3.1.4 Proteins Flashcards
How would you test for proteins in a sample?
Biuret test: confirms the presence of peptide bonds
- Add an equal volume of sodium hydroxide to a sample at room temp
- Add drops of dilute copper sulphate solution and swirl to mix
- Positive result: change from blue to purple
- Negative result: remains blue
How many amino acids are there and how do they differ?
20 and by their side ‘R’ group
How does a Peptide bond form?
Condensation reaction between 2 amino acids
How are Dipeptides formed?
Condensation reaction between 2 amino acids
What are Amino acids?
Monomers from which proteins are made
How are Polypeptides formed?
Condensation reaction between many amino acids
How many levels of a Protein structure are there?
4
Define Primary structure of a protein
Sequence , number and type of amino acids in the polypeptide is determined by the sequence of codons on the mRNA
Define Secondary structure of a protein
- It’s the shape that the chain of amino acids chains and is either alpha helix or beta pleated sheets
- Hydrogen in the - NH has a slight positive charge
- Oxygen in the -C=O has a slight negative charge
- As a result weak hydrogen bonds can form leading to alpha helices or beta pleated sheets
Describe the 2 types of Secondary protein structure
Alpha helix
- All N-H bonds are on the same side of protein chain
- Spiral shape
- Hydrogen bonds are parallel to the helical axis
Beta pleated sheets
- N-H and C=O groups alternate from one side to the other
Define Tertiary structure of a protein and name bonds present
3D structure formed by the further folding of the polypeptide
- Disulfide bridges
- Ionic bonds
- Hydrogen bonds
Describe Disulfide bridges
Strong covalent s-s bonds between molecules of the amino acid cystiene
Describe Ionic bonds
Relatively strong bonds between charged R groups (PH changes cause bonds to break)
Describe Hydrogen bonds
Numerous and easily broken
Define Quaternary structure of a protein
- Functional protein may consist of more than 1 polypeptide
- Precise 3D structure is held together by the same types of bonds as the tertiary structure
- May involve addition of prosthetic group e.g. metal ions or phosphate groups
Describe the structure and function of Globular proteins
- Spherical and compact
- Hydrophilic R groups face outwards and hydrophobic R groups face inward so usually water soluble
- Involved in metabolic processes e.g. enzymes and haemoglobin
Describe the structure and function of Fibrous proteins
- Can form long chains or fibres
- Insoluble in water
- Useful for structure/support (collagen in skin)
What are Enzymes?
Biological catalysts for intra and extracellular reactions
- Specific tertiary structure determines shape of active site which is complementary to a specific substrate
- Formation of enzyme-substrate (es) complexes lowers activation energy of metabolic reactions
Explain the Induced fit model of enzyme action
- Shape of active site is not directly complementary to substrate and is flexible
- Conformational change enables the es complex to form
- This puts strains on substrate bonds , lowering activation energy
How have models of Enzyme action changed?
- Initially lock and key model: rigid shape of active site is complementary to only 1 substrate
- Currently induced fit model: also explains why binding at allosteric sites can change shape of active site
How could a student identify the activation energy of a metabolic reaction from an energy level diagram?
Difference between free energy of substrate and peak of curve
Name 5 factors that affect the rate of Enzyme-controlled reactions
- PH
- Temp
- Concentration of inhibitors
- Substrate concentration
- Enzyme concentration
How does Enzyme concentration affect rate of reaction?
- Given that substrate is in excess rate increases proportionally to enzyme concentration
- Rate levels off when max number of es complexes form at any given time
How does Substrate concentration affect rate of reaction?
- Given that enzyme concentration is fixed , rate increases proportionally to substrate concentration
- Rate levels off when max number of es complexes form at any given time
How does Temperature affect rate of reaction?
- Rate increases as kinetic energy increases and peaks at optimum temperature
- Above optimum ionic and H-bonds in the 3D structure break and so the active site is no longer complementary to substrate (denaturation)
How does PH affect rate of reaction?
- Enzymes have a narrow optimum PH range
- Outside the range H+/OH- ions interact with the H-bonds and ionic bonds in the 3D structure leading to denaturation
Contrast competitive and non-competitive Inhibitors
Competitive:
- Similar shape to substrate so binds to active site
- Doesn’t stop reaction; es complex forms when inhibitor is released
- Increasing substrate concentration decreases their effect
Non-competitive:
- Binds at the allosteric binding site
- May permanently stop reaction and so triggers active site to change shape
- Increasing substrate concentration has no impact on their effect
Why is it advantageous to calculate initial rate?
Represents max rate of reaction before concentration of reactants decreases and ‘end product inhibition’
State the formula for PH
PH = -log10 (H+)
Outline how to calculate rate of reaction from raw data
Change in concentration of product or reactant / Time
Outline how to calculate rate of reaction from a graph
- Calculate gradient of line or gradient of tangent to a point
- Initial rate = draw tangent at 0
