TOPIC 3: CHEMISTRY OF LIFE 3.1 CHEMICAL ELEMENTS AND WATER 3.1.

1 STATE THE MOST FREQUENT OCCURRING CHEMICAL ELEMENTS IN LIVING THINGS

ARE CARBON , HYDROGEN , OXYGEN , AND NITROGEN .

3.1.2 STATE THE VARIETY OF OTHER ELEMENTS ARE NEEDED BY LIVING ORGANISM
INCLUDING SULFUR , CALCIUM , PHOSPHORUS , IRON AND SODIUM .

3.1.3 STATE ONE ROLE FOR EACH OF THE ELEMENTS MENTIONED IN 3.1.2 Element Sulfur Phosphorus Iron Calcium Role in plant In some amino acid Phosphate group in ATP molecules In cytochrome Co-factor in some enzyme In membrane function Role in animal In some amino acid Phosphate group in ATP molecules In cytochrome and hemoglobin Co-factor in some enzyme and as component of bones In membrane function and sending nerve impulse Role in prokaryote In some amino acid Phosphate group in ATP molecules In cytochrome Co-factor of enzyme

Sodium

In membrane function

3.1.4 DRAW AND LABEL WATER MOLECULES TO SHOW THEIR POLARITY AND HYDROGEN
BOND FORMATION

Hydrogen bond

Water molecule

3.1.5 OUTLINE THE THERMAL , COHESIVE AND SOLVENT PROPERTIES OF WATER .

Thermal Properties

water has high specific heat capacity which means that water can absorb or give off a great deal of heat without changing the temperature greatly. It has high heat of vaporization which means the water absorb a great deal of heat when it evaporate to act as cooling mechanism

Cohesive Properties

cohession is when molecules of the same type are attracted to each other. Water has this properties because of the hydrogen bond formed between the water molecules This properties enable the water to move as a column in the vascular tissue of plant

Solvent Properties

Many different substances dissolve in water because of its polarity inorganic molecules with positive or negative charge dissolve in water organic substances with polar molecules dissolve. water is the medium for metabolic reaction.

3.1.6 EXPLAIN THE RELATIONSHIP BETWEEN THE PROPERTIES OF WATER AND ITS USES
IN LIVING ORGANISMS AS A COOLANT , MEDIUM FOR METABOLIC REACTION AND TRANSPORT MEDIUM .

Properties of water Thermal properties

Solvent properties

Cohesive properties

Relationship between the properties of water and its uses in living organism Blood (mainly compose of water) can carry heat from warmer parts of the body to cooler parts Evaporation of water from plant (transpiration) and human skin (sweat) has useful cooling effect. Water act as a coolant Water is the medium for metabolic reaction Many substances to be carried dissolve in water in the blood of animals and the sap of plants. Strong pulling forces can be exerted to suck columns of water up to the tops of the tallest trees in the transport systems. Water is used as transport medium in the xylem of plants.

3.2 CARBOHYDRATES, LIPIDS, AND PROTEINS 3.2.1 DISTINGUISH BETWEEN ORGANIC AND INORGANIC COMPOUND Organic compound Are produced by living things and include all compound containing carbon that are found in living organism except for hydrogen carbonate(HCO3-), carbonate (CO32-) and oxide of carbon (CO2, CO) Inorganic Compound All compound that contain no carbon are inorganic

3.2.2 IDENTIFY AMINO ACID , GLUCOSE, RIBOSE AND FATTY ACID FROM DIAGRAMS
SHOWING THEIR STRUCTURE.

Amino Acid

Glucose

Ribose

Fatty Acid

3.2.3 LIST THREE EXAMPLES EACH OF THE MONOSACCHARIDE, DISACCHARIDES AND

POLYSACCHARIDES .

Subcategory Monosaccharide Disaccharide Polysaccharide

Examples Glucose, Galactose, Fructose Maltose, Lactose, Sucrose Starch, Glycogen and cellulose

3.2.4 STATE ONE FUNCTION OF GLUCOSE, LACTOSE AND GLYCOGEN IN ANIMALS AND OF
FRUCTOSE , SUCROSE AND CELLULOSE IN PLANTS .

Compound Glucose Lactose Glycogen Fructose Sucrose Cellulose

Function in living thing Chemical fuel for cell respiration Make up some of the solutes in milk Store glucose in liver and muscle Found in many fruits (make them sweet) Often transported from leaves of plants to other locations in plants by vascular tissues. One of the primary components of plants cell wall.

3.2.5 OUTLINE THE ROLE OF CONDENSATION AND HYDROLYSIS IN THE RELATIONSHIPS

BETWEEN MONOSACCHARIDES, DISACCHARIDES AND POLYSACCHARIDES , BETWEEN FATTY ACIDS , GLYCEROL AND TRIGLYCERIDES AND BETWEEN AMINO ACID AND POLYPEPTIDE .

