Chap 4 BIOLOGY BIO

8/13/2019 Chap 4 BIOLOGY BIO

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Introduction to cell biology

Chemical Bonds and Water


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Organisms are composed of matter.

Matter is anything that takes up space and has mass.

An elementis a substance that cannot bebroken down to other substances by chemicalreactions.

There are 92 naturally-occurring elements.

Each element has a unique symbol, usually from thefirst one or two letters of the name, often from Latinor German.


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A compoundis a substance consisting of two ormore elements in a fixed ratio.

Table salt (sodium chloride or NaCl) is a compoundwith 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.


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About 25 of the 92 natural elements are knownto 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 weightconsists of phosphorus (P), sulfur (S), calcium (Ca),

and potassium (K).

Life requires about 25 chemicalelements


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Trace elementsare required by an organism but

only in minute quantities.

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

Other trace elements arerequired only by some species.

For example, a daily intakeof 0.15 milligrams of iodineis required for normalactivity of the human

thyroid gland.

Fig. 2.4


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An elementconsists of a single type of atomthat 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 thoseatoms

C = Carbon, consists only single carbon atom


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1. Subatomic particles Atom= Greek word= indivisible

Consists of many subatomic particlesNeutrons (Neutral)

Protons (+ve charge)

Electrons (-ve charge) Neutron + Proton = Atomic nucleus

Electron move around nucleus= electron cloud


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Cloud of negative

charge (2 electrons)

Electrons

Nucleus

(a) (b)


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Protons and electrons attracted to each otherbecause of opposite charge, thus keeping theelectron 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 ofatom Unit for atom mass = dalton Proton + neutron = closed to 1 dalton


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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 2protons in its nucleus


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Usually, an atom is neutral in electricalcharge.

Equal number of electrons must balance itsproton. Therefore, the atomic number indicates the

number of protons or the number ofelectrons in an electrically neutral atom.


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Atomic mass = the sum of protons and neutronsin the nucleus atom (mass number)

Number of neutron= Atomic mass- Atomic number

Proton = 11Electron =11Neutron = Atomic mass-Atomic number

= 23-11=12


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Atomic number= no. of proton= no. of electronProton = 2Electron = 2Neutron = Atomic mass- Atomic number

= 4- 2=2


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Hydrogen, special case

Smallest atom

Made up of 1 proton, 1 electron, no neutron


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3. Isotopes Name given to the atoms from the same

element, but shows differences in terms ofthe subatomic particle numbers.

Element consists of mixture of atoms withdifferent numbers of neutrons, and thusdifferent masses.


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Radioactive isotope

Form of element that their nucleus decays

spontaneously Unstable, tend to give off particles and energy

easily.


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

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.


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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 metabolism-diagnostic tools in medicine (Kidney problem)


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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 ofproton- right pathway


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The pathway of electrons represents theirenergy level electron shell

Nucleus need less energy to attract theelectron when they are close to each other Periodic table shows the distribution of

electrons according to numbers of electronshell in their atom


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Left-right; refers to additional sequence ofelectrons

Top-bottom sequence of elements in eachcolumn represents the number of electronshell in their configuration

Similar no. of electrons in valence shell=similar chemical behavior

Completed valence shell- unreactive Incomplete valence shell- reactive

Figure 2.9


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g

First

shell

Secondshell

Third

shell

Hydrogen

1H

Lithium

3Li

Sodium

11Na

Beryllium

4Be

Magnesium

12Mg

Boron

5B

Aluminum

13Al

Carbon

6C

Silicon

14Si

Nitrogen

7N

Phosphorus

15P

Oxygen

8O

Sulfur

16S

Fluorine

9F

Chlorine

17Cl

Neon

10Ne

Argon

18Ar

Helium

2He2

He

4.00Mass number

Atomic number

Element symbol

Electron

distribution

diagram


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Electron orbital Orbital- 3D space where electron spends

most of its time 1stelectron shell-single orbital- 2 electrons 2ndelectron shell-4 orbital- 8 electrons

2s

2p (2px,2py, 2pz)


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The reactivity of atoms arises from the presence ofunpaired electron in one or more orbitals of their

valence shells


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Atoms with incomplete valence shell interactwith each other to complete their own

valence shell Atom stays close to each other bind by

chemical bonds

Covalent bonds

Ionic bonds

Hydrogen bond


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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.


