Option C - Human Biochemistry (HL)

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[edit] C.7 Enzymes

[edit] C.7.1

Characteristics:

• Most of the proteins in the organism are enzymes. They act as catalysts for biochemical reactions in the body.
• An enzyme's activity depends on its tertiary and quaternary structure. Different enzymes catalyse different reactions depending on their structure because substrates bind to the enzyme's active site during the reaction. This active site is only present in tertiary and quaternary structures. The properties and positions of the R-groups exposed at the active site determine which substrates will bind to the enzyme.
• Some enzymes do not bind to substrates unless their active sites don't contain additional ions or molecules.

Co-factor : A substance held to the protein by other bonds e.g. ions Ca²⁺.

Co-enzymes : Non protein organic molecules eg vitamins.

[edit] C.7.2

Substrate concentration :

A single enzyme can process only a limited amount of substrate in a given time,. When substrate concentration increases, reaction rate increases. When all the enzymes are bound to substrates, the rate depends on the enzymes' rate of processing the substrates. The reaction rate eventually reaches a maximum limit.

[edit] C.7.3

V_max and Michelis Constant (K_max) :

• The rate is expressed as the number of reactions catalyzed by a given enzyme molecule per unit time.
• In a graph of substrate concentration vs. rate of reaction, the graph rises in a curved fashion, with a decreasing slope. V_max is recognised as being the point in which the graph continues in a horizontal line, parallel to the x-axis.
• The K_max is the substrate concentration at which the reaction rate is ¹/₂ V_max. This is a measure of how readily the enzyme-substrate binding occurs. When K_max is low, the reaction proceeds at a rapid rate even at low substrate concentrations.
• K_max is recognised on a graph by finding the ¹/₂ V_max rate on the y-axis and drawing a perpendicular down to the x-axis. The perpendicular will reveal the concentration at K_max.

[edit] C.7.4

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[edit] C.7.5

Active Site :

• It is a cluster of chemical groupings formed as a part of the enzyme's folding pattern. The properties of the R-groups exposed at the active site determine which substrates will bind.
• When enzymes and substrates combine, they change shape: The active site is a flexible part of the enzyme, which increases the surface area between the substrate and enzyme.

[edit] C.7.6

Inhibition:

Competitive inhibition : Compounds that are similar to the substrate, which compete with the substrate by binding to the active site. This decreases the reaction rate because the enzyme cannot bind to the substrate.

Non-competitive inhibition : The inhibitor binds to a site other that the active site.

• Does not change the active site
• Increases the activation energy
• Does not effect Enzyme-Substrate binding

[edit] C.7.7

Effects on Enzyme Activity:

Heavy metal ions :

• Calcium ions are the most commonly found in animals, accounting for 1.5-2% of human body mass, of which 99% comes from bones and teeth.
• Half a gram phosphorous is required for attaching each gram of calcium to the bones
• Magnesium, potassium and sodium ions are also present in biological systems as ions in the fluids in and around the cells present in trace amounts in the human body.
• Iron was the first trace metal ion found to be essential in the human diet.

The first row transition metals such as Co, Cr, Cu, Mn and Zn are present in trace amounts in the human body. These are essential to many enzymes such as Zn²⁺ in carboxypeptidase.

• Zn is found in almost 100 enzymes and is also present in insulin.
• Co (3+) is found in vitamin B12 and iron is present in the hemoglobin molecule of red blood cells.
• Magnesium is a secondary element of bones and teeth as well as regulating intracellular chemical activity, helping to form protein and transmitting electrical signals from cell to cell.
• Mn is essential for healthy bones and Cr plays a key role in glucose metabolism.

• Iron deficiency produces anaemia and causes fatigue as cells are deprived of oxygen.
• Cu deficiency gives rise to bone disease.

The nees for trace amounts of some metal ions such as tin and arsenic has been established in animals such as rats but not yet in humans.

[Heaving metals poison enzymes by reacting with the –SH groups and replacing the hydrogen atom with a heavy metal atom or ion so that the tertiary structure is altered. ]

Temperature : When temperature rises, molecules move faster, colliding harder and more often, therefore they are more likely to react than at lower temperature. When the temperature increase is too high (above 60°C), the enzymes will be denatured permanently, and will no longer function since their 3-D structure will be destroyed. At low temp reactions proceed slowly, and at very low temperatures (below 0°C) the enzymes are denatured. They normally function at body temperature 37°C.

pH : Enzymes are electrically charged because R-groups may ionise when they dissolve in water. The pH therefore determines the changes in the enzyme. Enzymes will function only at given pH's depending on their electrical charge. Most enzymes function best at neutral pH's.

[edit] C.7.8

Biotechnology :

Protease in Biological detergents: Protease digest protein strains (blood and sweat) by hydrolyzing proteins to polypeptides and amino acids.

Glucose isomerase converting glucose to fructose: Starch is broken down by amylase to glucose. Glucose isomerase converts glucose to fructose. [Fructose is often used in manufacture of food as it is much sweeter than glucose]

[edit] C.8

(Missing)

C.8.4 Describe the principles and uses of DNA profiling Principles:

• Minute amounts of DNA can be amplified by PCR (polymerase chain reaction)

o Adv: can take very small samples from crime scenes (eg. Semen stains left behind in a rape case)

o Dis: even a small amount of contamination can ruin everything as the slight contamination will also be amplified.

• This is done in cycles each cycle doubling the amount of DNA. There are 3 steps:

1. Denaturation: The DNA is heated to about 90oC so that the DNA double strand breaks and there are 2 single strands.

2. Annealing: the temperature is then decreased to about 37oC and short DNA primers are allowed to bind to the single strand.

3. Extension: An enzyme then uses free nucleotides to fill in the gaps. (temperature about 70oC)

• Electrophoresis is then used to separate the DNA into bands.

Uses: • Determining parentage.

• Determining the person who committed an offense.

[edit] C.9 Metal Ions in Biological Systems

[edit] C.9.1

Roles in the body/Chemical properties :

• Sodium and Potassium are vital the the functioning of nerves and muscles.
• Calcium is necessary for muscular activity.
• Calcium and phosphorus are needed for bone formation (see p643 bio book (Which book?)).

[edit] C.9.2

Ion concentration across cell membrane :

• Active transport : Moves substances either with or against their electrochemical gradients, and requires energy. A source of energy may be Na⁺ of H⁺ concentration on the two sides of the membrane.
• Sodium/potassium pumps : It uses energy from ATP to transfer sodium ions out of the cell and potassium ions inside. This pump is responsible for the electrical potential across plasma membranes. In the membrane, 3 sodium ions are moved for every two potassium ions that move in. The cell becomes more negative compared with the outside. When the tendency of K⁺ leaving the cell balances its tendency to enter it, the membrane potential is reached, K⁺ movement ceases.
• This type of pump controls the water content of the cell. It also drives the transport of sugars and amino acids. This process controls; the ability of nerves to conduct electricity, kidneys to form urine, muscles to contract, absorption of food in digestive tract.

[edit] C.9.3

Copper ions in electron transport :

• The electron transport system accepts hydrogen atoms and passes their electrons from one member of the chain to the next.
• Cytochromes : Electron carrier molecule consisting of a protein and a porphyrin ring, containing a copper ion.

Iron ions in oxygen carriers :

• Haemoglobin : Respiratory pigment that carries oxygen in the blood.
• Contain a haemoglobin group with an iron atom at its centre. The iron atom binds to the oxygen. When O binds to Fe, the haemoglobin is oxygenated and appears bright red. Without the iron centre, oxygen wouldn't bind to haemoglobin, and oxygen couldn't be carried through the blood stream and to the cells in the body.