3.2.6 STATE THREE FUNCTIONS OF LIPIDS Role of lipids:As energy storage Thermal insulation Make up double layer of cell membrane

3.2.7 COMPARE THE USE OF CARBOHYDRATES AND LIPIDS IN ENERGY STORAGE . Carbohydrates Carbohydrates are more easily digested than lipid so the energy stored by them can be release rapidly. Carbohydrates are soluble in water, so are easier to transport to and from the store Lipids Contain more energy per gram than carbohydrates. Therefore, store of lipids are lighter than the store of carbohydrates that contain the same amount of energy. Lipids are insoluble in water, so they do not cause problem with osmosis in cells.

3.3 DNA structure

3.3.1 Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate. (2) A nucleotide is made of; Deoxyribose sugar (differs from ribose in having one less oxygen on carbon 2) A base (which can be either adenine, guanine, cytosine or thymine) and A phosphate group (PO43-)

3.3.2 State the names of the four bases in DNA. (1) Adenine (A), Guanine (G), Cytosine (C) and Thymine (T) A and G Purines (big 2-ring structure) C T and U Pyrimidines (small 1-ring structure) 3.3.3 Outline how DNA nucleotides are linked together by covalent bonds into a single strand. (2) DNA is composed of two strands of nucleotides. Nucleotides are linked into a single strand via condensation reaction; phosphate + deoxyribose sugar + organic base nucleotides + 2 H2O The phosphate group of one nucleotide (attached to the 5-end) joins to the hydroxyl group on sugar of the second nucleotide (3-end) The phosphate group creates a bridge connecting C5 on one pentose with the C3 on the next pentose. This results in a covalent bond, called phosphodiester bond.

3.3.4 Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds (3) i. ii. iii. iv. DNA is made up of two nucleotide strands. The nucleotides are connected together by covalent bonds within each strand. The sugar of one nucleotide forms a covalent bond (phosphodiester bond) with the phosphate group of another. The two strands themselves are connected by hydrogen bonds. The hydrogen bonds are found between the bases of the two strands of nucleotide; Adenine pairs with thymine (A = T) Guanine pairs with cytosine (G C) This is called complementary base pairing. Below is a digram showing the molecular structure and bonds within DNA

v.

3.3.5 Draw and label a simple diagram of the molecular structure of DNA (1) Two polynucleotide chains. Sugar and phosphate backbone run antiparallel forming the sides of the double helix with the organic bases pairs rung in between. Two chains are in opposite directions and are wound round each other to form a double helix They joined together by hydrogen bonds between the bases. Adenine hydrogen bonds to Thymine (2 Hydrogen bonds) Cytosine hydrogen bonds to Guanine. (3 hydrogen bonds) Bonds between the components of the nucleotides are covalently bonded, by condensation. However, the H bond strength < covalent bond strength. But, there abundant amount of H bonds that keep the DNA securely.

Phosphate group

Pentose sugar Nitrogenous base Covalent bond (phosphodiester bond)

Complementary base pairing

Hydrogen bond

7.1.1 Describe the structure of DNA, including the antiparallel strands, 35 linkages and hydrogen bonding between purines and pyrimidines. (2) 5 3 - Double helix shaped -Consists of nucleotides - Nucleotide have one base, one deoxyribose sugar and one phosphate - Consists of 4 different bases Adenine, Guanine, Thymine and Cytosine - Complementary base pairing: A bonds to T, G bonds to C - Bases bond with hydrogen bonds - Nucleotides linked up with covalent bond/sugar-phosphate bonds; 5 3 - 3 5 links between nucleotides; - Strands are anti-parallel

7.1.2 Outline the structure of nucleosomes. (2) -Nucleosome core consisting of 8 histone protein molecules -DNA wrapped twice around nucleosome core -Another histone protein holds the nucleosome together -Has DNA linker continuing to the next nucleosome

7.1.3 State that nucleosomes help to supercoil chromosomes and help to regulate transcription. (1) Supercoiling will condense the chromosome because only certain areas of supercoiled DNA are accessible to transcription enzymes.

7.1.4 Distinguish between unique or single-copy genes and highly repetitive sequences in nuclear DNA. (2) Single copy One locatable region on DNA molecule Long base sequence Have coding function May be translated Highly repetitive Can repeat up to 100 000 times on various location on DNA Short sequence/ 5-300 bases Have no know function Not translated

7.1.5 State that eukaryotic genes can contain exons and introns. (1) Exons are sequences of bases that are transcribed and translated, and introns are non-coding fragments that are transcribed but not translated.

3.4 DNA Replication

3.4.1 Explain DNA replication in terms of unwinding the double helix and separation of the strands by helicase, followed by formation of the new complementary strands by DNA polymerase (3) 7.2.2 Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates. (3) The cell produces many free nucleotides for DNA replication. Each nucleotide has 3 phosphate groups (deoxyribonucleoside triophosphate). During replication 2 phosphate groups are removed to release energy. 1. Helicase uncoils the DNA double helix and splits them into 2 template strands called lagging strand and leading strand by breaking the hydrogen bonds between the bases. 2. The leading and lagging strands of DNA are now templates for the new strands to form.

