Introduction to cell biology

Chemical Bonds and Water

Organisms are composed of matter.

Matter is anything that takes up space and has mass.

An element is a substance that cannot be broken down to other substances by chemical reactions.
There are 92 naturally-occurring elements. Each element has a unique symbol, usually from the

first one or two letters of the name, often from Latin or German.

A compound is a substance consisting of two or more elements in a fixed ratio.

Table salt (sodium chloride or NaCl) is a compound

with equal numbers of chlorine and sodium atoms.

While pure sodium is a metal and chlorine is a gas,

their combination forms an edible compound, an emergent property.

Life requires about 25 chemical elements

About 25 of the 92 natural elements are known to be essential for life.
Four elements - carbon (C), oxygen (O), hydrogen (H), and nitrogen (N) - make up 96% of living matter.

Most of the remaining 4% of an organisms weight consists of phosphorus (P), sulfur (S), calcium (Ca), and potassium (K).

 Trace elements are required by an organism but only in minute quantities.

Some trace elements, like iron (Fe), are required by all organisms.

Other trace elements are required only by some species.

For example, a daily intake of 0.15 milligrams of iodine is required for normal activity of the human thyroid gland.
Fig. 2.4

An element consists of a single type of atom that is different from other atoms that build up another element. Is the smallest unit of matter in biological or chemical organization. So small, symbolized with abbreviation used for the elements that are made up of those atoms
C = Carbon, consists only single carbon atom

1. Subatomic particles
Atom= Greek word= indivisible Consists of many subatomic particles

Neutrons (Neutral) Protons (+ve charge) Electrons (-ve charge) Neutron + Proton = Atomic nucleus Electron move around nucleus= electron cloud

Cloud of negative charge (2 electrons)

Nucleus

Electrons

(a)

(b)

Protons and electrons attracted to each other because of opposite charge, thus keeping the electron orbiting around the nucleus. Protons and neutrons have same mass Electrons are so light and small, their mass considered zero. Protons and neutrons contribute to mass of atom Unit for atom mass = dalton Proton + neutron = closed to 1 dalton

2. Atomic number and atomic weight Atomic number= the number of protons in the element The number is unique to that element 2He

Indicates atom of the element Helium has 2 protons in its nucleus

Usually, an atom is neutral in electrical charge. Equal number of electrons must balance its proton. Therefore, the atomic number indicates the number of protons or the number of electrons in an electrically neutral atom.

Atomic mass = the sum of protons and neutrons in the nucleus atom (mass number)
Number of neutron= Atomic mass- Atomic number

Proton Electron Neutron

= 11 =11 = Atomic mass-Atomic number = 23-11 =12

Atomic number= no. of proton= no. of electron Proton =2 Electron = 2 Neutron = Atomic mass- Atomic number = 4- 2 =2

Hydrogen, special case

Smallest atom Made up of 1 proton, 1 electron, no neutron

3. Isotopes Name given to the atoms from the same element, but shows differences in terms of the subatomic particle numbers. Element consists of mixture of atoms with different numbers of neutrons, and thus different masses.

Radioactive isotope
Form of element that their nucleus decays

spontaneously Unstable, tend to give off particles and energy easily.

 Carbon-12, Carbon-13 are stable- unable to decay

easily But, Carbon-14 are unstable or radioactive When an atomic nucleus of an element experience the decaying process, the atomic number change. As a result, the process transforms the atom into different atoms or different elements. E.g Carbon-14 transforms to N.

Radioactive isotopes applications:

Measurements of radioactivity in fossils to date

relics of past life Measure thickness of metal Testing for corrosion and monitoring purpose Treat cancerous cells Tracers to follow atoms through metabolismdiagnostic tools in medicine (Kidney problem)

4. Electron configuration

The arrangement and how electrons are distributed in the atom Determines the chemical behavior of atoms Electrons orbiting nucleus in spherical pathway- help from the opposite charge of proton- right pathway

The pathway of electrons represents their energy level electron shell Nucleus need less energy to attract the electron when they are close to each other Periodic table shows the distribution of electrons according to numbers of electron shell in their atom

Left-right; refers to additional sequence of electrons Top-bottom sequence of elements in each column represents the number of electron shell in their configuration Similar no. of electrons in valence shell= similar chemical behavior Completed valence shell- unreactive Incomplete valence shell- reactive

