IB Bio Topic 2 Chemistry of Life Notes

IB Biology/The Chemistry of Life

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Topic 2 The Chemistry of Life

Chemical Elements and Water

The most frequently occurring chemical elements in living things are carbon, hydrogen, nitrogen and oxygen.

A variety of other elements are needed by living organisms including nitrogen, calcium, phosphorus, iron, and

sodium.

State one role for each of the elements mentioned before

1. Nitrogen: Required by proteins. (Remember, nitrogen is included in the amino acid structure) Contains

enzymes essential for plant function.

2. Calcium: The mineral that strengthens bone and teeth uses calcium. Also important in nerve synaptic

transmission of nerve impulses and muscle contraction. Regulates the cell wall construction in plants.

3. Phosphorus: Part of the phosphate groups in ATP and DNA molecules. In plants it is needed for cell

reproduction and division. It is part of the cell membrane.

4. Iron: found in the structure of haemoglobin and essential for the production of red blood cells. It is

involved in the light energy transferring compounds involved in photosynthesis in plants.

5. Sodium: Major ion associated with the propagation of a nerve impulse. Can replace potassium in

some plants.

6. Sulfur: It is a component of amino acids.

Outline the difference between an atom and an ion

An atom is a single particle of a chemical element. When an atom either gains or loses an electron it then

becomes an ion. Ions are charged, while atoms are uncharged. An Ion has either a negative or positive

charge depending if it gained or lost an electron.

Outline the properties of water that are significant to living organisms, including transparency, cohesion,

solvent properties and thermal properties. Refer to the polarity of water molecules and hydrogen

bonding when relevant.

1. Water is transparent which allows light to filter into the oceans. This allows for aquatic plants to

absorb light and perform photosynthesis. Since the ancestor of all plants originated in the ocean, the

transparency of water has had an immeasurable influence on life as we know it.

2. Water is also cohesive, that is it binds to itself, due to the polarity of the water molecule. The positive,

hydrogen side of the molecule binds to the negative, oxygen side of another water molecule. This bond

is called a hydrogen bond. This property allows for transport of water against gravity in plants.

3. Water is a very versatile solvent. All the reactions in cells must take place in aqueous solution.

10/10/2010 IB Biology/The Chemistry of Life - Wikib…

…wikibooks.org/…/The_Chemistry_of_Life 1/11

4. Water's polarity also inhibits movement of its molecules. Since all the molecules are connected, they

cannot freely move about as other, non-polar molecules do. Heat, the kinetic energy of molecules, is

thus restricted and so water has a high specific heat (it must absorb large amounts of energy in order

to change states). This means that water can serve as a temperature insulator, and does so in

organisms of all kinds.

Explain the significance to organisms of water as a coolant, transport medium and habitat in terms of its

properties

1. 'Coolant: Allows us to perform homeostasis. (We sweat to cool ourselves down). Additionally,

water's high heat of vaporization allows water molecules to absorb large amounts of energy from the

body before evaporating - thus, the sweating individual loses heat.

2. Transport medium: Digestion, also important to help transport blood. Phloem in plants transport

nutrients dissolved in water using the cohesive and adhesive properties.

3. Habitat: Organisms need water; the ready availability of it is essential in the choosing of a habitat.

Water's high heat capacity (the amount of energy needed to increase the temperature of 1gm of water

by 1 Degrees Celcius) and high heat of vapourization (amount of energy absorbed by 1gm of liquid to

be converted to the gaseous form) prevents from plants and animals from overheating and dying.

- If water had a low heat capacity (was able to increase its' temperature by a relatively low amount of energy)

aquatic organisms can die and the water in organisms will heat quickly and can result in the destruction of the cell. -

If water had a low heat of vapourization, liquid water will be able to evaporate when absorbing a relatively low

amount of energy. Imagine on a hot day, the water in the lakes would evaporate (turned into a gaseous state) quite

easily.

Carbohydrates, Lipids, and Proteins.

Define organic

Organic compounds are defined as compounds containing carbon that are found in living organisms.

Compounds are considered inorganic when they contain carbon but are widely found in the

environment (carbon dioxide and hydrogen).

Draw the basic structure of a generalized amino acid

Generalized amino acid.