3. On the leading strand, the RNA primase synthesizes a short RNA primer on the DNA to begin replication. This acts as a primer, allowing the enzyme DNA polymerase III to bind. (The RNA primer will later be removed by DNA polymerase I) 4. DNA polymerase III then starts adding deoxynucleoside triphosphates to the strand in a 5 to 3 direction by complementary base pairing. 5. On the lagging strand, RNA primase synthesizes a short RNA primer complementary to the
exposed DNA for replication.

6. DNA polymerase III then starts adding deoxynucleoside triphosphates to the strand in a 5 to 3 direction by complementary base pairing, moving away from the replication fork. 7. DNA polymerase I removes the RNA primer and replaces it with deoxynucleoside triphosphates. Short lengths of DNA are formed between RNA primers, called Okazaki Fragments. 8. There is a nick where two nucleotides are still unconnected and DNA ligase seals the nick by making another sugar-phosphate bond. 10. Two identical DNA double helices are formed with each consisting of one old and one new strand. 11. The DNA strands then rewind to form a double helix. The replication process has produced a new DNA molecule which is identical to the initial one
Leading strand; The new strand that is synthesised continuously and follows the replication fork Lagging strand; The new strand that is synthesised in short fragments in the opposite direction to the movement of the replication fork

3.4.2 Explain the significance of complementary base pairing in the conservation of the base sequence of DNA. (3) i. ii. During DNA replication, base pairing occurs (A = T) and (G C) Thus, the sequence of bases in one strand exactly determines the sequence of bases in the other strand iii. This complementary base pairing allows the two DNA molecules to be identical to each other as they have the same base sequence. It ensures proper base/correct base incorporated into DNA strands. It also ensures the conservation of base sequence. iv. The new strands formed are complementary to the template strands but also identical to the other template. v. However, mistakes do occur, and these are called mutations.

3.4.3 State that DNA replication is semi-conservative (1) One strand will be from the original molecule and another strand will be newly synthesized.

7.2.1 State that DNA replication occurs in a direction. (1) The 5 end of the free DNA nucleotide is added to the 3 end of the chain of nucleotides that is already synthesized. This DNA replication occurs in a 5 to the 3 direction.

7.2.3 State that DNA replication is initiated at many points in eukaryotic chromosomes. (1) There are as many as 80 million bases to replicate in eukaryotic chromosome. That is why there are many replication forks on the chromosome.

3.5 Transcription and Translation

3.5.1 Compare the structure of RNA and DNA (3) Feature Number of strands Type of sugar Bases DNA 2 strands - Forming a double helix Deoxyribose (lack of one oxygen) A, G, C, T RNA 1 strand Ribose A, G, C, U

3.5.2 Outline DNA transcription in terms of the formation of an RNA strand complementary to the DNA strand by RNA polymerase. (2) Transcription is a process of synthesizing RNA from a DNA template and it happens in the nucleus Enzyme involved: RNA polymerase Involves a promoter and a terminator region Subunit used: RNA nucleotides Only one of the two DNA strands will be transcribed; Antisense strand: Transcribed Sense strand: Not transcribed The RNA polymerase attaches to the DNA; unwinds and separates the double strands. RNA polymerase covalently joins the complementary RNA nucleotides together to form a single strand (U instead of T). The RNA polymerase detaches from the DNA, so the double helix reforms.

Example of RNA made by transcription: Messenger RNA (mRNA), Transfer RNA (tRNA) and Ribosomal RNA (rRNA) 3.5.3 Describe the genetic code in terms of codons composed of triplets of bases (2) 1. Genetic information in DNA controls the manufacture of specific proteins by cell. 2. The codes require for protein synthesis are known as the genetic code. 3. The genetic codes are in the form of a series of triplets of bases in DNA, from which is transcribed into a complementary sequence of codons in messenger RNA. 4. Codons composed of triplets of bases. 5. The sequence of these codons determines the sequence of amino acids during protein synthesis. 6. There are 4 bases in DNA/RNA (A, G, C, T/U). 7. The 4 bases are based in sets of 3 called triplets. 8. Therefore, there are 43 possible triplets of DNA = 64 triplets (These are codons). 9. There are only 20 amino acids. 10. 64 triplets/codons are mapped to 20 amino acids. 11. Genetic code is degenerate. 12. Degenerate means more than one triplet or codon can code/map for one amino acid. 13. Genetic code is universal all living organisms on earth share the same genetic code. 3.5.4 Explain the process of translation, leading to polypeptide formation. (3) 1. 2. 3. 4. 5. 6. 7. Translation involves initiation, elongation/ translocation & termination. Translation takes place in the cytoplasm, ribosomes attach to the mRNA. mRNA binds to the small subunit of the ribosome. The ribosome covers an area of three codons on the mRNA. Slides along the mRNA to start codon. The ribosome read the mRNA in triplets of bases called codon (starting at AUG) The first tRNA carrying an amino acid will come in and the anti-codon exposed on the tRNA will have complementary binding with the start codon of the mRNA in the P site of the ribosome 8. The ribosome will move and the first tRNA will be in the P site on the ribosome. 9. The second tRNA with its own anti-codon, and carrying specific amino acid, will complementary bind to the second codon on the mRNA, filling the A site in the ribosome. 10. The second amino acid will attach to the first (formation of a peptide bond by a condensation reaction) and the first amino acid will be released from the first tRNA. 11. The ribosome will move by one codon in relation to the mRNA (5 3) 12. The first tRNA is now found in the E site of the ribosome. 13. The second tRNA will be in the P site and the A site is empty. 14. The anti-codon of the third tRNA will bind to the third codon of the mRNA in the A site of the ribosome.

