3.1.4 - proteins Flashcards
what are the monomers of proteins?
amino acids
what is formed when 2 amino acids join together?
a dipeptide
what is formed when more than 2 amino acids join together?
a polypeptide
what are proteins made up of?
proteins are made up of one or more polypeptides
general structure of an amino acid
- carboxyl group (COOH)
- amine or amino group (NH2)
- R group (also known as a variable side group) attached to a carbon atom
what do R groups generally contain?
carbon, only exception is glycine (its R group consists of just one H atom)
how many amino acids are there?
all living things share a bank of only 20 amino acids, the only difference between them is what makes up their R group
dipeptide and polypeptide formation
amino acids link together by condensation reactions to form dipeptides and polypeptides , a molecule of water is released during the reaction
what are the bonds that form between amino acids called?
peptide bonds
how do dipeptides/polypeptides break down
- hydrolysis reaction
what are the 4 ‘levels’ of a protein’s structure?
-primary
-secondary
-tertiary
-quaternary
what is the primary structure of a protein?
the sequence of amino acids in the polypeptide chain
secondary structure of proteins
polypeptide chain doesn’t stay flat but hydrogen bonds form between the amino acids in the chain which makes it automatically coil into an alpha helix or fold into a beta pleated sheet
what things are involved in the tertiary structure of a protein?
-hydrogen bonds
-ionic bonds
-disulfide bridges
tertiary structure - hydrogen/ionic bonds
coiled/folded amino acid chain is often coiled/folded further so more bonds form between different parts of the polypeptide chain e.g. hydrogen/ionic bonds (attraction between - and + charges on different parts of the molecule)
tertiary structure - disulfide bridges
- form when 2 molecules of the amino acid cysteine come close together
- sulfur atom in 1 cysteine bonds to the sulfur atom in the other
tertiary structure and single polypeptide chain proteins
for proteins made from a single polypeptide chain , the tertiary structure forms their final 3D structure
what is the quaternary structure?
some proteins are made of several different polypeptide chains held together by bonds , the quaternary structure is the way these polypeptide chains are assembled together
quaternary structure and proteins made from more than one polypeptide chain
for proteins made from more than 1 polypeptide chain (e.g. haemoglobin/insulin/collagen) the quaternary structure is the protein’s final 3D structure
proteins shape and function
a protein’s shape determines its function
how is haemoglobin’s shape adapted to its function?
haemoglobin is a compact/soluble protein so it is easy to transport so it is good at carrying oxygen around the body
enzyme’s shape
- usually roughly spherical in shape (tight folding of polypeptide chains)
enzyme’s function
- soluble, often have roles in metabolism e.g. some enzymes break down large food molecules (digestion enzymes), some help to synthesise large molecules
what are antibodies involved in/where are they found?
the immune response and are found in the blood
antibodies structure
- made up of 2 light (short) polypeptide chains and 2 heavy (long) polypeptide chains bonded together
- antibodies have variable regions - amino acid sequences in these regions vary greatly
how do you test for proteins?
biuret test
describe the biuret test?
- test solution needs to be alkaline so 1st add sodium hydroxide solution
- then add some copper(II) sulfate solution
what is a positive result from the biuret test?
purple colour indicates protein
what is a negative result from the biuret test?
solution staying blue indicates no protein
what are enzymes?
enzymes are proteins which act as a biological catalyst which lowers the activation energy of the reaction it catalyses but doesn’t get used up in the reaction
how do enzymes speed up reactions?
the lower the amount of activation energy needed, often making reactions happen at a lower temperature in comparison to without an enzyme. this speeds up the rate of reaction
what can enzymes catalyse?
metabolic reactions at a cellular level (e.g. respiration) and for the organism as a whole (e.g. digestion in mammals)
What can enzymes affect?
structures in an organism e.g. enzymes are involved in collagen production as well as functions e.g. respiration
what are the 2 types enzyme action can be
intracellular (within cells) or extracellular (outside cells)
active site of enzymes
- it has a specific shape , is where the substrate molecule binds to
why are enzymes highly specific?
due to their tertiary structure
how does the formation of an ESC lower the activation energy (repulsion)?
if 2 substrate molecules need to be joined, being attached to the enzyme holds them close together, reducing any repulsion between the molecule so they can bond more easily
how does the formation of an ESC lower the activation energy (strain on bonds)?