Figure 2.9

Hydrogen 1H
First shell

Mass number

2 He 4.00

Atomic number Element symbol Electron distribution diagram

Helium 2He

Lithium 3Li Second shell

Beryllium 4Be

Boron 5B

Carbon 6C

Nitrogen 7N

Oxygen 8O

Fluorine 9F

Neon 10Ne

Sodium Magnesium Aluminum 11Na 12Mg 13Al

Silicon 14Si

Phosphorus 15P

Sulfur 16S

Chlorine 17Cl

Argon 18Ar

Third shell

Electron orbital Orbital- 3D space where electron spends most of its time 1st electron shell-single orbital- 2 electrons 2nd electron shell-4 orbital- 8 electrons
2s 2p (2px ,2py, 2pz)

 The reactivity of atoms arises from the presence of unpaired electron in one or more orbitals of their valence shells

Atoms with incomplete valence shell interact with each other to complete their own valence shell Atom stays close to each other bind by chemical bonds
Covalent bonds Ionic bonds Hydrogen bond

1. Covalent bond Attraction due to sharing valence electrons by two atoms to fulfill their valence shells. Strong, not easily broken unless by enzymatic catalysis.

Two or more atoms held together by covalent bonds constitute a molecule. We can abbreviate the structure of this molecule by substituting a line for each pair of shared electrons, drawing the structural formula.
H-H is the structural formula for the covalent bond

between two hydrogen atoms.

The molecular formula indicates the number and types of atoms present in a single molecule.
H2 is the molecular formula for hydrogen gas

Single covalent bond: 2 atoms share a pair of electron valence- stable, complete configuration. For example, if two hydrogen atoms come close enough that their 1s orbitals overlap, then they can share the single electrons that each contributes.

Oxygen needs to add 2 electrons to the 6 already present to complete its valence shell.
Two oxygen atoms can form a molecule by

sharing two pairs of valence electrons. These atoms have formed a double covalent bond.

Every atom has a characteristic total number of covalent bonds that it can form - an atoms valence. The valence of hydrogen is 1. Oxygen is 2. Nitrogen is 3. Carbon is 4. Phosphorus should have a valence of 3, based on its three unpaired electrons, but in biological molecules it generally has a valence of 5, forming three single covalent bonds and one double bond.

Covalent bonds can form between atoms of the same element or atoms of different elements. While both types are molecules, the latter are also compounds. Water, H2O, is a compound in which two hydrogen atoms form single covalent bonds with an oxygen atom. This satisfies the valences of both elements.

 Methane, CH4, satisfies the valences of both C and H.

The attraction of an atom for the electrons of a covalent bond is called its electronegativity.
Strongly electronegative atoms attempt to pull

the shared electrons toward themselves.

If electrons in a covalent bond are shared equally, then this is a nonpolar covalent bond.
A covalent bond between two atoms of the same

element is always nonpolar.

If the electrons in a covalent bond are not shared equally by the two atoms, then this is a polar covalent bond. The bonds between oxygen and hydrogen in water are polar covalent because oxygen has a much higher electronegativity than does hydrogen.

 Compounds with a polar covalent bond have regions that have a partial negative charge near the strongly electronegative atom and a partial positive charge near the weakly electronegative atom.

2. Ionic bonds
Forms because of the attraction between positive and negative charged ion.
For example, sodium with one valence electron in its third shell transfers this electron to chlorine with 7 valence electrons in its third shell.
Now, sodium has a full valence shell (the second) and chlorine has a full valence shell (the third).

After the transfer, both atoms are no longer neutral, but have charges and are called ions. Sodium has one more proton than electrons and has a net positive charge.
Atoms with positive charges are cations.

Chlorine has one more electron than protons and has a net negative charge.
Atoms with negative charges are anions.