15. The anti-codon of the first tRNA will dissociate from the first codon of the mRNA in the E site of the ribosome. 16. The second amino acid will form a peptide bond with the third amino acid and the second amino acid will occupy the first site of the ribosome. 17. The second site is occupied by the third tRNA. The third site is free and the next tRNA will come in, carrying its own amino acid. 18. The process continues until a STOP codon is reached. The STOP codon doesnt code for an amino acid but terminates translation.

3.5.5 Discuss the relationship between one gene and one polypeptide. (3) i. ii. iii. iv. A polypeptide is formed by amino acids liking together through peptide bonds. There are 20 different amino acids so a wide range of polypeptides are possible. Genes store the information required for making polypeptides. The information is stored in a coded form by the use of triplets of bases which form codons. v. vi. The sequence of bases in a gene codes for the sequence of amino acids in a polypeptide. The information in the genes is decoded during transcription and translation leading to protein synthesis.

7.3.1 State that transcription is carried out in a direction. (1) Transcription is carried out in a 5 to 3 direction.

7.3.2 Distinguish between the sense and antisense strands of DNA. (2) Sense strand has the same base sequence as the mRNA, except for T instead of U. Anti-sense strand is the strand that is transcribed 7.3.3 Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator. (3) RNA Polymerase binds to the promoter region on the DNA. Then it unwinds the DNA strand by breaking the hydrogen bonds between the DNA. This forms the sense strand and anti sense strand. The antisense strand is used for transcription Direction for transcription is 5 to 3 Promoter region is where nucleoside triphosphates are added to extend the growth of the mRNA. When the RNA polymerase reaches the terminator, the RNA polymerase stops and transcription stops. mRNA detaches from the template, DNA rewinds RNA polymerase detaches from the DNA Introns removed in eukaryotes to form mature mRNA

7.3.4 State that eukaryotic RNA needs the removal of introns to form mature mRNA (1)

The non- coding introns are spliced out of the mRNA. The remaining mRNA is called mature mRNA and is exported from the nucleus to the cytoplasm for translation into the polypeptide

7.4.1 Explain that each tRNA molecule is recognized by a tRNA-activating enzyme that binds a specific amino acid to the tRNA, using ATP for energy. (3) 1. Amino acid is specific to each tRNA. 2. The amino acid will react with ATP and become activated. ATP loses energy in this process. 3. Activated amino acid will then bind to the acceptor stem of its own tRNA with the help of activating enzyme. 4. tRNA is composed of one chain of RNA nucleotides o 3 loops and is clover shaped o has double stranded sections formed by base pairing o has a site where amino acids attach to o has anti codon which bind to mRNA codon o 3 end terminal of ACC/CCA 7.4.2 Outline the structure of ribosomes, including protein and RNA composition, large and small subunits, three tRNA binding sites and mRNA binding sites. (2) Ribosomes consist of 2 subunits, one large and one small made up of protein and rRNA. There is a binding site for mRNA on the small unit of ribosome. There are 3 binding sites for tRNA on the large unit of ribosome. 7.4.3 State that translation consists of initiation, elongation, translocation and termination. (1) Translation consists of initiation, elongation, translocation and termination. 7.4.4 State that translation occurs in a direction. (1) Translation occurs in a 5 to 3 direction

7.4.5 Draw and label a diagram showing the structure of a peptide bond between two amino acids. (1)

- During translation amino acids will bind together with a peptide bond 7.4.6 Explain the process of translation, including ribosomes, polysomes, start codons and stop codons.(3) 1. The small unit of the ribosome binds to 5 end of mRNA. 2. Small subunit slides along mRNA until it reaches the START codon AUG. 3. An activated tRNA with the anticodon UAC carrying amino acid: Methionine, binds to the small subunit of the ribosome. 4. Then, the large subunit of the ribosome binds to the smaller unit 5. There are three binding sites for tRNA on the large sub unit. (A,P,E) 6. Another tRNA with the anticodon complementary to the next mRNA binds to the ribosome. Elongation of polypeptides now start. 7. The large subunit of the ribosome advances over the small subunit and detaches the polypeptide from the tRNA. 8. The small subunit slides across the large subunit and moves three nucleotides along the mRNA in a 5 to 3 direction. 9. A polypeptide chain is formed 10. When the ribosomes reach the STOP codon, UGA no tRNA has a molecule complementary to the anticodon. 11. The large subunit advances over the small subunit. The polypeptide is released from the tRNA. 12. The tRNA detaches and the large subunit, small subunit and mRNA all separate.

