Chapter 3: Proteins and Enzymes Flashcards
State the elements found in
a) all proteins
b) Some proteins
a) All = C, H, O, N
b) Some proteins = S
State the 3 groups found in all amino acids
- amine group
- carboxylic acid group
- residual group
Draw the structure of a generalised amino acid
State the residual groups for glycine and cysteine
Glycine = simplest amino acid as R group = H
Cysteine = R group is SH (important in forming disulfide bridges)
State the 6 main functions of proteins
Hint: think steam
Structural role e.g. keratin, collagen
Transport role i.e. Hb and Mb
Enzymes
Antibodies
Membranes i.e. intrinsic & extrinsic proteins
Hormones e.g. insulin, prolactin
Explain how to amino acids are joined together
- Condensation reaction joins two amino acids toegther
- i.e. removal of water resulting in the formation of a covalent bond
- Called peptide bond
- A series of condensation reactions are repeated to form a polypeptide chain (NB this is not an active functional protein at this stage)
Draw a diagram to show how a dipeptide is hydrolysed
Define the primary structure of a protein
Sequence of amino acids within the polypeptide chain (amino acids joined by series of condensation reactions resulting in peptide bonds)
Define the secondary structure of a protein
Folding of the polypeptide chain (ppc) to form one of 2 formations:
a) Alpha helices forms a coils
b) Beta pleated sheets forms pleated sheets
Define the tertiary structure of a protein
- Further folding of the ppc to produce complex 3-dimensional shape
- Results in globular arrangement (called G-protein)
Define the quaternary structure of a protein
Presence of 2 or more ppc joined together
OR
Presence of 1 ppc AND at least one non-protein, prosthetic group
Give 2 examples of quaternary proteins
Collagen – 3 ppc
Haemoglobin – 4 ppc and 4 haem groups
State and describe the 5 different bonds/interactions within proteins
i) Peptide: formed by condensation reaction between NH group of one AA and COOH group of adjacent AA
ii) Hydrogen: weak interactions between atoms with slight+ and slight- i.e. between dipoles
iii) Ionic: formed between R groups which have carboxyl groups (COO-) and amino groups (NH+)
iv) Disulfide: formed between the sulphur atom of R-groups of 2 cysteine amino acids
v) Hydrophobic interactions: water is repelled & excluded from hydrophobic, non-polar R-groups
Explain the principle behind how chromatography works
separates chemicals according to their solubility
State with an example the 2 different phases in chromatography
Stationary phase = paper, silica gel or column through which the solvent (mobile phase) runs
Mobile phase = liquid or gas, used to separate different chemicals
Write the formula used to calculate the Rf value
Retardation factor (Rf)
Rf = Distance travelled by the amino acid .
Distance travelled by the solvent
Explain how Rf values are used to determine the amino acids present
- Compare Rf value to Rf values of known standards
- Which have been run on chromatogram with same solvent
- At the same time i.e. same conditions
Give 2 reasons why pencil is used to draw the origin on a chromatogram
- To enable calculation of Rf
- Can’t use pen as the ink dye would also dissolve in the solvent & move up the SP
Explain how to apply a solution of amino acids to a chromatogram
- Use a narrow capillary tube
- To generate a spot with max diameter of 2-3mm
- On the, origin/starting line
- To generate/produce, a high concentrated spot (of the substance)
- Air dry between application of further spots
Explain why the chromatogram should be handled with gloves
- To avoid getting fingerprints on the stationary phase
- As the solvent may dissolve the oils in the grease
- This changes the rate the solute rises (and affects the spot formation and travel)
Explain why ninhydrin is applied to a chromatogram
To make the amino acids more visible
By forming a blue-violet compound
Explain how to confirm a spot on a chromatogram is not composed of 2 or more substances
- Run chromatogram again with different solvent
- Run chromatogram again in 2nd orientation
- i.e. 2-way chromatography
- This will increase the resolution of the spots obtained
Explain the advantage of using different solvents in chromatograms
- As different amino acids will have different solubilities in different solvents
- If only one solvent is used one (or more) amino acid may not dissolve in tit and hence give false results
- More solvent = increase probability that all amino acids present will dissolve in at least one solvent
Explain the importance of covering the chromatogram tank with a lid
- As solvent may have low heat of evaporation
- Hence could diffuse into surrounding atmosphere
- May have health risks e.g. corrosive when inhaled etc
Explain how the properties of amino acids affect the Rf value
- Amino acids with R-groups which are hydrophilic will have a higher solubility
- This means that they will have a larger Rf value e.g. serine
- Amino acids with R-groups which are hydrophobic will have a lower solubility
- This means that they will have a smaller Rf value e.g. glycine