Draw the ring structure of glucose and ribose

Glucose. Ribose.

Draw the structure of glycerol and a generalized fatty acid [1]

(http://www.public.iastate.edu/~cfford/101triacylglycerol.gif) click link for picture

Outline the role of condensation and hydrolysis in the relationship between monosaccharides,

disaccharides, and polysaccharides; fatty acids, glycerol and glycerides; amino acids, dipeptides, and

polypeptides.

In a condensation reaction, two molecules work together and form one big molecule along with water,

because water is released during this reaction. So, two amino acids could join together and form a

dipeptide and this would be a condensation reaction. Same applies for monosaccharides becoming

dissaccharides, you get the drift.

Now in a hydrolysis reaction, water molecules are used up to make a large molecule into a small

molecule. Think about it- "hydro" means water and "lysis" means splitting. So, water is used up to split

a disaccharide into a monosaccharide.

Draw the structure of a generalized dipeptide showing peptide linkage

http://homepages.ius.edu/GKIRCHNE/peptide.jpg

List two examples for each of monosaccharides, disaccharides, and polysaccharides

Monosaccharide: Glucose, Fructose and ribose

Disaccharide: Maltose (Glucose + Glucose) and Sucrose (Glucose + Fructose)

Polysaccharide: Starch (made of glucose subunits) and Glycogen (made of glucose subunits, but

linked differently from starch). (Plants use mostly starch, humans use mostly glycogen)

Also note that most polysaccharides are insoluble.

State one function of a monosaccharide and one function of a polysaccharide

Glucose, a monosaccharide has many important functions. Glucose molecules are used in respiration.

Glucose is building blocks larger carbohydrates such as starch, glycogen, and cellulose.

Starch, a storage polysaccharide for plants.

Cellulose and Chitin, are polysaccharides important for structure.

State three functions of lipids



Energy storage: Fat in humans. Oil in plants.

Heat insulation: A layer of fat under the skin reduces heat loss.

Buoyancy: Lipids are less dense than water.

Discuss the use of carbohydrates and lipids in energy storage.

Lipids and carbohydrates are excellent for storing energy in living organisms. Carbohydrates are

usually used to store energy in the short-term while lipids are used for the long-run.

Advantages of Lipids

1. Contain more energy per gram. Therefore lighter to store.

2. Lipids are insoluble in water; do not interfere with osmosis.

Advantages of Carbohydrates

1. More easily digested, so energy is released more easily from them.

2. Carbohydrates are soluble in water, so easier to transport.

Explain the four levels of protein structure

Primary structure

A linear sequence of amino acids joined by peptide linkages. There are about 20 different amino

acids.

Secondary structure

α -Helix is maintained by hydrogen bonds. The helix makes up keratin (skin, nails, hair)

β -Pleated Sheet flat zig-zag amino acid chain. The sheets make up fibroin (silk)

Both structures are fibrous and form structural proteins

Tertiary structure

Folded polypeptide chains into specific shapes. This means that tertiary proteins are globular

(hormones, enzmyes, membrane proteins)

Quaternary structure

Two or more polypeptide chains joined (e.g. haemoglobin).

Outline the difference between fibrous and globular proteins, with references to two examples of each

protein type

Fibrous proteins (such as keratin, collagen)

Chain extended

Insoluble

Resistance to pH/temperature changes

Structural material



Globular proteins (such as haemoglobin, amylase)

Chain folded

Soluble/colloidal

Susceptible to pH/temperature changes

Compact, rounded molecules

Enzymes

Define Enzyme and Active Site

1. Enzyme: Globular proteins used to catalyze chemical reactions.

2. Active site: The binding site on the surface of an enzyme where catalysis occurs.

Explain enzyme-substrate specificity

The active site for an enzyme is very specific in shape, with very precise chemical properties. Active

sites match the shape of their substrates. Other molecules do not fit or do not have the same chemical

properties. The enzyme is therefore substrate specific. This enzyme is a lock, and the substrate is the

key which can open it.

Explain the effects of temperature, pH and substrate concentration on enzyme activity

Temperature, pH and substrate concentration all affect the rate at which enzymes catalyse chemical

reactions.

