C3 - Proteins and Enzymes Flashcards
What is a protein?
A polymer made from repeating subunits of amino acids (monomers).
There are 20 naturally occurring amino acids (approx 100 overall).
What is the general structure of an amino acid?
A central carbon atom
An amino group (-NH2) which has basic properties
A carboxyl group (-COOH) which has acidic properties
A hydrogen atom (-H)
The R group - which varies between each of the 20 amino acids and makes each unique. The simplest R group is of the amino acid ‘glycine’ which is a H atom.
How do amino acids behave as a base or an acid in solutions like plasma or cytoplasm?
As a base - they accept protons (H+) to the amino group at the end of the molecule forming a positively charged amino acid ion.
As an acid - they donate protons from the carboxyl group which forms a negatively charged amino acid ion.
What does amphoteric mean?
It means that the molecule can behave as bases or acids which is important for the role of some proteins e.g. Haemoglobin which act as buffers.
How are amino acids joined together? (Name of reaction)
A condensation reaction which forms a dipeptide or polypeptide chain.
Water is removed as an -OH group is removed from the carboxyl group and a -H atom is removed from the adjacent amino acid.
What type of bond is formed when amino acids join together?
Peptide bonds
What is chromatography?
A technique used used to separate chemical substances according to their solubility.
It can be done in stationary phase (using paper, silica gel or columns) or mobile phase (liquid or gas)
Amino acids are separated using paper. Different substances have different weights, polarities and structures so move different amounts.
How is the Rf value (relative front) of a substance calculated?
Rf = distance travelled by substance / distance travelled by solvent
Different amino acids have different Rf values due to the different R groups they have.
What’s haemoglobin?
A complex protein that is essential for the transport of 98% of the oxygen.
It consists of 4 polypeptide chains.
What is the primary structure of a protein?
It is the sequence of amino acids in the polypeptide chain.
They are linked by peptide bonds.
A simple chain in a single amino acid can lead to a change in the shape and structure of the protein which may make it non-functional.
What is the secondary structure of a protein?
When the primary structure is folded or coiled into two different arrangements which are held in place by hydrogen bonds.
The -NH group has a slight + charge which is attracted to the - charge on oxygen of the -C=O group
What are the two different arrangements of the secondary structure of proteins?
Alpha helix: causes the polypeptide chain to coil into a tubular shape
Beta-pleated sheet: causes the polypeptide chain to fold back on itself in flat parallel sheets.
What is the tertiary structure of a protein?
When the secondary structure is further folded or coiled to produce a more complex 3D structure.
What type of interactions are present within tertiary structures of proteins?
Disulfide bonds - found between two cysteine amino acids. They’re very strong covalent bonds that form between a sulfur atom in each of the cysteine R groups.
Ionic bonds - weaker than above. Found between the carboxyl and amino R groups.
Hydrogen bonds - weaker than above. Found between the O of -C=O and H of -NH group.
Hydrophobic interactions - formed by non-polar R groups which are hydrophobic. They’re arranged so they’re positioned in the centre of the protein.
What is the quaternary structure of a protein?
When there is more than one polypeptide chain joined together.
E.g. Haemoglobin
How is haemoglobin assembled and what is it’s structure?
It’s made when four polypeptide chains made on the ribosomes within the cell are combined with four haem groups.
This occurs in the E.R. and Golgi apparatus.
When the haemoglobin content of the erythrocytes reaches 30% the nucleus, G.A., E.R. and mitochondria are broken down, creating space for the haemoglobin molecules to be stored and helps the formation of the biconcave discs essential for the erythrocytes functions.
What is an enzyme?
A globular protein that acts as a biological catalyst.
What are the four stages of enzyme activity?
1) The substrate collides successfully with the active site with sufficient energy and correct orientation.
2) The substrate binds to the active site of the enzyme to form an enzyme-substrate complex (ESC)
3) Once the substrates are bound to the active site the substrates are converted to the products
4) The products are released from the active site of the enzyme leaving it vacant for another substrate to bind again.
What are the functions of proteins?
Enzymes Antibodies Cell membranes Structural roles Hormones Transport
How do enzymes speed up reactions?
Converting a substrate into its products requires energy which cannot be achieved in living cells by simply heating the molecules.
Enzymes speed up reactions as they lower activation energy by using the enzyme ‘catalase’ so that the substrate ‘hydrogen peroxide’ doesn’t need to be raised to such a high energy level and can be converted into water and oxygen easier.
What is an endotherm?
An animal which is capable of internal generation of heat.
What is the significant difference between enzymes and non-biological catalysts?
Only substrates of a particular shape will fit into the active site of an enzyme.
What is carbonic anhydrase?
An enzyme which catalyses both forward and reverse reactions of some reversible reactions.
How does temperature affect enzymes?
As temperature increases, kinetic energy increases so random motion is faster. The faster the movement, the greater the chance of a (successful) collision, increasing reaction rate.
It temp’ exceeds 40’C, more vibrations occur between the atoms within each molecule which causes the hydrogen bonds in the enzyme structure to break. This results in the loss of its 3D shape and this distortion can cause it to denature and enzyme-substrate complexes cannot form.
How does the substrate concentration affect the rate of reactions with enzymes?
If enzyme concentration remains constant and substrate concentration is increased, reaction rate is increased as there is more substrate molecules in the same volume so there are more (successful) collisions occurring.
The rate increases until the number of enzymes becomes a limiting factor.
How does enzyme concentration affect the rate of reactions with enzymes?
The rate increases if enzyme concentration increases, only if there is an excess of substrate molecules.
This rate stops once the substance concentration becomes a limiting factor.
How do changes in pH affect enzymes?
2
- Different R groups of amino acids carry different charges which can be altered by a change of the environment’s pH. This affects amino acisd in the active site and can prevent substrates from binding to it, preventing ESC formations.
- A change in pH can cause the hydrogen and ionic bonds holding the secondary and tertiary structure of the enzyme in place to be broken which denatures the enzyme.
What are inhibitors?
Molecules which interfere with the functioning of the active site of an enzyme directly & indirectly, permanently and temporarily.
