Ib Topic 3 - Chemistry of Life

The Chemistry of Life

3.1 Chemical Elements and Water

3.1.1
State that the most frequently occurring chemical elements in living things are carbon, hydrogen, oxygen and nitrogen.
Carbon, hydrogen, oxygen and nitrogen are the most frequently occurring chemical elements in living things.
3.1.2
State that a variety of other elements are needed by living organisms, including sulphur, calcium, phosphorus, iron and sodium.
Other elements are needed by living organisms including sulphur, calcium, phosphorus, iron and sodium.
3.1.3
State one role for each of the elements mentioned in 3.1.2
|Element |Prokaryotic |Animal |Plant |
|Sulphur (S) |In some amino acids |Components of certain amino acids; |Component of proteins and some |
| | |needed for muscle growth |coenzymes |
|Calcium (Ca) |Co-factor in some enzymes |Formation of bones and teeth |Important in formation of cell wall |
|Phosphorus (P) |Phosphate group in ATP |Component of RNA and DNA |Component of phospholipids. |
| | | |Co-factor in protein synthesis |
|Iron (Fe) |In cytochromes |Component of haemoglobin and |Component of cytochromes (electron |
| | |myoglobin needed for oxygen |carriers in respiration and |
| | |transport in blood |photosynthesis) |
|Sodium (Na) |In membrane function |Needed for muscle and nerve |In membrane function |
| | |activity | |

3.1.4
Draw and label a diagram showing the structure of water molecules to show their polarity and hydrogen bond formation.

A covalent bond is a bond where electrons are shared between atoms (not taken). In a water molecule, a covalent bond occurs between the oxygen and hydrogen atoms to form a water molecule.
A polar molecule occurs in covalent bonded molecules. Electronegativity, which is the attraction of shared electrons, occurs in an atom of the bond and pulls the shared electrons towards the nucleus. In a water molecule, the oxygen has more electronegativity than the hydrogen; therefore it pulls the hydrogen towards itself. Oxygen then has a more negative charge as the electrons are closer to it, and hydrogen has a more positive charge as the electrons are further away (from the nucleus).
Hydrogen bonds join one water molecule to another. The hydrogen (+) of one molecule bonds with the oxygen (-) of another molecule. It is called a hydrogen bond because the hydrogen is the positively charged region of the bond. These bonds are not as strong as the covalent bonds in each water molecule.

3.1.5
Outline the thermal, cohesive and solvent properties of water.
Thermal Properties:
Boiling Point: • Boiling point is 100o – hydrogen bonds give water a high boiling point. • When water is heated the heat energy first disrupts the hydrogen bonds and then makes the water molecules move faster. • Significance: Water’s ability to resist temperature change creates a favourable environment for aquatic life.
Cooling Effect of Evaporation: • Water molecules absorb heat from the body. • Molecules on the surface evaporate, leaving behind cooler molecules. • This allows body temperature to regulate through sweating. Without the ability to cool down, body temperature would continue to rise – multisystem organ failure.
Heat Capacity: • Water molecules need a lot of heat energy to break the hydrogen bonds. As the hydrogen bonds break they absorb the heat energy – which prevents further heating. (Need a lot of energy to break). • It is good for regulating temperature in living things, because of the amount of energy needed.