State the two extremes of Rf values and explain their significance
Minimum = 0 and max = 1
Zero = amino acid doesn’t dissolve in the solvent/MP
One = amino acid has a high affinity for the MP So travels the same distance as the MP
Define the terms • repeatable • reproducible
If someone was to carry out the test again using the same method and got the same result, the data is said to be repeatable
If a measurement was taken using a different method and got the same result, the result is referred to as reproducible
State 7 key features/properties of enzymes
- biological catalysts i.e. speed up the rate of reaction
- lower the activation energy
- not altered or used up in the reaction
- can be reused many times
- are globular proteins
- are soluble
- have high turnover rates
Explain how enzymes lower the activation energy
- The enzyme provides an alternative pathway for the reaction
- The reactants are held in the active site by the R-groups of the amino acids
- The enzyme brings the reactants close together in the active site
- This puts strain on the reactants
- So that bonds can be made or broken more easily
- The enzyme can also transfer charges or groups from one reactant to another
Explain the difference between catabolic (C) and anabolic (A) reactions
- C: break large molecules down into smaller molecules vs A: join smaller molecules together
- C: break bonds within the initial substrate usually involve hydrolysis reactions vs A: form bonds between substrates to form larger product(s)
- C: are exergonic (give out energy) vs A: usually involve condensation reactions
State the 3 key properties of enzymes that are important in increasing the efficinecy of metabolism
Specificity
High turnover rate
Reversibility
Define the term specificity
- E only work on specific substrate(s)
- Shape of S must be complementary to the shape of the AS
Define the term reversibility
Some E catalyse reactions in either direction
Direction of reaction depends on environmental conditions
E.g. Carbonic anhydrase
Define the term high turnover rate (TOR)
- TOR = maximum number of chemical conversions of S molecules per second that a single catalytic site carries out at a given concentration of E
- E.g. catalase ~ 40million molecules of H2O2 broken down per second
Define a cofactor
additional non-protein component that is needed by the enzyme to enable it to function
Give 2 examples of cofactors
- inorganic ions (e.g. Ca2+, Zn2+)
- organic molecules (coenzymes) e.g. vitamins.
Define the term apoenzyme
An inactive enzyme which needs the presence of a co-factor to activate it
Define a holoenzyme
- A complex of an enzyme with its cofactor
- The complex is active i.e. enzyme will function
Explain how a cofactor such as chloride ions activates an aopenzyme such as salivary amylase
- Presence of Cl- ion alters shape of the enzyme
- Change in shape of the enzyme = allostery
- Causes the AS to become more complementary to the substrate
- Change in shape makes it easier for the substrate to bind to the active site
State what level of structure a holoenzyme must have to be active
Quaternary = as it must consist of at least one ppc to make the enzyme and must have a cofactor (specialised prosthetic group) to be active
State 4 factors that must be controlled when investigating the effect of enzyme concentration on the rate of reaction
- Substrate concentration
- pH
- Inhibitor concentration
- Temperature
Sketch a graph to show the effect of enzyme concentration on the rate of reaction
Sketch a graph to show the effect of substrate concentration on the rate of reaction
Sketch a graph to show the effect of pH on the rate of reaction
Sketch a graph to show the effect of temperature on the rate of reaction
Add dgm
Write the formula to calculate the pH of a solution You must be able to use this formula in exams
Add dgm
Explain the how enzymes can be permanently or temporarily denatured by changes in pH
small changes in pH can lead to temporary changes in the shape of the active site and can be reversed significant changes in pH will result in permanent denaturation as the changes are irreversible
Explain the Q10 rule
For every 1o oC rise in temperature the rate of an enzyme controlled reaction will double UP UNTIL its optimum temperature Remember: beyond the optimum temperature the RoR will decrease sharply to zero as the enzyme is denatured
Explain the difference between a collision and a successful collision
Collision: when a substrate impacts with an enzyme due to both molecules moving randomly as they possess kinetic energy Successful collision: when a substrate impacts with the active site of an enzyme in the correct orientation and with sufficient energy to form an ESC
Define an enzyme inhibitor
A small molecule that interacts with an enzyme to reduce the RoR
State the two type of inhibitor and state where they interact with the enzyme to reduce the RoR
Competitive inhibitor – interacts with the active site Non-competitive inhibitor – interacts with the allosteric binding site
Describe the relationship between a competitive inhibitor and the substrate
They are similar in shape to each other] Do NOT say they are the same