Substrate concentration: At low s.c. the enzyme activity is proportional to the substrate concentration, because of

random collision between substrate and enzyme. Thus the more substrate the higher the rate. However at a high

substrate concentration, at some point all active sites are occupied so raising the substrate concentration has no

effect.

Temperature: Enzyme activity increases as temperature increases, often doubling with each 10°C. This is because

collision between substrate and active site happen more frequently at higher temperatures, due to fast molecular

movement. However at high temperatures enzymes are denatured and stop working. This is because heat causes

vibrations inside the enzyme, which break bonds needed to maintain the structure.

pH: There is an optimum at which enzyme activity is fastest ( mostly pH 7), and as pH increases or decreases from

its optimum, enzyme activity is reduced. (acids and alkali denature enzymes)

Define Denaturation

Denaturation: A structural change in a protein that results in a loss of its biological properties. This

can be caused by pH or by temperature.

Explain the use of lactase in the production of lactose free milk

Lactose- The sugar present in milk. Lactose is obtained from Kluveromyces and lactis. Lactose can be converted

to glucose and galactose using the enzyme lactase (di-saccarharide). Biotechnology companies culture the yeast and



extract the enzyme in order to produce lactose free milk.

Advantages: Pectinase makes juice more fluid and easy to separate from pulp.

Fructose is widely used in food manufacturing because it is much sweeter than glucose. It is made

from starch, usually found in maize. Amylase is needed to break down the starch into glucose.

'Source of Enzyme: Amylase is obtained from fungi.

Use: Used to break Starch into glucose, which is then converted into fructose using the enzyme

glucose isomerase.

D1A Structure

Outline D1A nucleotide structure in terms of sugar (deoxyribose), base, and phosphate.

A DNA is composed of a deoxyribose, a phosphate group and a nitrogen base (Adenine, Cytosine,

Thymine, and Guanine). The phosphate group is covalently bonded to the carbon of the deoxyribose

and then nitrogenous base is attached to the deoxyribose.

State the four names of the bases of D1A

Adenine, Cytosine, Guanine, and Thymine.

Outline how the D1A nucleotides are linked together by covalent bonds into a single strand.

Two DNA nucleotides can be linked together by a covalent bond between the sugar of one nucleotide

and the phosphate of another. More nucleotides can be added to form a single strand.

Explain how the D1A double helix is formed using complementary base pairing and hydrogen bonds.

DNA molecules consist of two strands of nucleotides which are then wound together to form a double

helix. These are formed between the bases of two strands. However, it is formed by complementary

base pairing because Adenine only forms hydrogen bonds with Thymine and Cytosine only forms

hydrogen bonds with Guanine.

Draw a simple diagram of the molecular structure of D1A.

URL of a suitable picture: http://www.cem.msu.edu/~reusch/VirtTxtJml/Images3/dblhelx1.gif

D1A Replication

State that D1A replication is semi-conservative.

DNA replication copies DNA to produce new molecules with the same base sequence. It is semi-

conservative because each new molecule formed by replication uses one new strand and one old

strand which is conserved from the parent DNA molecule.

Explain D1A replication in terms of unwinding the double helix and separation of the strands by



helicase, followed by formation of the new complementary strands of D1A polymerase.

1. Stage 1: The DNA double helix is unwound and separated into strands by helicase breaking the

hydrogen bonds holding the strands together and creating a replication bubble.

2. Stage 2: The single strands act as blueprints for new strands. Free nucleotides are present in large

numbers. The enzyme primase places primers on the new strand, allowing DNA Polymerase III to

add to the strand in a 5-carbon to 3-carbon direction. Several small strands are made within the

replication bubble formed by helicase that are known as Okazaki fragments. DNA Polymerase III is

then removed, and DNA polymerase I replaces primers with corresponding base pairs. The enzyme

ligase then binds these new base pairs to the rest of the strand. The bases of these nucleotides form

hydrogen bonds with the bases of the parent strand. The nucleotides are connected to form a new

strand.

3. Stage 3: The daughter DNA molecules each rewind into a double helix.

The two daughter DNA molecules are identical in base sequence to each other and to the parent molecule, because

of complementary base pairing (Adenine pairs with Thymine and Cytosine with Guanine). Each of the new strand is

complementary to the template on which it was made and identical to the other template.