Atoms with 5, 6, 7 valence electron tend to gain electrons- become negatively charged. Atoms with 1, 2, 3 electrons tend to lose electrons- become positively charged

3. Hydrogen bonds Is the attractive force between hydrogen atom covalently bonded to one electronegative atom and is attracted to another electronegative atom from other molecules. Usually oxygen or nitrogen atoms E.g H2O, NH3

Hydrogen bonds between water molecules

Weak, but important The advantages

Support shapes of large molecules and help

molecules to attach to each other The contact can exist temporarily, not permanent
Chemical signal in brain One-brain cell signals other cell by releasing molecules that use weak bonds to tie up onto receptor molecules of the receiving cell If the signals strongly bonded, the transmission will continue to respond causing cell excited continuously

Do not the Unbelievers see that the heavens and the earth were joined together (as one unit of creation), before we clove them asunder? We made from water every living thing. Will they not then believe?- AlAnbiyaa 21: 30

Because water is the substance that makes possible life as we know it on Earth, astronomers hope to find evidence of water on newly discovered planets orbiting distant stars. Life on Earth began in water and evolved there for 3 billion years before spreading onto land. Even terrestrial organisms are tied to water.

Most cells are surrounded by water and cells are about 70-

95% water.

Water exists in three possible states: ice, liquid, and vapor.

a) Cohesive and adhesive properties Cohesive-capacity to stick to each other

tightly although under tension, normally occur among similar atoms and held together by hydrogen bonds.
The bonds are fragile, easily break and

reform with greater frequency. Make water more structured than most liquids hydrogen bonds hold water molecules, cohesion occur

 Cohesion among water molecules plays a key role in the transport of water against gravity in plants.

Water that evaporates from a leaf is replaced by water from vessels in the leaf.
Hydrogen bonds cause water molecules leaving the veins to tug on molecules further down. This upward pull is transmitted to the roots.

Adhesive- ability to cling to other substances. Also contribute to water transportation Adhesion of water to the wall of vessels helps to counter against gravity Ensure molecules move upward to every part of higher plants. Also can be seen during cleaning and cleansinghelp things become wet and remove all impurities

Adhesion to cell walls by hydrogen bonds- resist downward pull of gravity

Cohesion due to hydrogen bonds between water molecules helps hold together the column of water within the cells

Surface tension, a measure of the force necessary to stretch or break the surface of a liquid, is related to cohesion. Water has a greater surface tension than most other liquids because hydrogen bonds among surface water molecules resist stretching or breaking the surface. Water behaves as if covered by an invisible film. Some animals can stand, walk, or run on water without breaking the surface.

b. Water has high specific heat

Specific heat- amount of heat that must be absorbed or lost for 1g of substances to change its temperature by 1C. Specific heat of water- 1 cal/g/1C. Unusually high compared to others Ethanol- 0.6 cal/g/1C Acetone- 0.5 cal/g/1C Allows water to absorb or release large amount of heat without changing its temperature dramatically.

The property of specific heat closely related to hydrogen bonds. Absorption of heat- break bond Released of heat- bond formation Water needs more heat to raise its temperature as it need to break the hydrogen bond first before raising up the kinetic energy that cause the temperature to be increased.

When temperature drops, many additional hydrogen bonds form, slowing down the kinetic energy and releasing large amount of energy (heat). High specific water heat important in life for both large water bodies or the living cells of organisms.
In the ocean, large water bodies can absorb and store

large amount of heat from sun, while warming out only a few degrees, Gradually, cooling water can warm the air at night. Coastal area have mild climate compared to desert.

 Stabilizes ocean temperatures, sustaining

favorable environment for marine life. Keeps earth temperature fluctuating in water and on land within limit that permit life. Cells can resist extreme change in their own temperature so that it fluctuates within limits that permit life activities.

c. Water has high heat of vaporization Heat of vaporization= amount necessary to be absorbed by 1gm of water to convert from liquid to gas. Usually is the effect of heat energy. Heat of vaporization of water= 580 cal/g
Ethanol= 210 cal/g Benzene 120 cal/g

The heat is used to break off hydrogen bonds first before it moves faster and transforms into gaseous state.
Advantages in moderating earths climate Ocean capable of absorbing considerable amount of

heat for evaporation of surface water, it is then changes to moist tropical air and circulates upwards. The hot, moist tropical air meets with cool air at higher altitude and releases an amount of heat as it condenses to form rain.

