Biochemistry (Option B) Flashcards
What are biological polymers? How do they form? Provide an example
Biological polymers (biopolymers) are formed by condensation
reactions. These involve the reaction between two smaller
molecules to form one larger molecule with the evolution
o a small molecule such as water. For condensation
polymerization to occur each reacting molecule must possess
at least two reactive unctional groups. Classic examples
include the condensation o amino acids to form proteins and
the condensation o sugars to form starch
Describe and explain hydrolysis
Hydrolysis is the reverse of condensation. A molecule is hydrolysed when a water molecule (often in the presence
of acid or alkali) reacts with a larger molecule to break a
bond and form two smaller molecules.
State and explain the state of amino acids at room temperature
They are solids at room temperature and have quite high melting points. This solid state is because they
can exist as zwitterions in which the hydrogen atom from the carboxylic acid group protonates the amine group to form a carboxylate anion and a substituted ammonium cation within the same compound
What is a secondary structure of a protein?
The secondary structure describes the way in which the chain of amino acids folds itself due to intramolecular hydrogen bonding.
What is the tertiary structure and what forms it?
The tertiary structure describes the overall folding of the chain by interactions between distant amino acids (intra molecular) to give the protein its three-dimensional shape. These interactions may be due to
-hydrogen bonds,
-London dispersion forces between non- polar side groups
-ionic attractions between polar groups
-disulfide bridges
-hydrophobic interactions
What is a quaternary structure of a protein? what forms it?
Separate polypeptide chains can interact together (inter molecular bonding) to give a more complex structure of this is known as the quaternary structure.
These interactions may be due to
-hydrogen bonds,
-London dispersion forces between non- polar side groups
-ionic attractions between polar groups
-disulfide bridges
-hydrophobic interactions
State and explain the structure, function and properties of fibrous and globular protein providing one example for each
Haemoglobin is an example of a globular protein. Globular proteins have complex tertiary and sometimes quaternary structures (e.g. haemoglobin) folded into spherical (globular) shapes. They are usually soluble to some extent in water as the hydrophobic side chains tend to be in the centre of the structure. Fibrous proteins, such as collagen, have little or no tertiary structure and form long parallel polypeptide chains. Fibrous proteins have cross-linking
at intervals to form long fibres or sheets and have mainly structural roles such as keratin in hair and collagen, which is found in skin and the walls of blood vessels and acts as connective tissue.
Describe how you would carry out paper chromatography on amino acids
A small spot of the unknown amino acid sample is placed near the bottom of a piece of chromatographic paper. The paper is placed in a solvent, which then rises up the paper due to capillary action. As it meets the sample spots the different amino acids partition themselves between the solvent and
the paper to different extents, and so move up the paper at different rates. When the solvent has nearly reached the top, the paper is removed from the tank, dried, and then sprayed with a location agent (ninhydrin) and placed in a heated oven to develop the chromatogram by colouring the acids. The positions of all the spots can then be compared using Rf values.
Formula for Rf
Rf value = distance travelled by sample /
distance travelled by solvent
Rf value < 1 (ALWAYS)
What is the isoelectric point of proteins
For each amino acid there is a unique pH value (known as the isoelectric point) where the acid will exist as the zwitterion.
Predict with an explanation whether an amino acid will move towards the cathode or anode during electrophoresis when:
pH< isoelectric point
pH = isoelectric point
ph> isoelectric point
The structure of amino acids alters at different pH values. At low pH (acid medium) the amine group will be protonated, thus a general positive charge on the molecule and will move towards the negative anode. At high pH (alkaline medium) the carboxylic acid group will lose a proton and thus the molecule will have a general negative charge and move towards the positive cathode.
Explain why amino acids can function as buffers
The structure of amino acids alters at different pH values. At low pH (acid medium) the amine group will be protonated. At high pH (alkaline medium) the carboxylic acid group will lose a proton. This explains why amino acids can function as buffers. If H+ ions are added they are removed as NH4 + and if OH- ions are added the COOH loses a proton to remove the OH- ions as water
State and explain the effect of temperature, pH and heavy metals on enzyme activity
The action o an enzyme depends on its specific shape. Increasing the temperature will initially increase the rate
of enzyme-catalysed reactions, as more of the reactants
will possess the minimum activation energy. Additionally the collision frequency will increase according to kinetic theory. The optimum temperature for most enzymes is about 40ºC. Above this temperature enzymes rapidly become denatured as the weak bonds holding the tertiary structure together break.
At different pH values the charges on the amino acid change affecting the bonds between them, and so altering the tertiary structure and making the enzyme ineffective.
Heavy metals can poison enzymes by reacting with -SH groups replacing the hydrogen atom with a heavy metal atom or ion so that the tertiary structure is altered.
