2b- Biological Molecules: Proteins and Enzymes

What are proteins?

polymers made up of 1 or more chains of amino acid monomers forming polypeptide chains

What elements do all proteins contain?

• carbon

• hydrogen

• oxygen

• nitrogen

What are all amino acids made of?

• amine group

• carboxyl group

• a side chain

How many different amino acids are there?

20

What does an amino acid look like?

What is a dipeptide?

2 amino acids joined together

What is a polypeptide?

many amino acids joined together

What bond is formed between amino acids?

peptide bond

Describe how amino acids join together

Condensation reaction which removes a water molecule between the carboxyl and amine group of different amino acids, forming a peptide bond

Describe the primary structure of a protein

Sequence of amino acids in a polypeptide chain, joined by peptide bonds

Describe the secondary structure of a protein

Folding of the polypeptide chain due to hydrogen bonding between amino acids

What are the 2 structures formed in the secondary structure?

• a helix

• B pleated sheet

Describe the tertiary structure of a protein

3D folding of polypeptide chains into a specific shape due to interactions between R groups forming hydrogen and ionic bonds, and disulphide bridges

What is the order of strength of these bonds from weakest to strongest?

• hydrogen

• ionic

• disulphide

Where do hydrogen bonds form in the tertiary structure?

between amine and carboxyl groups of different amino acids

Where do ionic bonds form in the tertiary structure?

between variable groups

Where do disulphide bridges form in the tertiary structure?

between any variable group that has a sulphur atom

Describe the quaternary structure of a protein

protein containing more than 1 polypeptide chain

Describe the food test for proteins

Add biuret reagent (sodium hydroxide + copper II sulphate). Positive result blue to lilac. Indicates presence of peptide bonds

What is a fibrous protein?

• Form long parallel chains with cross-bridges

• Very stable

• Have a structural role in organisms

What is a globular protein?

Carry out metabolic functions e.g. enzymes and haemoglobin

What are some examples of fibrous proteins?

• collagen

• keratin

• elastin

What is chromatography used for?

used to separate mixtures of monosaccharides or amino aids

Why does chromatography work?

the molecules have different molecular sizes and solubilities

In chromatography, what does it mean if the molecule is smaller and more soluble?

the further it will be moved in a solvent

What is the equation to find the Rf value?

Rf= distance from origin to solute (spot) / distance from origin to solvent front

What are enzymes?

they are biological catalysts and act by lowering activation energy (never used up)

What is activation energy?

minimum amount of energy required to start a reaction

Why do we have enzymes in our body?

without, temperature would be too low to support life

What is meant by metabolism?

sum of all chemical reactions in the body

Distinguish between intracellular and extracellular enzymes

act inside and outside cells

What type of protein is an enzyme?

globular

Describe the ‘lock and key’ model

substrate fits exactly into active site as it is complementary. Enzyme-substrate complex formed. Reaction takes place and products are released

Describe the ‘induced fit’ model

the substrate does not fit perfectly into the active site (not complementary). The active site changes shape to allow the substrate to bind. E-S complex forms, causing bonds in substrate to distort, lowering activation energy to break bonds

Explain the specificity of enzymes

• Specific tertiary structure determines shape of active site= dependent on sequence of amino acids

• Active site is complementary to a specific substrate

• Only this substrate can bind to active site, inducing fit and forming an enzyme-substrate complex

What are the 2 calculations for rate of reaction?

• rate= amount of product / time taken

• rate= 1 / time

What are the units for per second?

S -1 (smaller -1)

What does it mean when the line levels off in a graph?

stopped-all substrate converted to products

Why is the enzyme reaction faster at the start?

the substrate used up as reaction progresses= more substrate at start so more ES complexes

What does the temperature graph for enzyme rate of reaction look like?

Describe and explain the effects of temperature on enzyme rate of reaction

• As temp increases up to optimum, rate increases= more kinetic energy so more collisions so more ES complexes form

• Temp above optimum, rate decreases= enzymes denature, bonds break so tertiary structure + active site change shape so no longer complementary so fewer ES complexes form

What does pH refer to?

concentration of hydrogen ions

What happens to enzyme rate of reaction when you change pH by 1?

changes aqueous H+ conc by 10 times

What is used to control pH in an enzyme investigation?

a buffer

Why is pH a log scale?

there is a huge range of H+ conc involved

What does the pH graph for enzyme rate of reaction look like?

Describe and explain the effects of pH on enzyme rate of reaction

• When not optimum= alters charges on amino acids which affects bonding= breaks bonds that hold tertiary structure and reform in different places= change shape of active site= not complementary= no ES complexes form= enzyme denatures

What does the substrate concentration graph for enzyme rate of reaction look like?

Describe and explain the effects of substrate concentration on enzyme rate of reaction

• As sub conc increases, rate increases= sub conc is limiting factor (too few enzymes to occupy all active sites)= more successful collisions= more ES complexes formed

• At maximum, rate stops increasing= enzyme conc is limiting factor as all active sites are saturated/ fully occupied

What does the enzyme concentration graph for enzyme rate of reaction look like?

Describe and explain the effects of enzyme concentration on enzyme rate of reaction

• As enzyme conc increases, rate increases= enzyme conc is limiting factor (excess substrate)= more available active sites= more ES complexes form

• At certain point, rate stops= substrate conc is limiting factor= all substrates in use

What is an inhibitor?

a substrate which decreases the rate of an enzyme- controlled reaction and may bring it to a halt

What are the 2 types of inhibitor?

• competitive

• non- competitive

What is a competitive inhibitor and how does it work?

• Have a similar shape to that of the enzyme’s substrate

• competes with substrate as it binds to the active site of the enzyme

• Active site is blocked so can’t be occupied by substrate= fewer ES complexes formed= reduced rate

What does the competitive inhibitor graph for enzyme rate of reaction look like?

Describe and explain the effects of competitive inhibitor on enzyme rate of reaction

• As conc of competitive inhibitor increases, rate decreases= similar shape to substrate= competes/binds/blocks active site= so substrate can’t bind= fewer ES complexes formed

• Increasing subsrate conc, reduces effect on inhibitors

What is a non-competitive inhibitor?

• Not similar shape

• Binds to another region of the enzyme (allosteric site)

• Changes tertiary shape therefore active site shape= substrate can’t bind= fewer ES complexes formed= rate decreases= once added, inactivates enzyme

What does the competitive inhibitor graph for enzyme rate of reaction look like?

Describe and explain the effects of enzyme concentration on enzyme rate of reaction

• As conc of non-competitive inhibitor increases, rate decreases= binds to allosteric site= changes active site shape= no longer complementary to substrate= can’t bind= fewer ES complexes formed

• increasing sub conc has no effect on rate, as change to active site is permanent