Proteins Flashcards
anabolic
building up
catabolic
breaking down
sequence to get a prot
roles of prots
- stryctural - collagen, keratin, fibroin
- movement - muscle fibres actin + myosin
- immune sys - antibodies
- endocrine sys - hormones + receptors
- transport - Hb, transferrin (Fe carrier)
- biological catalysis - enzs
general structure alpha aas
zwitterions
dipolar ion = no net charge unless R grp charged
aas in sol at normal physiological pH normally zwitterions
isomers alpha aas
asymmetric mols so 2 diff forms - optical isomers/enantiomers
* mirror images but can’t be superimposed onto each other
Types aas
- electrically charged side chains
- polar uncharged side chains
- hydrophobic side chains
- special cases
polar meaning
has pos + neg ends as charge not evenly distributed throughout
which aa tends to be found in coils
proline
prot primary structure
sequence aas joined peptide bonds bet carboxyl grp 1 aa + amino grp next
occur by condensation reaction where H20 mol removed
by convention: N-terminal on left
prot secondary structure
determined + maintained by H bonds bet O + H
* w/in prot backbone, not bet R grps
- alpha helix = folded into spiral w outer surface covered R grps to interact other prots etc
* CO grp residue n bonded NH grp residue (n+4) - beta-pleated sheets in parallel (sequences same direction) or anti-parallel (opp)
* can be diff peptide chains or 1 chain folded (therefore antiparallel)
prot tertiary structure
arrangement in space of aas, held together by diff interactions determined by sequence aas:
* disulphide bond
* side chain H bonding
* electrostatic attraction
* hydrophobic interactions - hydrophobic R grps sit together to avoid contact w water
* metal ion coordination
prot quaternary structure
interactions bet diff peptide chains by same side chain interactions:
* disulphide bond
* side chain H bonding
* electrostatic attraction
* hydrophobic interactions
* metal ion coordination
3 main types prot
- globular
- fibrous
- membrane
globular prots
- fold into compact structures - often w cleft for small mol
- usually hydrophobic side chains inside, hydrophillic outside to interact w aqueous environ = soluble
- majority prots
- e.g. enzs, antibodies
fibrous prots
- multiple strands held together strong bonding
- usually insoluble + structural
- e.g. collagen (skin, bone, tendon), keratin (hair, nails, horn), fibroin (silk)
mem prots
- hydrophobic regions sit in cell mem
- transmit mols + signals in/out cells
- e.g. channels + receptors
prion disease
disease starting from prot malformation:
genetic switch flipped + prot gradually to mainly beta sheets = sticky + aggregate , causing neuronal cell death
prions = infectious prots
bovine spongiform encephalopathy (BSE)
mad cow disease
neurodegenerative prion disease brain + spinal cord
* 2.5-8yr incubation
* transmissable to humans if you eat infected meat
role of enz
act as biological catalyst by increasing RoR w/o being changed themselves
* decrease activation E by:
1. bringing substrates together
2. excluding water
3. stabilising transition state
4. transferring chem grps
enz active site
3D region of enz that performs catalytic reaction, usually involving making/breaking bonds by binding substrate + converting it to product
binds specific aa side chains by weak forces:
* electrostatic interactions
* H bonds
* Van der Waals forces
* hydrophobic interactions
* sometimes reversible covalent bonds
forms predominantly non-polar environ
how are enzs made specific
properties + spatial arrangement relatively few aas at AS determine which mols can bind + so substrates
induced fit model for enz-substrate binding
as binds, aas move slightly to pull substrate in, change its structure slightly - for closer fit
so AS shape changes slightly
most enzs have this model
types enz-substrate binding
isosteric + allosteric
describe isosteric enz-substrate binding
RoR incrreases w substrate conc until enz saturated
parameters defining enz activity from ‘Michaelis-Menten’ plot initial rate + substrate conc, showing how quickly substrate converted product
most enzs
allosteric enz-substrate binding
enz changes to increase rate if substrate and/or effectors present
* e.g. multiple ASs - substrate binds 1, increasing activity others; or causes change in shape of all to fit (induced fit)
* each subunit own AS + allosteric sites where subunits join - something binds there + changes shape ASs so can accept substrate
allosteric site = anywhere other than AS where something can bind
don’t display Michaelis-Menten kinetics
interaction of 1 triggers same conformational change in all subunits = cooperativity
allosteric regulation
regulating effectors change enz’s shape + function by binding weakly allosteric site - inhibition or stimulation
* binding of activator stabilises conformation w functional AS
* binding of inhibitor stabilises inactive enz form
most have 2 or more polypeptide chains (subunits)
enz feedback regulation
metabolic pathway w several enzs + series of reactions to end-product, producing intermediates
* end-product can act allosteric inhibitor early stage enz to save E + prevent build-up intermediates
types enz inhibitor
- competitive - binds AS instead substrate
- non-competitive - binds allosteric site irrespective of whether substrate bound
- uncompetitive - only binds enz-subs complex
- allosteric - binds @ allosteric site; could be competitive if near AS, uncompetitive or non-competitive
factors affecting enz activity
- substrate/enz conc
- pH
- temp - more can overcome ae
- post-translational modifications
- cofactors
how post-translational modification affects enz activity
REVERSIBLE COVALENT ATTACHMENT
of small non-prot grp, most common phosphorylation-dephosphorylation as causes change 2/3 structure
* hydroxy side chains (serine, threonine, tyrosine) phophyd (OH grp to bind to)
* rapid reversible switch turn metabolic pathway on/off
PROTEOLYTIC ACTIVATION
enz synthed as larger, inactive precursor form (proenz/zymogen)
how cofactors affect enz activity
many enzs require presence small non-prot unit to function
* inorganic ions
* complex organic mols (=conenzs) - sometimesreded/oxed during reaction
what are proteinases
= proteases
enzs that cleave prots + may activate other enzs
e.g. blood clotting cascade where 1 removes prodomain enz + activates, does same for another + so on
types proteases
- serine
- cysteine
- aspartate
- metalloproteinases
- threonine proteinase
serine proteinases
reactive serine residue at AS, e.g. trypsin
cysteine proteases
cysteine at AS
aspartyl proteinases
aspartate at AS
metalloproteinases
metal ion (often Zn2+) at AS
threonine proteases
threonine at AS, e.g. proteasome
isoenzymes
= isozymes
diff forms of enz that cat same reaction, therefore similar AS
* usually derived diff genes + occur diff tissues
what is a multi-enz complex
aggregation several enzs/coenzs into single functional unit usually to perform multi-step transformation
proximity enzs to each other:
* increases RoR
* minimises side reactions
* intermediates immediately available as susbtrates for next reaction
e.g. fatty acid synthase involved lipid biosynthesis
