Week 2 (All) Flashcards
explain the existence of amino acids as optical isomers
- all amino acids (except glycine) exist as optical isomers termed D and L forms.
- only L forms are ever found in proteins
- D-amino acids occur as part of bacterial cell walls and in some antibiotics, and D-serine is used as a signal molecule in the brain
how many amino acids carry a charge?
five of the 20 amino acids - including lysine and glutamic acid - have side chains that form ions in solution. the rest are uncharged.
two types of abbreviations given to amino acids
three-letter and one-letter abbreviations
what structural feature of amino acids allows for the presence of L and D isomers?
the alpha carbon is asymmetrical
why are chains of amino acids very flexible?
the two single bonds around the C in the amide bond allow rotation
list the amino acids with basic side chains
- lysine (Lys, K)
- arginine (Arg, R)
- histidine (His, H)
positive charge
list the amino acids with acidic side chains
- aspartic acid (Asp, D)
- glutamic acid (Glu, E)
negative charge
list the amino acids with uncharged polar side chains
- asparagine (Asn, N)
- glutamine (Gln, Q)
amide N is not charged but is polar
- serine (Ser, S)
- threonine (Thr, T)
- tyrosine (Tyr, Y)
the OH group is polar
list the amino acids with non polar side chains
- alanine (ala, A)
- valine (val, V)
- leucine (leu, L)
- isoleucine (Ile, I)
- proline (pro, P)
- phenylalanine (Phe, F)
- methionine (met, M)
- tryptophan (trp, W)
- glycine (Gly, G)
- cysteine (Cys, C)
how is the polypeptide backbone formed?
from a repeating sequence of the core atoms (-N-C-C-) found in every amino acid
what constrains the shape of folded, long polypeptide chains/
many sets of weak non covalent bonds that form within proteins (hydrogen bonds, electrostatic attractions, and van der Waals)
how does the distribution of polar and non polar amino acids in a protein an important factor governing the folding of a protein?
- non polar (hydrophobic) side chains tend to cluster in the interior of the folded protein to avoid constant with the aqueous surroundings
- polar side chains arrange themselves near the outside of the folded protein, where they can form H bonds with water and other polar molecules
when polar amino acids are buried within the protein, they are usually hydrogen bonded to
other polar amino acids or to the polypeptide backbone
define the conformation of a polypeptide chain
the final folded structure
conformation is determined by
the shape in which its free energy is minimised.
the folding process is energetically —–. why?
favourable; it releases heat and increases the disorder of the universe
how can a protein be denatured and what does this mean?
protein is unfolded into a flexible polypeptide chain by treatment with solvents that disrupt the noncovalent bonds holding the folded chain together.
renaturation
when the denaturing solvent is removed, and the proper conditions are provided, the protein often refolds spontaneously into its original conformation
2 ways in which chaperone proteins work
- bind to partly folded chains and help them to fold along the most energetically favourable pathway
- form isolation chambers in which single polypeptide chains can fold without the risk of forming aggregates
function of chaperone proteins
assist protein folding in cells
function of bacterial transport protein HPr
facilitates transport of sugar into bacterial cells
4 types of 3D structure models
- backbone model
- ribbon model
- wire model
- space-filling model
in what protein was the alpha helix found?
in the protein alpha-keratin
in what protein was the beta sheet found?
in the protein fibroin
describe handedness of a helix
- depending on the way it twists, a helix is said to be either right-handed or left-handed
- handedness is not affected by turning the helix upside down, but it is reversed if the helix is reflected in a mirror
where are short regions of alpha helix especially abundant?
- in proteins that are embedded in cell membranes, such as transport proteins and receptors
- the portions of a transmembrane protein that cross the lipid bilayer usually form an alpha helix composed largely of amino acids with non polar Sid chains
- polypeptide backbone is hydrogen bonded to itself in the alpha helix, where it is shielded from the hydrophobic lipid environment of the membrane by the protruding non polar side chains
coiled coil
two or three alpha helices wrap around one another to form this stable structure. forms when the alpha helices have most of their nonpolar/hydrophobic side chains along one side, so can twist around each other with their hydrophobic side chains facing inward - minimising contact with the aqueous cytosol
distinguish between parallel and antiparallel beta sheets
parallel: when the neighbouring segments run in the same orientation (eg from N-terminus to C-terminus)
antiparallel: when they run in opposite directions
properties of beta sheets
- give silk fibres their tensile strength
- form basis of amyloid structures (beta sheets stacked together in long rows with their amino acid side chains interdigitated)
use of amyloid structures
- cells specialised for secretion store peptide or protein hormones in transport vesicles
- hormones adopt an amyloid structure to allow efficient packaging and unfold again once they reach cell exterior
how can amyloid structures cause disease?