Cohesion: • Cohesion is the attraction between same molecules. Stronger because of hydrogen bonding. • Enables surface tension – so can flow up plants/trees. • Shown in real life with cohesion – tension theory. • The hydrogen bonds keep the water molecules together as the move up the stem.
Solvent Properties: • Water is a polar molecule, therefore it is able to dissolve other polar substances. For example all Ionic salts are polar so water can dissolve them all. (like dissolves like). • This allows all living things to dissolve and absorb many mineral salts to use to live. Water is the universal solvent, water is also the main transport medium in organisms.
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.
|Name of the property |Outline of the properties of water (3.1.5) |Relationship between the properties of water and|
| | |its uses in living organisms (3.1.6) |
|Cohesion |Water molecules stick to each other because of |Strong pulling forces can be exerted to suck |
| |the hydrogen bonds that form between them |columns of water up to the top of trees in their|
| | |transport systems. Water is used as a transport |
| | |medium in the xylem of plants. |
|Solvent Properties |Many different substances dissolve in water |Most chemical reactions in living organisms take|
| |because of its polarity. Ions with + or – |place with all of the substances involved in the|
| |charges dissolve so they are attracted to the – |reactions dissolved in water. Water is the |
| |or + poles of water molecules |medium for metabolic reactions. The solvent |
| | |properties of water allow many substances to be |
| | |carried dissolved in water of blood of animals |
| | |and sap of plants. Water can be used as a |
| | |transport medium. |
|Thermal properties: heat capacity |Water has a large heat capacity–large amounts of|Blood, mainly composed of water, can carry heat |
| |energy are needed to raise its temperature. The |from warner parts of the body to cooler parts. |
| |energy is needed to break some of the hydrogen |Blood is used as a transport medium for heat. |
| |bonds. | |
|Thermal properties: boiling point |Boiling point of water (100OC) is high, because,|Water is below boiling point almost everywhere |
| |to change it from a liquid to a gas all of the |on Earth, and in most areas it is above freezing|
| |hydrogen bonds between the water molecules have |point. As a liquid, rather than a solid or gas, |
| |to be broken. |it can act as the medium for metabolic |
| | |reactions. |
|Thermal properties: the cooling effect of |Water can evaporate at temperatures below |Evaporation of water from plant leaves |
|evaporation |boiling point. Hydrogen bonds have to be broken |(transpiration) and from the human skin (sweat) |
| |to do this. The heat energy needed to do this is|has useful cooling effects. Water can be used as|
| |taken from the liquid water, cooling it down. |a coolant. |

3.2 Carbohydrates, lipids and proteins

3.2.1
Distinguish between organic and inorganic compounds
Organic compounds are defined as compounds containing carbon that are found in living organisms.
Three types of organic compounds are found in living organisms: • Carbohydrates • Lipids • Proteins
Some simple compounds are found in living organisms contain carbon but are inorganic. These include: • Carbon dioxide • Carbonates • Hydrogen carbonates
3.2.2
Identify amino acids, glucose, ribose and fatty acids from diagrams showing their structure.

3.2.3
List three examples each of monosaccharaides, disaccharides and polysaccharides.
Monosaccharides (simple sugars)
E.g. Glucose, fructose, galactose, ribose
Disaccharides (double sugars)
E.g. Maltose (2 glucose molecules), Sucrose (1 glucose and 1 fructose), Lactose (1 glucose and 1 galactose)
Polysaccharides
E.g. Starch (made of alpha glucose subunits), cellulose (made of beta glucose subunits), glycogen(made of glucose subunits that are linked differently to starch)
3.2.4
State one function of glucose, lactose and glycogen in animals, and fructose, sucrose and cellulose in plants.
|Carbohydrate |Function (in plants) |Function (in animals) |
|Glucose | |Main fuel molecule for cellular work (energy) |
|Lactose | |Main sugar in milk |
|Glycogen | |Storage compound in animal tissue, found mainly in |
| | |liver and muscle cells (make glycogen from glucose. |
| | |It can be converted back for energy.) |
|Fructose |Fruit sugar (during ripening, starch converted to | |
| |fructose) | |
|Sucrose |Main carbohydrate in plant sap and nourishes all | |
| |parts of the plant | |
|Cellulose |Structural component of plant cell walls | |

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 Reaction: Two molecules are joined together to form a larger molecule. Water is formed in the reaction.
Hydrolysis Reaction: Large molecules such as polypeptides, polysaccharides and triglycerides can be broken down into smaller molecules by hydrolysis reactions. Water molecules are used up in hydrolysis reactions.
Carbohydrates: Basic subunits of carbohydrates are monosaccharides. Two monosaccharides can be linked to form a disaccharide and more monosaccharides can be linked to form a large molecule called a polysaccharide.

Lipids: Fatty acids can be linked to a glycerol by condensation reactions to produce lipids called glycerides. Three fatty acids are linked to each glycerol producing a triglyceride.

+

Proteins: Amino acids can be joined to form a dipeptide. (New bond called peptide linkage) Further condensation reactions link amino acids to the dipeptide, forming a chain of amino acids called a polypeptide.

