Proteins Flashcards
Topic 1 revision
What is the general structure of an amino acid?
- COOH (carboxyl/ carboxylic acid group)
- R (variable side group consists of carbon chain & may include other functional groups e.g. benzene ring or -OH [alcohol]
- NH2 (amine/ amino group)
Describe how to test for proteins in a sample
Biuret test confirms presence of peptide bond
- Add equal volume of sodium hydroxide to sample at room temperature
- Add drops of dilute copper (II) sulfate solution. Swirl to mix. (steps 1 & 2 make Biuret reagent)
- Positive result: colour changes from blue to purple
Negative result: solution remains blue
How do dipeptides and polypeptides form?
- Condensation reaction forms peptide bond ( -CONH-) & eliminates molecule of water
- Dipeptide: 2 amino acids
- Polypeptide: 3 or more amino acids
Define ‘primary structure’ of a protein
- Sequence, number & type of amino acids in the polypeptide
- Determined by sequence of codons on mRNA
Define ‘secondary structure’ of a protein
Hydrogen bonds form between O S- (slightly negative) attached to -C=O & H S+ (slightly positive) attached to -NH
Describe 2 types of secondary protein structure
a-helix:
- all N-H bonds on same side of protein chain
- spiral shape
- H-bonds parallel to helical axis
B-pleated sheet:
- N-H & C=O groups alternate from one side to the other
Define ‘tertiary structure’ of a protein. (Name bonds present)
3D structure formed by further folding of polypeptide
- disulfide bridges
- ionic bonds
- hydrogen bonds
Describe each type of bond in tertiary structure of proteins
- Disulfide bridges: strong covalent S-S bonds between molecules of the amino acid cysteine
- Ionic bonds: relatively strong bonds between charged R groups )pH changes cause these bonds to break)
- Hydrogen bonds: numerous & easily broken
Define ‘quaternary structure’ of a protein
- Functional proteins may consist of more than one polypeptide
- Precise 3D structure held together by the same types of bond as tertiary structure
- May involve addition of prosthetic groups (e.g. metal ions or phosphate groups)
Describe structure and function of globular proteins
- Spherical & compact
- Hydrophilic R groups face outwards & hydrophobic R groups face inwards = usually water-soluble
- Involved in metabolic processes (e.g. enzymes & haemoglobin
Describe structure and function of fibrous proteins
- Can form long chains or fibres
- Insoluble in water
- Useful for structure and support (e.g. collagen in skin)
Outline how chromatography could be used to identify the amino acids in a mixture
- Use capillary tube to spot mixture onto pencil origin line & place chromatography paper in solvent
- Allow solvent to run until it almost touches other end of paper. Amino acids move different distances based on relative attraction to paper & solubility in solvent
- Use revealing agent or UV light to see spots
- Calculate Rf values & match to database
What are enzymes?
- Biological catalyst for intra & extracellular reactions
- Specific tertiary structure determines shape of active site, complementary to a specific substrate
- Formation of enzyme-substrate (ES) complexes lowers activation energy of metabolic reactions
Explain induced fit model of enzyme action
- Shape of active site is not directly complementary to substrate & is flexible
- Conformational change enables ES complexes to form
- This puts strain on substrate bonds, lowering activation energy
How have models of enzyme action changed?
- Initially lock & key model: rigid shape of active site complementary to only 1 substrate
- Currently induced fit model: also explains why binding at allosteric sites can change shape of active site
Name 5 factors that affect rate of enzyme-controlled reactions
- enzyme concentration
- substrate concentration
- concentration of inhibitors
- pH
- temperature
How does substrate concentration affect rate of reaction?
Given that enzyme concentration is fixed, rate increases proportionally to substrate concentration
Rate levels off when maximum number of ES complexed form at any given time
How does enzyme concentration affect rate of reaction?
Given that substrate is in excess, rate increases proportionally to enzyme concentration
Rate levels off when maximum number of ES complexes form at any given time
How does temperature affect rate of reaction?
Rate increases as kinetic energy increases & peaks at optimum temperature
Above optimum, ionic & H-bonds in 3 degrees structure break = active site no longer complementary to substrate (denaturation)
How does pH affect rate of reaction?
Enzymes have a narrow optimum pH range
Outside range, H+/ OH- ions interact with H-bonds & ionic bonds in 3 degrees structure = denaturation
Contrast competeiive & non-competitive inhibitors
Competitive inhibitors:
- similar shape to substrate = bind to active site
- do not stop reaction; ES complex forms when inhibitor is released
- increasing substrate concentration decreases their effect
Non-competitive inhibitors:
- bind to allosteric binding site
- may permanently stop reaction; triggers active site to change shape
- increasing substrate concentration has no impact on their effect
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 t=0
How to calculate rate of reaction from raw data
Change in concentration of product or reactant/ time
Why is it advantageous to calculate initial rate?
Represents maximum rate of reaction before concentration of reactants decreases & ‘end product inhibition’
