Biology topic 3
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.
-2 + 4 = 2 net yield ATP
3.4.3: State that DNA replication is semi-conservative.
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3.5.5 Explain the relationship between one gene and one polypeptide
A gene is a sequence of DNA which encodes a polypeptide sequence A gene sequence is converted into a polypeptide sequence via the processes of transcription (making an mRNA transcript) and translation (polypeptide synthesis) Translation uses tRNA molecules and ribosomes to join amino acids into a polypeptide chain according to the mRNA sequence (as read in codons) The universality of the genetic code means all organisms show the same relationship between genes and polypeptides (indicating a common ancestry and allowing for transgenic techniques to be employed) Some proteins may consist of a number of polypeptide chains and thus need multiple genes (e.g. haemoglobin consists of four polypeptide subunits encoded by two different genes) When a gene is mutated it may lead to the synthesis of a defective polypeptide, hence affecting protein function There are two exceptions to the 'one gene - one polypeptide' rule: Genes encoding for tRNA and rRNA do not code for polypeptide sequences (only mRNA sequences code for polypeptides) A single gene may code for multiple polypeptides if alternative splicing occurs (the removal of exons as well as introns)
3.7.1: Define Cell respiration
the controlled release of energy from organic compounds in cells to form 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.
Anaerobic respiration occurs when there is not sufficient oxygen being taken in by the body. The only source of energy, therefore, is glycolysis (as electrons can no longer move down the electron transport chain). As the electron transport chain will no longer occur, the NADH + H+ molecules that result from glycolysis are no longer oxidized. Without NAD+, glycolysis cannot occur. To account for this, pyruvate is reduced to form lactate (in animals) or ethanol and carbon dioxide (in yeast), thereby oxidizing the NADH + H+ molecules to form the NAD+ needed for glycolysis.
3.8.4: Outline the differences in absorption of red, blue and green light by chlorophyll.
Chlorophyll absorbs mainly red and blue light and reflects mainly green light. This is why we see plants as green.
3.4.2: Explain the significance of complementary base pairing in the conservation of the base sequence of DNA.
Complementary base pairing allows for the precise replication of DNA. This means that the two new strands formed during DNA replication have identical sequences to the original DNA. This is significant in that it allows for the conservation of the DNA sequence. As a result, all cells in an organism (with the exception of sex cells) contain the same DNA, even after cell division. No genes are lost, although there is the possibility of mutation.
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 acids and polypeptides.
Condensation: remove water to form new bonds Glucose + galactose → lactose + H2O (glycosidic linkage) Glycerol + 3 fatty acids → triglyceride + H2O (ester linkage) Amino acid + amino acid → polypeptide (peptide bond) Hydrolysis (dehydration synthesis): add water to break bonds
3.3.1: Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate.
DNA nucleotides are comprised of 3 parts: a 5-carbon sugar (deoxyribose), a phosphate and one of four nitrogenous bases. The nitrogenous base is attached to 1' carbon and the phosphate group is attached to the 5' carbon.
3.2.4: State one function of glucose, lactose and glycogen in animals, and of fructose, sucrose and cellulose in plants.
Glucose is a reactant in chemical respiration. Lactose is a sugar found in the milk of mammals. Glycogen is used as long term energy and stored in the liver. Fructose is responsible for the sweetness in fruit and hence helps with seed dispersal. Sucrose is a transportable form of energy that travels through the phloem. Cellulose forms the cell wall and helps to keep the plant's structure.
3.1.5: Outline the thermal, cohesive and solvent properties of water.
Hydrogen bonding occurs between water molecules, due to the presence of oxygen (which is highly electronegative and pulls electrons towards it, creating an unequal distribution of charge). This is when the partially positive hydrogen atom of one water molecule creates a bond with a partially negative oxygen atom of another water molecule. Water's thermal properties are a high heat of vaporization and a high specific heat. Heat of vaporization is the amount of energy required to evaporate 1g of water. A high specific heat is the amount of energy required to change the temperature of 1g of water 1 degree centigrade. These are both due to the hydrogen bonds which are difficult to break and therefore require more energy. Water is also cohesive: it sticks to itself, causing surface tension. This is because of the hydrogen bonds between water molecules that are difficult to break. Water is called the universal solvent as it very effective at dissolving polar molecules. Polar molecules have charges and include ionic and polar covalent compounds. The partially positive H atoms are attracted to the negative parts; the partially negative O atoms are attracted to the positive parts. The water molecules form hydration shells around these molecules, overcoming intermolecular forces and dissolving the compound.