3.2.6
State three functions of lipids.
Functions of Lipids • Energy storage in the form of fat in humans and oil in plants • Heat insulation as fat under the skin reduces heat loss • Shock absorption • Lipids allow buoyancy as they are less dense than water and so animals can float in water
3.2.7
Compare the use of carbohydrates and lipids in energy storage.
|Carbohydrates |Lipids |
|More easily digested than lipids so the energy stored can be released more |More concentrated source of energy than carbohydrates |
|rapidly | |
|Soluble in water and so are easier to transport to and from the store |Lipids are insoluble in water, so they do not cause problems with osmosis in |
| |cells |
|Energy storage over short term |Energy storage over long term |

3.3 DNA Structure

3.3.1
Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate.
Each nucleotide of DNA is composed of a phosphate group called deoxyribose (sugar) and a molecule that is called a nitrogen base.

3.3.2
State the name of the four bases in DNA. • Adenine • Thymine • Guanine • Cytosine
3.3.3
Outline how DNA nucleotides are linked together by covalent bonds into a single strand.
Two nucleotides can join together by a condensation reaction between the phosphate group of one nucleotide and the sugar of another nucleotide.
The bonds linking nucleotides are covalent bonds.
This process can be repeated to build a polynucleotide chain with a sugar-phosphate backbone and organic bases projected outward.

3.3.4
Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds.
DNA molecules consist of two strands of nucleotides wound together in a double helix.
Two sides are made up of phosphates and deoxyribose sugars. The “rungs” are made up of nitrogenous bases. There are two bases making up each rung and are complementary to each other (A-T and C-G)
Adenine and thymine are held together by two hydrogen bonds. Cytosine and Guanine are held together by three hydrogen bonds.
Because adenine and guanine are twice the size of cytosine and thymine, complementary base pairing is the only arrangement that gives a consistent distance from one strand across to the other strand and also leads to bending between the bases.
3.3.5
Draw and label a simple diagram of the molecular structure of DNA.

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. • Is the process that occurs in the nucleus of a cell to produce identical strands of DNA. • It occurs during mitosis in the first phase (interphase) of cell division. • DNA replication is semi-conservative because each strand of the new DNA molecules contains one strand of the original. • Complementary base pairing creates strands two strands that are identical and each nucleotide chain is complementary of the other. • Stages;
[pic]
3.4.2
Explain the significance of complementary base pairing in the conservation of the base sequence of DNA.

3.4.3
State that DNA replication is semi-conservative.
DNA replication is a process that occurs in the nucleus of a call to produce two identical strands of DNA. DNA replication occurs during the first stage of cell division (interphase). DNA replication is called semi-conservative because each of the new DNA molecules formed contains one strand from the original DNA molecule and one newly synthesized strand.
Stages of Replication
First the hydrogen bonds joining the two strands must be broken-the strands uncoil and separate. The enzyme required for this is helicase.
The resulting unpaired bases are then used as a template to synthesise a new strand by complementary base pairing.
Within the nucleus are free nucleotide units which are the building blocks of DNA.
Synthesis of the new strand is dependent on the shapes of the bases and their ability to form hydrogen bonds. (Adenine + Thymine, Guanine + Cytosine)
The enzyme DNA polymerase is needed to assemble the bases with their complementary base on the parental strand.
This process continues along the length of the DNA molecule until the synthesis of the new strand is completed.
The two daughter DNA molecules are identical in base sequence to each other and to the parent molecule because of complementary base pairing.
Each of the new strands is complementary to the template on which it was made and identical to the other template.

3.5 Transcription and Translation

3.5.1
Compare the structure of RNA and DNA.
|Property |RNA |DNA |
|Name of sugar |ribose |deoxyribose |
|Number of strands |1 |2 |
|Bases |adenine, uracil, guanine, cytosine |adenine, thymine, guanine, cytosine |

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 a process in which mRNA is made on a DNA template in the nucleus. It is the transfer of information from DNA to RNA
Formation of an RNA strand
DNA carries instructions for making proteins (genes). The information encoded in DNA is transferred to mRNA. The double helix unwinds separating the two polynucleotide chains exposing the nucleotide bases.

