Biology- Chapter 6

the most frequently occuring chemical elements in living things are carbon, hydrogen, oxygen and nitrogen

Sulphur- In some acids

Calcium- In bones and co-factor in enzymes

Iron- In haemoglobin and cytochromes

Phosphorus-As phosphate groups in ATP

Sodium- In membrane function and sending nerve impulses

Thermal: water changes temperature slowly and has a maximum density at +4°C
Cohesive: molecules of the same type are attracted to each other.
Solvent: water solves polar molecules.

 Thermal: Living things have a lot of water inside to keep a constant temperature.

Cohesive: the attraction causes surface tension, droplet and moving a column.

Solvent: solves carbon containing organic molecules with ionized groups.

                               All organic compounds contain carbon, however, a compound containing carbon doesn’t have to be organic.
Organic compounds are found in living organisms, inorganic are not.

 Monosaccharides: glucose, galactose, fructose
Disaccharides: maltose, lactose, sucrose
Polysaccharides: starch, glycogen, cellulose

Animals
Glucose: chemical fuel for cell respiration
Lactose: makes up some of the solutes in milk
Glycogen: stores glucose in liver and muscles

Plants
Fructose: found in many fruits (makes them sweet)
Sucrose: often transported from leaves of plants to other locations in plants by vascular tissue.
Cellulose: one of the primary components of plant cell walls.

When animals eat food, food is digested (hydrolysis) into building blocks each reaction requires a molecule of water as a reactant.

Examples:
Lactose + water à glucose + galctose
Starch + many water à many glucose
Triglyceride + three water à glycerol + three fatty acids.
Protein + many water à many amino acids

Condensation is often the reverse of hydrolysis reactions. Condensation reactions occur to reform molecules.
Both reactions are catalysed by enzymes.

          Three functions of lipids
- Energy storage: stores about twice as much as carbohydrates.
- Thermal insulation: to keep the body temperature.
- Cell membranes: phospholipids bilayer

Glycogen in a carbohydrate used by animals to store energy, starch is used by plants. Lipids store approximately twice as much chemical energy as the carbohydrates

Nucleotides are the building blocks of DNA. Each nucleotide of DNA is composed of a phosphate group, a sugar called deoxyribose and a molecule called a nitrogenous base.

DNA nucleotide structure:

The four nitrogenous bases of DNA are: adenine, thymine, guanine, cytosine

DNA is composed of two strands, each one shaped like a spiral staircase. Each   of the nucleotides in a single strand is covalently bonded together.

Imagine the double-stranded DNA molecule as a ladder; the two sides are made up of the phosphates and the deoxyribose sugars. The nitrogenous bases make up the rungs. The two bases making up a rung are complimentary. The bases are held together by hydrogen bonds.

There are two types of molecules that are particularly important for DNA replication:
Enzymes – including helicase and a group of enzymes called DNA polymerase.
Free nucleotides – not yet bonded, found floating freely (triphosphates)

1. The helicase moves one complimentary base pair at a time, breaking the hydrogen bonds, forming two separate strands. The double helix in now unwinded.

2. A triphosphate locates on one opened strand at one end and a second can come in to join the first. The two nucleotides become covalently bonded and they are the beginning of a new strand. The bonding is catalyzed by a DNA polymerase enzyme.

3. The process continues in a repetitive way, the other unzipped strand forms a new strand in the same way, but in opposite direction.

The pattern of DNA replication ensures that two identical copies of DNA are produced from one. This is why it is so important that the base-pairing is complementary and can only happen in one way.

                         DNA replication in semiconservative. This means that all DNA molecules, after having been replicated consist of a strand that was “old” now paired with a strand that is “new”. Half of the pre-existing DNA molecule is always conserved/saved. 

DNA

RNA

Contains a 5-carbon sugar

Contains a 5-carbon sugar

Deoxyribose

Ribose

Nucleotide has one nitrogenous base

Nucleotide has one nitrogenous base

Adeninde, Thymine, Guanine, Cytosine

Adenine, Thymine, Guanine, Uracil

Double-stranded

Single-stranded

Transcription: the DNA molecule is unzipped where the particular gene is found. Only one of the two unzipped strands of DNA is used as the template to create the mRNA (messenger) molecule. An enzyme called RNA polymerase is used as the catalyst for this process. Free RNA nucleotides float in to place by complementary base pairing. 

The genetic code is written in a language of three bases. Each groups of three bases is enough information to code for 1/20 amino acids. Any set of three bases is called a triplet. When a triplet is found in mRNA, it is called a codon (triplet).

