Sept 8 Protein Structure Flashcards
what are the bonds linking amino acids together?
peptide bonds
what is the basic biological point of DNA and RNA?
to allow the synthesis of specific proteins which carry out the chemical and physical functions of cells
what is the size of the smallest proteins?
~40 amino acids in length
what is the average size of a protein?
~300-400 amino acids
what is the largest known protein and how many amino acids long?
titin, muscle protein
~30,000 amino acids
what is the primary structure of proteins?
the specific sequence of amino acids
what kinds of shapes are created?
definite 3-D structures depending on the sequence of amino acids
what determines the function of a protein?
its overall shape (specific folding pattern) and the distribution of amino acids with distinctive chemical properties throughout the overall shape
what are the two major classes of amino acid side chains?
hydrophilic
water loving
polar electronic charge distribution
interact well with water
hydrophobic
non polar charge distribution
do not interact well with water
what is the hydrophobic effect?
water molecules surrounding hydrophobic molecules dispersed in water adopt a constrained, cage like organisation, which has low entropy (stable)
what happens if hydrophobic molecules coalesce? (come together to form one mass or whole)
total number of low entropy constrained water molecules is reduced
net increase in entropy
separate hydrophobic and aqueous phases
what favours the coalescence of hydrophobic molecules?
weak non covalent van der waals intermolecular interactions
what is the secondary structure of proteins?
local folding and hydrogen bonding
(alpha helix or beta sheets)
what is the tertiary structure of proteins?
overall conformation
spatial organization of the multiple secondary structure elements
what is the quaternary structure of proteins?
multimeric structure (when multiple proteins come together)
what are supramolecular structures?
large scale assembly of proteins
what are the different functions of proteins? (8)
structure
movement
molecular transformation
signalling
transport
binding
catalysis
regulation
what dictates the protein structure and function?
the amino acid sequence (primary structure)
indirectly determined by DNA
what proportion of a polypeptide do alpha helix and beta sheets occupy? and what is the rest?
60%
the rest is made of irregular structures, coils and turns, or is disordered.
where does the bonding occur to create those structures?
peptide bond carbonyl O atoms on one amino acid and amino group hydrogens on a different amino acid residue
what is the gross structure of an alpha helix?
a straight rod
what is an important covalent bond interaction that is important in an amino acid?
side chain of amino acid cysteine contains sulfhydryl group that can form covalent S-S (disulfide) bonds with other cysteine side chains
where can those disulfide bonds be found and what do they contribute to?
intrachain, contributing to the tertiary structure
interchain, contributing to the quaternary structure
what is a “motif” in protein structure?
combination of secondary structures forming distinct local 3D structure
do not contain enough bonds to maintain shape if it is cut away from the rest of the protein
rest of protein also contributes to its stability
motifs are not structurally independent entities
what are protein domains?
larger than motifs (less than 40 AA long)
compactly folded
can be made of various motifs
characteristic 3D structures within proteins
could maintain shape if cut away from rest of protein
rest of protein contributes little to the stability
structurally independent entities, covalently joined to the rest of the protein
what are the four major structural classes of proteins?
fibrous proteins
globular proteins
integral membrane proteins
intrinsically disordered proteins
what are intrinsically disordered proteins?
proteins or protein segments that exist as random coils under physiological conditions
may adopt a specific secondary/tertiary structure upon binging to a well structured partner protein
what are supramolecular complexes and an example?
large molecular machines made up of multiple distinct proteins, each of which may contain multiple subunits
example: transcription initiation complex
what are structural proteins?
determine the shape of cells and their extracellular environments
serve as guides to direct the movement of organelles and molecules
usually formed by assembly of multiple proteins subunits into very large and very long structures
what are scaffold proteins?
bring other proteins together into ordered arrays to perform specific functions more efficiently than if they were separate
what are enzymes?
proteins that catalyse chemical reactions
what are membrane transport proteins?
embedded in cellular membranes and permit the flow of ions and molecules across the membranes
what are regulatory proteins?
signals, switches and sensors to control activities of cells by altering the functions of other proteins and genes
what are signalling proteins?
hormones and cell surface receptors and transmit extracellular signals to cell interior
what are motor proteins?
responsible for the movement of other proteins
what are amino acids sometimes reffered to as?
residues
how many residues per turn in an alpha helix? and why is it that number and not a whole number?
3.6
(a 36 amino acid long helix will have 10 turns)
not 4 because Hydrogen bonds are tilted
how can the different strands be arranged in a beta sheet?
parallel (all strands point to the same side) or antiparallel (the strands point to different sides
what is a functional domain?
a region of a protein that exhibits a particular activity characteristic of that protein
what is the domain architecture?
the organisation (order) of domains within a multidomain protein
what are topological domains?
regions of proteins that are defined by their distinct spatial relationships to the rest of the protein
can comprise one or more structural and functional domains
what are proteins that have a common ancestor called?
homologs
what are globular proteins?
generally water soluble
compactly folded structures
often spheroidal
mixture of secondary structures (both alpha and beta)
what are fibrous proteins?
large, elongated
often stiff
long chain comprised of many tandem copies of a short AA sequence motif that forms a repeating pattern
usually play a structural role or participate in cellular movements
what is an intrinsically disordered region (IDR)?
a segment of a protein that is very flexible, with no fixed well ordered conformation
if the entire protein has no well ordered conformation, is it called an intrinsically disordered protein (IDP)
what is the native state of a protein?
one or a few closely related conformations that proteins are in when they are in their normal functional states
what is metabolic coupling?
when proteins assemble together to be more efficient
what are biomolecular condensates?
membraneless compartments in cells, often compared to liquid droplets
chemically and physically distinct from their surroundings
can break apart into smaller droplets or fuse together
what affects the capacity of proteins to form condensates?
depends on their structures and the surrounding environment (pH, temperature etc)
between what elements are hydrogen bonds created in protein secondary structure?
between carbonyl O (C double bond O) atoms on one amino acid and the amino group H (N–H) on another amino acid
which amino acid binds to which amino acid in an alpha helix?
amino acid n bonds with amino acid n+4
(1 to 5, 2 to 6, 3 to 7 etc)
explain how the coiled-coil motif is oriented/works?
heptad repeat of amino acids, and amino acids 1 and 4 are hydrophobic
hydrophobic amino acids cannot be exposed to water therefore two molecules join together (2 coils)
how are side chains arranged in a beta sheet and how does that affect the protein?
side chains protrude above and below the plane of the beta sheet
determines the interactions of the beta sheet with other parts of the protein and also its propensity to form
what type of stereoisomers are amino acids?
L stereoisomers
it’s the way it was chosen by nature
