IB Biology - Chemistry of Life

Where did cells first originate?

Cells first evolved in bodies of water

Water is a medium where most life process occur

What is water a medium of?

• solvent

• reactions

• transport of substances

• temperature regulator

• protection (brain, spinal cord, joints)

• absorption of nutrients

• excretion of waste

Polarity

When a molecule has both a partially negative (δ−) and positive charge (𝛿+)

What are a consequent of the polar bonds within water molecules

Hydrogen bonds

Causes of the polarity of covalent bonding in water molecules

Due to the unequal sharing of bonded electrons

What is the structure of a water molecule

1 O atom (partially negative) covalently bonds with 2 H atoms (partially positive)

Dipolar nature

TREAT THIS THE SAME AS POLAR, DIPOLAR = 2 OPPO. POLES

Polarity due to excess electrons surrounding O atom (not the usual excess of electrons due to ionic bonding) → hydrogen bonds (weak bonds) form between different water molecules → cause specific properties of water

Cohesion

binding together of molecules of the same substance due to H bonds (same molecules sticking together)

What is the direction of movement of water in the xylem vessels?

(against gravity) by water molecules “pulling each other up”

Surface tension

resistance of the surface of a liquid to breaking → caused by hydrogen bonding between surface molecules

Adhesion

H bonds form between water + other polar molecules (water sticking to other compounds) 

Adhesion enables #1

Movement of water in xylem (against gravity) by water molecules adhering to polar cellulose molecules in cell walls

Adhesion enables #2

Movement of water molecules between soil particles by adhering to polar organic matter in the soil → spreading due to plants’ uptake of water through roots

BOTH adhesion and cohesion contribute to capillary action

Role of solvent properties of water

• medium for metabolism

• for transport in plants + animals

What types of molecules dissolve in water?

A wide variety of hydrophilic molecules dissolve in water → most enzymes catalyse reactions in aqueous solutions

Functions of some molecules in cells depends on them being hydrophobic + insoluble

Why does water have a solvent property

Because of polarity, water molecules dissolve a number of other polar molecules

HYDROPHILIC (water-loving) SUBSTANCES = soluble in water

chemically attracted to water: polar charged or substances that water adheres to (glucose, cellulose, sodium chloride)

Hydrophilic substances

• extremely important for transport of nutrients + wastes 

• most metabolic enzymatic reactions happen in a watery environment

HYDROPHOBIC (“water-fearing”) SUBSTANCES = insoluble in water

nonpolar (uncharged) particles that can not be attracted to water (oils, fats, lipids, hydrocarbons) 

Importance of hydrophobic substance

extremely important that some substances remain hydrophobic → e.g. some lipid-based hormones, efficient energy storage as fats, transport of fatty substances in blood via “lipoprotein complexes” → hydrophilic exterior and hydrophobic interior

DON’T ASSUME that hydrophilic + soluble are together

CAN ASSUME hydrophobic + insoluble

How is glucose transported in blood

Mode of transport	How it works
(soluble) Dissovled in blood plamsa	Glucose is a polar molecule which dissolves in water. Blood plasma is mostly water.

How is amino acids transported in blood

Mode of transport	How it works
(soluble) Dissovled in blood plamsa	Amino acids is a polar molecule which dissolves in water. Blood plasma is mostly water.

How is cholesterol + other lipids transported in blood

Mode of transport	How it works
(insoluble) Lipoprotein complexes	Cholesterol and lipid molecules are nonpolar, and will not dissolve in blood plasma, which is mostly water.

How is sodium chloride transported in blood

Mode of transport	How it works
(soluble) Dissovled in blood plasma	Sodium chloride is an ionic compound which dissolves in water. Blood plasma is mostly water.

How is oxygen transported in blood

Mode of transport	How it works
(insoluble) Mostly bound to hemoglobin, some dissolved in blood plasma	Oxygen is nonpolar, and does not readily dissolve in water.

Physical Properties of water: water anomaly (thermal)

most substances increase in density as their temperature decreases until they reach a solid state → water is densest at 4°C rather than 0°C → ice is less dense than water, so it floats on the surface → enables survival of aquatic plants + animals

Physical Properties of water: HBP (thermal)

high because of high heat of vaporization → boiling point is the max temp. in which substance is still liquid

Physical Properties of water: high latent heat of vaporization (thermal)

high amount of heat (energy) required for a water molecule to break H bonds (set free from the liquid) → become a water vapor molecule  

• evaporation has a cooling effect (sweating) on organisms → e.g. humans

• very large span of liquid water availability on Earth (0-100C)

Physical Properties of water: high specific heat capacity (thermal)

Specific heat capacity = amount of energy required to raise 1 g of a substance by 1°C.