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.
In order to directly measure photosynthesis, one can measure the amount of reactant used (i.e. carbon dioxide) or the amount of product produced (i.e. oxygen). The more carbon dioxide used up, the higher the rate of photosynthesis; the more oxygen produced, the higher the rate of photosynthesis. The rate of photosynthesis can be indirectly measured by an increase in biomass. Glucose production results in an increase in biomass, so the greater the increase in biomass, the greater the rate of photosynthesis. However, biomass is also affected by many other factors, which is why this measurement is considered indirect.
3.8.8: Outline the effects of temperature, light intensity and carbon dioxide concentration on the rate of photosynthesis.
In the beginning, an increase in temperature results in an increase in the rate of photosynthesis. This is because increased temperature results in the increased kinetic energy of the particles, resulting more successful collisions for the reaction. This activity increases until it reaches the optimum temperature. After this point, however, enzymes that allow photosynthesis to occur (like NADP reductase) begin to denature, thereby decreasing the photosynthetic rate. Photosynthetic rate increases with light intensity up as this allows for faster light dependent reactions. This occurs up to a point when the light dependent reactions are occurring at a maximum rate. The rate then plateaus and continues at the maximum rate despite increases in light intensity. As the concentration of carbon dioxide increases, the rate of photosynthesis increases as it allows for the Calvin Cycle to create glucose more often. This occurs up to a point, which is the maximum rate of photosynthesis (i.e. all enzymes are saturated).
3.2.3: List three examples each of monosaccharides, disaccharides and polysaccharides.
Monosaccharides: glucose, galactose, fructose Disaccharides: sucrose, maltose, lactose Polysaccharides: cellulose, glycogen, starch
3.1.1: State the most frequently occurring chemical elements in living things
Carbon, hydrogen, oxygen, nitrogen → most frequently occurring elements in living things.
3.8.3: State that chlorophyll is the main photosynthetic pigment.
Absorbs energy from light
3.3.2: State the names of the four bases in DNA.
Adenine - thymine Guanine - cytosine
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.
Aerobic cell respiration occurs when there is sufficient oxygen for oxidative phosphorylation to occur. The pyruvate produced from glycolysis in the cytoplasm is transported into the mitochondrion where it is broken down further and oxidized to form water, carbon dioxide and a large yield of ATP.
3.2.2: Identify amino acids, glucose, ribose and fatty acids from diagrams showing their structure.
Amino acid → amine group + central carbon Glucose → 6 carbons Ribose → 5 carbons Fatty acid → CH3 + lots of Cs and Hs
3.2.7: Compare the use of carbohydrates and lipids in energy storage.
Both carbohydrates and lipids are used for the storage of energy in organisms. Carbohydrates are more immediate forms of energy; they break down much faster than lipids. This means that they release energy faster than lipids. However, carbohydrates have less energy per gram than lipids, making lipids a more concentrated form of energy. Furthermore, carbohydrates are hydrophilic and therefore easier to transfer to and from the storage sites than lipids. Therefore, carbohydrates are better as short-term energy stores (like glucose) whereas lipids are more effective as long-term energy stores (fat).
3.4.1: Explain DNA replication in terms of unwinding the double helix and separation of the strands by helicase, followed by the formation of the new complementary strands by DNA polymerase.
DNA replication starts off with a DNA double helix molecule. An enzyme called helicase breaks the hydrogen bonds between complementary base pairs, separating the two strands of DNA. This starts at a position called the origin of replication, with the helicase unzipping the double helix at a position called the replication fork. The two separated strands of DNA can be used as templates to create new strands. DNA polymerase is the enzyme that synthesizes the two new strands. There is an abundant supply of free nucleotides in the nucleus, which are bonded to their complementary bases in the original strand by DNA polymerase. DNA polymerase also creates phosphodiester bonds between the nucleotides that are being added. At the end of the replication process, there are two identical DNA double helices.
3.6.4: Define denaturation.
Denaturation: the structural change in a protein that results in the loss (usually permanent) of its biological properties. Heat and pH are agents.