The hydrogen bonds holding the double helix of DNA together are broken by the enzyme helicase. Only one of the strands is used as a template for the synthesis of mRNA. An enzyme RNA polymerase attaches to the strand at a particular base sequence-the promoter site-initiating-transcription. During transcription the enzyme moves along the transcribing strand and builds up mRNA by adding complementary nucleotides. Uracil pairs with adenine and cytosine with guanine. On reaching a special ‘stop’ sequence called a terminator, the enzyme detaches and the mRNA separates from the DNA and the DNA reforms
3.5.4
Describe the genetic code in terms of codons composed of triplets of bases.
The genetic code is held in the order of the bases along the DNA molecule. Selections of DNA (genes) contain the information to make a particular polypeptide.
Twenty amino acids make all the proteins in living organisms. Each of the twenty amino acids used to make proteins is represented by a three letter abbreviation-a base triplet in DNA or a codon in mRNA.
3.5.4
Explain the process of translation, leading to polypeptide formation.
Translation
mRNA moves into the cytoplasm and combines with ribosomes to direct protein synthesis
It is the conversion of the information in mRNA to make polypeptides
Initiation
mRNA binds to a small ribosomal subunit tRNA binds to the start codon (AUG) of the mRNA to begin translation by carrying the amino acid methionine.
A large ribosomal subunit binds to the small one creating a functional ribosome.
A ribosome moves along the mRNA strand and codons are read sequentially.
Elongation
Amino acids are now added one by one
The amino acid is attached to tRNA by a specific enzyme using energy from ATP
The anticodon of a tRNA (carrying its amino acid) pairs with then mRNA codon.
The large subunit has binding sites for tRNA.
-1 holds the tRNA carrying the growing polypeptide chain
-1 holds a tRNA carrying the next amino acid
Complementary base pairing between anticodons on tRNA and codons on mRNA ensures the correct sequence of amino acid is built in the polypeptide chain.
Termination
Elongation continues until a stop codon is reached.
3.5.5
Discuss the relationship between one gene and one polypeptide.
In the 1940’s a hypothesis was stated “every one gene of DNA produces one enzyme”
It was amended to include all proteins. However, proteins are composed of more than one polypeptide. Each individual polypeptide requires a separate gene. (One gene, one polypeptide hypothesis)
Some genes aren’t that straightforward.
For example, one gene may lead to a single mRNA molecule, but the mRNA may then be modified in many different ways. Each modification may result in the production of a different polypeptide during the translation portion of protein synthesis.

3.6 Enzymes

3.6.1
Define enzyme and active site
Most enzymes are proteins. They are biological catalysts.
Each enzyme is specific as they catalyse only one type of reaction. The reaction that the enzyme catalyses are reversible and the same enzyme can catalase a reaction in either direction.
Substrate molecule: Substrate molecules are the chemicals that an enzymes acts on. They are drawn into the cleft of the enzyme.
Active site: the part of the enzyme’s surface into which the substrate is bound and undergoes a reaction.
3.6.2
Explain enzyme-substrate specificity.
The active site of an enzyme is very specific to its substrates as it has a very precise shape. This results in enzymes being able to catalyse only certain reactions as only a small number of substrates fit in the active site. This is called enzyme-substrate specificity. Some other enzymes have lower specificity and will accept a wide range of substrates of the same general type (e.g. lipases break up any fatty acid chain length of lipid). This is because the enzyme is specific for the type of chemical bond involved and not an exact substrate.

3.6.3
Explain the effects of temperature, pH and substrate concentration on enzyme activity. • Substrate Concentration: Initially the rate of reaction increases rapidly before the rate slows and levels off. The enzymes are then at maximum capacity (all the active sites are in use)

• Temperature: At low temperatures, it is too cold for the enzymes to operate as there is not enough energy. The enzyme activity increases until the optimum temperature is reached (the temperature of the enzyme’s natural environment). At higher temperatures the enzymes denature. • pH: Enzymes are denatured at extremes of pH. Each enzyme has an preferred range of pH for optimum activity.