7.4.7 State that free ribosomes synthesize proteins for use primarily within the cell, and that bound ribosomes synthesize proteins primarily for secretion or for lysosomes. (1) Free ribosomes in the cytoplasm are associated with the synthesis of proteins for internal use in the cell. Ribosomes which are attached to the wall of the endoplasmic reticulum are associated with proteins which will be placed into vesicles and secreted form the cell.

7.5.1 Explain the four levels of protein structure, indicating the significance of each level. (3) Primary Structure The number and sequence of amino acids in a polypeptide Linked by peptide bonds Determines the 2 and 3 structures and function Reflects genetic information of the protein

Secondary structure: Folding of polypeptides to form beta - pleated sheets Coiling of polypeptides to form alpha-helix; Held together by hydrogen bonds Contributes to the strength of fibrous proteins Eg: Keratin

Tertiary Structure: A 3 dimensional conformation of a polypeptide Due to intramolecular bonds between amino R-groups: Hydrogen bonds, Ionic Bonds, Disulphide Bridges, Sulphur bonds Determines overall shape of the protein Eg: Lysozyme

Quaternary Structure: Linking together of two or more polypeptides to form a single protein Same type of bonding as in tertiary structure Linking of non-polypeptide (prosthetic group) 4 polypeptides are linked to heme group Eg: Hemoglobin and insulin

7.5.2 Outline the difference between fibrous and globular proteins, with reference to two examples of each protein type. (2) Type Shape Solubility in water Functions Fibrous Long, narrow Insoluble Providing strength and support to tissue Myosin: Contraction in muscle fibers for movement in animals. Collagen: Strengthen tendons, bone and skin. Globular Rounded shape Soluble Act as pigments and transport proteins Hemoglobin: Bind to oxygen in lungs to transport to tissues

Example

Immunoglobulin: Act as antibodies.

7.5.3 Explain the significance of polar and non-polar amino acids (3) Polar amino acids are hydrophilic, water soluble, become channels for transport of ions/polar substances Non polar acids are hydrophobic, non-soluble, are embedded in the within the lipid membrane 7.5.4 State four functions of proteins, giving a named example of each (1) Hormones- Insulin Transport- Haemoglobin Movement- Myosin Enzymes- Amylase

3.6 Enzymes
3.6.1 Define enzyme and active site (1) Enzymes: Globular proteins which act as catalysts of chemical reaction. Active site: The site on the surface of an enzyme to which substrates bind / the site on the enzyme where it catalyzes a chemical reaction. 3.6.2 Explain enzymesubstrate specificity (3) Enzyme has a specific shape. Active site of enzyme binds to specific substrate. Shape of the active site and substrate fit/complement each other. Active site works as a lock and substrate as a key. Active site fits substrate molecule. Enzyme-substrate complex formed. Weakens the bonds in substrate to lower activation energy. 3.6.3 Explain the effects of temperature, pH and substrate concentration on enzyme activity (3) Temperature

Rate of reaction increases as temperature increases (or vice versa).. This is because molecules have more kinetic energy [or faster in movement of molecules] that result in more collisions between active site of enzyme and substrate. Optimum temperature rate of enzymecatalyzed reaction is fastest; At a very high temperatures enzymes are denatured and stop working. Denatured means change of structure resulting in loss of its biological properties which makes it no longer can carry out its function;

pH

Optimum pH is rate of enzyme-catalyzed reaction is fastest. Rate of reaction reduced as increase or decrease pH (from optimum). Strong acids and alkalis can denature enzymes. Affect (weak, ionic, hydrogen) bonds that hold enzyme in specific shape alter the intermolecular interactions within the protein. Example; Pepsin pH of 2 (active in acidic stomach) Trypsin pH of 8 (active in alkaline duodenum & small intestine) Most enzymes in human cells pH of 7

Substrate concentration

At low substrate concentrations, as increase concentration get increase in rate of reaction. More chance of collision between substrate and active site of enzyme (more enzymesubstrate complex forms). At high substrate concentration, have no change in rate as increase concentration as all active sites occupied. Additional substrate will not lead to a greater rate of product formation at this point 3.6.4 Define denaturation (1) Denaturation: The changing of the structure of an enzyme (or other protein) so it can no longer carry out its function. It is usually permanent.