3.3.4: Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds.
Each nitrogenous base found in DNA corresponds to another nitrogenous base, called its complementary base pair (A-T, C-G). When two polynucleotide chains are positioned anti-parallel to each other (in opposite directions: one is 3' to 5', other is 5' to 3'), hydrogen bonding occurs between these complementary base pairs. Adenine and thymine form two hydrogen bonds; cytosine and guanine form three hydrogen bonds. Adenine and guanine are purines: they are twice as big as thymine and cytosine (pyrimidines). This means that an equal distance is always maintained between the two polynucleotides. The DNA strand then twists itself into its optimal energy configuration: a double helix.
3.6.1: Define enzyme and active site.
Enzyme: globular protein that increases the rate of a biochemical reaction by lowering the activation energy Active site: site on the surface of the enzyme that binds to the substrate molecule
3.6.2: Explain enzyme-substrate specificity.
Enzymes fit together with specific substrates and catalyze reactions involving those substrates. This is because the active site of an enzyme has a particular shape and charge that are complementary to the shape and charge of the substrate. For example, the enzyme succinate dehydrogenase has an active site that allows its substrate succinate to be held in the optimum position to carry out chemical reactions.
3.6.3: Explain the effects of temperature, pH and substrate concentration on enzyme activity.
In the beginning, increased temperature results in an increase in enzyme activity. This is because the average kinetic energy of the particles are increased, allowing for more collisions between the active site and the substrate. The activity gradually increases until it reaches the optimum temperature, where enzyme activity is at its peak. If the temperature increases after the optimal temperature, however, the enzyme begins to denature as the various bonds that make up the enzyme begin to break. Generally, enzymes function at an optimum pH of about 7.4; however this varies depending on the environment they are required to function in. As the pH is lowered, the concentration of H+ ions increases. As the pH is increased, the concentration of OH- ions increases. This causes the denaturation of the enzyme as these ions disrupt its ionic bonds. As substrate concentration increases, enzyme activity increases, up till a point. This is because increased substrate concentration means an increased chance of a substrate particle colliding with an active site. However, eventually all the enzymes will be in use and adding more substrate concentration will not have any effect on the rate of enzymatic activity. This is the maximum rate of enzymatic activity.
3.6.5: Explain the use of lactase in the production of lactose-free milk.
Lactose is a disaccharide found in milk and is broken down into glucose and galactose by the enzyme lactase. Lactase is usually produced by the human body, but some people lose this ability over time. This is called lactose intolerance is and is particularly common in Asian and Aboriginal societies. Humans need milk because of nutritional value (contains calcium and vitamin D). Therefore, lactose-free milk is produced to cater to lactose intolerant people. This is done by pouring milk through alginate beads (which have lactase on them, obtained from yeast extraction). This predigests the lactose, breaking it down into glucose and galactose. This milk is now lactose-free and can be consumed by lactose intolerant people. Lactose-free milk is also sweeter, reduces crystallization in ice cream and shortens the production time of yogurt and cheese.
3.8.5: State that light energy is used to produce ATP, and to split water molecules (photolysis) to form oxygen and hydrogen.
Light dependent reactions splits water molecules into oxygen, hydrogen ions and electrons.
3.8.1: State that photosynthesis involves the conversion of light energy into chemical energy.
Light energy from sun → chemical energy stored in bonds of glucose molecules
3.8.6: State that ATP and hydrogen (derived from the photolysis of water) are used to fix carbon dioxide to make organic molecules.
Light independent reaction → ATP and hydrogen (from photolysis) used to fix carbon molecules and create organic molecules (glucose made of carbon, hydrogen and oxygen)
3.2.6: State three functions of lipids.
Lipids are used for energy storage (fats in animals), thermal insulation (blubber in seals and polar bears) and make up the structure of the cell membrane (phospholipid bilayer).
3.2.1: Distinguish between organic and inorganic compounds.
Organic compounds are compounds that contain carbon and found in living organisms (with the exception of hydrogencarbonates, carbonates and oxides of carbon).
3.1.2 + 3.1.3: State that a variety of other elements are needed by living organisms which are.... + State one role for each of the elements mentioned in 3.1.2.
