 1st and 7th a.a are hydrophobic so these go on the inside
other name for Coiled-coil motif + its exact shape
(leucine) zipper. Looks like a straight rod but is a little tilted
What is the function of coiled-coil motif
Involved in protein-protein interactions
EF hand/helix-loop-helix motif description
loop between 2 helices contains amino acid that binds calcium
Function of EF hand/helix-loop-helix motif
Ca 2+ binding motif
Zinc-finger motif description
Part is an alpha helix and other part is a sheet of antiparallel beta strands. These parts bind a zinc 2+ ion
Zinc-finger motif function/ex of molecule it can help bind to/protein where we saw it
Common in transcription factors : binds to DNA/RNA
4 major structural classes of proteins
Fibrous, Globular, Transmembrane and intrinsically disorder proteins
Intrinsically disorder proteins def.
Random coils under physiological conditions and therefore exposed to proteolysis by proteases and phosphorylation by kinases
Typical function of intrinsically disorder proteins (3) (very generally)
1) signaling molecules
2) regulators of other molecules
3) scaffolds for multiple proteins, small molecules and ions.
2 main things intrinsically disorder proteins do
1) Interact with partner proteins
2) Fold into well-defined conformation after binding to partner proteins
what could make a protein intrinsically disorder (2)
High net charge (rich in polar amino acids such as proline) and poor in hydrophobic residues
What drives intrinsically disorder protein’s function
their flexibility
4 exemples of function/advantages of intrinsically disorder regions within a protein
1) Flexibility
2) Site for post-translational protein modification
3) Site for protease digestion (autoinhibition)
4) Intracellular sorting of proteins
2 exemples of disorder proteins seen with Zetka
CTD tail of Pol II (phosphorylated)
N-termini of histones (PTMs such as acetylation, methylation)
2 exemples of tests for identifying intrinsically disorder proteins
1) Protease digestion sensitivity (more disordered = more vulnerable)
2) Spectroscopy
