3.1.4 - proteins

3.1.4.1 (general properties of proteins) - 3.1.4.2 (many proteins are enzymes)

• what monomers are polypeptides made from

• what do polypeptides combine to form

• amino acids

• proteins (note: amino acids are still the MONOMERS proteins are made from!)

diagram of general structure of amino acids

more visual diagram of general structure of amino acids

what does each part in the diagram represent?

• NH₂ - an amine group, the AMINO part of amino acid

• COOH - a carboxyl group. an acidic group, the ACID part of amino acid

• H atom

• R - a side chain

the R group can be a v_______ of different groups

variety

how many amino acids are common in all organisms?

20

what is the only way in which they differ?

in their R (side) group

how is a peptide bond formed between 2 amino acids

by a condensation reaction (and hence the removal of a water molecule)

what are dipeptides formed by?

the condensation of 2 amino acids

how is the water molecule made

by combining an —OH from the carboxyl group of one amino acid

and a —H from the amino group of another amino acid

what is the resulting peptide bond between (like what atoms is it between)

• the C atom of one amino acid

• and the N atom of the other

what can the peptide bond of a dipeptide be broken by (to give 2 amino acids)

hydrolysis (the same way a glycosidic bond of a disaccharide can be broken by the addition of water)

diagram of formation of a peptide bond

what are polypeptides formed by?

the condensation of many (hundreds of!) amino acids

what forms the primary structure of a protein

the sequence of amino acids in a polypeptide chain

what is this sequence determined by

DNA

why is there an almost limitless number of possible combinations (and therefore types) of protein structures

• polypeptides have many of the 20 naturally occurring amino acids

• and these are joined in different sequences

what does the primary structure of a protein determine

• shape

• function

• what can lead to a change in the shape of the protein

• what may this stop the protein from doing

• a change of just a single amino acid in the primary sequence

• carrying out its function

hence, a protein’s shape is v___ s________ to its function. change its shape and it will function l___ w____, or differently. 

hence, a protein’s shape is very specific to its function. change its shape and it will function less well, or differently. 

how many polypeptides does a functional protein contain?

a simple protein may consist of 1.

more commonly, a protein is made up of more / lots of polypeptides

on either side of every peptide bond, what 2 groups are there? 

—NH group and —C==O groups

the H of the —NH group has an o________ p_________ c_______ while the O of the —C==O group has an o_________ n__________ c_______

the H of the —NH group has an overall positive charge while the O of the —C==O group has an overall negative charge

therefore, what do these 2 groups readily form

weak bonds (hydrogen bonds)

what does this cause the long polypeptide chain to twist into

a 3D shape

hence, what is the secondary structure of a protein

the shape which the polypeptide chain forms as a result of hydrogen bonding

give 2 examples of the secondary structure of proteins

• alpha helix (α-helix), which is a coil

• beta-pleated sheet

diagram of the structure of the α-helix

• what can the α-helices (plural of helix) of the secondary protein structure be twisted + folded even more into

• what is this known as

• the complex (and often specific) structure of each protein

• the tertiary structure

what is the tertiary structure maintained by

different bonds

where the bonds occur depends on…

the primary structure of the protein

what 3 bonds do these include

• disulfide bridges

• ionic bonds

• hydrogen bonds

• describe strength of disulfide bridges

• are they easily broken?

• fairly strong

• no

• what are the ionic bonds formed between

• describe their strength compared to disulfide bonds

• what are the ionic bonds easily broken by?

• any carboxyl and amino groups that are not involved in forming peptide bonds

• weaker than disulfide bonds

• changes in pH

in summary, what is the tertiary structure of proteins

• the bending and twisting of the polypeptide helix into a compact structure

• all 3 types of bond (hydrogen, ionic and disulfide) contribute to the maintenance of this structure

diagram of tertiary structure of proteins

what is the quatenary structure of proteins

• when large proteins form complex molecules

• containing a no. of individual polypeptide chains

• that are linked in various ways

• what may also be associated with the molecules

• give an example of these

• non-protein (prosthetic) groups

• the iron-containing haem group in haemoglobin

diagram of the quaternary structure

relationship between primary, secondary, tertiary and quaternary structure, and protein function

• basically, the 3D shape of the protein (determined by primary, secondary, tertiary and quatenary structure) is essential for the protein’s function

• 3D shape of the protein allows it to be distinctive, to recognise and be recognised by other molecules so it can interact with them in a v. specific way (this is the protein’s function)

• what is the test for proteins

• what exactly does it detect

• biuret test

• peptide bonds

how to carry out a biuret test

• place sample in a test tube

• add an equal vol. of NaOH at room temp.

• add a few drops of v. dilute copper (II) sulfate solution

• (or check if you can just say add biuret’s reagent)

• mix gently

• what indicates peptide bonds (and hence proteins) are present

• what means proteins aren’t present

• if solution turns purple

• if solution stays blue

• what are fibrous proteins

• what are their functions

• long, insoluble strands of polypeptide chains

• structural functions, e.g. to provide strength, to support tissues like skin, bone, hair

describe the structure of a fibrous protein in more detail

• long, rope-like shape

• repetitive, stable amino acid sequences

• many H bonds between polypeptide chains —→ these provide strong cross-linkages (remember, even though the H bonds are weak on their own, altogether, they are strong)

why are fibrous proteins insoluble

• have a large proportion of hydrophobic R groups

give 2 examples of fibrous proteins

• collagen —→ forms connective tissues

• keratin —→ found in hair and nails

• what are globular proteins

• what is their function

• compact, spherical macromolecules

• to perform vital biological functions

describe the structure of globular proteins in more detail

• have hydrophobic amino acid side chains clustered in the center

• have hydrophilic amino acids on the surface

what does this structure allow to happen (i.e. how is it suited to its function)