Sulfur is part of some R-groups in amino acids. Calcium is a co-factor in some enzymes. Phosphorus used in phosphate groups in ATP. Iron found in cytochromes. Sodium is part of membrane functions.
3.5.3 Describe the genetic code in terms of codons comprised of triplets of bases
The genetic code is the set of rules by which information encoded in mRNA sequences is converted into proteins (amino acid sequences) by living cells Codons are a triplet of bases which encodes a particular amino acid As there are four bases, there are 64 different codon combinations (4 x 4 x 4 = 64) The order of the codons determines the amino acid sequence for a protein The coding region always starts with a START codon (AUG) and terminates with a STOP codon The genetic code has the following features: It is universal - every living thing uses the same code (there are only a few rare and minor exceptions) It is degenerate - there are only 20 amino acids but 64 codons, so more than one codon may code for the same amino acid (this allows for silent mutations whereby a change in the DNA sequence does not affect the polypeptide sequence)
3.3.3: Outline how DNA nucleotides are linked together by covalent bonds into a single strand.
The phosphate group attached to 5' carbon in the deoxyribose sugar of one nucleotide will form a covalent bond (called a phosphodiester bond) with the 3' carbon of the deoxyribose of another nucleotide. This creates the sugar-phosphate backbone of DNA.
3.5.2 Outline DNA transcription in terms of the formation of an RNA strand complementary to the DNA strand by RNA polymerase
Transcription is the process by which an RNA sequence is produced from a DNA template: RNA polymerase separates the DNA strands and synthesises a complementary RNA copy from one of the DNA strands It does this by covalently bonding ribonucleoside triphosphates that align opposite their exposed complementary partner (using the energy from the cleavage of the additional phosphate groups to join them together) Once the RNA sequence has been synthesised, RNA polymerase will detach from the DNA molecule and the double helix will reform The sequence of DNA that is transcribed into RNA is called a gene Transcription occurs in the nucleus (where the DNA is) and, once made, the mRNA moves to the cytoplasm (where translation can occur) Three main types of RNA are predominantly made: Messenger RNA (mRNA): A transcript copy of a gene used to encode a polypeptide Transfer RNA (tRNA): A clover leaf shaped sequence that carries an amino acid Ribosomal RNA (rRNA): A primary component of ribosomes
3.5.4 Explain the process of translation, leading to polypeptide formation
Translation is the process of protein synthesis in which the genetic information encoded in mRNA is translated into a sequence of amino acids in a polypeptide chain Ribosomes bind to mRNA in the cell's cytoplasm and move along the mRNA molecule in a 5' - 3' direction until it reaches a start codon (AUG) Anticodons on tRNA molecules align opposite appropriate codons according to complementary base pairing (e.g. UAC will align with AUG) Each tRNA molecule carries a specific amino acid (according to the genetic code) Ribosomes catalyse the formation of peptide bonds between adjacent amino acids (via a condensation reaction) The ribosome moves along the mRNA molecule synthesising a polypeptide chain until it reaches a stop codon, at this point translation stops and the polypeptide chain is released
3.1.6: Explain the relationship between the properties of water and its uses in living organisms as a coolant, medium for metabolic reactions and transport medium.
Water's high heat of vaporization makes it an effective coolant in living organisms. Sweat is comprised of water, and is secreted when the human body gets too warm. Because of the high heat of vaporization, evaporating the sweat absorbs a great deal of energy from the body, lowering the body temperature and hence making it cooler. Water's solvent properties make it an effective medium for metabolic reactions. Water is polar and can therefore dissolve polar substances, which the majority of organic compounds are. This is why water is a main component of our blood and cytoplasm as it allows for the presence of reactants and products of metabolic reactions. Water's cohesive properties make it an effective transport medium in plants. The Cohesion-Tension theory states that transpiration (evaporation of water through leaves) creates a negative pressure. The cohesive property of water allows it, along with minerals, to be pulled up through the xylem, against gravity. It also shows adhesion to the walls of the xylem.
3.8.2: State that light from the Sun is composed of a range of wavelengths (colors).
White → all colors Black → no colors
charge/polar/hydrophilic/soluble in water no charge/nonpolar/hydrophobic/insoluble in water
charge/polar/hydrophilic/soluble in water no charge/nonpolar/hydrophobic/insoluble in water