Biological Molecules Flashcards
what is the general basic structure of an amino acid
- COOH (carboxyl group)
- A R variable side group
- NH₂ amine / amino group
How many naturally occurring amino acids are there and how are they distinguished ?
- 20
- differ only by side ‘R’ group
Describe how a peptide bond is formed between two amino acids to form a dipeptide (2)
- Peptide bonds are formed from a condensation reaction
- between the amine and carboxyl groups (or NH2 and COOH)
What is a polypeptide and how is it formed
- condensation reaction forms a peptide bond between 3 or more amino acids
How many levels of protein structure are there?
4
Describe the ‘primary’ structure of a protein
- linear sequence , number and type of amino acids in the polypeptide
- determined by sequence of codons on mRNA
The secondary structure of a polypeptide is produced by bonds between amino acids. Describe how.
[2 marks]
- Hydrogen bonds form between the slightly positive NH group on one amino acid and the slightly negative C=O group on another.
Describe the 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 another
Define tertiary structure of a protein. Name the bonds present.
3D structure formed by further folding of polypeptide:
- disulfide bonds
- 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 cysteine
ionic bond: relatively strong bonds between charged R groups (pH changes cause these to break
hydrogen bonds: numerous & easily broken
Define quaternary structure of a protein
- functional proteins which consist of more than one polypeptide
- may involve the addition of prosthetic groups (moieties)
Describe how to test for proteins in a sample.
Biuret Test confirms presence of peptide bond
1. Add equal volumes of sodium hydroxide to sample at room temperatures
2. Add drops of dilute copper (||) sulfate solution . Swirl to mix
3. Positive result: colour changes from blue to purple
negative result: solution remains blue
What are enzymes?
- biological catalysts for intra & extracellular reactions
- specific tertiary structure determines shape of active site, complementary to a specific sustrate
- formation of (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 ES complexes to form
- this puts strain on substrate bonds , lowering activation energy
how have models of enzyme action changed ?
- Lock and key method : rigid shape of active site complementary to only use 1 substrate
- Current induced fit model : explains why binding at allosteric sites can change shape of active site
Describe the structure and function of globular proteins
- spherical and compact
- hydrophilic R groups face outwards & 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 & place chromatography paper in solvent.
- Amino acids move different distances during the mobile phase based on relative attraction to paper & solubility in solvent.
- Remove paper when the solvent has nearly reached the top and draw a line to show where the solvent has reached, this is the SOLVENT FRONT.
- The chromatogram is dried in a fumes cupboard and then sprayed with NINHYDRIN SPRAY. When the chromatogram dries, the amino acids will appear as purple spots at different distances up the chromatogram.
- The unknown amino acid(s) can then be identified by comparing and matching them with the chromatograms of the known standard solutions of different amino acids
- Calculate Rf values
How could a student identify the activation reaction from an energy level diagram?
- difference between free energy of substrate & 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 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 E 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 and H-bonds in tertiary structure break.
- active site is no longer complementary to substrate ( denaturation)
How does pH affect rate of reaction?
- Below and above the optimum pH of an enzyme, solutions with an excess of H+ ions (acidic solutions) and OH- ions (alkaline solutions) can cause H+ and ionic bonds to break
- This alters the shape of the active site, which means enzyme-substrate complexes form less easily.
- denaturation of the enzyme occurs
Explain how competitive inhibitor reduce the rate of an enzyme catalysed reaction (3)
- Inhibitor is a similar shape to substrate
- This binds to the active site
- Thus preventing an enzyme substrate complex from Forming
Describe how a non-competitive inhibitor can reduce the rate of an
enzyme-controlled reaction. (3)
- Attaches to the enzyme at a site other than the active site ( the allosteric site)
- Changes (shape of) the active site
- (So active site and substrate) no longer complementary so
no substrate can bind.
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 max rate of reaction before concentration of reactants decreases &’ end product inhibition’
state the formula for pH.
pH = −log10 ([H+])
H+ = hydrogen ion concentration of a solution