Water has high SHC → resists temperature change due to hydrogen bonds absorbing energy → large bodies of water resist temperature change → stable aquatic ecosystems

Physical Properties of water: thermal conductivity (thermal)

water conducts heat much more effectively than air → means aquatic animals lose body heat more rapidly → animals must be adapted to reduce heat loss

Physical Properties of water: buoyancy (the ICE floats on the water)

upwards force (drag) exerted by a fluid on an object immersed in it → liquid water is a denser fluid than air, providing greater buoyancy for aquatic animals → allows them to float or swim more easily

• helps many aquatic animals conserve energy → allows them to stay afloat without expending a lot of effort

• Aquatic mammals have a layer of blubber that provides buoyancy → helps them float on the surface of the water (also provides thermal insulation)

Physical Properties of water: viscosity

• measure of a fluid’s resistance to flow → the higher the viscosity, the more difficult it is for animals to move through the fluid

• Water has a higher viscosity than air, so most aquatic animals have various hydrodynamic shapes → streamlined body shape which allows them to smoothly move through water

Ringed seal - buoyancy

layers of blubber → allows to remain buoyant while in sea → reduces energy required to swim

Ringed seal - viscosity

• streamlined body → allows them to efficiently move through water

• flippers → use drag to facilitate movement

Ringed seal - thermal conductivity

• layer of blubber → insulates them in water

• fur → can trap air → helps with insulation

• seals tend to huddle → reducing exposed surface area + heat loss when on land

Ringed seal - high specific heat capacity

• endotherms (able to make their own heat) = adapted to maintain a constant body temperature → the high specific heat capacity of the water in their bodies help maintain a stable body temperature

Black throated loons - buoyancy

• able to adjust its density by changing the volume of air in special 'air sacs' (in their lungs) → allows them to control the depth when diving for food

• by spreadings its wing → stabilise + distribute weight on water surface → able to increase its buoyancy

• bones → dense to help them dive down to hunt for food

Black throated loons - viscosity

• streaming shape of loons → allows them to efficiently move through air + water

• webbed feet → helps the birds to move through water

Black throated loons - thermal conductivity

• endotherm = maintains a constant body temp

• feather trap air and provide insulation

• feather are covered in hydrophobic oil → keeps feathers dry

Black throated loons - high specific heat capacity

• water has HSHC → aquatic environments change temperature slowly → reduces rapid heat loss when diving → help loons to regulate its body temp

Why was there no water on “proto-Earth”?

• Earth + other rocky planets of the inner solar system formed by clumping together

• Water was not present as ice since the temp. were too high for it to exist as ice → any gaseous water would have been moved by solar winds

How did Earth gain its water?

• Solid water was formed in the outer solar system (due to low temperatures) since the sun was far

• ice formed comets + asteroids

• Earth's water came from asteroids (have similar heavy hydrogen atoms as Earth's water)

• Water came during the Late Heavy Bombardment (4 billion years ago)

How did Earth retain its water?

• Earth's large mass creates enough gravity to retain the liquid water + vapor inside. The moon is smaller --> less gravity --> cannot retain water vapor

• Earth is in a habitable zone of the solar system --> water exist in liquid here. Earth's temp. is suitable for the water cycle --> water vapor condenses to liquid water --> falls back to Earth as precipitate

What is required for life to exist? - Liquid water

acts as a solvent → enables chemical reactions

What is required for life to exist?

• Source of energy

What is required for life to exist? (essential chemical elements)

• Carbon  

• Hydrogen

• Oxygen

• Nitrogen

• Phosphorus 

• Sulfur

What is required for life to exist? (stable environment)

Habitable zone around a star = zone in which liquid water can form and remain = the Goldilocks zone 

Carbon atom’s structure

Carbon atoms contain 4 electrons in their outer shell → can pair up with electrons of other atoms → able to form single/double/triple covalent bonds with other atoms

Covalent bonding

Covalent bonds are strongest type of bond between atoms → stable molecules can be formed 

Carbon on Earth

Carbon very abundant on the planet → forms the backbone of every single organic molecule

Carbon forming with others

Carbon can form molecules with many different elements → e.g. other carbon atoms, metallic + non-metallic atoms.

Carbohydrates

Lipids

Protein

Nucleic acids

SI Metric Units Prefixes

Hydrolysis

• Breaking apart polymers (bonds) into monomers using water

• Catabolic

• In: water

• Out: energy (exergonic react.) 

Hydrolysis defintion

breaks down complex polymers into monomers by adding a water molecule to break covalent bonds

Condensation

• Polymerization of monomers

• Anabolic

• In: energy (endergonic react.)