Explain the significance of complementary base pairing in the conservation of the base sequence of

D1A.

Because the nitrogenous bases that compose DNA can only pair with complementary bases, any two

linked strands of DNA are complementary. This ensures that the old base sequence is conserved.

Transcription and Translation

Compare the structure of R1A and D1A

1. The number of strands.

DNA has two strands forming a double helix.

RNA has one strand.

2. The type of sugar.

DNA has a deoxyribose.

RNA has a Ribose.

3. The 1ucleotides.

DNA has A,C,G,T

RNA has A,C,G,U, (Uracil replaces Thymine)

Outline D1A transcription in terms of the formation of the R1A strand complimentary to the D1A

strand by R1A polymerase.

Transcription: The copying of the base sequence of a gene by making an RNA molecule.



1. The DNA double helix uncoils and the two strands separate.

2. RNA Polymerase attaches to promoter regions of the DNA strand

3. RNA polymerase binds free RNA nucleotides to create mRNA that are a copied template of the

corresponding DNA strand.

4. The mRNA separates from the DNA.

5. The DNA strands reforms into a double helix.

Describe the genetic code in terms of codons composed of triplets and bases. The genetic code is a triplet

code- three bases code for one amino acid. A group of three bases is :*called a codon.

Explain the process of translation, leading to peptide linkage of bases

1. Before the mRNA strand is translated, it must be processed. A cap and tail are added to the mRNA

strand to allow the mRNA strand out of the nucleus.

2. There are intron and exon segments of the strand. The introns are removed by the introduction of a

splicesome. The splicesome pushes out the introns and binds the exons together.

3. The mRNA then passes through the nuclear pore and enters the cytoplasm.

4. The two subunits of a ribosome (60s and 40s) lock onto the mRNA at the ribosome-binding site.

5. Transfer RNA (tRNA) are clover-leafed shaped molecules that have a specific amino acid attached.

6. Each tRNA also has three bases called the anticodon that binds to the mRNA. The anticodon

determines which amino acid the tRNA carries.

7. The tRNA can only bind to the mRNA in the presence of a ribosome. In each ribosome there are two

tRNA binding sites (Aminoacyl tRNA binding site or A site and Peptidinal tRNA binding site or P

site) and a tRNA exit site (E site).

8. The mRNA is divided into groups of three bases each called a codon. The anticodon on the tRNA

binds to the complementary codon on the mRNA. In so doing it brings the amino acid into position.

9. The mRNA is fed between the small and large subunits of the ribosome. The first tRNA molecule with

the attached start amino acid, methanine, attaches at the A site and is transferred to the P site. The

next tRNA binds to the mRNA and contains an amino acid.

10. When two tRNA molecules are bound to the mRNA at the ribosome a ribosomal enzyme forms a

peptide bond between the two amino acids.

11. The first tRNA becomes detached from its amino acid and moves off from the ribosome after it slides

into the exit site.

12. The ribosome moves a distance of one codon and a new tRNA binds bringing in another amino acid

to be joined to the polypeptide chain.

13. The first codon translated on any mRNA is always AUG. This is called the initiation codon and it sets

the reading frame of the mRNA.

14. There are also three codons that signal the end of the mRNA and stop translation. They are the stop

codons UAG, UAA and UGA.

15. Several ribosomes may all be translating the same mRNA at the same time. This is called a polysome.

Define the terms degenerate, and universal as they relate to the genetic code

Degenerate: Having more than one base triplet to code for one amino acid.

Universal: Found in all living organisms.

Explain the relationship between one gene and one polypeptide



Polypeptides are long chains of amino acids.

Amino acids must be linked up in a precise sequence to make a polypeptide.

Genes store the information needed to make a polypeptide in a coded form.

The sequence of bases in a gene codes for the sequence of amino acids in a polypeptide.

The information in the gene is decoded during the making of the polypeptide.

This process is conducted in two stages known as transcription and translation.

Cell Respiration

Define Cell-Respiration

Cell Respiration: controlled release of energy in the form of ATP from organic compounds in cells.

In cell respiration, glucose in the cytoplasm is broken down into pyruvate with a small yield of ATP

Glucose is organic compound that is sometimes used in cell respiration. Chemical reactions break Glucose

into a simpler compound called pyruvate. A small amount of ATP (2 ATP) is produced by using energy

released from glucose.

