Atoms are the smallest forms of matter that retain the chemical characteristics of a given element
Atoms have a nucleus , which:
Contains protons (p)
May contain neutrons (n)
Clouds of electrons (e) surround the nucleus
Protons, Electrons, & Neutrons
Protons have +1 charge and have a mass of 1 atomic unit (AU)
Neutrons have no charge but have a mass of 1.005 AU
Electrons have a -1 charge and a mass of 1/1800 AU
The Periodic Table
Atomic Number & Atomic Weight
The number of protons is called the atomic number
The atomic number defines the element – if the number of protons changes, the element changes
The number of protons + the number of neutrons = the atomic weight
In an uncharged atom, the number of protons equals the number of electrons
The net charge on an atom is usually zero, because the number of electrons is usually equal to the number of protons.
If the number of electrons does not equal the number of protons, the atom is called an ion .
Ions have a net charge.
Elements are substances that cannot be broken down into simpler substances
account for >
Other elements are important too but are present in small quantities
• Nitrogen which is found in protein (CHON)
• Calcium which is found in bones / teeth
• Iron which is to be found in hemoglobin (animal)
• Sodium which is needed for a nerve impulse
• Phosphorus found in cell membrane structures
Most common chemical elements ( 98 % of mass of living organisms comes from O, C, H, N, Ca, and P ): • Carbon (C) • Oxygen (O) • Hydrogen (H)
Examples of Fe
Black Smoker Hydrothermal vents
Atoms stick together by linkages we call bonds .
Bonds come about because of reorganization of electron structure in the valence shells of the constituent atoms.
All biological reactions involve some sort of reorganization of bonds.
Bond reorganization (breakage or building of bonds) results in the uptake or release of energy.
Bond energy is the energy needed to break a given bond.
1. Covalent Bonds
In covalent bonds , two electrons are shared per bond
More than one bond can occur between two atoms
2. Ionic Bonds
In ionic bonds, electrons are donated by one atom to another
An electronegative atom steals an electron from another atom to fill its valence shell
That is, one or more electrons LEAVE one atomic center to ‘live’ with another
Ionic Bonds in Salt
Electronegative O pulls e- from H in water
This causes a partial (+) charge on the H, and a partial (-) charge on the O
Partial charges are indicated by lower case deltas (d)
The bonds between O and H are polar covalent bonds
3. Polar Covalent Bonds
Van der Waals
Short-lived charges on the surface of molecules induce opposite charges in adjacent molecules: Van der Waals ‘bonds’
Water is Polar
Water is a dipole
O pulls electrons from H
O end is partially (-), H ends are (+)
Partial charges interact
H’s attracted to O’s
Causes water to self-associate
Water Forms Hydrogen Bonds
Properties of water 1. Transparency 2. Water is “Sticky” Cohesive – sticks to itself Adhesive – sticks to other things creating a Meniscus 3. Solvent Properties 4. Thermal Properties 5. B uffering agent
Transparency: light can pass through water
• Light reaching the chlorophyll molecules within a plant cell.
• Light passing through the vitreous humour and aqueous humour of the eye to reach the retina.
• Light passing through aquatic habitats allowing vision for these organisms
Cohesion: because of the hydrogen bonds the water molecules stick together
At a surface, the cohesion of water molecules makes it difficult for small objects to break through. This creates niche opportunities both above and below the surface.
Water has High Surface Tension
Water sticks to itself strongly and so has high surface tension
Small animals can ‘skate’ on surface
Many different substances dissolve in water because of its polarity. Inorganic particles such as sodium ions and organic substances such as glucose can dissolve.Causes ions to come apart
Makes ‘hydration shells’ of water around an ion
• Water temperatures tends to remain fairly stable.
• As temperature rises the energy is absorbed by the many hydrogen bonds.
• Therefore water is a useful substance for living things both physiologically and ecologically.
Physiology: Cooling effects
• Blood (water in the plasma) can carry heat away from hot parts of the body to the cooler parts.
• Water can evaporate at temperature below boiling. Heat energy can absorbed by the water molecules. They enter the vapour phase and carry away heat from the body surface. Hence the process of sweating and panting.
Ecological effects: •Oceans, lakes and ponds have fairly stable temperature which means that organisms that live in them need not waste energy on thermoregulation. Surrounding air temperatures may show marked changes but water water in the same vicinity will remain relatively stable
• In natural habitats water rarely boil because it takes so much energy to break all the hydrogen bonds. However there are some organisms that thrive in high temperatures, the so called extremophiles.
• Water has a high freezing point. As water freezes the molecules for a crystal structure less dense than water itself. Therefore ice floats. This important if you are a fish or a polar bear.
Water acts as Buffers
Acids release protons ( proton donors )
Acid molecule H + + Anion
Bases absorb protons ( proton acceptors )
Base is an anion
Anion + H + Acid
HCl (acid – actually a gas, dissolves in water) H + + Cl -
NaOH (base - solid dissolves in water) Na + + OH -
pH is Very Important
Cell function is greatly dependent on pH
Normal physiological pH is usually close to pH 7.4
Minor deviations from physiological pH can be very devastating to biochemical reactions (and therefore, to life processes)
Buffers Minimize Changes in pH
Buffers are molecules that act as acids or bases or both
They are weakly (i.e., incompletely) ionizing
Many buffers are both acid and base at the same time
Bicarbonate ( HCO 3) is an important buffer in vertebrate blood:
The branch of chemistry that specializes in the study of carbon compounds
Organic molecules are molecules containing carbon and hydrogen (except hydrogencarbonates, carbonates and oxides of carbon
Are organic compounds made of sugars and their
Monosaccharides Single units callled monomers.
Disaccharides 2 monomers joined.
Polysaccharides long chains of repeating units
The ring structure of Glucose and Ribose
Below is the structure of Glucose .
• C 6 H 12 O 6
• Carbon 5 is connected to Carbon 1
• Each Carbon has an -OH group
• Each Carbon has an -H (C6 has 2)
Properties of Glucose
• reducing sugar
• monomer of Starch/ Glycogen
This is the structure of Ribose
• C 5 H 10 O 5
• Carbon 1 is attached to Carbon 4
• Each Carbon has a -H group (C5 has 2)
• Each Carbon has a -OH group
Properties of Ribose
• part of the structure
of nucleic acids
• e.g. Deoxy ribo nucleic acid
Sugar which is less sweet than glucose.
It is found in dairy products, in sugar beets and gums. When combined with glucose, through a dehydration reaction, the result is the disaccharide lactose found in most milks.
Difference in the Structure Galactose Glucose
Are double sugars that contain two monosaccharides.
Are formed through the process of condensation synthesis.