 Due to evaporation, evaporative cooling occur as the

hottest molecule transform into gas leaving remaining molecule to cool down. Contributes to the stability of temperature in lakes and ponds, prevent overheating for terrestrial organism. Example Evaporation of water from leaves and plants helps to keep plant tissues from overheating on hot day Evaporation of sweat from human skin transfers body heat to surrounding.

d. Water expands as it freezes When water is cooled, it does contract as usual until the temperature is approximately 4c, then expanding slightly until it reach freezing point. Therefore, water become less dense as solid than liquid-ice floats. Temperature reaches 0c- water molecules locked into crystalline lattice; maximum 4 neighboring partner through hydrogen bond, forming hexagon. Hydrogen bonds keep molecules at certain length , so there are more empty space inside compared to liquid water 10% less density.

Advantages to the fitness of environment Floating ice insulate water below, prevent freezing. Life under frozen surface.

Ice

Liquid

e. Water is versatile solvent

Because of their polarity-due to polar covalent bond when a water molecule bears partial positve and partial negative charges. Hydrogen atom of water molecule with its partial positive charge attracted to oxygen atom of neighboring water molecule. Partial negative charge form hydrogen bond. The opposite charges attracted another ionic compounds such as NaCl, sugar and protein.

The polarity of water-capable to dissolve many substances, polar and ionic compounds. Water provides efficient medium in facilitating chemical rxn. Able to interact with H2O hydrophilic Unable to interact with H2O hydrophobic

 Oxygen- negatively charge, attracted to Na+

Hydrogen- positively charge, Attracted to Cl NaCL- Solute Water- Solvent Mixture of more than one substance in waterhomogenous liquid- Solution The region of water molecules around dissolved ions-hydration cell Any polar-molecules compound can be dissolved

Mixture in which water is the solvent. Solute- must be hydrophilic substance, dissolve and interact readily with water. Important for physiological and enzymatic activity. Solute concentration Units of mole (mol)= molecular weight of a substance Avogadros number= number of molecules in a mole=6.02 x 1023 Molarity refers to the number of moles of solute per liter of solution- M or mol/l

How to prepare a 0.5 M of NaCl

0.5 M equals to 0.5 mol NaCl in 1 liter of water solution Na(23) + Cl (35) = 58 grams (1 mol) = 0.5 x 58 g = 29 g

1. How to prepare a 2.0 M of K2HPO4?

39K 1H 31P 16O

2. How many grams of salt (NaCl) must be dissolved in water to make 2 L of a 2M salt solution? 23Na 34Cl

Acids and bases

Acid-substances that dissociate in solution to yield

hydrogen ion (H+) and anion inside aqueous solution HCl H+ + ClProton donor because of the +ve charge Acidic solution- always has higher hydrogen ion [H+] concentration compared to hydroxide ion [OH-] Strong acid-If the dissociation happens completely Weak acid- incomplete, reversible Litmus paper- blue -> red

 Base- substance that dissociates to yield

hydroxide ion [OH-] and cation when dissolved in water. Proton acceptor Basic solution- lower hydrogen ion [H+] concentration than hydroxide ion [OH-] . [OH-] acts as base by accepting a proton to form H2O indirectly. Strong base- dissociate completely in water Litmus paper- red -> blue

Neutral-solution which have equal concentration of [H+] and [OH-]. When acid and base added to each other, they react to neutralize each other provided if an equal number of hydrogen and hydroxide ions present. Produce salt and water

pH scale Measure the strength of acid and base Ranges from 0-14 pH of solution= the negative logarithms (base 10) of the hydrogen ion concentration: pH = - log [H+] [ ] = the molar concentration for the substance. Neutral, [H+] = 10-7 = - log [10-7] =7

In any solution, the product of H+ and OHconcentration = 10-14 Helps to determine pH if either concentration of H+ or OH- are given. pH declines as concentration of H+ increase pH scale based on H+ concentration, but also can imply OH- concentration.

Buffers- substances that resists extreme changes in the concentrations of H+ and OHin a solution. Resists changes in pH when acids or bases are introduced. How? Buffer work by accepting H+ from the solution if excess, donating H+ if depleted. Normally, buffer solutions contain weak acid and weak base, which combine reversibly with H+.

 One important buffer in human blood and other

biological solutions is carbonic acid.

The chemical equilibrium between carbonic acid

and bicarbonate acts at a pH regulator.

The equilibrium shifts left or right as other

metabolic processes add or remove H+ from the solution.

FIN
Verily, after each difficulty, there are relief- Al-Insyirah
Athirahs