- when proteins fold incorrectly, they sometimes form amyloid structures that can damage cells
- brain is particularly vulnerable to the damage caused by an accumulation of amyloid aggregates
- most neurone cannot regenerate -> neurodegenerative diseases like Alzheimer’s, Parkinson’s, Huntington’s
prions
- misfolded proteins
- infectious: amyloid form can convert properly folded molecules of the protein into the abnormal, disease-causing conformation
- move up the food chain and find their way to the brain where they form aggregates that spread from cell to cell
- scrapie in sheep, BSE/mad cow, CJD in humans
draw a diagram for how prions lead to amyloid fibrils
- normal protein can adopt an abnormal misfolded prion form
- prion form can bind to normal form, inducing conversion to abnormal conformation
- abnormal prion proteins propagate to form amyloid fibrils
give an example of the different functions of different protein domains
bacterial catabolite activator protein (CAP) has two domains:
- small domain that binds to DNA
- large domain that binds to cyclic AMP, an intracellular signalling molecule
- when the large domain binds cyclic AMP, it causes a conformational change in the protein that enables the small domain to bind to a specific DNA sequence and thereby promote the expression of an adjacent gene.
unstructured sequences
- larger proteins can contain many domains which are often connected by relatively short, unstructured lengths of polypeptide chain
- continually bend and flex due to thermal buffeting
why is only a minuscule fraction of the unimaginably large collection of potential polypeptide sequences actually made by cells?
- most biological functions depend on proteins with stable, well-defined 3D conformations
- functional proteins must not engage in unwanted associations with other proteins
- vast majority of potential protein sequences has been eliminated by natural selection through trial-and-error process
an example of a protein family
serine proteases, a family of protein-cleaving enzymes including digestive enzymes
- portions of amino acid sequences nearly the same
- most of the detailed twists and turns in their polypeptide chains are virtually identical
- distinct enzymatic activities
define a binding site
any region on a protein\s surface that interacts with another molecule through sets of noncovalent bonds
define a subunit
- if a binding site on one protein binds to a second protein, this will form a larger protein with a quaternary structure
- each polypeptide chain in such a protein is called a subunit
dimer
two identical, folded polypeptide chains form a symmetrical complex of two protein subunits held together by interactions between two identical binding sites
proteins can assemble into three main assemblies:
filaments (eg helical actin filaments), sheets, spheres, hollow tubes, rings
globular proteins
polypeptide chain folds up into a compact shape like a ball with an irregular surface
fibrous proteins
- have roles in the cell that require them to span a large distance
- have a simple, elongated 3D structure
intermediate filaments
- coiled-coil regions are capped at either end by globular domains containing binding sites that allow them to assemble into ropelike intermediate filaments
- component of the cytoskeleton that gives cells mechanical strengths
what is the role of fibrous proteins outside of the cell?
form the gel-like extracellular matrix that helps bind cells together to form tissues
describe collagen
- most abundant fibrous extracellular protein in animal tissues
- consists of 3 long polypeptide chain, each containing glycine (non polar) at every third positioin
- regular structure allows chains to wind around one another to generate a long, regular triple helix with glycine at its core
- collagen molecules bind to one another forming strong fibrils
describe elastin
- formed from loose and unstructured polypeptide chains that are covalently cross-linked
- resulting elastic fibers enable skin, arteries, lungs to stretch and recoil without tearing
how do protein molecules attached to the surface of a cell’s plasma membrane/secreted as part of the extracellular matrix maintain their structures among the potentially harsh extracellular conditions?
- stabilised by covalent cross-linkages
- can either tie together 2 AAs in the same polypeptide chain or join together many polypeptide chains in a large protein complex
- most common are disulphide bonds
how are disulphide bonds formed?
before a protein is secreted, by an enzyme in the endoplasmic reticulum that links two -SH groups from cysteine side chains
example of disulphide bonds
lysozyme retains its antibacterial activity for a long time due to disulfide cross-links
why do disulfide bonds generally not form in the cell cytosol?
proteins do not require this type of structural reinforcement in the relatively mild conditions inside the cell
how do proteins proceed in a singular direction (eg when walking along a cytoskeletal fibre)?