3.6.5 Explain the use of lactase in the production of lactose-free milk. (3) Lactose is the sugar found in milk. Lactase is the enzyme and is obtained from Kluveromyces lactis. Lactose-free milk can be made in two ways; a) Adding the enzyme lactase to the milk so that the milk contains the enzyme. b) Immobilizing the enzyme on a surface or in beads of a porous material. The milk is then allowed to flow past the beads or surface with the immobilized lactase. Avoids having lactase in the milk. Reasons for using lactase in food processing; a) Lactose intolerance high in some human population lactase is used to produce lactose-free / low-lactose milk. b) Galactose and glucose are sweeter than lactose no need to add extra sugar in manufacture of flavoured milk drinks / frozen desserts. c) Lactose tends to crystallize during production of ice cream, giving gritty structure. Glucose and galactose are more soluble and thus remain dissolved smoother texture of ice cream. d) Bacteria ferment glucose and galactose more quickly than lactose, results in faster production of cottage cheese and yogurt. 7.6.1 State that metabolic pathways consist of chains and cycles of enzyme catalysed reactions (1) Metabolic pathways consist of chains and cycles of enzyme catalysed reactions.

7.6.2 Describe the induced-fit model (1) Substrate approaches active site. Shape of the active site will change to fit the substrate As this occurs the substrates bonds are weakened and lowers its activation energy This permits some enzymes to bond with several substances Eg: Protease

7.6.3 Explain that enzymes lower the activation energy of the chemical reactions that they catalyse. (2) 1. Activation energy is the energy needed for a reaction to occur. 2. Enzymes lower the activation energy of the chemical reaction that they catalyse 3. In the activated complex, energy is put into the substrate and weakens the structure. This allows the reaction to occur with a minimal amount of additional energy required. 4. Normal activation energy would cause damage to the proteins of the cell. Thus reduced activation energy makes these reactions possible in a cell. 5. After the product is formed energy is released. 7.6.4 Explain the difference between competitive and non-competitive inhibition, with reference to one example of each (3) Type Binding Competitive Inhibitor binds to the same active site of enzyme Substrate and inhibitor are chemically similar When inhibitor occupies the active site, substrate cannot bind to it. Activity of enzyme is decreased. Non Competitive Inhibitor binds to enzyme at different site from active site (allosteric site) Substrate and inhibitor are not similar When inhibitor binds to the allosteric site, this can cause the enzymes active site to change shape (conformation change). Thus the substrate will not be able to bind to the active site.

Similarity Activity

Example

Malonate- inhibitor Succinate- substrate

Opioid- inhibitor Nitric Oxide- substrate

7.6.5 Explain the control of metabolic pathways by end-product inhibition, including the role of allosteric sites. (3) 1. Allostery is a form of non-competitive inhibition. 2. The allosteric site is an area of the enzyme separate from the active site. 3. The end product in the pathway inhibits the enzyme that catalyses the first reaction of the pathway. This is called end-product inhibition and shape of allosteric enzymes and the active sites are altered by this process. So the substrate is less likely to bind to the enzyme 4. Once the inhibitor is released from the allosteric site, the active site returns to its original conformation and the substrate is able to bind again. 5. End product inhibition is an example of negative feedback. 6. When there is an excess of end-product, the whole metabolic pathway is shut down. Therefore less of the end product gets produced and by inhibiting the first enzyme it also prevents the formation of intermediates. 7. When the levels of the end product decrease, the enzymes start to work again and the metabolic pathway is switched on.

3.7 Cell respiration

3.7.1 Define cell respiration (1) Cell respiration is the controlled release of energy from organic compounds (glucose) in cells to form ATP. It occurs in every living cell. 3.7.2 State that, in cell respiration, glucose in the cytoplasm is broken down by glycolysis into pyruvate, with a small yield of ATP (1)

Location: Process: Substrate: Products:

Cytoplasm Glycolysis (does not require O2) Glucose 2 pyruvates and small amount of ATP

3.7.3 Explain that, during anaerobic cell respiration, pyruvate can be converted in the cytoplasm into lactate, or ethanol and carbon dioxide, with no further yield of ATP. (3) Humans: Yeast (Fermentation process without O2): No ATP produced in this reactions Location: cytoplasm These reactions start with glycolysis.

3.7.4 Explain that, during aerobic cell respiration, pyruvate can be broken down in the mitochondrion into carbon dioxide and water with a large yield of ATP. (3)

With the presence of O2 Location: Mitochondria (Pyruvate and O2 diffuses into mitochondria) Substrate: Pyruvate Products: CO2, H2O, large amount of ATP and heat The overall equation of glycolysis and aerobic respiration: The overall equation of glycolysis and anaerobic respiration: (The ATP comes from glycolysis)

Topic 8 : Cell Respiration And Photosynthesis Cell respiration

8.1.1 State that oxidation involves the loss of electrons from an element, whereas reduction involves a gain of electrons; and that oxidation frequently involves gaining oxygen or losing hydrogen, whereas reduction frequently involves losing oxygen or gaining hydrogen.
Comparison of oxidation and reduction oxidation loss of electron loss of hydrogen atoms gain of oxygen atoms reduction gain of electron gain of hydrogen atoms loss of oxygen atoms

REMEMBER OIL RIG = OXIDATION IS LOSS (in terms of electron and hydrogen) , REDUCTION IS GAIN (in terms of electron and hydrogen)

8.1.2 Outline the process of glycolysis, including phosphorylation, lysis, oxidation and ATP formation.

4 Main Stages in Glycolysis 1. Phosphorylation

Two phosphate groups are added to a molecule of glucose to form hexose biphosphate . These two phosphate groups are provided by two molecules of ATP.

