proteins and enzymes

amino acids

the monomers from which proteins are made

explain the general structure of an amino acid

NH2 represents an amine group, COOH represents a carboxyl group and R represents a carbon-containing side chain

how do the 20 amino acids that are common in all organisms differ?

only in their side group

how is a peptide bond formed?

by a condensation reaction between two amino acids

how are dipeptides formed?

by the condensation of two amino acids

how are polypeptides formed?

by the condensation of many amino acids

functional protein

may contain one or more polypeptides

proteins

• proteins consumed are broken down into amino acids

• amino acids are then transported to tissues in the body to create: muscle cells, antibodies, blood cells, hormones, etc.

what are the 4 levels of protein structure?

1. primary

2. secondary

3. tertiary

4. quaternary

what is the monomer of a protein?

amino acids

why are R groups important?

they can attract or repel each other

what causes polypeptides to fold?

R groups forming bonds with other amino acid R groups in the polypeptide

what bonds can R groups form?

disulfide bonds, hydrogen bonds, ionic bonds

where are hydrophilic R groups found?

on the outside of the protein

where are hydrophobic R groups found?

on the inside of the protein (away from water)

primary structure

• polymerisation

• sequence of amino acids → determined by DNA

• determines proteins ultimate shape and therefore function

• type of bonding: peptide

polymerisation

condensation reaction → amino acid monomers join together

secondary structure

• hydrogen bonds cause folding of the polypeptide chain into alpha helix or beta pleated sheet

• weak hydrogen bonds form

alpha helix

chain coils in a spiral shape

beta pleated sheet

chain runs parallel to itself

tertiary structure

• further 3D folding of the polypeptide chain

• type of bonding: disulfide bridges, ionic bonds, hydrogen bonds

• disulfide bridges: strong bonds between S-S

• ionic bonds: between amino acid side chains (weaker than disulfide bridges and easily broken by changes in pH)

• hydrogen bonds: numerous but easily broken

• if 1 amino acid in the primary structure is altered or changes position disulfide, ionic, and hydrogen bonds will form in different places → creates a different tertiary structure and different 3D shape

quaternary structure

• more than one polypeptide chain bonded together

• sometimes contains prosthetic groups (non-protein)

• type of bonding: disulfide, ionic and hydrogen bonds

globular proteins

• have complex tertiary and sometimes quaternary structures

• folded into spherical (globular) shapes

• usually soluble as hydrophobic side chains in centre of structure

• roles in metabolic reactions

examples of globular proteins

enzymes, haemoglobin in blood

fibrous proteins

• little or no tertiary structure

• long parallel polypeptide chains

• cross linkages at intervals forming long fibres or sheets

• usually insoluble

• many have structural roles

examples of fibrous proteins

keratin in hair and the outer layer of skin, collagen (a connective tissue)

biochemical test for proteins

• biuret test (detects peptide bonds)

• heat protein with biuret solution

• positive result → biuret solution turns from blue to purple/lilac

• negative result → biuret remains blue

enzymes

• proteins

• biological catalysts - reduce activation energy

• facilitate chemical reactions - increase rates of reaction without being consumed

• highly specific

how do enzymes react with their substrates?

• both substrates must collide with sufficient energy to alter the arrangement of their atoms

• an initial amount of energy is required to start the reaction off - activation energy

how does the temperature affect the rate of an enzyme-controlled reaction?

• gives enzymes and substrate kinetic energy causing them to move around quicker resulting in more collisions → more e-s complexes form

• optimum e-s complexes made at optimum temp (also optimum rate of reaction)

• when temp exceeds optimum it denatures enzymes active site → bonds that hold enzymes 3D shape (H + I bonds) break → tertiary structure changes → active site no longer complementary to substrate → no more e-s complexes form

how does the pH affect the rate of an enzyme-controlled reaction?

• enzymes have an optimum pH at which they work fastest (normally pH 7-8)

• a few enzymes can work at extreme pH

• in highly acidic or alkaline environments H+ or OH- ions affect ionic and hydrogen bonds, altering tertiary structure and shape of the active site

• when pH exceeds optimum it denatures enzymes active site resulting in no more e-s complexes forming

how does the substrate concentration affect the rate of an enzyme-controlled reaction?

• higher substrate concentration increase rate of reaction as not all active sites are occupied

• max rate of reaction at saturation point → all active sites are occupied

• despite high conc of substrate rate of reaction would not increase any further as all the active sites are occupied

• graph plateaus

how does the enzyme concentration affect the rate of an enzyme-controlled reaction

• substrate in excess; the rate of reaction increases as enzymes are re-used and the substrate continues to be available

• substrate limited; the rate of reaction increases until the enzymes are limited by the concentration of substrate, no more substrate is available

lock and key theory

• suggests enzymes and substrate are rigid structures

• random movement, collision

• substrate bind to enzyme’s active site, charged groups attract, distorting the substrate

• forming e-s complex

• products released, enzyme left unchanged, ready to bind again

strength of lock and key model

explains how the enzyme is specific; 1 substrate, will fit into active site

limitations of lock and key model

• states the enzyme is rigid but enzyme structure is flexible not rigid

• doesn’t explain how other molecules (e.g. activators and inhibitors) can bind to enzyme at sites other than active site and change its activity

the active site

• the functional site of the enzyme

• a relatively small number of amino acids

induced fit model

• an enzymes shape is flexible

• initially the substrate and active site of th enzyme are not complementary

• the proximity of the substrate causes a change in the environment of the enzyme

• leads to a change in the shape of the active site, this puts a strain on the substrate and distorts bonds, allows an e-s complex to form

why is the induced fit model a better explanation of enzyme controlled reactions than the lock and key model?

• explains how other molecules effect enzyme activity (enzyme flexible) e.g. activators and inhibitors

• explains how the activation energy is lowered (by putting a strain on the bonds)

factors that affect the rate of enzyme catalysed reactions

1. temperature

2. pH

3. substrate concentration

4. enzyme concentration

5. concentration of competitive inhibitors

6. concentration of non-competitive inhibitors

inhibitors

substances that directly or indirectly interfere with the functioning of the active site of an enzyme

what are the two types of inhibitors?

1. competitive inhibitors

2. non-competitive inhibitors

competitive inhibitors

• similar molecular shape to substrate

• bind to active site (not permanently)

• this prevents the substrate from binding with the enzyme

• increasing substrate concentration increases rate of reaction

non-competitive inhibitors

• bind to allosteric site

• this alters the shape of the enzyme and its active site

• the substrate can no longer bind to the enzyme → decreases rate if reaction

• increasing substrate concentration will have no effect on rate of reaction

activation energy

• the minimum amount of energy needed to activate the reaction

• forming new bonds and breaking bonds requires energy

the specificity of an enzyme

• tertiary structure

• active site shape almost complementary to shape of substrate

• substrate binds to active site

• e-s complex is produced