IB Chemistry

The activity of enzymes depends on…

(in terms of structure)

tertiary and quatenary structures
stereoselectivity
controls which optical isomer is formed
differences between inorganic catalysts and organic catalysts (enzymes)

1. enzymes are proteins and catalysts are inorganic elements or compounds

2. enzymes are more efficient than inorganic compounds

3. inorganic compounds are not temperature sensitive, whereas enzymes are

4. enzymes only work in a narrow pH range

5. enyzme action takes place in aqueous solutions in biological organisms, whereas inorganic catalysts can be homogeneous or heterogeneous 

the rate of reaction is ____ order with respect to enzyme concentration 

(if pH, temperature and concentration are constant)

first
there is a maximum rate at which the reaction can occur with enzymes because…
all of the active sites will eventually be occupied
Michalis constant
equal to the substrate concentration when the velocity (rate) is equal to half the maximum value (Vmax)

Michaelis constant for a particular substrate

(Km)

will always be the same 

indicates the level of substrate where the enzyme works most efficiently

relationship between Km value and enzyme-substrate stability
a low Km value means the enzyme-substrate comples is more stable than when the Km value is higher

relationship between Vmax and Km in terms of

non-competitive and competitive inhibitors

for non-competitive inhibitors, Vmax is lower but Km is the same

for competitive inhibitors, Vmax is the same by Km has increased

effect of temperature on the reaction rate of an enzyme

as the temperature goes up, the rate increases as there are more molecules that exceed the required Ea and collisions are more frequent

As the optimal temperature is exceded the rate of reaction decreases as the enzyme becomes denatured

Effect of metal ions on the reaction rates of enzymes
can poison enzymes by reacting with -SH groups replacing the H atom with a heavy metal atom, or ion, so that the tertiary structure is altered
reason why enzymes give the reaction a lower activation energy
enzymes changes the shape with substrate, altering the substrate position so that it is in a more favourable orientation and position
nuclei acids fall into two classes
DNA and RNA
DNA and RNA are polymers of….
nucleotides linked in a chain through phosphodiester bonds
purines vs pyrimidines 

purines (A and G)

pyrimidines (C,T and U)

nucleoside structure
consists of a base and a sugar
nucleotide structure
consists of a base, a sugar and a phophate group
bonding between a base and a sugar
covalently bonded through a condensation reaction

Explain the double helix structure of DNA

( 8 points)

1. DNA has a seconding structure that results in the formation of a double helix

2. The double helix consists of 2 strands of nucleic acid that interact through intermolecular hydrogen bonding between the bases attached to the strands to form the double helix

3. The base pairings result because only a base combination of a purine and a pyrimidine give a similar distance between the 2 backbones of DNA (double and single rings)

4. The intermolecular hydrogen bonding that occurs between the base pairs is a major factor holding the double stranded DNA molecule

5. Adenine forms 2 hydrogen bonds wih thymine and cytosine forms 3 hydrogen bonds with guanine

6. The double helix is also stabilised by other interactions such as Van der Waal’s forces

7. To minimise the electrostatic repulsions between negatively charged phosphate residues, the sugar-phosphate backbone adopts a helical configuration

8. The combination of H-bonding between the base pairs and the twisting of the sugar-phophate backbone result in DNA’s secondary structure – a double stranded, helical shape with a ‘ladder’ of bases spanning the gap between the 2 strands

Protein synthesis

(5 points)

1. Protein synthesis takes place in the cytoplasm

2. the information required is passed from DNA to mRNA through transcription

3. the coded information held in the mRNA is used to direct protein synthesis using a triplet code by translation

4. each sequence of 3 bases represents one amino acid and is known as a triplet code. The triplet code allows for up to 64 different permutations know as codons, which is more than sufficient to account for the 20 amino acids

5. tRNA acts as an amino acid carrier in the formation of proteins

DNA profiling

1. DNA is extracted and broken down into smaller fragments using restriction enzymes

2. DNA is then replicated and separated using gel electrophoresis (opposite charges at either end)

3. Since DNA has a negatively charged phosphate group it is attracted to the positive end

4. As the graments of DNA move, the smaller fragments move quicker

5. A fluorescent dye is added which makes the DNA glow in UV light

6. The sequence and hence fragment sizes are unique for each individual (except identical twins)

Respiration

1. sugars undergo glycolysis as the first stage in cellular respiration (one molecule of glucose breaks down into 2 pyruvic acid molecules)

2. Pyruvic acid is a weak acid and it dissociates to form pyruvate ions:

C3H4O3 — C3H3O3 + H+

3. The beakdown of glucose involves the removal of hydrogen atoms by a carrier called

nictotinamide adenine dinucleotide (NAD+) to form NADH

4. Once glucose is converted into the pyruvate ion aerobic oxidation takes place (pyruvate is converted into carbon dioxide and water)

5. When anaerobic respiration takes place the pyruvate ion is converted to lactic acid, and if oxygen becomes available the lactic acid can be oxideise to CO2 and H2O

Electron Transport chain in the mitochondria

1. transition metals exist in multiple oxidation states

(can catalyse redox reactions)

2. glucose is oxidised by a series of redox reactions

(in the mitochondria of cells)

3. The oxidising enzymes are called cytochromes, containing Cu2+ or Fe3+ which transports the electrons

4. Cytochromes are part of the electron transfer chain which generates adenosine triphosphate

(a form of short term stored chemical energy)

5. The Cu2+ or Fe3+ in cytochrome oxidase is surrounded by a porphyrin ligand, containing 4 N atoms each with donates a pair of electrons and occupies four of the sites arround the metal ion (tetradentate ligand)

6. Reduced co-enzymes such as NADH carry hydrogen ions and eletrons from the metal ions and serve as intermediates to form water and produce energy

Haemoglobin as an oxygen carrier

1. the ability of iron to form complexes is important in Hb

2. Hb contains 4 large polypeptide groups, and 4 Fe2+ which are surrounded by flat porphyrin ligands known as haem groups

4. At high oxygen concentrations, Hb binds to the Fe2+ in the haem group as an extra ligand, and at low concentrations the reverse reaction occurs

5. CO and cyanide ions are poisonous because they form irreversible complex ions with the iron preventing it from carrying oxygen (have a much higher affinity than oxygen) 

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