2.

Lysis

Hexose biphosphate is split to form 2 molecules of triose phosphate

3.

Oxidation

Two atoms of hydrogen are removed from each triose phosphate. The energy released by the oxidation is used to add another phosphate group to each molecule. This will result in two 3-carbon compounds, each carrying two phosphate groups. NAD+ is the hydrogen carrier that accepts the hydrogen atoms lost from each triose phosphate molecule.

4. ATP Formation Two pyruvate molecules are formed by removing two phosphate groups from each molecule. These phosphate groups are given to ADP molecules to form ATP.Four ATP will be produced.

Glycolysis occurs in the cytoplasm of cells. Two ATP molecules are used and 4 ATP molecules are produced. Therefore there is a net yield of two ATP molecules. Also, two NAD+ are converted into NADH + H+ during glycolysis.

8.1.3 Draw and label a diagram showing the structure of a mitochondrion as seen in electron micrographs.

8.1.4 Explain aerobic respiration, including the link reaction, the Krebs cycle, the role of NADH + H+, the electron transport chain and the role of oxygen. Anaerobic respiration Glycolysis can take place without oxygen. Pyruvate produced from glycolysis cannot be oxidised further without the presence of oxygen

Aerobic respiration occurs in the mitochondria of cells. consists of three stages ;Link reaction, The Krebs Cycle, The Electron Transport Chain

The Link Reaction Pyruvate from glycolysis is absorbed by the mitochondria Enzymes within the matrix of the mitochondrion remove hydrogen #(oxidation) and carbon dioxide *(decarboxylation) from the pyruvate. Therefore, the process is called oxidative decarboxylation The hydrogen removed is accepted by NAD+ results in the formation of an acetyl group which then accepted by CoA and forms acetyl CoA.

# = removal of hydrogen or addition of oxygen * = removal of carbon dioxide

The Krebs Cycle

Step 1 - In the first stage of the Krebs cycle, the acetyl group from acetyl CoA is transferred to a four carbon compound. This forms a six carbon compound. Step 2 - This six carbon compound then undergoes decarboxylation (CO2 is removed) and oxidation (hydrogen is removed) to form a five carbon compound. The hydrogen is accepted by NAD+ and forms NADH + H+. Step 3 - The five carbon compound undergoes decarboxylation and oxidation (hydrogen is removed) again to form a four carbon compound. The hydrogen is accepted by NAD+ and forms NADH + H+. Step 4 - The four carbon compound then undergoes substrate-level phosphorylation and during this reaction it produces ATP. Oxidation also occurs twice (2 hydrogens are removed). One hydrogen is accepted by NAD+ and forms NADH + H+. The other is accepted by FAD and forms FADH2. The four carbon compound is then ready to accept a new acetyl group and the cycle is repeated.

Summary: Carbon dioxide is removed in two reactions Hydrogen is removed in 4 reactions NAD+ accepts the hydrogen in 3 reactions FAD accepts the hydrogen in 1 reaction ATP is produced in one of the reactions

The carbon dioxide that is removed in these reactions is a waste product and is excreted from the body. The oxidations release energy which is then stored by the carriers when they accept the hydrogen. This energy is then later on used by the electron transport chain to produce ATP.

The Electron Transport Chain

Series of electron carriers,located in the inner membrane of the mitochondrion NADH + H+ supplies 2 electrons to the first carrier in the chain. FADH2 also donates electrons but at a later stage than NADH. The electrons come from oxidation reaction in earlier stages of cell respiration As the electrons are passed from one carriers to another,energy is released . The energy released is used to synthesize ATP via ATP synthase ATP synthase is an enzyme that is also found in the inner mitochondrial membrane.

The oxygen-dependent synthesis of ATP within mitochondria using energy released from redox reaction is called oxidative phosphorylation The final electron acceptor is oxygen where it will combine with hydrogen ions to form water.

The Role of Oxygen = as the terminal electron acceptor Oxygen is important for cell respiration as at the end of the electron transport chain, the electrons are donated to oxygen. This occurs in the matrix at the surface of the inner membrane. At the same time oxygen binds with hydrogen ions and forms water. This is the only stage that oxygen is used in cell respiration. If there is no oxygen then electron flow along the electron transport chain stops and NADH + H+ can no longer be reconverted into NAD+. Eventually supplies of NAD+ in the mitochondrion runs out and therefore the link reaction and Krebs cycle no longer take place.