3.6.4
Define denaturation.
Denaturation is the structural change in a protein that results in the loss (usually permanent) of its biological properties. (Temperature and pH effects)
3.6.5
Explain the use of lactase on the production of lactose-free milk.
Lactose is the sugar found in milk. It can be broken down by the enzyme lactase into glucose and galactose. However some people lack this enzyme and so cannot break down lactose leading to lactose intolerance. Lactose intolerant people need to drink milk that has been lactose reduced. Lactose-free milk can be made in two ways. The first involves adding the enzyme lactase to the milk so that the milk contains the enzyme. The second way involves 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. This method avoids having lactase in the milk.

3.7 Cell Respiration

3.7.1
Define cell respiration
Cell respiration is the controlled release of energy from organic compounds in cells to form ATP.
It is represented by the equation: Glucose + Oxygen →Carbon dioxide + Water + Energy
The chemical bonds that link the last two phosphate groups in ATP are energy rich, when broken, lots of energy is released
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.
In cell respiration, glucose in the cytoplasm is broken down by glycolysis into pyruvate with a small yield 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.
In anaerobic cell respiration the pyruvate stays in the cytoplasm and in humans is converted into lactic acid which is then removed from the cell. In yeast the pyruvate is converted into carbon dioxide and ethanol. In either case, little ATP is produced (2ATP)
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.
If oxygen is available, the pyruvate is taken up into the mitochondria and is further broken down in the Kreb cycle resulting in carbon dioxide and water with a net ATP of 36

3.8 Photosynthesis

Plants and other photosynthetic organisms produce foods that begin food chains. We count on the Sun to be a constant energy source for both warmth and food production. The sunlight that strikes our planet must be converted into a form of chemical energy in order to be usefull to all non-photosynthetic organisms. The most common energy produced from photosynthesis is the molecule glucose.

Sunlight (energy) + Carbon Dioxide + Water [pic] Glucose + Oxygen

3.8.1
State that photosynthesis involves the conversion of light energy into chemical energy.
Photosynthesis involves the conversion of light energy into chemical energy.
3.8.2
State that light from the Sun is composed of a range of wavelengths (colours).
The light from the sun is composed of a range of wavelengths (colours).
3.8.3
State that chlorophyll is the main photosynthetic pigment.
Chlorophyll is the main photosynthetic pigment.
3.8.4
Outline the differences in absorption of red, blue and green light by chlorophyll.
Chlorophyll can absorb red and blue light more than green. Chlorophyll cannot absorb green light and so instead reflects it making leaves look green.
3.8.5
State that light energy is used to produce ATP, and to split water molecules (photolysis) to form oxygen and hydrogen.
Stage 1 of photosynthesis
Light energy is used to produce ATP and 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.
Stage 2 of photosynthesis.
ATP and hydrogen (derived from photolysis of water) are used to fix carbon dioxide to make organic molecules.
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.
Photosynthesis can be measured in many ways as it involves the production of oxygen, the uptake of carbon dioxide and an increase in biomass. For example, aquatic plants release oxygen bubbles during photosynthesis and so these can be collected and measured. The uptake of carbon dioxide is more 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. Finally, photosynthesis can be measured through an 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.
Temperature:
As the temperature increases the rate of photosynthesis increases at an increasing rate as there is increased molecular collisions.
At a certain temperature the rate peaks. Above this temperature there is a dramatic decline in the photosynthetic rate as the enzymes denature.

Light intensity:
There is a positive correlation between light intensity and photosynthetic rates until limiting factors stop a further increase.
Factors include enzymes already working at maximum rate and lack of carbon dioxide.

Carbon Dioxide concentration:
There is a positive correlation between the concentration of carbon dioxide and photosynthetic rate.
At a certain carbon dioxide level rate plateaus unless another variable is also increased.

-----------------------
(+))

(+)

H

H

(-)

Amino acid

General structure

Glucose

6 Carbon (hexose sugar)

Ribose

5 Carbon (pentose sugar)

Fatty acid

[OH-OC-(CH2)nCH3]

Poly.

Di.

Mono.

Triglyceride

Fatty acids

Gly.

Polypeptide

Dipeptide

a.a

Phosphate

Deoxyribose (sugar)

Base

Covalent bond-2 nucleotides

Deoxyribose (sugar)

A

T

A

T

G

C

A

T

Phosphate

DNA Template

mRNA

Nucleus