- conformational change must be unidirectional
- one of the steps must be made irreversible
- this is achieved by coupling one of the conformational changes to the hydrolysis of an ATP molecule tightly bound to the protein
- great deal of free energy is released when ATP is hydrolysed, making it very unlikely that the protein will undergo the reverse shape change needed to move backward
motor proteins are also known as
ATPases
the most complex tasks within cells are carried out by
large protein assemblies formed from many protein molecules
how do protein machines work?
the hydrolysis of bound nucleoside triphosphate (ATP or GTP) drives an ordered series of conformational changes in some of the individual protein subunits, enabling the ensemble of proteins to move coordinately
how do proteins locate their partners - and assemble into complexes that are activated only when and where they are needed - within the crowded conditions inside the cell?
many protein complexes are brought together by scaffold proteins
define a scaffold protein
large molecules that contain binding site recognised by multiple proteins
how do scaffold proteins work
they bind a specific set of interacting proteins, greatly enhancing the rate of a particular chemical reaction while also confining the chemistry to a particular area of the cell
give an example of cells that use scaffold proteins
nerve cells use scaffold proteins to organise the specialised proteins that localise at the synapse between one cell and the net
describe the structure of scaffold proteins
- though some scaffolds are rigid, the most abundant ones are very elastic
- contain long unstructured regions that bend, enhancing the collisions between the specific molecules bound to the scaffold
define a bimolecular condensate
- assemblies which often contain RNA and protein, forming fluid, membrane less subcompartments that perform a particular biochemical function
- contains at least one type of scaffold protein or scaffold RNA molecule that can interact w ‘clients’ which become concentrated
give an example of a biomolecular condensate
nucleolus
phase separation
property where the dynamic network of weak interactions that allows individual molecules to come and go, while the condensate as a whole remains intact and separated from its surroundings
the existence of condensates is
transient but stable
describe the process of purifying proteins from cells or tissues
- breaking open the cells to release their contents
- initial fractionation procedure to separate out the class of molecules of interest
- isolating the desired protein
- can be used in biochemical assays to study the details of its activity
cell homogenate or extract
resulting slurry after breaking open cells to release their contents
how does chromatography purify the protein
different materials are used to separate the individual components of a complex mixture into fractions, based on the properties of the protein such as size, shape, or electrical charge
affinity chromatography
- most efficient form of protein chromatography
- separates polypeptides on the basis of their ability to bind to a particular molecule
electrophoresis
- used to separate proteins based on size and net charge
- yields a number of bands or spots that can be visualised by staining; each band or spot contains a different protein
how was protein sequencing done in earlier years?
- protein broken down into smaller pieces using a selective protease
- identities of the aas in each fragment determined chemically
describe how mass spectrometry is performed
- peptides derived by digestion with trypsin are blasted with a laser - this heats the peptides, causing them to become ionised and then ejected as a gas
- peptide ions are accelerated by a powerful electric field and fly toward a detector
- time it takes them to arrive is related to their mass and charge
tandem mass spectrometry
- complex mixture of proteins
- after peptides pass through first mass spec, they are broken into even smaller fragments and analysed by a second mass spec
what methods do scientists use to determine experimentally the structure of purified proteins?
X-ray crystallography, NMR spec, cry-electron microscopy
how do we know the vast majority of proteins may fold up to a limited number of structural domains?
although the number of multi domain families in protein databases is growing rapidly, the discovery of novel single domains is levelling off
how are proteins useful in the industry?
bacteria, yeast, and cultured mammalian cells are now used to mass-produce a variety of therapeutic proteins, such as insulin, human growth hormone, and even the fertility-enhancing drugs used to boost egg production in women undergoing IVF
give an example of how investigators have designed proteins with completely novel functions
they have built a synthetic protein that contains a special cage that can be made to swing open like a latch when exposed to a compound that serves as its molecular key. this can be used to dispense a drug or to deliver a molecule
parts of an amino acid
- alpha carbon to which all other atoms and groups are attached
- amino group (NH2)
- carboxyl group (COOH)
- R group - side chain
how is a peptide bond formed?
- there is a reaction between the carboxyl group on one amino acid and the amino group on the other.
- the OH group on the carboxyl end of one amino acid reacts with the hydrogen atom on the amino group of the other to eliminate a molecule of water
what two features are always present in polypeptides, even in short chains?
an amino end (N-terminus) and a carboxyl end (C-terminus)
residues
what amino acids are referred to as once they have joined together into a polypeptide chain
in an alpha helix, where does hydrogen bonding occur between residues?
- there is hydrogen bonding between an oxygen atom of the carbonyl group of residue ‘n’ and the hydrogen atom of the amide group of the residue ‘n+4’ on the same polypeptide chain
- this is repeated in a regular fashion (1 and 5, 2 and 6, 3 and 7)
- the peptide chain thus twists around on itself and forms a cylindrical structure (a stable alpha helix)
are R-groups involved in the formation of alpha helices?
no
give the hierarchy of protein structure and examples for each
- primary; AA sequence
- secondary; local folding, like alpha helix and beta sheet
- tertiary; long-range folding, essentially 3D structure
- quaternary; multimeric organisation (the organization of multiple polypeptide chains with respect to each other)
- multiprotein complexes
major categories of amino acids
- acidic: negatively charged
- basic: positively charged
- uncharged polar: tends to form H=bonds, interact with h2o on the outside of proteins
- non polar: on the inside of proteins, ‘hydrophobic core’ due to hydrophobic interactions. found in lipid bilayer
what type of amino acids usually have enzymatic functions?
polar amino acids
what is unique about the structure of cysteine?
