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LET US LEARN ABOUT PROTEINS
THE BASICS
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Proteins are involved in all things
They are structural, hormones, enzymes, carrier molecules, they form pigments
V large molecules
Vary species to species, although they can be SIMILAR- indirect evidence of
evolution, used to investigate evolutionary relationships ~
All contain hydrogen, oxygen, nitrogen, carbon
Some contain other elements
Most important thing to remember about proteins is that their SHAPE determines
their FUNCTION
Basic monomer is amino acid ~

AMINO ACIDS
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Consist of a central carbon bonded to:
o A hydrogen atom
o A basic amino group (NH2)
o An acidic carboxyl group (COOH)
o An R group
The R group is what creates diversity between the amino acids
Only 20 used in proteins of all organisms, indirect evidence for evolution ~
Combine very CONDENSATION reactions to form dipeptides, polypeptides etc
OH taken from carboxyl group, H taken from amino group
Water released, PEPTIDE bond

PRIMARY STRUCTURE OF POLYPETIDES
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Sequence of amino acids in polypeptide chain, brought together via condensation
reactions, forms the primary structure
Polymerisation brings ‘em all together
Primary sequence is determined by DNA, and the order of the amino acids
determines how they interact with each other to form secondary and tertiary
structures of the polypeptide
o Determines SHAPE and therefore FUNCTION

SECONDARY STRUCTURE OF POLYPEPTIDES

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Hydrogen bonds form between the H of the NH group, and the O of the C=O group,
which causes the long polypeptide chain to be twisted into a 3D shape
o Most commonly the alpha helix
o But also the beta pleated sheet is quite common

TERTIARY STRUCTURE

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Alpha helices of 2ndary structure can be twisted and folded into COMPLEX,
COMPACT, and ofen SPECIFIC 3D shapes
(Makes them distinctive, allows them to recognise and be recognised, and interact
with other components in a v specifc way)
Maintained by a number of diferent bonds which depend on primary structure
o Disulphide bonds/bridges, fairly strong, not easily broken
o Ionic bonds, formed between any carboxyl and amino groups found in the R
groups, weaker than disulphide bonds, easily broken by changes in pH
o Hydrogen bonds, which are numerous but easily broken

QUATERNARY STRUCTURE OF POLYPEPTIDES

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Large proteins ofen form complex molecules containing a number of DIFFERENT
individual polypeptide chains that are linked in various ways
May also contain prosthetic groups, eg iron in haemoglobin

TEST FOR PROTEINS

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Biuret test 4 peptide bonds
Add equal volume NaOH at room temperature, then a few drops of copper sulfate
solution, mix gently
Purple colouration = peptide bonds = protein
Negative result = solution stays blue

PROTEIN SHAPE AND FUNCTION

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Roles depend on shape
Globular proteins, eg enzymes, carry out metabolic functions
Fibrous proteins have structural functions
o Eg, keratin
o eg, collagen
o from long chains which run parallel to each other, linked by cross bridges, v
stable
o primary structure is unbranched polypeptide chain
o secondary, chain is v tightly wound
o tertiary, chain twisted into second helix

o quaternary, three such polypetide chains wound together, held together by
bonds between the adjacent amino acids of adjacent chains
o collagen is found in tendons
ENZYMES

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globular proteins, act as catalysts, remain chemically unchanged so are v efective at
low concentrations
specifc 3D shape, region of enzyme that is functional = active site, made of only a
few amino acids
induced ft model
o active site forms fully as enzyme and substrate interact
o proximity of substrate leads to a change in the enzyme and the formaton
of a functonal actie site
o active site already has general shape
o enzyme moulds around substrate
o as the enzyme changes shape, a strain is put on the substrate molecule
 distorts a partcular bond or bonds in the substrate and
consequently lowers the actiaton energy needed to break the
bond
old model was lock and key model
o supported by enzymes being specifc
o considered the enzyme rigid, which couldn’t have been true as other
molecules can bind with enzymes @ places other than their active site
measuring enzyme catalysed reactions- either measure the formation of the
product(s) or the disappearance of he substrate
o steep graph @ frst bc lots of substrate, easy for enzyme to come into
contact with
o eventually all active sites are flled at any given point, rate is maximum,
substrate rapidly broken down
o as reaction proceeds, less and less substrate and more and more product,
rate slows
 more difficult for enzyme to come into contact with substrate
molecule, fewer substrate molecules, product molecules get in the
way
o rate continues to slow until no further change can be detected, graph tails of
and faaens
o gradient = rate, use a tangent
temperature
o all enzymes haie an optmum
o raising increases Ek and therefore rate up to a point

at frst, active site distorted and so rate slowed
eventually enzyme becomes denatured, bonds break, new ones form,
no more reactons
o lowering temperature decreases Ek and therefore activity
o many human enzyme’s optimums is higher than body temp
 maintaining higher temp would require a FUCK TONNE MORE FOOD
 other proteins may denature at the higher temperature
 leaves no room for a further rise, eg in illness
o birds have higher bc fight
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pH
o alters charges on amino acids that make up active site, preient substrates
from bonding
o if signifcant, may cause tertiary structure to break
o pH fuctuations within organisms are v small, unlikely to denature
enzyme concentration
o increasing the enzyme concentration will increase the rate SO LONG AS
THERE IS AN EXCESS OF SUBSTRATE
o afer that the graph will plateau
Substrate concentration
o Rate of reaction will increase UNTIL EVERY ACTIVE SITE IS OCCUPIED AT A
GIVEN TIME, THE ENZYMES ARE WORKING AS FAST AS THEY CAN
o Then no increase

ENZYME INHIBITION

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Inhibitors directly or indirectly interfere with functioning of active sites and so
reduce enzymatic activity
Competitive
o Similar molecular shape to substrate molecule, sit in active site, do not bind,
prevent substrate molecules from binding with enzymes and forming
enzyme-substrate complexes
o Competing with substrate for active sites
o Increasing concentration of substrate will therefore reduce the afect of the
inhibitor
Non-competitive
o Bind to enzymes at binding sites that are not the active site, causes change of
active site to change, substrate molecules can no longer occupy the enzyme
o Changing the concentration of substrate does jack shit

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