1. The mRNA will locate a ribosome and align with it so that the first two codon triplet are within the boundaries of the ribosome.
2. tRNA (transfer) floats in and brings the first amino acid (decided by DNA). A second tRNA floats in and brings the second one. These amino acids catalyse a condensation reaction (building up) between them, resulting in a covalent bonding called a peptide bond.
3. The first tRNA floats away and reloads with another amino acid of the same type. The ribosome moves and a third RNA floats in with a new amino acid, and so on.
4. The final codon triplet will NOT act as a code for an amino acid. It signals to “stop” the process of translation.
5. The entire polypeptide breaks away from the tRNA and floats freely in the cytoplasm of the cell.

           In 1940, it was believed that each gene coded for one polypeptide. This was later proven to be wrong, since each gene codes for one protein; built up of many polypeptides.

Enzyme: Enzymes are proteins which consist of long chains of amino acids that have taken on a very specific three-dimensional shape.

Active site: The active site of the enzyme is an area that is design to match a specific molecule known as that enzyme’s substrate. (Key in the lock)

             The shape of an enzyme is very complex and the active site matches the substrate in a similar way that a glove fits over hand. All substrates do not fit, but the active site may change shape. The enzymes and the substrate are specific for each other.

Temperature: the rate of the motion of the enzyme and the substrate depends on the temperature of the fluid. Higher temperate à more kinetic energy. Reactions which use enzymes have an upper limit (55° in humans).

pH-value: the pH of a solution is dependent on the relative number of hydrogen ions (H⁺) compared to hydroxide ions (OH^-). Different enzymes need different pH-values to reach their greatest enzyme activity.

Substrate concentration: as the concentration of a substrate increases, the rate of reaction will increase as well due to more molecular collision. But there is a limit because the enzyme has a maximum rate at which it can work.

Denaturation: when the enzyme begins to lose its three-dimensional shape due to intramolecular bonds being stressed and broken. This can happen when the temperature is too high or when the pH-value is either too acidic or too basic/alkali.

The enzyme lactase digests the disaccharide lactose into two monosaccharides, which are more easily absorbed into the blood stream. So, when milk products are treated with lactase before consumption, the lactose is pre-digested (without affecting the nutritional value).

Cell respiration: the controlled release of energy from organic compounds in cells to form ATP. It refers variety of biochemical pathways that can be used to metabolize glucose. If glucose is not available, other organic molecules may be substituted, such as fatty acids or amino acids.

In cell respiration, glucose in the cytoplasm is broken down by glycolysis into pyruvate, with a small yield of ATP (net. gain of two ATP).

Anaerobic respiration: cell respiration without oxygen, a.k.a. fermentation.

Alcoholic fermentation: both of the three carbon pyruvate molecules are converted into two carbon ethanol molecules. The two carbon molecules that are not included are a waste product and “lost” in this conversion.

Aerobic pathway:
- Pyruvate loses CO₂ and becomes Acetyl-CoA (2C).
- Acetyl-CoA enters Krebs cycle where two CO₂ molecules are produced.
- Some ATP is directly generated from Krebs cycle and some indirectly through reactions involving 0₂.
- Aerobic cell respiration breaks down or completely oxidizes a glucose molecule.
- The end-products are CO₂ and H₂O.
- Total net gain of 36 ATP molecules.

Photosynthesis involves the conversion of light energy into chemical energy.
The sunlight that strikes our planet must be converted into a form of chemical energy in order to be useful to all non-photosynthetic organisms.

Photosynthesis formula:
carbon dioxide + water + sunlight (light energy) à water + glucose + oxygen (chemical energy)

- Light from the Sun is composed of a range of wavelengths (colours)
- Light from the Sun is a mixture of different colours of light, all with different wavelengths. These wavelengths can be separated if you let light pass through a prism.

            Chlorophyll is the main photosynthetic pigment. It absorbs all wavelengths except for green, which is reflected. So, almost all energy is absorbed and used for photosynthesis.

Chlorophyll absorbs the red- and blue end of the visible part of the spectrum, but reflects the green middle.

Chlorophyll absorbs light energy and converts it into a form of chemical energy, especially ATP, and the light energy splits the water molecules (photolysis) to form oxygen and hydrogen.

ATP and hydrogen (derived from the photolysis of water) are used to fix carbon dioxide to make organic molecules. The conversion of an inorganic form (CO₂) to an organic form (glucose) is known as a fixation à CO₂ and H₂O are fixed into glucose, and O₂ is produced as a waste product. The fixation requires energy, which comes directly from ATP and hydrogen.

Photosynthetic rate depends on environmental factors, including intensity of light and air temperature. During daytime, the rate of photosynthesis might be very high, and if so, the rate of CO₂ taken in by a plant, and the rate of O₂ given off will both be very high. At night, the rate may drop to zero, since there is no sunlight available.

Measuring the rate of O₂ production or CO₂ intake, is a direct measurement of photosynthetic rate (as long as correction is made for cell respiration).
An indirect reflection of photosynthetic rate is the change in biomass, which may be traced to a whole variety of factors, beside photosynthetic rate.