8.1.5 Explain oxidative phosphorylation in terms of chemiosmosis

Chemiosmosis = is the coupling of ATP synthesis to electron transport via a concentration

gradient of protons There is a link between electrons being passed down the electron transport chain and the production of ATP. NADH + H + and FADH2 deposit their electrons to the electron transport chain in the inner membrane As the high energy electrons pass through the electron transport chain,they release energy. The energy released is used to pump H+ from the matrix across the inner mitochondrial membrane into the intermembrane spaces A concentration gradient of H+ is formed ,which is a store of chemical potential energy (high concentration of protons in the intermembrane spaces and a low concentration of protons in the matrix.) ATP synthase (enzyme) located in the inner mitochondrial membrane transport the H+ back across the membrane down the concentration gradient As the protons pass across the membrane ,they release energy and this is used by ATP synthase to convert ADP to ATP. Since the electrons come from previous oxidation reactions of cell respiration and the ATP synthase catalyses the phosphorylation of ADP into ATP, this process is called oxidative phosphorylation.

8.1.6 Explain the relationship between the structure of the mitochondrion and its function. Matrix: Watery substance that contains ribosomes and many enzymes. These enzymes are vital for the link reaction and the Krebs cycle. Inner membrane: The electron transport chain and ATP synthase are found in this membrane. These are vital for oxidative phosphorylation. Space between inner and outer membranes: Small volume space into which protons are pumped into. Due to its small volume, a high concentration gradient can be reached very quickly. This is vital for chemiosmosis. Outer membrane: This membrane separates the contents of the mitochondrion from the rest of the cell. It creates a good environment for cell respiration. Cristae: These tubular projections of the inner membrane increase the surface area for oxidative phosphorylation.

3.8 Photosynthesis
3.8.1 State that photosynthesis involves the conversion of light energy into chemical energy (1) Photosynthesis is the process used by plants & some other organisms to produce their own organic substances. Reaction: Traps light energy (photons) and converts it into chemical energy Substrates: CO2, H2O Products: Organic compounds (sugar), CO2 3.8.2 State that light from the Sun is composed of a range of wavelengths (colours) (1) Sunlight is called white light, but it is actually made up of a wide range of wavelengths (colours) including red, green and blue. 3.8.3 State that chlorophyll is the main photosynthetic pigment (1) Some substances called pigments can absorb light Chlorophyll is the main photosynthetic pigment. This is where light energy is trapped and turned into chemical energy. The structure of chlorophyll allows it to absorb some colours or wavelengths of light better than others. Red and blue light are absorbed more than green Green light is reflected chlorophyll, chloroplast and plant leaves look green

3.8.4 Outline the differences in absorption of red, blue and green light by chlorophyll. (2)

The 'peaks' show which wavelength of light is being absorbed. The x-axis shows the colours of light that is being absorbed at the 'peaks'. The main colour of light absorbed by chlorophyll is red and blue. The main colour reflected (not absorbed) is green.

3.8.5 State that light energy is used to produce ATP, and to split water molecules (photolysis) to form oxygen and hydrogen. (1) Light energy is used to; i. Produced ATP ii. To split water molecules (photolysis) to form oxygen and hydrogen

3.8.6 State that ATP and hydrogen (derived from the photolysis of water) are used to fix carbon dioxide to make organic molecules. (1) ATP and hydrogen derived from photolysis of water are used to combine with carbon dioxide to form organic compounds like sugar. Bonds are formed between the carbon, hydrogen and oxygen using the energy from ATP (which came from the sun). C, H, O are enough to form lipids and carbohydrates 3.8.7 Explain that the rate of photosynthesis can be measured directly by the production of oxygen or the uptake of carbon dioxide, or indirectly by an increase in biomass (3) Measuring the rate of photosynthesis; Production of oxygen Aquatic plants release oxygen bubbles during photosynthesis and so the volume can be collected and measured. The uptake of carbon dioxide Difficult to measure so it is usually done indirectly. When carbon dioxide is absorbed from water the pH of the water rises and so this can be measured with pH indicators or pH meters. Increase in biomass If batches of plants are harvested at a series of times and the biomass of these batches is calculated, the rate increase in biomass gives an indirect measure of the rate of photosynthesis in the plants.

3.8.8 Outline the effects of temperature, light intensity and carbon dioxide concentration on the rate of photosynthesis. (2) Temperature As temperature increases, the rate of photosynthesis increases more and more steeply (as the kinetic energy of the reactants increase) until the optimum temperature is reached If temperature keeps increasing above the optimum temperature then photosynthesis starts to decrease very rapidly (denaturation of enzymes) Light intensity As light intensity increases so does photosynthesis until a certain point. At high light intensities photosynthesis reaches a plateau and so does not increase any more At low and medium light intensity the rate of photosynthesis is directly proportional to the light intensity. CO2 concentration As the carbon dioxide concentration increases so does the rate of photosynthesis. There is no photosynthesis at very low levels of carbon dioxide At high concentration of CO2, the rate reaches a plateau because other factors become the limiting factor.