- contains interchain disulphide bonds
- whether these occur can be controlled by the cell based on redox conditions
- helps the protein hold its shape with physical or chemical stress
how is the primary structure of a protein numbered?
from the amino group (N-terminus)
give an example of how differences in primary amino acid sequence matter
- vasopressin and oxytocin
- both are 9AA long neuropeptide hormones
- AA sequence is identical except at 2 positions
- vasopressin controls urine production rates and oxytocin is involved in birth, lactation, and pair bonding
give an example of how the order of AA’s is important too
- Leu-Enkephalin (pentapeptide N-Tyr-Gly-Gly-Phe-Leu-C) is a natural opioid peptide which down modulates the perception of pain
- the pentapeptide N-Leu-Phe-Gly-Gly-Tyr-C, basically a reversal, has no pharmacological effects
- the NH2-COOH orientation of the peptide is essential for function
describe the structure of the beta sheet
- H-bonding between carbonyl oxygen (C=O) of 1aa and amide hydrogen (N-H) of aa in neighbouring strand
- R groups not involved but alternately project up and down
- beta sheets typically contains 4-5 beta strands but can have more than 10
types of beta sheets
- anti-parallel
- parallel
where are beta sheets found
strong, rigid structure found in silk
compare and contrast hydrogen bonding in alpha helices and beta sheets
- H bonds formed between carbonyl oxygen, amide hydrogen in peptide backbone
Alpha: - 4 AA’s apart and within the same segment of
pp chain
Beta: - Between AA’s in different segments or
strands of pp chain
coiled coil
- when alpha helices are twisting together
- amphipathic alpha helix
- these are found in alpha-keratin of skin, hair, and also myosin motor proteins
- helices wrap around each other to minimise exposure of hydrophobic amino acid side chains to aqueous environment
tertiary structure
- 3D overall structure of a protein
- held together by hydrophobic interactions, non-covalent bonds (hydrogen bonds, dipole-dipole and van der Waals), and covalent disulphide bonds
What determines the confirmations into which proteins fold?
proteins generally fold into the conformation that is the most energetically favourable
what helps fold proteins?
Proteins will fold into the shape dictated by their
amino acid sequence, but chaperone proteins help make the process more efficient and reliable
in living cells.
3 types of hydrogen bonding within tertiary structure of a protein
backbone to backbone: hydrogen bond between atoms of two peptide bonds
backbone to side chain: hydrogen bond between atoms of a peptide bond and an amino acid side chain
side chain to side chain: hydrogen bond between atoms of two amino acid side chains
What are protein domains?
- portion of a protein that has its own tertiary structure, often functioning in a semi-independent manner
- eukaryotic proteins often have 2 or more domains connected by intrinsically disordered sequences
- domains are important for the evolution of proteins
domains are often specialised for
different functions
Src protein kinase
- contains SH3 domain, SH2 domain, and kinase domain with 2 lobes
- phosphorylates amino acids to change the activity of proteins
- SH2 regulates kinase domain
- SH3 regulates kinase domain in a different way
- kinase domain phosphorylates the amino acids
protein families
- have similar amino acid sequences and tertiary structures
- however, members have often evolved to have different functions
- most proteins belong to families with similar structural domains
quaternary structure
proteins that have more than one polypeptide chain
describe haemoglobin
- 4 separate polypeptide chains
- 2 alpha subunits and 2 beta subunits
- each subunit is a separate polypeptide
- sickle cell anaemia is caused by a mutation in the beta subunit
give 3 types of multi protein complexes
- many identical subunits (eg actin filaments)
- mixtures of different proteins and DNA/RNA (eg viruses and ribosomes)
- very dynamic assemblies of proteins to form molecular machines (eg machines for DNA replication initiation or for transcription)
scaffold proteins
assemble other proteins needed for a particular process, getting them close together so work can be carried out
how are proteins studied?
- first purify protein/proteins of interest via various types of electrophoresis and affinity chromatography
- then determine amino acid sequence (eg mass spectrometry)
- discover precise 3D structure using techniques such as x ray crystallography, nuclear magnetic resonance spectroscopy or cry-electron microscopy
what properties can be exploited to separate proteins from one another so they can be studied individually?
- size, shape, charge, hydrophobicity, and their affinity for other molecules.
AI used to predict protein structure
alphafold to predict protein structure from linear amino acid sequences
proteomics
large scale study of proteins
- identity and structure of proteins
- protein-protein interactions, regulation of these interactions and their position within a pathway
- abundance and turnover of proteins
- location within a cell or tissue
- bioinformatics, statistics, and artificial intelligence often in combination with other ‘omics’ data