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Two or more atoms held together by covalentbonds constitute a molecule.

We can abbreviate the structure of this molecule

by substituting a line for each pair of sharedelectrons, drawing the structural formula. H-H is the structural formula for the covalent bond

between two hydrogen atoms.

The molecular formulaindicates the numberand types of atoms present in a single molecule. H2is the molecular formula for hydrogen gas


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Single covalent bond: 2 atoms share a pairof electron valence- stable, completeconfiguration.

For example, if two hydrogen atoms comeclose enough that their 1s orbitals overlap,then they can share the single electrons

that each contributes.


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Oxygen needs to add 2 electrons to the 6already present to complete its valence shell.

Two oxygen atoms can form a molecule bysharing twopairs of valence electrons.

These atoms have formed a double covalent

bond.


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Every atom has a characteristic total number ofcovalent 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 onits three unpaired electrons, but in biological

molecules it generally has a valence of 5, forming

three single covalent bonds and one double bond.


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Covalent bonds can form between atoms ofthe same element or atoms of differentelements.

While both types are molecules, the latterare also compounds.

Water, H2O, is a compound in which two

hydrogen atoms form single covalentbonds with an oxygen atom. This satisfies the valences of both

elements.


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


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The attraction of an atom for the electrons ofa covalent bond is called itselectronegativity.

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 covalentbond.

A covalent bond between two atoms of the sameelement is always nonpolar.


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If the electrons in a covalent bond are notshared equally by the two atoms, then this is

a polar covalent bond. The bonds between oxygen and hydrogen

in water are polar covalent because oxygenhas a much higher electronegativity thandoes hydrogen.


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Compounds with a polarcovalent bond have regions

that have a partial negativecharge near the stronglyelectronegative atom and apartial positive charge near

the weakly electronegativeatom.


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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 7valence electrons in its third shell.

Now, sodium has a full valence shell (the second) andchlorine has a full valence shell (the third).


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After the transfer, both atoms are no longerneutral, 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.


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Atoms with 5, 6, 7 valence electron tend togain electrons- become negatively charged.

Atoms with 1, 2, 3 electrons tend to loseelectrons- become positively charged


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3. Hydrogen bonds Is the attractive force between hydrogen

atom covalently bonded to oneelectronegative atom and is attracted toanother electronegative atom from othermolecules.

Usually oxygen or nitrogen atoms E.g H2O, NH3


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Hydrogen bonds between water molecules


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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 moleculesthat use weak bonds to tie up onto receptor moleculesof the receiving cell

If the signals strongly bonded, the transmission willcontinue to respond causing cell excited continuously


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Do not the Unbelievers see that the heavens and theearth were joined together (as one unit of creation),

before we clove them asunder? We made fromwaterevery living thing. Will they not then believe?- Al-Anbiyaa 21: 30


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Because water is the substance that makes possiblelife as we know it on Earth, astronomers hope tofind evidence of water on newly discovered planetsorbiting distant stars.

Life on Earth began in water and evolved there for 3billion 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, andvapor.


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

tightly although under tension, normally

occur among similar atoms and held togetherby 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


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

Water that evaporates from a leaf is replaced bywater from vessels in the leaf.

Hydrogen bonds cause water molecules leavingthe veins to tug on molecules further down.

This upward pull is transmitted to the roots.


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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 cleansing-help things become wet and remove all impurities

Adhesion to cell walls byhydrogen bonds resist


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hydrogen bonds- resistdownward pull of gravity

Cohesion due to hydrogenbonds between water

molecules helps holdtogether the column ofwater within the cells


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Surface tension,a measure of the force necessaryto stretch or break the surface of a liquid, is relatedto cohesion.

