1.4 Proteins Flashcards
General structure of an amino acid
- COOH carboxyl group
- R variable side group consists of carbon chain and may include other functional groups e.g. benzene ring
- NH2 amine group
What does Biuret test do?
Confirms presence of peptide bond
Describe how to test for proteins in a sample
- Add 2cm3 food sample to test tube
- Add equal volume of sodium hydroxide to sample at room temp
- Add two drops of dilute copper (II) sulfate solution. Mix
- Positive result: colour changes from blue to purple
How many amino acids are there and how do they differ from one another?
- 20
- Differ only by side ‘R’ group
How do dipeptides and polypeptides form?
- Condensation reaction forms peptide bond (-CONH-) and eliminates molecule of water
- Dipeptide: two amino acids
- Polypeptide: 3 or more amino acids
How many levels of protein structure are there?
4
Define ‘primary structure’ of a protein
- Sequence, number and 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 delta-negative (slightly negative) attached to -C=O and H delta-positive (slightly positive) attached to -NH
Describe the 2 types of secondary protein structure
Alpha helix
- All N-H bonds on the same side of protein chain
- Spiral shape
- H-bonds parallel to helical axis
Beta pleated sheet
- N-H and C=O groups alternate from one side to the other
Define tertiary structure of a protein.
3D structure formed by further folding of polypeptide
Name the bonds present in the tertiary structure of a protein
- Disulfide bridges
- Ionic bonds
- Hydrogen bonds
Describe disulfide bonds in tertiary structure of proteins
Strong covalent S-S bonds between molecules of the amino acid cysteine
Describe ionic bonds in the tertiary structure of proteins
Relatively strong bonds between charged R groups (pH changes causes these bonds to break)
Describe hydrogen bonds in tertiary structure of proteins
Numerous and 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 and compact
- Hydrophilic R groups face outwards and hydrophobic R groups face inwards = usually water-soluble
- Involved in metabolic processes e.g. enzymes and haemoglobin
Describe structure and function of fibrous proteisn
- 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 amino acids in a mixture
- Use capillary tube to spot mixture onto pencil origin line and 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 and solubility in solvent
- Use revealing agent or UV light to see spots
- Calculate Rf values and match to database
What are enzymes
- Biological catalysts for intra and extracellular reactions
- Specific tertiary structure determine shape of active site, complementary to a specific substrate
- Formation of enzyme-substrate complexes lowers activation energy of metabolic reactions
Explain induced fit model of enzyme action
- Shape of active site not complementary to substrate and is flexible
- conformational changes enables ES complexes to form
- Puts a strain on substrate bonds, lowering activation energy
How have models of enzyme action changed?
- Initially lock and 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 the shape of active site
How could a student identify the activation energy of a metabolic reaction from an energy level graph?
Difference between free energy of substrate and peak of curve
Name 5 factors that affect the 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 complexes 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 and peaks at optimum temperature
- Above optimum, ionic and H-bonds in tertiary 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 and ionic bonds in tertiary structure = denaturation
Contrast competitive and non-competitive inhibitors
- Competitive: similar shape to substrate=bind to active site, non-competitive: bind at allosteric binding site
- Competitive: do not stop reaction - ES complex forms when inhibitor is released, non-competitive: may permanently stop reaction - triggers active site to change shape
- Competitive: increasing substrate concentration decreases their effect, non-competitive: 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
Outline 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 and ‘end product inhibition’
State formula for pH
pH=-log10[H+]
