1.4 Proteins Flashcards
What is the general structure of an amino acid?
-COOH carboxyl/carboxylic acid group
- R variable side group consists of carbon chain and 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 and 2 make biuret reagent)
- Positive result: colour changes from blue to purple
Negative result : solution remains blue
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: 2 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 formed between O (slightly negative) attached to -C=O and H (slightly positive) attached to -NH
Describe the two types of secondary protein structure
Alpha helix
All N-H bonds on same side of protein chain
Spiral shape
H-bonds parallel to helical axis
Beta pleated sheet
N-H & C=O groups alternate from one side to the other
Define ‘tertiary structure’ of a protein. Name the bonds present
3D structure formed by further folding of polypeptide
- disulfide bridges
-ionic bonds
-hydrogen bonds
Describe each type of bond in the tertiary structure of proteins
Disulfide bridges: strong covalent S-S bonds between molecules of the amino acid cycsteine
Ionic bonds: relatively strong bonds between charged R groups (pH changes cause these to break)
Hydrogen bonds: numerous and easily broken
Define ‘quaternary structure’ of a protein
Two or more polypeptide chains
Describe the 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 the 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 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 determines shape of active site, complementary to a specific substrate
Formation of enzyme-substrate (ES) complexes lowers activation energy of metabolic reactions
Explain the induce fit model of enzyme action
Shape of active site is not directly complementary to substrate and is flexible
Conformational change enables ES complexes to form
This puts strain on substrate bonds, lowering activation energy
How have models of enzymes 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 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 substance and peak of curve
Slide 38
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 meaning 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 range, H+/OH- ions interact with H-bonds and ionic bonds in tertiary structure = denaturation
Contrast competitive and 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 at 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
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 the formula for pH
pH = -log10[H+]