List three types of lipids
Three important types of lipids are:
-triglycerides (fats and oils)
-phospholipids (lecithin)
-steroids (cholesterol).
What are fats and oils and how do they form?
Fats and oils are triesters (triglycerides) formed from the condensation reaction of propane- 1,2,3-triol (glycerol) with long chain carboxylic acids (fatty acids).
What are the four components of a phospholipid?
A backbone such as propane-1,2,3-triol (glycerol), linked by esterifcation to two fatty acids and a phosphate group which is itself condensed to a nitrogen-containing alcohol
What is characteristic of all steroid structures. Provide an example
Cholesterol has the characteristic our-ring structure possessed by all steroids
Explain why unsaturated fats exist as oils at room temp and saturated fats are solid at room temp
The regular tetrahedral arrangement of saturated fatty acids means that they can pack together closely, so the London dispersion forces holding molecules together are stronger as the surface area between them is greater. As the bond angle at the C=C double bonds changes from 109.5º to 120º they are unable to pack so closely and the London dispersion forces between the molecules become weaker, which results in lower melting points
Describe how hydrogenation of unsaturated fats occurs and discuss the possible concerns
Unsaturated fats can be hydrogenated to saturated fats by adding hydrogen under pressure in the presence of a heated nickel catalyst.
However during the hydrogenation process, partial hydrogenation can occur and the trans-isomers may be formed. Unlike natural mono- and poly-unsaturated oils, trans-unsaturated fats increase the formation of LDL cholesterol (bad cholesterol) and thus increase the risk of heart disease.
When has a lipid gone rancid (common terms)
Lipids (fats and oils) in food become rancid when our senses perceive them to have gone off due to a disagreeable smell, texture or appearance.
Describe the two ways in which a lipid may go rancid
-Hydrolysis o the triesters (hydrolytic rancidity) as shown above to produce disagreeable smelling fatty acids
-Oxidation of the fatty acid chains due to the addition of oxygen across the C=C double bonds in unsaturated fatty acids. The process proceeds by a free radical mechanism catalysed by light in the presence of enzymes. Volatile aldehydes and ketones are the products that make the fat rancid.
What does 1/2 Vmax mean?
This is the substrate concentration at which the reaction rate is equal to one half its
maximum value. In other words, [S] = Km when the rate is Vmax/2.
What is the effect of adding excess substrate to enzyme solution which contains;
A competitive inhibitor
Non-competitive inhibitor
In the comp. situation adding excess substrate will allow Vmax too be reached as the probability of substrate-enzyme complex forming increases
In non-comp situation excess reactant will have no effect as inhibitor is still able to affect the enzymes allosteric site irreversibly
What is end product inhibition?
The product of a reaction sometimes acts as an inhibitor of the enzyme for its synthesis, thereby setting up a feedback loop regulating its own concentration. This is known as product inhibition.
Beer–Lambert law
I0 = the intensity of light before passing through the sample
I = the intensity of light after passing through the sample
The absorbance depends on:
* the molar absorptivity, ε, defined as the absorbance of a 1.00 mol dm–3 solution in a 1.00 cm cell at a specified wavelength
* the concentration of the solution, c * the path length, l.
log10(I0/I) = εlc
Are Saturated or Unsaturated fats more stable and why>
As they cannot undergo auto-oxidation, saturated fats are more stable than unsaturated fats.
4 roles of lipids in the body
-Energy storage. Because they contain proportionally less oxygen than carbohydrates they release more energy when oxidized.
-Insulation and protection of organs. Fats are stored in adipose tissue, which provides both insulation and protection to parts of the body.
-Steroid hormones. Examples include female and male sex hormones such as progesterone and testosterone and the contraceptive pill. Sometimes steroids are abused. Anabolic steroids have similar structures to testosterone and are taken to build up muscle.
-Cell membranes. Lipids provide the structural component of cell membranes.
What is the iodine number and how is it calculated?
Since one mole of iodine will react quantitatively with one mole of C=C double bonds. Iodine is coloured. As the iodine is added to the unsaturated fat the purple colour of
the iodine will disappear as the addition reaction takes place. Once the colour remains the amount o iodine needed to react with all the C=C double bonds can be determined. Often fats are described by their iodine number, which is the number of grams o iodine that add to 100 g o the at.
What are the features of carbohydrates and how may they be subdivided?
they contain a carbonyl group (C=O) and at least two -OH groups. I the carbonyl group is an aldehyde they are known as an aldose, if the carbonyl
group is a ketone they are known as a ketose.
What are the most common forms of amino acids and carbohydrates found i nature?
D - Sacharides
L - Amino acids