• Out: water 

Condensation definition

joins two monomers together to form a polymer, releasing a molecule of water as a by-product

Hexoses

A type of monosaccharide

Pentoses

A type of monosaccharide

What is an example of a monosaccharide?

Glucose is a monosaccharide

Solubility of glucose

Glucose is a polar molecule which readily dissolves in water

Transportability of glucose

Since glucose is soluble in water, it is transported within bodily fluids, such as the bloodstream in humans

Chemical stability of glucose

Glucose is a relatively stable compound, so it does not degrade as it is being transported

Energy yield of glucose

Glucose is the primary fuel for respiration in cells - it is repeatedly oxidized to produce a net gain of up to 36 ATP molecule

Properties of starch and glycogen

- large compact polymers of α - glucose due to

1. spiral coiling (1-4 glycosidic bonds)

2. branching (1-6 glycosidic bonds)

- insoluble (due to size), which allows efficient storage of many glucose molecules (which can be quickly released when needed)

Properties of cellulose

- polymer of β - glucose (1-4 glycosidic bonds)

1. the position of the C1 -OH group repels the C4 -OH group on the neighboring molecule, which causes every other molecule to flip 180 --> long straight chains called microfibrils

- microfibrils are held together by hydrogen bonds which gives them a very high tensile strength = structural integrity of the cell walls in plants

- hydrophilic, but insoluble

Structure of cellulose

Structure amylose

Structure of amylopectin

Condensation + hydrolysis in α - glucose monomers

condensation → build energy stores

hydrolysis → mobilize (making it more readily available) energy stores

Condensation + hydrolysis effect in α - glucose monomers

α-glucose monomers are added by condensation reactions + removed by hydrolysis → allows rapid building + mobilization of energy stores

alpha (α) - glucose

beta (β) - glucose

Cellulose

• β-glucose units alternate (every other one flipped 180°)

• This prevents coiling → chains stay straight

• Parallel chains form microfibrils

• Hydrogen bonds between chains give tensile strength (plant cell walls)

Amylose

Amylopectin

Glycogen

Glycoproteins

Glycoproteins = integral membrane proteins 

(located within the phospholipid bilayer of cells’ membranes) with short outside-facing carbohydrate chains attached to them → recognized by other receptors

Glycoproteins functions - cell to cell adhesion

Cell to Cell Adhesion → interact with glycoproteins on neighboring cells → allows formation of tissues

Glycoproteins functions - receptors for hormones

when a hormone binds to a specific glycoprotein receptor → changes metabolism. within the cell

Glycoproteins functions - cell to cell communication

neurotransmitters bind to glycoproteins → allows communication between cells

Glycoproteins functions - immune responses

act as markers on cells → allows the immune system to distinguish between self + non-self cell 

Structure of red blood cells

All red blood cells carry the same “stem” glycoprotein (H) on their membrane surface, plus different glycoproteins on it → depending on the alleles that the person has

Determining blood group

• Blood group A – glycoprotein A

• Blood group B – glycoprotein B

• Blood group AB – glycoproteins A & B

• Blood group O – no glycoprotein 

Importance of glycoprotein

they help the immune system cells to recognize “own self” cells from “non-self” cells

Non - self cells

“Non-self” cells = containing any glycoprotein that the person doesn’t already have) → can cause a very dangerous immune reaction → they are recognized as antigens (much like actual pathogens) by the immune system cells → starts making antibodies to fight them off = extremely important to watch out for during transfusion 

Lipids

Groups of lipids

diverse group of organic compounds which all have long chains of hydrocarbons

Lipids’ charge

hydrophobic, non-polar compounds → dissolve in other nonpolar compounds, but do not dissolve in water 

Fats

• Long - term energy reserve + concentrated source of energy for animals

• supply essential fatty acids + fat soluble vitamins (A, D, E, K)

• constituent of cell membranes

• stored in adipose tissue for insulation + energy

Oils

• triglycerides liquid at room temperatures

• relatively low melting points

• usually unsaturated fatty

• plants (and fish) use oils as an energy store

Waxes

• long fatty acid chain esterifies to long chain alcohols

• covers some aquatic birds' feathers and some plants' leaf surfaces - they prevent water from sticking on the surface

Steriods

• Lipids with a structure of 4 fused carbon rings

• Cholesterol is a component of animal cell membranes + helps regulate membrane fluidity

• Some steroids (steroid hormones) are lipid-soluble and can diffuse through the phospholipid bilayer to bind to intracellular receptors

• Act mainly as signalling molecules in organisms