special topic 2 - protein structure Flashcards
what atoms are amino acids all made of
C, O, N, H and occasionally S
what is the alpha carbon
the central carbon of an amino acid (stereogenic centre)
how is the polymerisation of amino acids reversed
hydrolysis reaction to return to amino acid monomers
describe the joining of amino acids
large ribosomal unit catalyses dehydration condensation reaction in which carboxyl and amino groups join to form peptide bond.
4 possible characteristics of amino acids
hydrophobic, hydrophilic, acidic and negatively charged, basic and positively charged
differentiate between an amino acid and a residue
amino acids are usually referred to as residues once in a polypeptide chain
what is the secondary structure
local folding of the polypeptide chain - the beginning of hydrogen bonding and folding. alpha helices and beta sheets are formed.
what does the artemis protein do
involved in antibody production. without it we would need to live in a sterilised environment.
what is the hydrophobic effect, and its role in proteins
the interaction of non-polar or hydrophobic side chains with an aqueous environment, and subsequent burial into the proteins internal environment . important for protein folding, means most hydrophobic residues are found facing inward and hydrophilic residues are found on outside.
what are alpha helices and beta sheets
helices are helical structures of spiralling backbones with side chains pointing outwards, with hydrogen bonds maintaining the twisting structure.
beta sheets backbones extend our then double back on themselves, hydrogen bonds extend straight across between backbones.
what is the tertiary structure
full folding of polypeptide to make a large structure, this is many proteins final form
what is quaternary folding
multiple tertiary polypeptide subunits joining to form a larger protein structure
what is a tetramer and an example of one?
4 protein subunits forming a quaternary structure. hemoglobin is a tetramer.
structure of malic enzyme
2 dimers joined together
structure, function, and examples of a globular protein
globular proteins are highly folded and look like ‘globs’, usually have metabolic function. examples are artemis and alpha amylase.
structure, function, and examples of a fibrous protein
tend to be long and spindly, usually involved in structural elements. e.g actin and collagen.
what is alpha amylase
an enzyme secreted in saliva to break down food
four types of bonds holding together proteins
hydrogen bonding, electrostatic interactions, disulphide bonds, hydrophobic interactions.
how many amino acids can participate in electrostatic interactions, give example of 2
5, e.g glutamic acid and lysine.
what does code E116 (or similar) refer to.
letter corresponds to protein where possible, but is often not the first letter. number indicates number of residues downstream from the N terminus the amino acid is.
what is the second strongest type of bond in a protein, explain its structure and location
disulfide bond. two sulfide bonds form a disulfide ‘bridge’ between two cysteine amino acids.
what are hydrophobic interactions
clustering of hydrophobic side chains together away from water
explain how an egg becomes insoluble in heat
albumin proteins unravel in heat, then the unravelled proteins form new permanent disulfide bonds. proteins can’t return to original folding, become protein aggregate with hydrophobic amino acids on the outside.
proteins are _______ stable, as they are both ______ and can be ________
marginally stable, are maintained but can be denatured
what denatures proteins
pH, temperature, salt concentration,
what is a protein aggregate
large misfolded or damaged protein structures, which often are insoluble and have lost their original function.
experimental methods of determining protein structure
crystallography, cryo electron microscopy, NMR
how does crystallography work
protein crystals are made, and their diffraction patterns are used to map electron density to determine atomic structure
what does malic enzyme do
catalyses conversion of malate to pyruvate, in presence of NAD+/NADP+
what is warburg effect/warburg glycolysis
the preferential conversion of pyruvate to lactate rather than entering the mitochondria for CAC. it is a crucial part of cancer cells ability to upregulate their own growth.
what role does malic enzyme play in cancer
in warburg conditions in cancer cells, glutamine amino acid is used to make malate, which magic enzyme converts to pyruvate for acetyl CoA to fuel CAC
what is NPD-389, what is its medicinal function
an inhibitor for the malic enzyme, which malate competes unsuccessfully for. used in anti-cancer, as it disables cancer cells from making pyruvate for the CAC via malic enzyme.
ben krinkel’s new drug potency proportionate to NPD-389
4 times as potent