if the enzyme is catalysing a breakdown reaction, fitting into the active site puts a strain on bonds in the substrate, so the substrate molecule breaks up more easily
lock and key model
active site and substrate have a complementary shape and fit into each other like a lock and key
why wasn’t the lock and key model completely accurate?
enzyme and substrate don’t have to fit together in the 1st place , ESC changed shape slightly to complete the fit - locks the substrate even more tightly to the enzyme
induced fit model
substrate doesn’t only have to be the right shape to fit into the active site but has to make the active site change shape in the right way as well
what are enzyme’s properties related to?
their tertiary structure
why are enzymes very specific?
as only one complementary substrate will fit into the active site. each enzyme has a different tertiary structure and so a different shaped active site
what is the active site’s shape determined by?
the enzyme’s tertiary structure (which is determined by the enzyme’s primary structure)
what happens if the substrate shape doesn’t match the active site?
ESC won’t be formed, reaction won’t be catalysed
what could cause the shape of the active site to change?
a change in the enzyme’s tertiary structure - substrate won’t fit into active site, no ESC, enzyme no longer able to carry out its function (denaturing)
what could cause a change in the enzyme’s tertiary structure?
changes in pH or temperature
how may the primary structure of an enzyme be altered and what else can this affect?
primary structure is determined by a gene, if a mutation occurs in that gene it could change the tertiary structure of the enzyme produced
how can you measure enzyme activity?
- how fast the product is made
- how fast the substrate is broken down
what factors affect enzyme activity?
temperature
pH
substrate concentration
enzyme concentration
how does temperature initially affect enzyme activity?
as temp increases so does rate of reaction (more kinetic energy=molecules move faster) .substrate molecules more likely to collide with the enzyme’s active site. energy of collisions also increases = each collision more likely to result in a reaction
what happens to enzyme activity when temperature gets too high?
rise in temp=enzyme’s molecules vibrate more. if temp goes above the optimum = vibration breaks some of the bonds that hold the enzyme in shape . active site changes shape so substrate no longer fits, enzyme is now denatured and no longer functions as a catalyst
how does pH affect enzyme’s rate of reaction?
above/below optimum pH = H+/OH- ions found in acids/alkalis disrupt the ionic/hydrogen bond holding the enzyme’s tertiary structure in place. enzyme becomes denatured, active site changes shape
how does substrate concentration affect enzyme’s rate of reaction initially?
higher substrate concentration =faster reaction (collision between enzyme and active site is more likely so more active sites occupied)
what happens to rate of reaction for enzyme’s when substrate concentration gets too high?
when a ‘saturation’ point is reached = so many substrate molecules that all the active sites are full so adding more substrate molecules makes no difference
how does enzyme concentration affect an enzyme’s rate of reaction?
more enzyme molecules, more likely a substrate molecule is to collide with one and from an ESC
how does enzyme concentration affect an enzyme’s rate of reaction if the amount of substrate is also limited?
initially rate if reaction increases but eventually all the enzyme molecules active site’s are full so rate of reaction plateaus
what are enzyme inhibitors
molecules that bind to the enzyme they they inhibit
what are the 2 types of enzyme inhibitors?
competitive and non competitive
how do competitive inhibitors work?
they have a similar shape to the substrate molecule so compete with the substrate molecules to bind to the active site so no substrate molecules can fit in it
how do competitive inhibitors affect rate of reaction when the concentration of competitive inhibitors are high?
higher concentration of inhibitors= takes up nearly all of the active sites and not many substrates get to the enzymes = rate of reaction is low
how do competitive inhibitors affect rate of reaction when the concentration of substrate molecules are high?
substrate’s chances of getting into the active site before the inhibitor increase, rate of reaction is higher
how do non-competitive inhibitors work?
bind to the enzyme away from its active site, causes active site to change shape so substrate molecules can no longer bind to it
what result will increasing substrate molecules in the presence of non-competitive inhibitors have?
non-competitive inhibitors don’t compete with the substrate molecules for the active site as they are a different shape so increasing substrate concentration won’t make a difference, enzyme activity will still be inhibited
what is the 1st step of measuring the rate of an enzyme controlled reaction (RP1)
immerse equal volumes of trypsin and milk in different test tubes in a water bath for 5 mins for the temp to equilibrate
what is the 2nd step of measuring the rate of an enzyme controlled reaction (RP1)
mix the two test tubes together and immediately start timing until the milk has become hydrolysed completely (become colourless)
what is the 3rd step of measuring the rate of an enzyme controlled reaction (RP1)
repeat with at least 5 temperatures, with at least 3 repeats for each temperature