Water has a greater surface tension than mostother liquids because hydrogen bonds amongsurface water molecules resist stretching orbreaking the surface.

Water behaves as if covered by an invisible film.

Some animals can stand,walk, or run on waterwithout breaking thesurface.


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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.


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The property of specific heat closely relatedto 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 thekinetic energy that cause the temperature tobe increased.


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When temperature drops, many additionalhydrogen bonds form, slowing down the kineticenergy and releasing large amount of energy

(heat). High specific water heat important in life forboth large water bodies or the living cells oforganisms. In the ocean, large water bodies can absorb and store

large amount of heat from sun, while warming outonly a few degrees,

Gradually, cooling water can warm the air at night. Coastal area have mild climate compared to desert.


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Stabilizes ocean temperatures, sustainingfavorable 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.


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The heat is used to break off hydrogen bondsfirst before it moves faster and transforms intogaseous state.

Advantages in moderating earths climate

Ocean capable of absorbing considerable amount ofheat 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 itcondenses to form rain.


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Due to evaporation, evaporative cooling occur as thehottest molecule transform into gas leavingremaining molecule to cool down.

Contributes to the stability of temperature in lakesand ponds, prevent overheating for terrestrialorganism.

Example

Evaporation of water from leaves and plants helpsto keep plant tissues from overheating on hot day

Evaporation of sweat from human skin transfersbody heat to surrounding.


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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 thanliquid-ice floats.

Temperature reaches 0c- water molecules lockedinto 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 liquidwater 10% less density.


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Advantages to the fitness of environment

Floating ice insulate water below, prevent freezing.

Life under frozen surface.

Ice Liquid


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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.


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The polarity of water-capable to dissolvemany substances, polar and ioniccompounds.

Water provides efficient medium infacilitating chemical rxn.

Able to interact with H2O hydrophilic Unable to interact with H2O hydrophobic

Oxygen- negatively charge,attracted to Na+


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attracted to Na+

Hydrogen- positively charge,

Attracted to Cl-

NaCL- Solute Water- Solvent Mixture of more than one

substance in water-homogenous liquid- Solution

The region of water

molecules around dissolvedions-hydration cell

Any polar-molecules

compound can be dissolved


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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 asubstance

Avogadros number= number of molecules in amole=6.02 x 1023

Molarity refers to the number of moles of solute perliter of solution- M or mol/l


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How to prepare a 0.5 M of NaCl

0.5 M equals to 0.5 mol NaCl in 1 liter of watersolution

Na(23) + Cl (35) = 58 grams (1 mol)

= 0.5 x 58 g= 29 g


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1. How to prepare a 2.0 M of K2HPO4?

39K 1H 31P 16O

2. How many grams of salt (NaCl) must bedissolved in water to make 2 L of a 2M salt

solution?23Na 34Cl


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Acids and bases Acid-substances that dissociate in solution to yield

hydrogen ion (H+) andanion inside aqueoussolution

HClH++ Cl-

Proton 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


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Base- substance that dissociates to yieldhydroxide ion [OH-]and cationwhen dissolved inwater.

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


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Neutral-solution which have equalconcentration of [H+] and [OH-].

When acid and base added to each other,they react to neutralize each other provided ifan equal number of hydrogen andhydroxide ionspresent.

Produce salt and water


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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


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In any solution, the product of H+and OH-

concentration = 10-14

Helps to determine pH if either concentrationof H+or OH- are given.

pH declines as concentration of H+increase pH scale based on H+ concentration, but also

can imply OH- concentration.


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Buffers- substances that resists extremechangesin the concentrations of H+and OH-

in 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 reversiblywith H+.


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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.


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FINVerily, after each difficulty, there arerelief- Al-Insyirah

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Chap 4 BIOLOGY BIO