In anaerobic cell respiration pyruvate is converted into lactate or ethanol dioxide in the cytoplasm with

no further yield of ATP

Lactic fermentation: In the process of glycolysis glucose is transferred into two pyruvate. Since no

oxygen is available, the Krebs cycle cannot run which therefore also stops the process of the electron

transport chain. Too much pyruvate is built up in the cytoplasm and we need to get rid of it. Therefore,

it is transferred into the waste product - lactate - that can be removed from the cell. No ATP is

produced.

Alcohol fermentation: since there is no oxygen, pyruvate is transferred into ethanol/alcohol and carbon

dioxide is created as a bi-product. This is how an one-celled organisms overcome oxygen deficiency.

In aerobic respiration pyruvate is broken down in the mitochondrion into carbon dioxide and water with a

large yield of ATP If oxygen is available, the pyruvate is absorbed by mitochondrion. The pyruvate is then broken

down into carbon dioxide and water. A large amount of ATP is produced.

1ote: How to remember the difference! Aerobic sounds healthy- so something good comes

out of it! Anaerobic sounds like unaerobic and that sounds unhealthy! Easy to remember, right?

Also, think of doing aerobics, which is healthy as well and makes you breathe a lot!

2.8 Photosynthesis

State that photosynthesis involves the conversion of light energy into chemical energy.

Photosynthesis involves energy conversion. Light energy, usually sunlight, is converted into chemical

energy.



State that white light from the sun is composed of a range of wavelengths.

Sunlight is called white light, but it is actually made up of a range of wavelengths including red, blue,

and green.

State that chlorophyll is the main photosynthetic pigment

The structure of chlorophyll allows it to absorb some colours of wavelength better than others.

Outline the differences in absorption of red, blue and green light by chlorophyll

Red and blue light are absorbed more than green. The green light that cannot be absorbed is reflected

giving plants (and the pigment chlorophyll) their green colour.

State that light energy is used to split water molecules (photolysis) to give oxygen and hydrogen and to

produce ATP

Some of the energy absorbed by chlorophyll is used to produce ATP

Some of the energy absorbed by chlorophyll is used to split water molecules. This is called photolysis

of water

Photolysis of water results in the formation of oxygen and hydrogen. The oxygen is released as a

waste product

State that ATP and hydrogen (derived from photolysis of water) are used to fix carbon dioxide to make

organic molecules.

Carbon dioxide is absorbed for use in photosynthesis

The carbon from it is used to make a wide range of organic substances

The conversion of carbon in a gas to carbon in solid compounds is called carbon fixation

Carbon fixation involves the use of hydrogen from photolysis and energy from ATP.

Explain that the rate of photosynthesis can be measured directly by the production of oxygen or the

uptake of carbon dioxide, or indirectly by the increase of biomass

Uptake of carbon dioxide: Since carbon dioxide is important in the light-independent reactions of

photosynthesis, its consumption by plants can be measured as a means to determine the rate of ATP

and electron carriers used for carbon fixation.

Production of oxygen: Aquatic plants release bubbles of oxygen when they carry photosynthesis. e.g.

these bubbles are collected; their volume can be measured.

Increase in Biomass: If batches of plants are harvested at a series of times and their biomass

determined, then the rate of photosynthesis can be determined by an increase in biomass.

Outline the effects of temperature, light intensity, and carbon dioxide concentration on the rate of

photosynthesis:

Light - At low medium light intensities the rate is directly proportional to light intensity. At high light

intensities the rate reaches a plateau.

Carbon Dioxide - No photosynthesis at very low CO2 concentrations. At low to fairly high CO2

concentrations the rate is positively correlated with CO2 concentration. At very high CO2



concentrations the rate reaches a plateau.

Temperature - As temperature increases the rate increases more and more steeply. If the temperature

increases with 10¤C it roughly doubles the rate. When it reaches it maximum point it is said to be its

Optimum Temperature which is around 40¤C. Above the optimum temperature the rate slows down

rapidly and then stops. This happens because the excessive heat destroys the enzymes which are

responsible for catalyzing chemical reactions.

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IB Bio Topic 2 Chemistry of Life Notes