• H2O molecules can surround the protein

• so the protein is soluble in water

• this = essential for their transport and involvement in metabolic processes / transport

extra: why are globular proteins considered more unstable than fibrous proteins

they can undergo denaturation from environmental changes, whereas fibrous proteins have strong cross-linkages (from the H bonds)

give four examples of globular proteins, and the aforementioned vital biological functions they carry out 

• enzymes —→ catalyzing reactions

• haemoglobin —→ transports molecules (O₂)

• hormones

• antibodies

what do catalysts do

• alter the rate of a chemical reaction

• w/o undergoing permanent changes themselves

spec points to make flashcards on

3.1.4.2, all the bullet points and everything after that, and the RQ1

how many times can catalysts be used

so they are therefore effective in…

repeatedly

small amounts

what is activation energy

minimum amnt. of energy req. for a chemical reaction to occur

what does an enzyme do in the reaction it catalyses

lowers the activation energy

so reactions can take place at a l_______ t_________________ than normal

lower temperature

what is formed when a substrate binds to an active site

enzyme-substrate complex

KIND OF EXTRA: how is the substrate molecule held within the active site

• by bonds

• that temporarily form between certain amino acids of the active site

• and groups on the substrate molecule

what does the induced fit model of enzyme action propose

• that the active site forms as the enzyme and substrate interact

• the enzyme has a certain general shape, but it is flexible and can alter in the presence of the substrate by molding itself around the substrate

what does the enzyme do to the substrate molecule when it changes shape

puts a strain on it

what does this strain do

• distorts a particular bond / bonds in the substrate

• consequently = lowers the activation energy required to break the bond

any change in the enzymes’s e______________ is likely to change its s_______

environment, shape

the very act of colliding with its substrate is a change in its environment

and so its shape changes —→ induced fit

say substrate is COMPLEMENTARY to active site

diagram of all the mechanism of enzyme action

what do almost all the factors that affect the rate of enzyme-controlled reactions affect?

• the substrate

• the active site

what are these factors

• enzyme conc

• substrate conc

• conc of competitive + non -competitive inhibitors

• pH

• temperature

to investigate how enzymes are affected by various factors, we need to be able to measure the rate of the reactions they catalyse. we do this by…

measuring its time-course (how long it takes for a particular event to run its course). this includes:

• the formation of the products of the reaction

• the disappearance of the substrate

graph for formation of the product

graph for disappearance of the substrate

explanation of these graphs is the same:

• at first = a lot of substrate and not product

• easy for substrates to come into contact w empty active sites

• all active sites = filled, and substrate is broken down into products

• as reaction proceeds = less substrate, more product

• becomes more difficult for substrates to come into contact w/ active sites BECAUSE there are fewer substrates + product molecules may get in the way of substrates reaching the active sites

• so, takes longer for substrate molecules to be broken down by the enzyme, so rate of disappearance slows, and consequently, rate of formation of product also slows

• when graphs flatten out = all substrate has been used up, so no new product can be produced

how to measure rate of change in a a reaction at a certain point on a curved graph

• draw a tangent to graph at the point (make sure the tangent doesn’t cut THROUGH the graph)

• find the gradient of this (change in y / change in x)

rate is always expressed…

per unit time (NOT hertz 💔)

when investigating the effect of a named variable on the rate of an enzyme reaction…

all other variables must be kept constant

EFFECT OF TEMP:

• a rise in temp. increases the k_______ e______ of molecules

• what happens as a result

• kinetic energy

• molecules move around more rapidly + collide w/ each other more often

• more enzyme-substrate complexes are formed

• so RoR = increases.

graph of effect of temp. on an enzyme controlled reaction

description of graph

• gives a rising curve

• curve peaks at optimum temp, where enzyme works most efficiently.

• but increasing temp = causes H bonds + other bonds in molecule to break

• so enzyme starts to change shape —→ substrate fits less easily into changed active site —→ slowed rate of reaction. curve starts to fall.

• at some point (usually around 60 degrees) = enzyme denatures. (permanent change, enzyme does not function again)

how to calculate pH of a solution

• press log button on calc

• in the bracket, enter the H ion conc (given)

• press equals. should give you the answer

• example: H ion conc = 1 × 10^-9. so do log (1 × 10^-9) which gives pH = 9.

effect of pH on enzyme action

• each enzyme has a optimum pH. an increase / decrease in optimum pH

• if change in pH = extreme, then beyond a certain pH, enzyme denatures.

what does a change in pH do to the active site

• alters the charges on the amino acids that make up the active site

• so substrate can no longer attach to it

• and enzyme-substrate complex can no longer be formed

• may also cause bonds maintaining enzyme’s tertiary structure to break —→ active site therefore changes shape

kinda extra: why is the bonding in the active site changed

• arrangement of active site = partially determined by H bonds and ionic bonds between —NH2 and —COOH groups of the polypeptides that make up the enzyme

• change in H+ ions affects this bonding (so active site changes shape)

graph of effect of pH on the rate of an enzyme-controlled reaction

description of graph

• increasing pH (towards optimum): activity rises as environment becomes more favorable

• decreasing pH (away from optimum): activity drops as H+ interfere with enzyme-substrate binding

• extreme pH: at very low / high pH, enzyme denatures —→ reaction rate falls to zero

effect of enzyme conc. on rate of reaction

as long as there is an excess of substrate, an increase in the amount of enzyme leads to a __________ in the rate of reaction

(proportionate) increase

on a graph of rate of reaction against enzyme conc…

• RoR = low. enzyme conc is limiting —→ more substrates than enzyme’s AS can deal w

• then RoR = increase as enzyme conc. = increases. bc excess substrate can be acted upon